support_disc_reads	support_breakpoint	cancer_type	sample	fiveprimepartner	threeprimepartner	fiveprime_symbol	threeprime_symbol	Fusion_sequence	Fusion_description	Fusion_finding_method	Predicted_effect	Counts_of_common_mapping_reads	Spanning_pairs	Spanning_unique_reads	Longest_anchor_found	fiveprime_chr	fiveprime_junction_hg38	fiveprime_strand	threeprime_chr	threeprime_junction_hg38	threeprime_strand	fiveprime_fpkm	threeprime_fpkm	fiveprime_is_mirna_host	threeprime_is_mirna_host	fiveprime_is_snorna_host	threeprime_is_snorna_host	multi_juncion	is_reciprocal	fiveprime_is_top10_tumor	threeprime_is_top10_tumor	fiveprime_gene_type	threeprime_gene_type	detected_by_TumorFusions	TumorFusions_WGS_validation	listed_in_Mitelman_database	is_recurrent
TRUE	FALSE	Glioblastoma	TCGA-06-0152-02A	ENSG00000146648	ENSG00000129244	EGFR	ATP1B2	CGCATCATTGTACTCCAGCCTGGGCAACAAGAGTGAAACTCCATCTCGAA*AAAAAAAAAACAAAAACAAAAACAAAAAAACCCATAATGCCCACAGAATG	oncogene,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	2	1	18	7	55047754	+	17	7657381	+	241.3126	310.3258	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0152-02A	ENSG00000146648	ENSG00000129244	EGFR	ATP1B2	CAAAATATTAAACCTGTCTTACACACACACACACACACACACACACACAC*ACACCCCCCGCCACACACACACACAAACGTGCACACGCGTCTCATTTGAC	oncogene,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	2	1	17	7	55020589	+	17	7656256	+	241.3126	310.3258	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0152-02A	ENSG00000146648	ENSG00000129244	EGFR	ATP1B2	CCCCATCATCACTAAAGCAGACATGGCAATGATGGCCATGCACACTTTCC*CTGCCCCCACCATCCTTTCTCTGGCTTCTTTTAGCAAGTTATCAACTAAT	oncogene,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	2	1	16	7	55034058	+	17	7657235	+	241.3126	310.3258	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0152-02A	ENSG00000146648	ENSG00000116016	EGFR	EPAS1	CCGAGCACCTGTTTGCCATTTTGGATGTTTCCAAACATGAACCAAACTTC*CAAGTTTGGTGCATGTCTGTTCTTCTGTAGGGAGAAGCTTTAGCTTCATT	oncogene,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	2	1	16	7	55171872	+	2	46384996	+	241.3126	44.3884	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0152-02A	ENSG00000146648	ENSG00000075785	EGFR	RAB7A	AACTGTTTGGAAATTCAAAATATATCTTATCATTTTAAAAACATCTTTCT*CACACGCACACACACACACACAGATCTGACGTAATCAAACTCCAGCCCTT	oncogene,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	2	1	14	7	55090775	+	3	128813598	+	241.3126	51.6141	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0152-02A	ENSG00000132434	ENSG00000198121	LANCL2	LPAR1	CCACGGCGCCCCGGGGGTCATCCACATGCTCATGCAGGCGTACAAGGTCA*TCCACATCCTTATGCCTTCTTTTGAATCTATGATTTGATAACTTAAGAAA	cancer	BOWTIE+STAR	intronic/intronic	0	2	1	15	7	55412093	+	9	110998916	-	297.0929	13.601	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0152-02A	ENSG00000204956	ENSG00000131095	PCDHGA1	GFAP	GATTATGAAGAAACCGGTTTCTATGAAATAGAAATACAAGCAGAAGATGG*ATGACTTTGTCCCATTTCTAAAGGCCTCTTCCTTGCTGTGTCATACCAGG	NA	BOWTIE+STAR	intronic/UTR	0	2	1	14	5	141414158	+	17	44906213	-	0.8029	1141.3953	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0152-02A	ENSG00000204956	ENSG00000131095	PCDHGA1	GFAP	GATTATGAAGAAACCGGTTTCTATGAAATAGAAATACAAGCAGAAGATGG*CAGCCTCTGAGCCCCTGGGACTGCTGCTTCTTAACCCCAGTAAGCCACTG	NA	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	14	5	141414158	+	17	44906157	-	0.8029	1141.3953	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0152-02A	ENSG00000204956	ENSG00000131095	PCDHGA1	GFAP	GATTATGAAGAAACCGGTTTCTATGAAATAGAAATACAAGCAGAAGATGG*TGTGTACGTGGAGAGGGATGAGGTGCTGGGAGGGATAGAGGGGGGCTGCC	NA	BOWTIE+STAR	intronic/UTR	0	2	1	14	5	141414158	+	17	44906499	-	0.8029	1141.3953	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0152-02A	ENSG00000204956	ENSG00000131095	PCDHGA1	GFAP	AACCCTGTCAAGAAAGAAAGGAAGGAATGAGGGAGGGAGGGAGAGAGGAA*GGGAGGGATAGAGGGGGGCTGCCTGGCCCCCAGCTGTGGGTACAGAGAGG	NA	BOWTIE+STAR	intronic/UTR	0	2	1	14	5	141452735	+	17	44906472	-	0.8029	1141.3953	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0152-02A	ENSG00000204956	ENSG00000131095	PCDHGA1	GFAP	AAACCCAGAGCTGGTGCTGGAGCGCGCCCTGGACAGGGAGGAGGCAACTG*GGAGGGGACGCTGGTAGAGATGGAGGAGGAGGCAATTGGGATGGCGCTAG	NA	BOWTIE+STAR	intronic/UTR	0	2	1	14	5	141403571	+	17	44906391	-	0.8029	1141.3953	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0152-02A	ENSG00000204956	ENSG00000131095	PCDHGA1	GFAP	CTACCAGCTCAGCCCCAATCACCACTTCTCCCTGAACGTGCAGACTGGAG*GGGGGGCTGCCTGGCCCCCAGCTGTGGGTACAGAGAGGTCAAGCCCAGGA	NA	BOWTIE+STAR	intronic/UTR	0	2	1	14	5	141403508	+	17	44906460	-	0.8029	1141.3953	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0152-02A	ENSG00000081853	ENSG00000131095	PCDHGA2	GFAP	CCACGCTGTGTGAGCCGATCCGCTACTCGATTCCGGAGGAGCTGGCCAAG*GTAGGGGTTGTGGGTGACCAGTTGCACTTGGCCTCTGGATTGTGGGAATT	NA	BOWTIE+STAR	intronic/UTR	0	2	1	16	5	141417988	+	17	44906333	-	1.137	1141.3953	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0152-02A	ENSG00000081853	ENSG00000131095	PCDHGA2	GFAP	ATTATGAAGAAACCGGTTTCTATGAAATAGAAATACAAGCAGAAGATGGA*ATACAAGTAGGGGTTGTGGGTGACCAGTTGCACTTGGCCTCTGGATTGTG	NA	BOWTIE+STAR	intronic/UTR	0	2	1	15	5	141414159	+	17	44906339	-	1.137	1141.3953	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0152-02A	ENSG00000075785	ENSG00000146648	RAB7A	EGFR	CAGGAACGGTTCCAGTCTCTCGGTGTGGCCTTCTACAGAGGTGCAGACTG*TCTCCCACCATCACCATCGCACCTCAGGAACCAGAGAACTTTTTAATGGA	oncogene,cancer,tumor	BOWTIE+STAR	CDS(truncated)/intergenic	0	2	1	15	3	128806439	+	7	55211788	+	51.6141	241.3126	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0152-02A	ENSG00000075785	ENSG00000146648	RAB7A	EGFR	TCAACGTGGAGCAGGCGTTCCAGACGATTGCACGGAATGCACTTAAGCAG*TGCCATGGAATTCCCTAAGGCCGTGCAGGGAGCAGGTTGCCAAGCTGGGT	oncogene,cancer,tumor	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	15	3	128807671	+	7	55104268	+	51.6141	241.3126	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0152-02A	ENSG00000075785	ENSG00000146648	RAB7A	EGFR	GAATTGGGAAATCCAGCTAGCGGCAGTATTCTGTACAGTAGACACAAGAA*AAGTCTTCTGCTTGTTAACTTAATTAGAGATACATGAGTTTGCAGCTGTG	oncogene,cancer,tumor	BOWTIE+STAR	UTR/intronic	0	2	1	14	3	128814233	+	7	55135266	+	51.6141	241.3126	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0152-02A	ENSG00000132432	ENSG00000132434	SEC61G	LANCL2	AGCTCCAGTGCTACGTGTCCCTGGCATTTTAGGTGTCGGTTGGGTAG*TTTGCAGAGTGGTGTCTAGATTACGGAGCACACGGGTGCCGCATTCC	known,gliomas,exon-exon	BOWTIE	UTR/CDS(truncated)	0	1	1	13	7	54759158	-	7	55428375	+	685.883	297.0929	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-2570-01A	ENSG00000179912	ENSG00000257921	R3HDM2	AC025165.3	ATGTGATGCCATTCCAGCACTGGACTCATGGAGGCTGAGCATTTATTCAG*GCTGGGTCTCTTCTGCGTCAGTCGCCCCAGCCAAGGCACACATTTTATGC	exon-exon	BOWTIE+STAR	UTR/CDS(no-known-start-or-end)	0	24	4	17	12	57395749	-	12	57783110	+	9.4912	0	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-2570-01A	ENSG00000179912	ENSG00000257921	R3HDM2	AC025165.3	TGTGATGCCATTCCAGCACTGGACTCATGGAGGCTGAGCATTTATTCAGG*GGGGGATGTTACCATCACTGACCTGCCCCTGGCCCTAGAACAGATCCAGG	NA	BOWTIE+BOWTIE2	intronic/intronic	0	24	1	26	12	57395748	-	12	57780256	+	9.4912	0	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-2570-01A	ENSG00000257443	ENSG00000123297	AC068305.3	TSFM	TTAGGGTCCGATTTGTGAAGGTTGATGTCCTGCCCAGATATCAGAGTAGT*CCAGCTGTAAGGCAGATTTTGACATTCTTGTGCCAGAAACAGAAATTAGA	antisense	BOWTIE+STAR	intronic/UTR	0	21	1	16	12	58928443	+	12	57797201	+	23.5824	2.7111	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-2570-01A	ENSG00000123297	ENSG00000257443	TSFM	AC068305.3	TAAATTGCAAGAAAGCTCTGGAGACTTGTGGCGGGGACCTCAAACAG*GGTGGGAGAAGGAATGTTCTCTGGAGAAATCTGTATGATAGAATAGT	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	21	22	29	12	57783283	+	12	59056006	+	2.7111	23.5824	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-2570-01A	ENSG00000257921	ENSG00000257443	AC025165.3	AC068305.3	TTGTAAATTGCAAGAAAGCTCTGGAGACTTGTGGCGGGGACCTCAAACAG*GGTGGGAGAAGGAATGTTCTCTGGAGAAATCTGTATGATAGAATAGTGAA	antisense,exon-exon	BOWTIE+STAR	CDS(no-known-start-or-end)/exonic(no-known-CDS)	0	19	3	16	12	57783283	+	12	59056006	+	0	23.5824	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-2570-01A	ENSG00000257443	ENSG00000135506	AC068305.3	OS9	TTGATAAACCTTTGGTCCAAGTGATTAAGAAAAAGGGAAGAAGAGACAAA*AAGAAGAGGAGGATGAGGATGAGGATGAGGATGAAGATGAGGATGAACGG	antisense	BOWTIE+STAR	intronic/CDS(truncated)	0	7	1	18	12	58999605	+	12	57718252	+	23.5824	359.0332	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-2570-01A	ENSG00000257443	ENSG00000135506	AC068305.3	OS9	TTTGGTTTTTTGTCCTTGTGATAGTTTGCTGAGAATGATGGTTTCCAGTT*CCGGCTCCGTTCGGAGGTGAAGGCTGGCATGGAGCGGGAACTGGAAAACA	antisense	BOWTIE+STAR	intronic/CDS(truncated)	0	7	1	18	12	58992792	+	12	57718361	+	23.5824	359.0332	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-2570-01A	ENSG00000257443	ENSG00000135506	AC068305.3	OS9	AGAAATTGAACATCCTCCATAGCCTCCTGCCTCAGGGACAGGACAGGAGC*AGGAGGATGAGGATGAGGATGAGGATGAAGATGAGGATGAACGGCAGTTA	antisense	BOWTIE+STAR	intronic/CDS(truncated)	0	7	1	16	12	58976023	+	12	57718258	+	23.5824	359.0332	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-2570-01A	ENSG00000257443	ENSG00000135506	AC068305.3	OS9	TAGTGCATTTTGGCCTTCTGCTGATTCTACCATATTAATCTACAGGTAGG*CAGTAGGATCTTTTGAGTGGAGGTGGGTAGAGAGAGCAAGGAGGGCAGGA	antisense	BOWTIE+STAR	intronic/UTR	0	7	1	15	12	59009994	+	12	57721226	+	23.5824	359.0332	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-2570-01A	ENSG00000257443	ENSG00000135506	AC068305.3	OS9	TGATTTGCCCCCTCCCTATCCATTTCCATAGGTACAAATAACAGTACCTA*GGGAGAATTTGAGAAGGAACTGGAAGGGATCCTGCTTCCGTCAGACCGAG	antisense	BOWTIE+STAR	intronic/CDS(truncated)	0	7	1	14	12	59008544	+	12	57718310	+	23.5824	359.0332	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-2570-01A	ENSG00000257443	ENSG00000135506	AC068305.3	OS9	ACATAAATGTATATAATTTTGAATATAAAACCATTTGTAGAATGTAATAG*GCTCTCCTGAACTCTCACTCAATCCTCTTCCTCTCCTCTGTGGCTTTTCC	antisense	BOWTIE+STAR	intronic/UTR	0	7	1	14	12	58968803	+	12	57721126	+	23.5824	359.0332	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-2570-01A	ENSG00000257443	ENSG00000135506	AC068305.3	OS9	TCTCTGACAGTCATTTGCTCCTCTTTGTAACTTCCATATTAAATTGCCTG*GGGCAGGACACTTAGCAGGCACTGAGCAAGCAGGCCCCCACCTGCCCTTA	antisense	BOWTIE+STAR	intronic/UTR	0	7	1	14	12	58982778	+	12	57721268	+	23.5824	359.0332	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-2570-01A	ENSG00000135506	ENSG00000257443	OS9	AC068305.3	GGTCCAAGTGCGACCTTAATGGGAGGCCCCGGGAGGCCGAGGTTCGG*GGTGGGAGAAGGAATGTTCTCTGGAGAAATCTGTATGATAGAATAGT	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	7	6	22	12	57696373	+	12	59056006	+	359.0332	23.5824	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-2570-01A	ENSG00000135506	ENSG00000257443	OS9	AC068305.3	ATGGGTCCAAGTGCGACCTTAATGGGAGGCCCCGGGAGGCCGAGGTTCGG*TTTAGCTTCATCTCCAGCTGCTCCTAAGAAGCCCAGCCATCAAGCCAACT	antisense	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/intronic	0	7	1	33	12	57696373	+	12	59038290	+	359.0332	23.5824	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-2570-01A	ENSG00000135506	ENSG00000257443	OS9	AC068305.3	GAATTTGACTTCTGAGACCAACACTACACTTGACCCTTCACGGAATCCAG*GAAGAGTCTGGATGCAGTGGCTCACACCTGTAATTCCAGTACTTTGGGAG	antisense	BOWTIE+STAR	UTR/intronic	0	7	1	18	12	57720944	+	12	59049298	+	359.0332	23.5824	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-2570-01A	ENSG00000135506	ENSG00000257443	OS9	AC068305.3	ACCATCATCCCTTTGCGTGTTTACCTCCTATTCATCCCTCTGGGAAGCAG*CTGTGCTCTAAAAGCTGCAGTGTCACAGTTACAGAAAGGTCAAGAGCTTC	antisense	BOWTIE+STAR	UTR/intronic	0	7	1	18	12	57719388	+	12	59025029	+	359.0332	23.5824	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-2570-01A	ENSG00000135506	ENSG00000257443	OS9	AC068305.3	TGATATTTGCTCTCCTGAACTCTCACTCAATCCTCTTCCTCTCCTCTGTG*GTTTTTGTTTTCCTGAAATCCCACCAGTTTCCCTCACCTCCTACAAGACC	antisense	BOWTIE+STAR	UTR/intronic	0	7	1	15	12	57721167	+	12	59041038	+	359.0332	23.5824	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-2570-01A	ENSG00000135506	ENSG00000257443	OS9	AC068305.3	CACCATGTTCTTGAACAATCAGGTTTCTAAATAAACAACTGGACCATCAA*TCCATGAAAACAAATGAGCTCTAAGATAAAGTAGGAATAGTTCCCCAGTA	antisense	BOWTIE+STAR	UTR/intronic	0	7	1	14	12	57721557	+	12	59032977	+	359.0332	23.5824	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-2570-01A	ENSG00000135506	ENSG00000257443	OS9	AC068305.3	GGCAATGCTGGCTCTCACATCCACTCTCAACAAACTCATCAAAAGACTGG*ATGTGAGAGCCAGCACGTGCACGTTATTCTCTTTTCTCTGCCACTGTGAT	antisense	BOWTIE+STAR	CDS(truncated)/intronic	0	7	1	14	12	57719095	+	12	59061716	+	359.0332	23.5824	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-2570-01A	ENSG00000135506	ENSG00000257443	OS9	AC068305.3	AGGGAACCAGAGAAGGAAAGGGGTGATCCAGAACGGCAGAGAGAGATGGA*GCCCCCATTTCCTTCACTGGGAAAAGCTGTTGATATATGAAAAATAGATG	antisense	BOWTIE+STAR	CDS(truncated)/intronic	0	7	1	14	12	57718252	+	12	59008215	+	359.0332	23.5824	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-2570-01A	ENSG00000135506	ENSG00000257443	OS9	AC068305.3	GCCTGTGATATTTGCTCTCCTGAACTCTCACTCAATCCTCTTCCTCTCCT*TAACTCTCACACAATGTAGTTAATTCATGGGCCTTTGACAAGACTGTAAT	antisense	BOWTIE+STAR	UTR/intronic	0	7	1	14	12	57721162	+	12	59029028	+	359.0332	23.5824	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-2570-01A	ENSG00000135506	ENSG00000257443	OS9	AC068305.3	CGTGGACGAGCCCTTGTCCTGCTCTTATGTGCTGACCATTCGCACTCCTC*AAGCCCAATTCCAGTTAGCATGAGCAAACAAAGGTGGTTTATTGGTACTT	antisense	BOWTIE+STAR	CDS(truncated)/intronic	0	7	1	14	12	57715856	+	12	59059515	+	359.0332	23.5824	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-2570-01A	ENSG00000135506	ENSG00000257443	OS9	AC068305.3	TGATGCTGCAGAAGTCCCTCAGAGGGAACCAGAGAAGGAAAGGGGTGATC*TTGGCCTAGAGTTGTTTCTGCCAGAGGATGAAATAACAGAGAAGTGAGAG	antisense	BOWTIE+STAR	CDS(truncated)/intronic	0	7	1	14	12	57718230	+	12	59061445	+	359.0332	23.5824	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-2570-01A	ENSG00000179912	ENSG00000257443	R3HDM2	AC068305.3	TGATGCCATTCCAGCACTGGACTCATGGAGGCTGAGCATTTATTCAG*GGTGGGAGAAGGAATGTTCTCTGGAGAAATCTGTATGATAGAATAGT	antisense,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	UTR/exonic(no-known-CDS)	0	7	11	29	12	57395749	-	12	59056006	+	9.4912	23.5824	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-2570-01A	ENSG00000162174	ENSG00000256824	ASRGL1	AP000721.2	GAAAAAGAGAAGCATGAAAAAGGTGCTCAGAAAACAGATTGTCAAAA*GTGAGGAAGCAGGCAGTGGGCGAGAAGATGGATTCCTTTTTGGACAG	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	3	2	30	11	62357144	+	11	64103194	+	4.0907	0.026	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-2570-01A	ENSG00000115816	ENSG00000055332	CEBPZ	EIF2AK2	AATTCTCAGCAGACAATATCGGATCGATATTACACAGCATTATACAG*GATACGGGAAGAAGAAATGGCTGGTGATCTTTCAGCAGGTTTCTTCA	known,tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	2	1	14	2	37227544	-	2	37147822	-	5.7993	5.1612	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000127314	PPM1H	RAP1B	ATTTGCCTTTTGGGGAAGCTGTATGTTGCAAATGCTGGGGATAGCAG*GTACTAGGTTTTGACAAGCTTGCATCATGCGTGAGTATAAGCTAGTC	cell_lines,18cancers,cancer,m263,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	511	35	30	12	62788226	-	12	68648699	+	9.7382	27.1903	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000127314	PPM1H	RAP1B	ATTTGCCTTTTGGGGAAGCTGTATGTTGCAAATGCTGGGGATAGCAG*ACTGTACAATTTGTTCAAGGAATTTTTGTAGAAAAATACGATCCTAC	cell_lines,18cancers,cancer,m263,exon-exon	BOWTIE	out-of-frame	0	511	5	24	12	62788226	-	12	68650400	+	9.7382	27.1903	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000127314	PPM1H	RAP1B	ATTTGCCTTTTGGGGAAGCTGTATGTTGCAAATGCTGGGGATAGCAG*GTTTTGACAAGCTTGCATCATGCGTGAGTATAAGCTAGTCGTTCTTG	cell_lines,18cancers,cancer,m263,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	511	5	23	12	62788226	-	12	68648706	+	9.7382	27.1903	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000127314	PPM1H	RAP1B	ATGAGTGCCTGGTCATCGGAGCGCTTGAAAGTGCATTCAAGGAAATG*GTACTAGGTTTTGACAAGCTTGCATCATGCGTGAGTATAAGCTAGTC	cell_lines,18cancers,cancer,m263,exon-exon	BOWTIE	CDS(truncated)/UTR	0	511	3	29	12	62801816	-	12	68648699	+	9.7382	27.1903	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000127314	PPM1H	RAP1B	CCTGTAATCCCAGCTACTCGGGAGGCTGAGGCGGGAGAATCGCTTGAACC*CGGGAGGCTGATGTGGGAGAATGGCCTGAACCCGGGAGGCAGAGGTTGCA	cell_lines,18cancers,cancer,m263	BOWTIE+STAR	intronic/UTR	0	511	1	34	12	62932729	-	12	68650005	+	9.7382	27.1903	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000127314	PPM1H	RAP1B	GTGATTTGCCTTTTGGGGAAGCTGTATGTTGCAAATGCTGGGGATAGCAG*TAGAGACAGGGTTTCACCATGTTAGCCAGGATGGTCTCGATCTCCTGACC	cell_lines,18cancers,cancer,m263	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	511	1	32	12	62788226	-	12	68654661	+	9.7382	27.1903	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000127314	PPM1H	RAP1B	CTTTTGGAGGCCGAGGCAAGGTGGATTCCCTGAGCTCAGGAGTTCGCAAC*CAGCCTGGCCAATATAGTGAAACCCCGTCTCTACTAAAAATATAAAAATT	cell_lines,18cancers,cancer,m263	BOWTIE+BLAT	intronic/UTR	0	511	1	22	12	62819036	-	12	68649916	+	9.7382	27.1903	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000127314	PPM1H	RAP1B	GGTCTCTTGCGGTGGCCATCTTGAGTGTGTGCATCTACATTGCTGGCTTG*CAACAGGGAGCCACAGTATTTAAATTGACCAACCTAATGTTACAACTACT	cell_lines,18cancers,cancer,m263	BOWTIE+STAR	intronic/UTR	0	511	1	21	12	62921486	-	12	68660361	+	9.7382	27.1903	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000127314	PPM1H	RAP1B	GTGATTTGCCTTTTGGGGAAGCTGTATGTTGCAAATGCTGGGGATAGCAG*AATTCTTTTTTTTTTTTTCCTTTAATAAGGTACTAGGTTTTGACAAGCTT	cell_lines,18cancers,cancer,m263,exon-exon	BOWTIE+STAR	CDS(truncated)/UTR	0	511	1	15	12	62788226	-	12	68648670	+	9.7382	27.1903	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000127314	PPM1H	RAP1B	CTTACATTAACATAAAGCACGGAAGCTATATAAACGTGTCTGGGCTGTTC*GGATGTGAATGTGGGAAGTAATTTTAATCATATGTAATTGGTCACAAGGC	cell_lines,18cancers,cancer,m263	BOWTIE+STAR	intronic/UTR	0	511	1	14	12	62874782	-	12	68660221	+	9.7382	27.1903	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000127314	PPM1H	RAP1B	GTCCGTCATTAGGCTGGCTAGATTCCTAAGGAGCAGCAAGGTCCACATCT*AGCACAGTCCACATTTAACGATTTACAAGACCTGAGAGAACAGATTCTTC	cell_lines,18cancers,cancer,m263	BOWTIE+STAR	intronic/CDS(truncated)	0	511	1	14	12	62887361	-	12	68654183	+	9.7382	27.1903	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000127314	ENSG00000111110	RAP1B	PPM1H	TGCATTAGTTTATTCCATCACAGCACAGTCCACATTTAACGATTTACAAG*GATTTGTATTAGTTTATTCTCACGCTGCTGAGACATACCAGAGATTGGGT	cell_lines,18cancers,cancer,m263	BOWTIE+STAR	CDS(truncated)/intronic	0	511	2	19	12	68654211	+	12	62811903	-	27.1903	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000127314	ENSG00000111110	RAP1B	PPM1H	TTTCACATAAGTATTCTTTTTTTGAGATGGAGTTTCACTCTGTCACCCAG*CCTGGGTGACAGAGTGAGACTCTGTCTCAAAAAAAAAAAAAAAAAAAAAA	cell_lines,18cancers,cancer,m263	BOWTIE+BLAT	UTR/intronic	0	511	1	20	12	68657449	+	12	62867623	-	27.1903	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000127314	ENSG00000111110	RAP1B	PPM1H	CCACTATTTTAGCATAATAAAAGAAAGTCCAAAGAGCTCCTATATAGACT*TCATTTTATTATGCTAAAATTTTGTTCCTTGTTCTGCACATGTGAAGAAA	cell_lines,18cancers,cancer,m263	BOWTIE+STAR	UTR/intronic	0	511	1	19	12	68659674	+	12	62817567	-	27.1903	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000127314	ENSG00000111110	RAP1B	PPM1H	GGTAATAAGTGTGACTTGGAAGATGAAAGAGTTGTAGGGAAGGAACAAGG*ATTTGTATTAGTTTATTCTCACGCTGCTGAGACATACCAGAGATTGGGTG	cell_lines,18cancers,cancer,m263	BOWTIE+STAR	CDS(truncated)/intronic	0	511	1	18	12	68656373	+	12	62811902	-	27.1903	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000127314	ENSG00000111110	RAP1B	PPM1H	GGCGGATGAAAGCTACTATATCAGTTTGCACATTCTAATCACTTTCCAGT*GCTGGTACACTTTAAATTGCATTTTAAGGCTGGGCGTGGTGGCTCATGCC	cell_lines,18cancers,cancer,m263	BOWTIE+STAR	UTR/intronic	0	511	1	15	12	68659429	+	12	62727987	-	27.1903	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000127314	ENSG00000111110	RAP1B	PPM1H	CATCATGTCAGCTGCTTTAATATACTAAATGCATTGTAGCTCTGAGCCAG*CCCTCTATTTCTTTTGCTTCACTTTTCACACTGCACTGTAACTGGGTGTC	cell_lines,18cancers,cancer,m263	BOWTIE+STAR	UTR/intronic	0	511	1	15	12	68657217	+	12	62765683	-	27.1903	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000127314	ENSG00000111110	RAP1B	PPM1H	TTATTTAACAATGCCTTGTTGCTTTGTATGCATTAATGTTTGGATGTAAA*CGTGGGAAGTGATTTATGTTGATGATGCCAAAGTGTGAACTCTAGGTTCC	cell_lines,18cancers,cancer,m263	BOWTIE+STAR	UTR/intronic	0	511	1	14	12	68660345	+	12	62702508	-	27.1903	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000127314	ENSG00000111110	RAP1B	PPM1H	TATTGGAGAGTACAATAATGTAAATCCTAAAAGCACCACTATTTTAGCAT*TTTCATTATTGGACCTTTGTATATGTTCTTCAGAGAAATGTCTATTCAAG	cell_lines,18cancers,cancer,m263	BOWTIE+STAR	UTR/intronic	0	511	1	14	12	68659639	+	12	62828845	-	27.1903	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000127314	ENSG00000111110	RAP1B	PPM1H	GTGTACAGTGGGGGTCTACAACAAGAAGTGTATATTTTCAAACAATTTTT*ATAGTCATGTTTACCCATATCTCCTTATTTGCTTAAAGCCTTAAGAAGAT	cell_lines,18cancers,cancer,m263	BOWTIE+STAR	UTR/intronic	0	511	1	14	12	68660028	+	12	62858761	-	27.1903	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000127314	ENSG00000111110	RAP1B	PPM1H	CAAATGTAAACTAAAAGCCTTAATTAAAGTGGTGCAATTTTGTATAACTT*TACTTAAGGTTTTTCCCGGAGCAGAGTATGACTGGTGTGTGGTTAGAATG	cell_lines,18cancers,cancer,m263	BOWTIE+STAR	UTR/intronic	0	511	1	14	12	68660470	+	12	62760930	-	27.1903	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000127314	ENSG00000111110	RAP1B	PPM1H	TCATGCATAAGTGTATTTGCAATACCAAATATACAGGTTTAGTATTTTTG*GTATTGGAATTACAGGCGTTAGCCACCGTGCCTGGCTTCCATTTGCTCTT	cell_lines,18cancers,cancer,m263	BOWTIE+STAR	UTR/intronic	0	511	1	14	12	68660154	+	12	62790331	-	27.1903	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000127314	ENSG00000111110	RAP1B	PPM1H	AGTATAAGCTAGTCGTTCTTGGCTCAGGAGGCGTTGGAAAGTCTGCTTTG*CTGATGGTAGTTTGTATTTCTGTGGGATTGGTGGTGATATCCCCTTTATC	cell_lines,18cancers,cancer,m263	BOWTIE+STAR	CDS(truncated)/intronic	0	511	1	14	12	68648781	+	12	62823100	-	27.1903	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000127314	ENSG00000111110	RAP1B	PPM1H	TGAGTATAAGCTAGTCGTTCTTGGCTCAGGAGGCGTTGGAAAGTCTGCTT*TCCTTGTGCAATTTGCTCATTTCTGCAGAACTCCATTTTCTCCATTACTA	cell_lines,18cancers,cancer,m263	BOWTIE+STAR	CDS(truncated)/intronic	0	511	1	14	12	68648779	+	12	62907392	-	27.1903	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000248995	ENSG00000135679	LINC02231	MDM2	AAAAAAGATCATGGCTTCTGTCTTAGTCTCTCTCTCTCTCTGTCTCTCTC*AATAAAATCAACTGAACTGTAAGCTTAGAATAGGACTGAGGTAATTCTGC	lincrna,oncogene,cancer,tumor	BOWTIE+BLAT	intronic/UTR	0	146	3	24	12	64944844	-	12	68843612	+	12.4738	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000248995	ENSG00000135679	LINC02231	MDM2	TCTCTGTCGCCAGACTGGAGTGCAGTGGTGTGATCTTGGCTCACTGCAAT*CTCTGCCTCCTGGCTGTGTTCAAGTGGTTCTGCTTCAGCCTCCCAAGTAG	lincrna,oncogene,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	146	1	35	12	64925284	-	12	68844849	+	12.4738	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000248995	ENSG00000135679	LINC02231	MDM2	TGATGTGATCTCGGCACACTGCAACCTCCACCTCCCAGGTTAAAGCGATT*TCCTGCCTCAGCCTTCCAAGTAACTGGGATTACAGGCATGTACCACCATA	lincrna,oncogene,cancer,tumor	BOWTIE+BLAT	intronic/UTR	0	146	1	22	12	64970503	-	12	68840953	+	12.4738	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000248995	ENSG00000135679	LINC02231	MDM2	ATGTACCCTAAAACTTAGAGTATAATAAAAAAAAAAAGAAAAAAAAAAGA*AATAAGCCCTGCCCAGTATGTAGACAACCAATTCAAATGATTGTGCTAAC	lincrna,oncogene,cancer,tumor	BOWTIE+STAR	intronic/CDS(truncated)	0	146	1	19	12	64972493	-	12	68839787	+	12.4738	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000135679	ENSG00000248995	MDM2	LINC02231	TATTAAAGTCTGTTGGTGCACAAAAAGACACTTATACTATGAAAGAG*AGAATCATGGGAACCATTATAACAAAGAAGTCAAGAGTGTTGGTGTG	lincrna,oncogene,cancer,tumor,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	146	31	30	12	68813628	+	12	64921070	-	438.8763	12.4738	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000135679	ENSG00000248995	MDM2	LINC02231	CTAGGAGATTTGTTTGGCGTGCCAAGCTTCTCTGTGAAAGAGCACAG*AGAATCATGGGAACCATTATAACAAAGAAGTCAAGAGTGTTGGTGTG	lincrna,oncogene,cancer,tumor,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	146	14	28	12	68816945	+	12	64921070	-	438.8763	12.4738	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000135679	ENSG00000248995	MDM2	LINC02231	AGTTATTAAAGTCTGTTGGTGCACAAAAAGACACTTATACTATGAAAGAG*GAGCCCACTTGGATCTCTTCCAAGGGATCTTTCTTTCTTCTCTTATTAAG	lincrna,oncogene,cancer,tumor	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	146	4	27	12	68813628	+	12	64921666	-	438.8763	12.4738	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000135679	ENSG00000248995	MDM2	LINC02231	GCACTAGAGATACATGAGTACAGTATACTGATCTTTCTGGGATAGAG*AGAATCATGGGAACCATTATAACAAAGAAGTCAAGAGTGTTGGTGTG	lincrna,oncogene,cancer,tumor,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	146	2	20	12	68814689	+	12	64921070	-	438.8763	12.4738	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111581	ENSG00000123297	NUP107	TSFM	TTAGAGTCTAAATAATGGAAAACTGAAAAATTTATTCTTCATTGTTTGTT*TTATGTCCACGGAGCAATGCAGAGTCCCTCACTTCACAAGCTGGTGCTGG	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	UTR/CDS(truncated)	0	131	1	14	12	68690562	+	12	57796250	+	283.5483	11.2876	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000123297	ENSG00000111581	TSFM	NUP107	GCCTGACAGAGAAGGCTCACTCAAGGATCAGTTGGCTTTAGCAATTG*GCTGTTAATGCCAGTGAAAAAACAGTTGTGGAAGCGTTATTTCAGAG	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	131	31	30	12	57793073	+	12	68709238	+	11.2876	283.5483	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000123297	ENSG00000111581	TSFM	NUP107	TGATGCATTGTCAGACCCTAAAGGATCAACCCTCTGCATACAGTAAA*GCTGTTAATGCCAGTGAAAAAACAGTTGTGGAAGCGTTATTTCAGAG	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	131	20	29	12	57787162	+	12	68709238	+	11.2876	283.5483	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000123297	ENSG00000111581	TSFM	NUP107	TACAGGCTAAATAGATTTTAGAAATAATCATCTTAAAATTGAAAACAAAG*GCTGTTAATGCCAGTGAAAAAACAGTTGTGGAAGCGTTATTTCAGAGGGA	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	131	11	37	12	57797533	+	12	68709238	+	11.2876	283.5483	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000123297	ENSG00000111581	TSFM	NUP107	CATTACAAAAAGGAATATTTCCCAAACCTCTTCAGACCGAGAATGCATGG*GCTGTTAATGCCAGTGAAAAAACAGTTGTGGAAGCGTTATTTCAGAGGGA	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	131	7	37	12	57796684	+	12	68709238	+	11.2876	283.5483	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000123297	ENSG00000111581	TSFM	NUP107	GCCTGACAGAGAAGGCTCACTCAAGGATCAGTTGGCTTTAGCAATTG*GACCCTGATGCTCCCATAAGACAGAAAATGCCCCTTGATGATCTGGA	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	131	2	30	12	57793073	+	12	68715627	+	11.2876	283.5483	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000123297	ENSG00000111581	TSFM	NUP107	TGATGCATTGTCAGACCCTAAAGGATCAACCCTCTGCATACAGTAAA*GACCCTGATGCTCCCATAAGACAGAAAATGCCCCTTGATGATCTGGA	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	131	2	28	12	57787162	+	12	68715627	+	11.2876	283.5483	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000123297	ENSG00000111581	TSFM	NUP107	GCCTGACAGAGAAGGCTCACTCAAGGATCAGTTGGCTTTAGCAATTG*CTGGTGGTAGATTGGTTAGAGAGTATTGCCAAAGATGAAATTGGAGA	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	131	2	26	12	57793073	+	12	68710005	+	11.2876	283.5483	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000123297	ENSG00000111581	TSFM	NUP107	CCTTGGAACCATGATGCATTGTCAGACCCTAAAGGATCAACCCTCTGCAT*ACACTAAAGAAGTCTATTTTTAGAAAGAGGAAAAGACTTCAAGAAAATAC	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	131	1	14	12	57787154	+	12	68699397	+	11.2876	283.5483	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000123297	ENSG00000111581	TSFM	NUP107	GCCTGATTGGGCTGTTGCAGGAAGGAAACACAACTGTATTAGTAGAG*GGAAAATACTCTGCATACCTTAAAACAACGGCAGCTGACTTCTTACG	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	131	1	13	12	57786291	+	12	68713730	+	11.2876	283.5483	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000146648	ENSG00000111110	EGFR	PPM1H	GCTGGCTGCGCTCTGCCCGGCGAGTCGGGCTCTGGAGGAAAAGAAAG*GAATCCGAGGGTGTTTCCTGCCACTATTGGTCGCTGTTTGACGGGCA	oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	94	28	30	7	55019365	+	12	62802160	-	266.3115	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000146648	ENSG00000111110	EGFR	PPM1H	GTCACATTTTATTTCACAAGTTAGTCCATTAAAAGTTTCCTGCAGTGAGG*TTACATGTTAATATAAGATGATGTAGCTCTTCAGCCACAGGGGTATAAAC	oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+STAR	intronic/intronic	0	94	2	16	7	55026351	+	12	62925686	-	266.3115	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000146648	ENSG00000111110	EGFR	PPM1H	CTGTTTGAAGAATTTGAGCCAACCAAAATATTAAACCTGTCTTACACACA*CACACACACACACACACACACACACACACACACGCTTTCTCTCTCTTTCA	oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+BOWTIE2	intronic/intronic	0	94	1	34	7	55020566	+	12	62704008	-	266.3115	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000146648	ENSG00000111110	EGFR	PPM1H	GCTCCCGGGGAGGGGTGGTGCTGGCGGCGGTTAGTTTCCTCGTTGGCAAA*AGGAATCCGAGGGTGTTTCCTGCCACTATTGGTCGCTGTTTGACGGGCAC	oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+STAR	intronic/intronic	0	94	1	32	7	55020121	+	12	62802162	-	266.3115	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000146648	ENSG00000111110	EGFR	PPM1H	TGGCCCAGAACATGAGCAGCCTCTCTCTCTCACTCTCACTGTCTCTCTTT*CACTCTCACTGCCATCCACCTGGTGACATCATCCTAGCACCATCGCCTCT	oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+STAR	intronic/intronic	0	94	1	14	7	55149361	+	12	62700722	-	266.3115	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000135679	ENSG00000111110	MDM2	PPM1H	AGAGTGATACAGATTCATTTGAAGAAGATCCTGAAATTTCCTTAGCT*GAATCCGAGGGTGTTTCCTGCCACTATTGGTCGCTGTTTGACGGGCA	known,oncogene,18cancers,cancer,tumor,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	35	14	29	12	68836749	+	12	62802160	-	438.8763	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000135679	ENSG00000111110	MDM2	PPM1H	GAGGTAATTCTGCACAGCAACTTTACTAATGGTACATTGTTGCTTCAAAA*CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTAGCTCAAGGTCATG	known,oncogene,18cancers,cancer,tumor	BOWTIE+STAR	UTR/intronic	0	35	3	35	12	68843698	+	12	62702578	-	438.8763	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000135679	ENSG00000111110	MDM2	PPM1H	CTTAATAAGGGTTTTATTTTATTTTTATTTATTTTTTGAGACGGAGTCTT*GCCACTGCACTCCAGCCTGGGTGAAAGAGTGAGACTCTGTCCCAAAAAAA	known,oncogene,18cancers,cancer,tumor	BOWTIE+BLAT	UTR/intronic	0	35	1	34	12	68844797	+	12	62665108	-	438.8763	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000135679	ENSG00000111110	MDM2	PPM1H	TCCTGCCTCAGCCTTCCAAGTAACTGGGATTACAGGCATGTACCACCATA*CCAGCTACTTGGAAGGCTGAGGCAGGAGAATTGCTTGAACTCGGGAGGTG	known,oncogene,18cancers,cancer,tumor	BOWTIE+STAR	UTR/intronic	0	35	1	28	12	68841002	+	12	62779172	-	438.8763	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000135679	ENSG00000111110	MDM2	PPM1H	CTGCACAGCAACTTTACTAATGGTACATTGTTGCTTCAAAACTCTCTCTC*TCTCTCTCTCTCTCTCTCTCTCTCTGCATTAGCATGGTCCTAAGCAGATA	known,oncogene,18cancers,cancer,tumor	BOWTIE+STAR	UTR/intronic	0	35	1	26	12	68843707	+	12	62717476	-	438.8763	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000135679	ENSG00000111110	MDM2	PPM1H	GATGTTATCTCAGTGCCTTTTGCAATTTGTTGTGTGGGTTTTTTTTTTTT*TTAAAAACACAAAATAAGTTTTCATATGTGTGTGTATATATGACTGCAAA	known,oncogene,18cancers,cancer,tumor	BOWTIE+STAR	UTR/intronic	0	35	1	21	12	68843105	+	12	62652550	-	438.8763	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000135679	ENSG00000111110	MDM2	PPM1H	CTTCAGCCTCCCAAGTAGCTGGGGTTAGAGCACCCTGTCACCACGCCCCG*CTACTTGGGAGGCTGAAGCGGGAGAATCGCTTGAACCCTGGAGGCGAAGG	known,oncogene,18cancers,cancer,tumor	BOWTIE+BLAT	UTR/intronic	0	35	1	19	12	68844930	+	12	62668506	-	438.8763	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000135679	ENSG00000111110	MDM2	PPM1H	CTTCCGCCTTCTGGGTTCAAGCTATTCTCCTGCCTCAGCCTTCCAAGTAA*TTGGAAGGCTGAGGCAGGAGAATTGCTTGAACTCGGGAGGTGGAAGTTGC	known,oncogene,18cancers,cancer,tumor	BOWTIE+STAR	UTR/intronic	0	35	1	17	12	68840975	+	12	62779164	-	438.8763	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000135679	PPM1H	MDM2	TTATTTCTCTCGCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTCT*CAATAAAATCAACTGAACTGTAAGCTTAGAATAGGACTGAGGTAATTCTG	known,oncogene,18cancers,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	35	9	27	12	62840048	-	12	68843611	+	9.7382	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000135679	PPM1H	MDM2	TGGGAGGCCCAGGTGGGCAGATCACTTGAGGCCAGGAGTTCGAGACCAGC*CTGGGCAACATGGTGCAACCCTGTCTTAACTAAAAATACAAAAATTAGCC	known,oncogene,18cancers,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	35	5	31	12	62795940	-	12	68850092	+	9.7382	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000135679	PPM1H	MDM2	CGCCACCATGCCTGGCTAATTTTTTGTATTTTTAGTAGAGACAGGGTTTC*CATGCTAGCCTTGAACTCCTGACCTTGTGATCTGCCTGCCTCGGCCTC	known,oncogene,18cancers,cancer,tumor	BOWTIE+BOWTIE2	intronic/UTR	0	35	3	36	12	62768475	-	12	68849609	+	9.7382	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000135679	PPM1H	MDM2	TAGTACCGATGGTTTTGCCATGTTGGCTAGGCTGGTCTCGAACTCCTTAC*CTCAGGTGATCCAGTCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGATG	known,oncogene,18cancers,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	35	2	24	12	62846286	-	12	68849844	+	9.7382	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000135679	PPM1H	MDM2	CAACCTCCACCTCCCGGGTTCAAGCAATTCTCCTGCCTCAACCTCCCGAG*TAGCTTGGCCTACAGTCATCTGCCACCACACCTGGCTAATTTTTTGTACT	known,oncogene,18cancers,cancer,tumor	BOWTIE+BOWTIE2	intronic/UTR	0	35	1	38	12	62793614	-	12	68840273	+	9.7382	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000135679	PPM1H	MDM2	AGGCTGGAGTGCAGTGGCGCAATCTCGGCTCACTGCAACCTCCGCCTCCT*GGCTGTGTTCAAGTGGTTCTGCTTCAGCCTCCCAAGTAGCTGGGGTTAGA	known,oncogene,18cancers,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	35	1	38	12	62846425	-	12	68844860	+	9.7382	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000135679	PPM1H	MDM2	TGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCG*GCCTCCCAATTAGCTTGGCCTACAGTCATCTGCCACCACACCTGGCTAAT	known,oncogene,18cancers,cancer,tumor	BOWTIE+BOWTIE2	intronic/UTR	0	35	1	35	12	62838687	-	12	68840263	+	9.7382	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000135679	PPM1H	MDM2	GTGGGTGGATCACTTGAGGCCAGGAGTTTGAGACCAGCCTGGGCAACATG*GTGCAACCCTGTCTTAACTAAAAATACAAAAATTAGCCAGGCGTCATGGC	known,oncogene,18cancers,cancer,tumor	BOWTIE+BOWTIE2	intronic/UTR	0	35	1	34	12	62802783	-	12	68850104	+	9.7382	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000135679	PPM1H	MDM2	TTTCTCTCGCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTCTCTC*TCAATAAATGGCCAAAGGGATTAGTAGTTTACCTGTGGAGGTCCTCCAAG	known,oncogene,18cancers,cancer,tumor	BOWTIE+BOWTIE2	intronic/UTR	0	35	1	34	12	62840045	-	12	68843724	+	9.7382	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000135679	PPM1H	MDM2	ACATGATCACGAAGGTGGTTTTCCCAGGGCGAGGTTTATCCATTGCACTC*AAAAAAACTATAGTGAATGATTCCAGAGAGTCATGTGTTGAGGAAAATGA	known,oncogene,18cancers,cancer,tumor	BOWTIE+STAR	intronic/CDS(truncated)	0	35	1	33	12	62850829	-	12	68839460	+	9.7382	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000135679	PPM1H	MDM2	GGCTCACACCTGTAGTCCCAGCACTTTGGGAGGCCAAGGCAGGTTGATTG*CTCGAACTCCTGGGCTCAAGAGATCCTCCTGTCTTGGCCTCGCAAAGTGC	known,oncogene,18cancers,cancer,tumor	BOWTIE+BLAT	intronic/UTR	0	35	1	32	12	62850204	-	12	68841314	+	9.7382	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000135679	PPM1H	MDM2	GATGGGGTTTCACCATGGCTGGTCTCGAACTCCTGGCCTCAGGTGATCCG*CCTGCCTCAGCCTCCCAGTAGTTGGAATTACAGGCGCATGCCACCATGCA	known,oncogene,18cancers,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	35	1	32	12	62908189	-	12	68849519	+	9.7382	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000135679	PPM1H	MDM2	CCAGCACTTTGGGAGGCCGAGGCAGGCAGATCACAAGGTCAGGAGTTCGA*GGCCAACATGGTGAAACCCTGTCTCTACCAAAAATACAAAAATTATCCAG	known,oncogene,18cancers,cancer,tumor	BOWTIE+BLAT	intronic/intronic	0	35	1	30	12	62779267	-	12	68827940	+	9.7382	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000135679	PPM1H	MDM2	GTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCG*CTGCGCCTGGCCGTTTTTTTTTTTGTTGTTGTTGTTGTTTGTTCGTTTGT	known,oncogene,18cancers,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	35	1	22	12	62838696	-	12	68849378	+	9.7382	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000135679	PPM1H	MDM2	TATGTTGTGTGTGTTTTTGTTTTTTATTTCTCTCGCTCTCTCTCTCTCTC*ACTCTCTCTCTCTCTCTCTGTCTGTCTCAATAAATGGCCAAAGGGATTAG	known,oncogene,18cancers,cancer,tumor	BOWTIE+BLAT	intronic/UTR	0	35	1	20	12	62840071	-	12	68843698	+	9.7382	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000135679	PPM1H	MDM2	TTCCTTTCCTTTCGAGACAGAGTCTTACTCTGTCACAAGGCTGGAGTGCA*GTGAGCCGAGATCCCACCACTGCACTCCAGCCTGGGTGACAGAGCGAGAC	known,oncogene,18cancers,cancer,tumor	BOWTIE+BLAT	intronic/UTR	0	35	1	20	12	62778893	-	12	68850228	+	9.7382	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000135679	PPM1H	MDM2	TTCCAGCTTCATCCGTGTCCCTAAAAAGGGCATGAACTCATCCTTTTTTA*AAAGAAAAAGTATTTCTTCAGCTTAAAAAATTGTTTAAAAGTTTGTGATC	known,oncogene,18cancers,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	35	1	20	12	62879433	-	12	68845208	+	9.7382	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000135679	PPM1H	MDM2	GTTTAATTTAAAGTTGACTTACGGGGATTTATCAATTGTACATATTTTCT*TCAAAACTCTCTCTCTCTCTCTCTGTCTGTCTCAATAAATGGCCAAAGGG	known,oncogene,18cancers,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	35	1	17	12	62830739	-	12	68843693	+	9.7382	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000135679	PPM1H	MDM2	GACAGGGTTTCATCATGTTGATCAGGCTGGTCTCAAAATCCTGACCTCAG*GTGGGTGGATCACTTGAGGCCAGGAATTCAAGACCAACCTGGGCAACATG	known,oncogene,18cancers,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	35	1	17	12	62791703	-	12	68850054	+	9.7382	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000135679	PPM1H	MDM2	TCACCGCCAGTGTGATGGTTTTTGGAGGTGGAGCCTTTTGAAATTGTTCA*GACAGATAGTTGGGGATGAGAGCCGAATAAGGTTTGCCTGAAATAACTGA	known,oncogene,18cancers,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	35	1	16	12	62840337	-	12	68842909	+	9.7382	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000135679	PPM1H	MDM2	GGTGCGGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGACTGAGGTGG*GAGGATCACTTGAGGCCAGGAGTTTGAGATCAGCCTGGGCAACATAATGA	known,oncogene,18cancers,cancer,tumor	BOWTIE+BLAT	intronic/UTR	0	35	1	15	12	62745307	-	12	68847938	+	9.7382	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000135679	PPM1H	MDM2	CTAGGCTCAAGCAGTCCTTTCACCTCAGCCTCTCAAGTACCTGGGACTAT*TAATTGCACACAAAACCACTTTTAATGGGTACAGAGTTAAATTTGAAGGA	known,oncogene,18cancers,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	35	1	15	12	62839915	-	12	68843159	+	9.7382	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000135679	PPM1H	MDM2	AGTTCTTTAGGCTTTCACGTGCCGTCATCTTCGGCCGTTCAATTGGCTCC*GCTTCAGCCTCCCAAGTAGCTGGGGTTAGAGCACCCTGTCACCACGCCCC	known,oncogene,18cancers,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	35	1	14	12	62756736	-	12	68844880	+	9.7382	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000180806	ENSG00000170473	HOXC9	PYM1	ACAGAGTCTTCTGGGTCTCTCTGCCTGAGGCCCTGGAGGGAGAGAAG*GCAAGTATATCGCGTCAACACAGCGACCTGACGGGACCTGGCGCAAG	18cancers,exon-exon	BOWTIE;BOWTIE+STAR	UTR/CDS(truncated)	0	26	21	29	12	53995016	+	12	55903480	-	1.3571	16.8195	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000180806	ENSG00000170473	HOXC9	PYM1	TGCAAATTTCCTTGCGACACATACATCACACAAAAGATCAG*GCAAGTATATCGCGTCAACACAGCGACCTGACGGGACCTGGCGCAAG	18cancers,exon-exon	BOWTIE	UTR/CDS(truncated)	0	26	2	25	12	53995549	+	12	55903480	-	1.3571	16.8195	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000180806	ENSG00000170473	HOXC9	PYM1	ACAGAGTCTTCTGGGTCTCTCTGCCTGAGGCCCTGGAGGGAGAGAAG*ATATGAAAACAAGTATGTGAAGTTTTTCAAGAGTAAACCAGAGTTGC	18cancers,exon-exon	BOWTIE	UTR/CDS(truncated)	0	26	1	13	12	53995016	+	12	55902355	-	1.3571	16.8195	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111581	ENSG00000111012	NUP107	CYP27B1	ACGTCTTGTTGTTTGTTGATGGAGGGTGGATGGTGGATGTTAGAGAG*ACTGTACCCTGTGGTACCTGGAAATTCTCGTGTCCCAGACAAAGACA	18cancers,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	11	17	30	12	68735344	+	12	57764176	-	283.5483	121.1904	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111581	ENSG00000111012	NUP107	CYP27B1	TATAACGTCTTGTTGTTTGTTGATGGAGGGTGGATGGTGGATGTTAGAGA*GGGCTGCAGCCCCTAGCCTCATCTTGTTGTCTCCATTTTGTGCTTTGCAA	18cancers	BOWTIE+STAR	CDS(truncated)/intronic	0	11	7	25	12	68735343	+	12	57764231	-	283.5483	121.1904	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111581	ENSG00000111012	NUP107	CYP27B1	GGTCTGAGGTAGGGCTGGGGTTTATTTTTGTTTTTTTAATCACTTGCAGT*GCTGCAGCCCCTAGCCTCATCTTGTTGTCTCCATTTTGTGCTTTGCAACC	18cancers	BOWTIE+STAR	intronic/intronic	0	11	1	29	12	68735821	+	12	57764229	-	283.5483	121.1904	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000135679	ENSG00000154978	MDM2	VOPP1	AAAAGTACTAATCCCTTTGGCCATTTATTGAGAGAGAGAGAGAGAGAGAG*AGTAGGGTGACTATAGTTAATAATATATTTTATAATAGCTAGAAGAGAAT	known,oncogene,cancer,tumor	BOWTIE+STAR	UTR/intronic	0	10	4	21	12	68843316	+	7	55457001	-	438.8763	98.8104	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000135679	ENSG00000154978	MDM2	VOPP1	TATTTTATTTTTATTTATTTTTTGAGACGGAGTCTTGCTCTGTGGCTCAG*CCAGGAGGCAGAGGTTGCAGTGAGCCAAGATCGCACCACTGCACTCCAGC	known,oncogene,cancer,tumor	BOWTIE+BLAT	UTR/intronic	0	10	1	27	12	68844811	+	7	55531444	-	438.8763	98.8104	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000135679	ENSG00000154978	MDM2	VOPP1	CTTTTAATGGGTACAGAGTTAAATTTGAAGGAATAAGTTCTAGCTGAAGT*GCTGTGGGCTCCAAAGGCCCCATCATGTTCTCCTCTCCTCCTCAGGGCCT	known,oncogene,cancer,tumor	BOWTIE+STAR	UTR/intronic	0	10	1	14	12	68843226	+	7	55468368	-	438.8763	98.8104	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000154978	ENSG00000135679	VOPP1	MDM2	GCCAGCCTGCGAAGGTGGCGGCGCTGCTGCTCGGGCTGCTCTTGGAG*AATCATCGGACTCAGGTACATCTGTGAGTGAGAACAGGTGTCACCTT	known,oncogene,cancer,tumor,exon-exon	BOWTIE	in-frame	0	10	6	29	7	55572271	-	12	68824363	+	98.8104	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000154978	ENSG00000135679	VOPP1	MDM2	GCCAGCCTGCGAAGGTGGCGGCGCTGCTGCTCGGGCTGCTCTTGGAG*GAAAATATATACCATGATCTACAGGAACTTGGTAGTAGTCAATCAGC	known,oncogene,cancer,tumor,exon-exon	BOWTIE	in-frame	0	10	4	29	7	55572271	-	12	68820325	+	98.8104	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000154978	ENSG00000135679	VOPP1	MDM2	GATCTTAGCTCACTGCAACCTCCGCCTCCCGGGTCCAAGCGATTCTCCTG*CCTCAGCCTTCCAAGTAACTGGGATTACAGGCATGTACCACCATACCAGC	known,oncogene,cancer,tumor	BOWTIE+BOWTIE2	intronic/UTR	0	10	1	38	7	55539250	-	12	68840958	+	98.8104	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000154978	ENSG00000135679	VOPP1	MDM2	GTGTGTGTCTGTGTGTGTATGTCTGTGTGTGTGTGTGTGTGTCTGTGTGT*GTGGATGCTGAATTACATTTTGATTTGATACTTATAAAAAGAAAAAGTAT	known,oncogene,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	10	1	37	7	55445237	-	12	68845171	+	98.8104	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000154978	ENSG00000135679	VOPP1	MDM2	TTTGTTTAGTAGAGACGGGGTTTCACTGTGTTAGGCAGGATGGTCTCGAT*CTCCTGGGCTCAAGAGATCCTCCTGTCTTGGCCTCGCAAAGTGCTAAGTA	known,oncogene,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	10	1	31	7	55442910	-	12	68841320	+	98.8104	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000154978	ENSG00000135679	VOPP1	MDM2	GCTTATTTTTTGTATTTTTAGTAGAGATGGGGTTTCACCGTGTTAGCCAG*GCTGGTCTCGAACTCCTGACCTCATGATCCGCCCACCTCGGCCTCCCAAA	known,oncogene,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	10	1	23	7	55443360	-	12	68846166	+	98.8104	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000154978	ENSG00000135679	VOPP1	MDM2	GCTTATTTTTTGTATTTTTAGTAGAGATGGGGTTTCACCGTGTTAGCCAG*GCTGATCTTGAACTCCTAAACTCAAGTGATCTACTCACCTCAGCCTCCCA	known,oncogene,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	10	1	23	7	55443360	-	12	68841057	+	98.8104	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000154978	ENSG00000135679	VOPP1	MDM2	TGCAATCTCAGCTCACTTCCACCTCCTCCTCCCGGGTTCAAGGGATTCTC*CTGCCTCAGCCTTCCAAGTAACTGGGATTACAGGCATGTACCACCATACC	known,oncogene,cancer,tumor	BOWTIE+BLAT	intronic/UTR	0	10	1	19	7	55468179	-	12	68840955	+	98.8104	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000154978	ENSG00000135679	VOPP1	MDM2	ATTTCCTTCACGGATTTTAACAAGCCAGGACACAGTGACAGCTATTAGAA*CAAGCAGAATCTGTTTTTTTCTGAGGAGTATCGGTAGCATAAATGTGATT	known,oncogene,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	10	1	18	7	55534069	-	12	68843977	+	98.8104	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000154978	ENSG00000135679	VOPP1	MDM2	GAGTGCTTGCCTAAGCACTCTGCGGTGTCATCTCCAGAGAGCTGGGGATG*AGAACAAAATGGCCTTATATAATGAAGCCTAGTTATGCTGGACTGTTTTG	known,oncogene,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	10	1	16	7	55514717	-	12	68842841	+	98.8104	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000154978	ENSG00000135679	VOPP1	MDM2	CCTTTGACTGCCGTTTCAACTCCCACCATACTTGAAGACCCTCAGGTGGT*CGCCTCGGCCTCCCAAAGTGCTGGGATTACAGATGTGAGTCACTACGCTT	known,oncogene,cancer,tumor	BOWTIE+STAR	UTR/UTR	0	10	1	16	7	55561886	-	12	68849859	+	98.8104	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000154978	ENSG00000135679	VOPP1	MDM2	GAAGTGGATGGAGTTTTCCCATCGACAGATAGTTTTCTTCCTTTCCAGCA*CCTCAAAGCATTATTGGAGTTCATAATACTGAAGCTAGAACCAAGCAGAA	known,oncogene,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	10	1	16	7	55487283	-	12	68843936	+	98.8104	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000154978	ENSG00000135679	VOPP1	MDM2	GAGGACTCTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAATCTTGCTC*GTGGCTCAGGCTGGAGTACAGTGGTGCAATCTTGGCTCACTGCAACCTCT	known,oncogene,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	10	1	15	7	55529348	-	12	68844803	+	98.8104	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000154978	ENSG00000135679	VOPP1	MDM2	CATTTTTAATGGCTTCTGTTTTTGATATTGAGCGGTAAGACTTTAAATAC*CCTCTTTTGTATAAACCATAGTAAGGGATGGGAGTAATGATGTTATCTGT	known,oncogene,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	10	1	14	7	55541064	-	12	68841424	+	98.8104	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000154978	ENSG00000135679	VOPP1	MDM2	GATAGGATCCTGTTTCCTATGTGTGCAAAATAAAAATAAATTTGGGC*ATGTGCAAAGAAGCTAAAGAAAAGGAATAA	known,oncogene,cancer,tumor,exon-exon	BOWTIE	UTR/CDS(truncated)	0	10	1	13	7	55470614	-	12	68839762	+	98.8104	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000197757	ENSG00000170473	HOXC6	PYM1	AGCTAACAGAAACGCCAGGAGCAGCAGGAGGAGGAGGCAGCGACAAG*GCAAGTATATCGCGTCAACACAGCGACCTGACGGGACCTGGCGCAAG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	9	4	26	12	53990814	+	12	55903480	-	1.1359	16.8195	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000257921	ENSG00000111581	AC025165.3	NUP107	AAGGCCTGATTGGGCTGTTGCAGGAAGGAAACACAACTGTATTAGTAGAG*ATGGATTTTGGTATTTGGAAAGGGCATTTGGATGCCCTAACTGCTGATGT	exon-exon	BOWTIE+STAR	UTR/CDS(truncated)	0	8	1	18	12	57786291	+	12	68735231	+	0	283.5483	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000165304	ENSG00000224596	MELK	ZMIZ1-AS1	CCTGTCCTTCTGTCGGGCGCCGCTCAGCCGTGCCCTCCGCCCCTCAG*GGAGCTCAGGAGGGGGAATTGCACTGAAGATTTGTCCCATCGTGAAG	antisense,18cancers,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	UTR/exonic(no-known-CDS)	0	8	3	19	9	36573007	+	10	78945989	-	14.1642	1.6305	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000165304	ENSG00000224596	MELK	ZMIZ1-AS1	TCCCTGGATAAGATATTTGACCTTTCCGACCCGCGGTTTTCTTCTCC*GGAGCTCAGGAGGGGGAATTGCACTGAAGATTTGTCCCATCGTGAAG	antisense,18cancers,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	8	2	19	9	36573198	+	10	78945989	-	14.1642	1.6305	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000273049	ENSG00000170473	AC012531.3	PYM1	GGGACAGAGTCTTCTGGGTCTCTCTGCCTGAGGCCCTGGAGGGAGAGAAG*GCAAGTATATCGCGTCAACACAGCGACCTGACGGGACCTGGCGCAAGCAG	NA	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	7	4	22	12	53995016	+	12	55903480	-	0	16.8195	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000273049	ENSG00000170473	AC012531.3	PYM1	AGCAGCTAACAGAAACGCCAGGAGCAGCAGGAGGAGGAGGCAGCGACAAG*GCAAGTATATCGCGTCAACACAGCGACCTGACGGGACCTGGCGCAAGCAG	NA	BOWTIE+STAR	intronic/CDS(truncated)	0	7	1	17	12	53990814	+	12	55903480	-	0	16.8195	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000273049	ENSG00000170473	AC012531.3	PYM1	GGCCAAAGCTGCCGACTCCAGCCCAGACACCTCGGATAACGAAGCGAAAG*GCAAGTATATCGCGTCAACACAGCGACCTGACGGGACCTGGCGCAAGCAG	exon-exon	BOWTIE+STAR	in-frame	0	7	1	14	12	53986010	+	12	55903480	-	0	16.8195	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000111490	PPM1H	TBC1D30	GTGATTTGCCTTTTGGGGAAGCTGTATGTTGCAAATGCTGGGGATAGCAG*ATGGAATCTTGCTGTGTTGCCCAGGCCGGAGTGCAGTGGTGCGATGTTGG	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	5	1	22	12	62788226	-	12	64792591	+	9.7382	21.6381	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000111490	PPM1H	TBC1D30	TCAGCTTCTTTCAAGGACTGGTGATGCTTCAGGCAAAGGGTTTAACCATG*GACAGTCTCGTGCTGTTGCCAGGCTGGAATGCTGGAATGCAGTGGCGCAA	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/intronic	0	5	1	16	12	62929622	-	12	64818455	+	9.7382	21.6381	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111490	ENSG00000111110	TBC1D30	PPM1H	GAAATCATCCTAAGGGTGTCGCTGGCTATCTGGGCAAAATTAGGAGA*GGTTATCAATGCCGGGAAGAGCACACACAATGAAGACCAAGCCAGCT	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	5	11	25	12	64838851	+	12	62832279	-	21.6381	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111490	ENSG00000111110	TBC1D30	PPM1H	TCAGAAATCATCCTAAGGGTGTCGCTGGCTATCTGGGCAAAATTAGGAGA*ACTCGGGTGTGTCTTTATCAGCAGCATGAAAATAGACTAATACACCCTCA	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/intronic	0	5	1	35	12	64838851	+	12	62884962	-	21.6381	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111490	ENSG00000111110	TBC1D30	PPM1H	GTGGGTTCCTGGCTCCTGAACTGCAGAAGTACCAAAAACAAATTAAAGGT*GACCTTGAACAAAATGCCTAACCTCTCTGTGCCTTCCTTATCAGGGAAAT	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/intronic	0	5	1	15	12	64866905	+	12	62770365	-	21.6381	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111490	ENSG00000111110	TBC1D30	PPM1H	GGCTGGGGGCAGCAGAGGCATTCCCCTCTGGTTGTACAGCGACAGCTGGG*GCCAGCAGTGGCATTGAAAAGGGAATTCATATTAGGTTCAATTAGTAATA	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	5	1	15	12	64875359	+	12	62778266	-	21.6381	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111490	ENSG00000111110	TBC1D30	PPM1H	GGGTGCACCCACCCTGCCAGCGGCACTGCCCAGAGCCGCCGAGTGCACCC*ACCCTGCCAGTGGAACTAAGTTCCTTTGAAGGCTGTCAACTATGACTCCC	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	5	1	14	12	64875569	+	12	62649585	-	21.6381	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111490	ENSG00000111110	TBC1D30	PPM1H	AAGACCAATGGGCTGGGGGCAGCAGAGGCATTCCCCTCTGGTTGTACAGC*AGGACCTATGGGCTAATTCTCAGCCTATTTTTAGGATCCCATTTCTAAGG	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	5	1	14	12	64875349	+	12	62708668	-	21.6381	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000135407	ENSG00000132434	AVIL	LANCL2	AAGTTTTCCAGGATAAATTTGATGTGACTCTGCTACACACCAAGCCAGAG*TCAGATCATTCATAATTTCATAAGACGGATCCAGACCAAAATTAAAGATC	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	29	12	57808242	-	7	55391789	+	20.5013	433.6163	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000132434	ENSG00000135679	LANCL2	MDM2	TCTACTAAACATACAAAAATTAGCCGGGTGTGGTGGCGGGCACCTGTAGT*CTCAGCCTCCCAATTAGCTTGGCCTACAGTCATCTGCCACCACACCTGGC	oncogene,cancer,tumor	BOWTIE+BLAT	intronic/UTR	0	2	1	36	7	55384433	+	12	68840259	+	433.6163	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000132434	ENSG00000135679	LANCL2	MDM2	CTGGGAGGCGGAGGTTGCAGTGAGCTATGATCATGCCACTGCACTCCAGC*CTGGGTGACAGAGCGAGACTTCGTCCCAAAAAAAAAAAAAAAAGCTGCAA	oncogene,cancer,tumor	BOWTIE+BLAT	intronic/UTR	0	2	1	27	7	55414956	+	12	68850259	+	433.6163	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000132434	ENSG00000135679	LANCL2	MDM2	TTTGTATTTTTAGTAGAGATGGGGTTTCACCGTGTTAGCCGGGATGGTCT*CATTCTCCTGCCTCAGCCTCCCAATTAGCTTGGCCTACAGTCATCTGCCA	oncogene,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	2	1	26	7	55417199	+	12	68840248	+	433.6163	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000132434	ENSG00000135679	LANCL2	MDM2	GAGCTAAGACGGCATGTGAGTGTGCATTAGGCCTGGAAAACTCAACTTAA*CCTGAAGATAAAGGGAAAGATAAAGGGGAAATCTCTGAGAAAGCCAAACT	oncogene,cancer,tumor	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	18	7	55379288	+	12	68839364	+	433.6163	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000132434	ENSG00000135679	LANCL2	MDM2	TTAATAAATAAGTGACTAAATGAAACTATCAAGGAAAAAAATCAAAGAGA*AGAACATGTGTCTGTTAATTGCACACAAAACCACTTTTAATGGGTACAGA	oncogene,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	2	1	18	7	55395624	+	12	68843144	+	433.6163	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000132434	ENSG00000135506	LANCL2	OS9	TCGGCATCAGGGGGAGACCGTGGAAAGAGAGGGAGAGGGAGAGGGAGAGG*GACCCAGATGGGCTGAAGAAGGAGTCAGAGCGGGATCGGGCAATGCTGGC	NA	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	18	7	55403460	+	12	57719008	+	433.6163	964.1605	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000132434	ENSG00000135506	LANCL2	OS9	GTCCCAGCTACTCGGGAAGCTGAGGCAGGAGAATGGTGTGAAGGCAGGAG*TGAAACGGGAAAACCCACAGCTGAAACAAATCGAGGGGCTGGTGAAGGAG	NA	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	16	7	55379060	+	12	57720183	+	433.6163	964.1605	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000135679	ENSG00000132434	MDM2	LANCL2	CATGCATGGGAGACTGAGGTGGGAGGATCACTTGAGCCCAGGAGTCCAAT*GTTGCAGTGAGCTATGATCATGCCACTGCACTCCAGCCTGGGTGACACAG	oncogene,cancer,tumor	BOWTIE+STAR	UTR/intronic	0	2	5	33	12	68848064	+	7	55414920	+	438.8763	433.6163	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000135679	ENSG00000132434	MDM2	LANCL2	GCCCAAAGTTAAGCATTTTTTAACCACAAGGTGGGAGGTGGAAGTATCTC*GCTGGTCTCAAACTCCTGACCTCATGATCCGCCCACGTCAGCCTCCCAAA	oncogene,cancer,tumor	BOWTIE+STAR	UTR/intronic	0	2	1	31	12	68849057	+	7	55403783	+	438.8763	433.6163	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000135679	ENSG00000132434	MDM2	LANCL2	AAATTTAAACGTTGAAGTCTAGGTAAATATACCAGGGAACTTCTGCTTAA*GAGGCTGAGGTGGGTGGATCACTTGAGGCCAGGAGTTCAAGACCATTCTG	oncogene,cancer,tumor	BOWTIE+BLAT	UTR/intronic	0	2	1	28	12	68850356	+	7	55378220	+	438.8763	433.6163	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000135679	ENSG00000132434	MDM2	LANCL2	GCCTCCCAGTAGTTGGAATTACAGGCGCATGCCACCATGCATGGCTAATT*TTTTTGTGTTTTTAGTAGAGACAGGATTTCACCATGTAGGCCAGGCTGGT	oncogene,cancer,tumor	BOWTIE+STAR	UTR/intronic	0	2	1	25	12	68849577	+	7	55419569	+	438.8763	433.6163	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000135679	ENSG00000132434	MDM2	LANCL2	CCTGCCTCAGCCTCCCAATTAGCTTGGCCTACAGTCATCTGCCACCACAC*CTGGCTAACACGGTGAAACCCTGTCTCTACTAAAAATACAAAAAATTAGC	oncogene,cancer,tumor	BOWTIE+BLAT	UTR/intronic	0	2	1	23	12	68840303	+	7	55378938	+	438.8763	433.6163	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000135679	ENSG00000132434	MDM2	LANCL2	ACCATGCCTGGCAAATTTTTGTATTTTCAGTAGAGATGGGGTTTTGCTAT*GCTAGTCTTGAACTCCTGACCTTAGGTGATCTGCCTGCCTTGGCCTCCAA	oncogene,cancer,tumor	BOWTIE+BLAT	UTR/intronic	0	2	1	22	12	68849814	+	7	55415826	+	438.8763	433.6163	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000135679	ENSG00000132434	MDM2	LANCL2	AGTCTTGCTCTGTGGCTCAGGCTGGAGTACAGTGGTGCAATCTTGGCTCA*GGCTAGAGTACAGTGGTGCAATCACAGCTCTCTACAGCCTTGACCTCCTG	oncogene,cancer,tumor	BOWTIE+STAR	UTR/intronic	0	2	1	20	12	68844841	+	7	55392395	+	438.8763	433.6163	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111581	ENSG00000111110	NUP107	PPM1H	CTCAGAGAGTCCTCTCTAATGCTCCTAGACCAGGGACTTGACCCATTAGG*ACAGGGTCTCAATCTGTTGCCTAGGCTGGCGTGCAGTGGTGCAGTTTCGG	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	22	12	68742443	+	12	62743349	-	283.5483	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111581	ENSG00000111110	NUP107	PPM1H	CTCAGAGAGTCCTCTCTAATGCTCCTAGACCAGGGACTTGACCCATTAGG*ACAGATTCTCCCTCTGTTGCCTAGGCTGGAGTGCAGTGGCGCCATCTCGG	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	22	12	68742443	+	12	62843313	-	283.5483	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111581	ENSG00000111110	NUP107	PPM1H	TAACGTCTTGTTGTTTGTTGATGGAGGGTGGATGGTGGATGTTAGAGAGG*ATGTTAAAGAAGACCATCTGGTTACTTGGCTTTTATTTAGATCGCAATAG	NA	BOWTIE+STAR	intronic/intronic	0	2	1	17	12	68735345	+	12	62700880	-	283.5483	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111581	ENSG00000135452	NUP107	TSPAN31	CAGATCACGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAAC*CCTGTCATTACTAAAAGTACAAAAATTAGCTGAGCATGGTGGCGTGCACC	NA	BOWTIE+STAR	intronic/UTR	0	2	2	35	12	68692404	+	12	57749823	+	283.5483	275.7682	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111581	ENSG00000135452	NUP107	TSPAN31	GGTTTGGTGACGCACACCTGTAATCCCAGCTACTTGGGAGGCTGAGGCAG*GGTGATCCACCCGCGTTGGCCTCCCAACGTGCTGGGATTATAGGCGTGAG	NA	BOWTIE+BOWTIE2	intronic/UTR	0	2	1	37	12	68710562	+	12	57747977	+	283.5483	275.7682	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111581	ENSG00000135452	NUP107	TSPAN31	TGAGAGGCTGAGGCAGGAGCACCGCTTGAACCTGGGAGGTGGAGGTTGCA*GCGGCTCACGCCTGTAATCCTAGCACTTTGGGAGTCTGATGTGGGTGGAT	NA	BOWTIE+BLAT	intronic/UTR	0	2	1	18	12	68696306	+	12	57749728	+	283.5483	275.7682	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111581	ENSG00000135452	NUP107	TSPAN31	AGAGGTGACACGGACTGCACGGAAACAGAGTGCTCAGAAAAGAGTTTTAC*TACATGATCATCCTTGGTTTGGTCTTCATCTTCCAATTTGTAATCTCTTG	exon-exon	BOWTIE+STAR	out-of-frame	0	2	1	18	12	68689053	+	12	57746176	+	283.5483	275.7682	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111581	ENSG00000135452	NUP107	TSPAN31	ATAGTGTTATGACCACTGTACAAGCATTAACTCATGTAATCCTTATGGTG*ATAAGAGTGCTGCAGAGCTCGAAAGGCAGAGATTCGCTTGTGTGGGTTAA	NA	BOWTIE+STAR	intronic/UTR	0	2	1	15	12	68693977	+	12	57748555	+	283.5483	275.7682	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000135407	PPM1H	AVIL	ATTTGCCTTTTGGGGAAGCTGTATGTTGCAAATGCTGGGGATAGCAG*ACTTCAGCAGGAAATCCTAGATGTCCAGTCTCGTCTCTTTGAATGTT	known,exon-exon	BOWTIE	in-frame	0	2	3	26	12	62788226	-	12	57803391	-	9.7382	20.5013	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000135407	PPM1H	AVIL	ATCCTCAAGGAGACTCGGCGGCTGCCCTGGGCCACTGGCTACGCAGA*ACTTCAGCAGGAAATCCTAGATGTCCAGTCTCGTCTCTTTGAATGTT	known,exon-exon	BOWTIE	in-frame	0	2	1	13	12	62934492	-	12	57803391	-	9.7382	20.5013	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000111581	PPM1H	NUP107	TCTAACTCGCATGGCTGGATAACATCCTTGGGTCCTGACAGAAGAGGCAG*AACGACTCTGTAAACGCTGTGGTCAAGCATGGAGAGCTGCAACACTTGAA	NA	BOWTIE+STAR	intronic/CDS(truncated)	0	2	2	15	12	62837779	-	12	68719345	+	9.7382	283.5483	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000111581	PPM1H	NUP107	AATACAGGAGGCAGAGGTTGCAGTGAGCTGAGATCATGCCACTGCACTCC*AGCCTTGGGGACAGAGCGAGACACTGTCTCCAAAAAAAGAAAGAATTACA	NA	BOWTIE+BOWTIE2	intronic/UTR	0	2	1	34	12	62800385	-	12	68743372	+	9.7382	283.5483	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000111581	PPM1H	NUP107	CCATTGGAGAATTGTTTCTTTTGAGAAATACTTGGTAAGAAGAGAAAGAT*CAGATGGATTTTGGTATTTGGAAAGGGCATTTGGATGCCCTAACTGCTGA	NA	BOWTIE+STAR	intronic/intronic	0	2	1	14	12	62666461	-	12	68735228	+	9.7382	283.5483	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000111581	PPM1H	NUP107	ATTTGCCTTTTGGGGAAGCTGTATGTTGCAAATGCTGGGGATAGCAG*GGAAAATACTCTGCATACCTTAAAACAACGGCAGCTGACTTCTTACG	exon-exon	BOWTIE	in-frame	0	2	1	13	12	62788226	-	12	68713730	+	9.7382	283.5483	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000175782	PPM1H	SLC35E3	TGTTTTCTTGCTGTTTCATTCATATATATATATGTGTGTGTGTGTGTGTG*TATATATATATATGTGTGTGTGTGTGTGTGTATACATATATACACATATA	NA	BOWTIE+STAR	intronic/UTR	0	2	10	24	12	62890739	-	12	68765623	+	9.7382	93.7991	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000175782	PPM1H	SLC35E3	ATTTGCCTTTTGGGGAAGCTGTATGTTGCAAATGCTGGGGATAGCAG*GGAACAGATTGACCCCAAACATCTGACATAACCTACGTAAGTGACAG	exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	2	6	30	12	62788226	-	12	68793288	+	9.7382	93.7991	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000175782	PPM1H	SLC35E3	CGATCACACCACTGCACTCCAGCCTGGGCAGCAGAGCAAGACTCCGTCTC*AATAATAATAATAATAACAAAGCAGCAACATTAATCAAGCACTCTGTATT	NA	BOWTIE+STAR	intronic/UTR	0	2	4	34	12	62665755	-	12	68769245	+	9.7382	93.7991	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000175782	PPM1H	SLC35E3	CTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAGAAAAA*TTAGTCAGCTGTGATGGTGTGCACCTGTAGTCCCAGCTACTCTGAAAGCT	NA	BOWTIE+BOWTIE2	intronic/UTR	0	2	3	37	12	62804671	-	12	68776537	+	9.7382	93.7991	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000175782	PPM1H	SLC35E3	TTAACAAATTTTTGTTTCAATTAGTTGGGCATGGTGGCACATGCCTGTGG*TCCCAGCTGCTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCAGGAGG	NA	BOWTIE+STAR	intronic/UTR	0	2	3	24	12	62780438	-	12	68766367	+	9.7382	93.7991	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000175782	PPM1H	SLC35E3	CAGCCTGGCGACAGAGTGAGACTCCATCTCAAAAAAAAAAAAAAAAAAGC*CCTATGTTTAAATGGCTCAAAGAAAAGACTATAAATGGAATTGAACATGT	NA	BOWTIE+BOWTIE2	intronic/UTR	0	2	1	34	12	62819129	-	12	68766509	+	9.7382	93.7991	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000175782	PPM1H	SLC35E3	ATTACAGGCATGTGCCACCACGCCCAGCTAATTTTGTATTTTTAGTAGAG*ACAGGAGAATCGCTTGAACCAGGGAGGCAGAGGTTGCAGTGAGCTGAGAC	NA	BOWTIE+BLAT	intronic/UTR	0	2	1	33	12	62663823	-	12	68774483	+	9.7382	93.7991	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000175782	PPM1H	SLC35E3	AAAATTAGTCGGGCGTGGTGGCACATGCCTGTAATCCCAGCTACTTGGGA*AGGCTGAGGCAGGAGAATCACTTGAACCCGGGAGGCGGCGGTTGCAGTGA	NA	BOWTIE+STAR	intronic/UTR	0	2	1	31	12	62800458	-	12	68765152	+	9.7382	93.7991	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000175782	PPM1H	SLC35E3	GGCTATTTTTGTATTTTTAGTAGAGACAGGGTTTCGCCATGTTGGCCAGG*CTGGGTGACGAGAGTGAAACTCTGTCTCAAAAAAAGAAAAAAAAAAAGAA	NA	BOWTIE+BLAT	intronic/UTR	0	2	1	30	12	62826256	-	12	68768262	+	9.7382	93.7991	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000175782	PPM1H	SLC35E3	CGTCAGTAGTTCCAGCTGCTTGGAGGCTGAGGGAGGAGGATTGCTTGAGC*CGAGATCATGCCATTGCTCTCCAGCCTGGGCAACAAGAGTGAAACTCCAT	NA	BOWTIE+BLAT	intronic/UTR	0	2	1	30	12	62850058	-	12	68766434	+	9.7382	93.7991	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000175782	PPM1H	SLC35E3	TTGAGATGGAGTCTCACTCTGTTGCCCAGGCTGGAGTGCAGTGGTGCAAT*CCTGGGCAACAAAGTGAGACCCTGACTCTAAAAGTAAAATTAAATTAAAT	NA	BOWTIE+STAR	intronic/UTR	0	2	1	30	12	62687961	-	12	68779909	+	9.7382	93.7991	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000175782	PPM1H	SLC35E3	TAACAAATTTTTGTTTCAATTAGTTGGGCATGGTGGCACATGCCTGTGGT*CTCAACCTCCCCAGTAGCTGGGACTACAGGTGCACACCAACATACCTGGC	NA	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	24	12	62780437	-	12	68766699	+	9.7382	93.7991	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000175782	PPM1H	SLC35E3	GAAAGAGAAACCTGTTAGAAGTGAGCCCTTTAGGCCAGGCATGGTGGCTC*GCGCCTGTAATTCCAGCTACTCGGGAGGCTGAGACAGGAGAATCACTTGA	NA	BOWTIE+BLAT	intronic/UTR	0	2	1	21	12	62865779	-	12	68768160	+	9.7382	93.7991	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000175782	PPM1H	SLC35E3	GTGATTTGCCTTTTGGGGAAGCTGTATGTTGCAAATGCTGGGGATAGCAG*TGACTGTGAGGCAGATCCTCATCAGGGAGGAGGCGCAGTGTCTTTTTAAC	NA	BOWTIE+STAR	CDS(truncated)/UTR	0	2	1	20	12	62788226	-	12	68793481	+	9.7382	93.7991	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000175782	PPM1H	SLC35E3	AATCTCAGCTACTCAGGAGACTGAGAGGCCAGAGAATCACTTGAGCCCAG*GAGTTTGAGACCAGCCTAGCCAACATGGCGAAACCTCGTCTCTACTAAAA	NA	BOWTIE+BLAT	intronic/UTR	0	2	1	17	12	62682593	-	12	68778582	+	9.7382	93.7991	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000175782	PPM1H	SLC35E3	ATCCACCTGCCTCAGCCTCCCAAAATGTAGGGATGACAGGCGTGAGCCAC*CACGCCTGTCATCCCAGCAGTTTGGGAGGCTGAGGCAGATGGATCACCTG	NA	BOWTIE+STAR	intronic/UTR	0	2	1	17	12	62927389	-	12	68775683	+	9.7382	93.7991	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000175782	PPM1H	SLC35E3	TGGCTAGAAGGGAGCCAGTCCAGCCTCCCAGCAGGGCAGAGGGCCCCAGG*TGGTGAGAGACTTCTTGTTCCTGGGAACTCTCTGCAGAGACCCAAGGTGG	NA	BOWTIE+STAR	intronic/UTR	0	2	1	16	12	62691844	-	12	68775403	+	9.7382	93.7991	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000175782	PPM1H	SLC35E3	CTCTAGCCTGGGTGACAGAGCGACCCTCTGTCACAAAACAAAAAAAAAGA*AAAAAAAAAAAAGTGTTGAGCAGCTAAAACAATGCCGTTAGATGCCCTAT	NA	BOWTIE+STAR	intronic/UTR	0	2	1	15	12	62666716	-	12	68774767	+	9.7382	93.7991	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111110	ENSG00000175782	PPM1H	SLC35E3	CCTCCGCCTCCCGGGTGCAAGCAGTTCTCCTGCCTCTGCCTCCTGAGTAG*CCTCCTGCCTCAACCTCCCCAGTAGCTGGGACTACAGGTGCACACCAACA	NA	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	14	12	62926841	-	12	68766691	+	9.7382	93.7991	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000175782	ENSG00000111110	SLC35E3	PPM1H	GCACTCCAGCCTGGGCGACAGAGCAAGACACTGTCTCTCTCTCTCTCTCC*ATATATATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATAC	NA	BOWTIE+STAR	UTR/intronic	0	2	28	32	12	68765599	+	12	62890763	-	93.7991	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000175782	ENSG00000111110	SLC35E3	PPM1H	CACTGTCTCTCTCTCTCTCTCCATATATATATGTGTGTGTGTGTATATAT*ATATATATATATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT	NA	BOWTIE+STAR	UTR/intronic	0	2	11	33	12	68765627	+	12	62890767	-	93.7991	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000175782	ENSG00000111110	SLC35E3	PPM1H	TGGGCGACAGAGCAAGACACTGTCTCTCTCTCTCTCTCCATATATATATG*TGTGTGTGTGTGTGTATACGTATATATATGTGTGTATATATATATACACG	NA	BOWTIE+STAR	UTR/intronic	0	2	7	35	12	68765610	+	12	62831805	-	93.7991	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000175782	ENSG00000111110	SLC35E3	PPM1H	CAGCTAAAACAATGCCGTTAGATGCCCTATCTCTTAAAAAAAAAAAAAAA*AAAGAAAAAAAAAACAAAATGGGAGAGGAAGAAAGGTCTTGGAAGTTCTC	NA	BOWTIE+STAR	UTR/intronic	0	2	2	20	12	68774836	+	12	62764615	-	93.7991	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000175782	ENSG00000111110	SLC35E3	PPM1H	ATGGTGTGCACCTGTAGTCCCAGCTACTCTGAAAGCTAAGGCACGAGAAT*CGCTTCCTGGGTTCAAGCGATTCTCCTGCCTCGGCCTCCCGAGTAGCTGG	NA	BOWTIE+STAR	UTR/intronic	0	2	1	36	12	68776599	+	12	62710002	-	93.7991	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000175782	ENSG00000111110	SLC35E3	PPM1H	GTAGAGATGGGGTTTCACCATGTTGCCCTGTCTAGTCTTGAAACCTTGAG*CCAAGGTGGGTGGATCACTTGAGGCCAGGAGTTTGAGACCAGCCTGGGCA	NA	BOWTIE+BOWTIE2	UTR/intronic	0	2	1	35	12	68780403	+	12	62802837	-	93.7991	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000175782	ENSG00000111110	SLC35E3	PPM1H	TGCTTGGAGTTTTGTTTTGTTTTTATTTTGTTTTGTTTTGGAGATAGGTT*CTCCAGCCTGGGTGACAGAGAGAGACTCTGTCTCAAAAAAAAAAAAAACC	NA	BOWTIE+STAR	UTR/intronic	0	2	1	35	12	68773434	+	12	62732623	-	93.7991	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000175782	ENSG00000111110	SLC35E3	PPM1H	TAGAGACGGGGTCTTGCTATGTTGCCAGGCTGGTCTCCAACTCCTGGCCT*CAGGTGATCCTCCCACTTCAGCCTCCTGAGTAGCTGGGACTACAGGCGCA	NA	BOWTIE+BLAT	UTR/intronic	0	2	1	34	12	68773635	+	12	62691742	-	93.7991	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000175782	ENSG00000111110	SLC35E3	PPM1H	GAATGCAGTGGCACAATCATGGCTCACTGCAGCCTCAGCCTCCTGGGCTC*AGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGAACTACAAGCGCGCG	NA	BOWTIE+BLAT	CDS(truncated)/intronic	0	2	1	32	12	68766683	+	12	62773065	-	93.7991	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000175782	ENSG00000111110	SLC35E3	PPM1H	ATGATTGTATAAAATGTATGGAATGGTTAGCCTGGTGTGGTGGTGCACAC*CTGTAATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTGAACCT	NA	BOWTIE+BLAT	UTR/intronic	0	2	1	29	12	68765461	+	12	62747279	-	93.7991	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000175782	ENSG00000111110	SLC35E3	PPM1H	CACTGTCTCTACTAAAAATACAAAAATTAGCTGGGCATGGTGGCGGGCGC*CTATAATCCCAGCTACTCAGGAGGCTGAGGTGGGCAGATCACCTGAGCCC	NA	BOWTIE+STAR	UTR/intronic	0	2	1	25	12	68768163	+	12	62782971	-	93.7991	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000175782	ENSG00000111110	SLC35E3	PPM1H	TAATCCCAGTGTTTTGGGAGGCCAAGGCAGGAGGTGCACTTGAGGCCAGG*AGATGGACTTGAACTCCTGGGCTCAAGTAATCTCTCGCCTCAGCCTTGTG	NA	BOWTIE+STAR	UTR/intronic	0	2	1	19	12	68779731	+	12	62889464	-	93.7991	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000175782	ENSG00000111110	SLC35E3	PPM1H	GTTTTGCCATGTTGCTCAGGCTGATCTCAAACTCTTGAGCTCAAGCCATC*CTCCTGCCTCGGCCTCCCGAGTAGCTGGGATTACAGGCATGTGCCACCAC	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	18	12	68766826	+	12	62709980	-	93.7991	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000175782	ENSG00000111110	SLC35E3	PPM1H	TACTAAAAATACAAAAATTAGCTGGGCATGGTGGCGGGCGCCTGTAATTC*CGGCCTCCCGAGTAGCTGGGATTACAGGCATGTGCCACCACGCCCAGCTA	NA	BOWTIE+STAR	UTR/intronic	0	2	1	15	12	68768172	+	12	62709971	-	93.7991	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000175782	ENSG00000111110	SLC35E3	PPM1H	ATAATAAATTGAGACATATCATTACTCTTGTAATAATTCATTTTCTAAAT*GGGAGTTGATAAATAGACATTTAAGCTATTAAAAAATGGTGCATCTTTAC	NA	BOWTIE+STAR	UTR/intronic	0	2	1	15	12	68767272	+	12	62921354	-	93.7991	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000175782	ENSG00000111110	SLC35E3	PPM1H	GAGACAGAGTTTTGCCATGTTGCTCAGGCTGATCTCAAACTCTTGAGCTC*GAGATCAGCCTGAGAAACATGATGAAACTCGTCTCTACAAAAAGTAAAAA	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	14	12	68766818	+	12	62673936	-	93.7991	9.7382	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000157625	ENSG00000135679	TAB3	MDM2	GGCGTGGTGGCTCACGCCTGTAATCTCAGCACTTTGGGAGGCCGAGGAGG*GAGGATCACTTGAGGCCAGGAGTTTGAGATCAGCCTGGGCAACATAATGA	oncogene,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	2	5	38	X	30896150	-	12	68847938	+	1.8044	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000157625	ENSG00000135679	TAB3	MDM2	CAGCACTTTGGGAGGCCGAGGCGGGCAGATCACTTGAGGTCAGGAGTTTG*CGCCCAGCCTAATAAGGGTTTTAAAGATAATTAGTGTGTAGGTCTGTAGG	oncogene,cancer,tumor	BOWTIE+BOWTIE2	intronic/UTR	0	2	1	36	X	30921129	-	12	68845059	+	1.8044	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000157625	ENSG00000135679	TAB3	MDM2	TAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCAATCTCCTG*CCTCAGCCTCCCAATTAGCTTGGCCTACAGTCATCTGCCACCACACCTGG	oncogene,cancer,tumor	BOWTIE+BOWTIE2	intronic/UTR	0	2	1	36	X	30947015	-	12	68840258	+	1.8044	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000157625	ENSG00000135679	TAB3	MDM2	TTACAGGCATGTGCCACCACACCTGGCTAATTTTTGTATTTTTAGTAGAG*ACAGTTTCACCATGTTGCCCAGGCTGGTCTCAAACTCCTGGGGTCAAGTG	oncogene,cancer,tumor	BOWTIE+BLAT	intronic/UTR	0	2	1	29	X	30924016	-	12	68846276	+	1.8044	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000157625	ENSG00000135679	TAB3	MDM2	TTGGGAGGCTGAGGTGGGAGGATCTCTTGAGCCCAGGAGTTTGAGGCCAG*CCTGGGCTCAAGAGATCCTCCTGTCTTGGCCTCGCAAAGTGCTAAGTAGG	oncogene,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	2	1	26	X	30970438	-	12	68841322	+	1.8044	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000157625	ENSG00000135679	TAB3	MDM2	ATTGATATACAATTGTTGTACATATTTATAGAGCACAACATGATGCTTTG*AGGACCTCCAAAGGTAAAAGTACTAATCCCTTTGGCCATTTATTGAGAGA	oncogene,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	2	1	18	X	30925488	-	12	68843252	+	1.8044	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000157625	ENSG00000135679	TAB3	MDM2	TAATGGCCCCCTAACAGATAAATCAAAAAAAATTTTTAAATTTTAGATAC*TTTTTTTTTTTTTTTTTTTTTTTTTGAGACAGAGTCTTGCTCCATCACCC	oncogene,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	2	1	16	X	30915735	-	12	68840838	+	1.8044	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000157625	ENSG00000135679	TAB3	MDM2	CAGTAAATCAGAAGTGTTGACCAGCTAAATGGTAACAATATAAGTACTTT*TAACCATTTCTATATTTACATTTGAAAATCTCCTTTGGAGACTTAGAACC	oncogene,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	2	1	14	X	30849085	-	12	68842403	+	1.8044	438.8763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2624-01A	ENSG00000111490	ENSG00000132434	TBC1D30	LANCL2	ACTTTCAATGAAAGGAGTAATCCTGATGATGACTCCATGGGAATTCAGAT*CAATATTTGCATAGTATAGTCTGTAAAGAACACAGGATTATGGATGGTGA	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	19	12	64830495	+	7	55409915	+	21.6381	433.6163	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000135452	ENSG00000111581	TSPAN31	NUP107	AACTCCTGACCTCAGGTGATCCACCCGCGTTGGCCTCCCAACGTGCTGGG*ATTACAGGTGTGCACCACCACGCCTGGCTAATTTTGTATTTTTAGTAGAG	NA	BOWTIE+STAR	UTR/intronic	0	2	9	37	12	57748012	+	12	68729580	+	275.7682	283.5483	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000135452	ENSG00000111581	TSPAN31	NUP107	GTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATACGCCCACCTT*GTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGACCCACCTGCCTT	NA	BOWTIE+BLAT	UTR/intronic	0	2	1	36	12	57748957	+	12	68736904	+	275.7682	283.5483	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2624-01A	ENSG00000135452	ENSG00000111581	TSPAN31	NUP107	GACCTCAGGTGATCCACCCGCGTTGGCCTCCCAACGTGCTGGGATTATAG*GCGTGGTGGCTCACGCCTGTACTCCTAGCACTTTGAGAGGCTGAGGTGGG	NA	BOWTIE+BLAT	UTR/intronic	0	2	1	16	12	57748019	+	12	68737289	+	275.7682	283.5483	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0745-01A	ENSG00000100014	ENSG00000100239	SPECC1L	PPP6R2	TGCCCCTGCCATGACCACCGTGGAGAACAAATCCAAGATTAGCACAG*GTGATTACGTTTTTGAAGAAGAAGGACAAGTTCATCAGCCTGGTGTT	known,tcga,18cancers,chimerdb3seq,m5,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	6	11	28	22	24313466	+	22	50414552	+	2.1446	7.689	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-06-0745-01A	ENSG00000258555	ENSG00000100239	SPECC1L-ADORA2A	PPP6R2	ATCTGCCCCTGCCATGACCACCGTGGAGAACAAATCCAAGATTAGCACAG*GTGATTACGTTTTTGAAGAAGAAGGACAAGTTCATCAGCCTGGTGTTGAA	m5,exon-exon	BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	6	3	18	22	24313466	+	22	50414552	+	0	7.689	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0745-01A	ENSG00000267173	ENSG00000018607	AC245748.1	ZNF806	CAGAATCCTGCCCTTTCCAAAAGGAAGACGGTATGATTAAGTTCCAG*GAAAGGGTGACATTCAAGGACATAGCTGTTATCTTCACCAAGGAAGA	pseudogene,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	2	4	29	19	44397199	-	2	132312869	+	0	0.1591	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	unprocessed_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0745-01A	ENSG00000100150	ENSG00000183765	DEPDC5	CHEK2	GAAGCTTACGTCCAACAGAAGGCGCTGGATGCACACTTTTCCTGTGG*GTCGTGATGTCTCGGGAGTCGGATGTTGAGGCTCAGCAGTCTCATGG	cancer,tumor,exon-exon	BOWTIE	out-of-frame	0	2	3	24	22	31819225	+	22	28734727	-	0.8404	2.0144	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-14-2554-01A	ENSG00000114302	ENSG00000229453	PRKAR2A	SPINK8	CGACGCCAAAGGGGACAGCGAGTCGGAGGAGGACGAGGACTTGGAAG*ATTTGAAGGGCTTAACATAACTAAACTGTATGATGGACAATGTGAAA	18cancers,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	23	24	30	3	48847335	-	3	48309946	-	9.9274	21.6592	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-14-2554-01A	ENSG00000114302	ENSG00000229453	PRKAR2A	SPINK8	CGCCGACGCCAAAGGGGACAGCGAGTCGGAGGAGGACGAGGACTTGGAAG*GGTCTCACTTTGTCACCCAAGCTGGAGTGAAGTGGCACGATCTTGGTTCA	18cancers	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	23	8	34	3	48847335	-	3	48312635	-	9.9274	21.6592	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-14-2554-01A	ENSG00000166025	ENSG00000257057	AMOTL1	C11ORF97	TGAGTTTGTGGAAGCCTCGCCCGCATCCTACAGCCCAGACGAGTTAG*GGAAGAAATTTTTATATTGTGAGCCACATAAGAGAATTAAGGAAGTA	18cancers,100K<gap<200K,exon-exon	BOWTIE	CDS(no-known-start-or-end)/CDS(truncated)	0	6	19	29	11	94740988	+	11	94517583	+	2.1757	9.999	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-14-2554-01A	ENSG00000166025	ENSG00000257057	AMOTL1	C11ORF97	TGAGTTTGTGGAAGCCTCGCCCGCATCCTACAGCCCAGACGAGTTAG*TGGCCCTGGAAGGGATTTGGAGCATTAAAAGGAATCTGCCTGTGGGA	18cancers,100K<gap<200K,exon-exon	BOWTIE	CDS(no-known-start-or-end)/CDS(truncated)	0	6	5	28	11	94740988	+	11	94528084	+	2.1757	9.999	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-14-2554-01A	ENSG00000166025	ENSG00000257057	AMOTL1	C11ORF97	GCGCGGACGGCGGCGGGAGCGCGCGAGAAGCTCTAGGACCCAGCAGCGGT*GTGCCCAGGGCTCTCGGAAGACCGCTGCGGCATGACAGGCGAGGAGGCGG	18cancers,100K<gap<200K	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	UTR/UTR	0	6	1	30	11	94768388	+	11	94512498	+	2.1757	9.999	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0125-02A	ENSG00000117713	ENSG00000092098	ARID1A	RNF31	TCTATCGCCTCTATGTGTCTGTGAAGGAGATTGGTGGATTGACTCAG*ATGCAGGCCCTGACTTCCTGTGAGTGCACCATCTGTCCTGACTGCTT	known,tcga,cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	25	24	30	1	26767999	+	14	24155157	+	6.7519	0.0597	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0125-02A	ENSG00000054965	ENSG00000048471	FAM168A	SNX29	CCGCCTCAGCCGCCGCCGCCGCCGTTTTCGCCTGCAGCTGCTCACCG*GTCTACATCCGGATAAAAGACGATGAATGGAATATTTATCGCCGGTA	18cancers,cancer,tcga-cancer,exon-exon	BOWTIE;BOWTIE+STAR	UTR/CDS(truncated)	0	10	14	30	11	73597923	-	16	12477719	+	22.9138	8.0134	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0125-02A	ENSG00000048471	ENSG00000054965	SNX29	FAM168A	CAGTGTTTCTCCGGGGCAAAGCAGCAAATGCATTCCACGTGTATCAG*GATCCTCAGTCTTCCACAATGAACCCTGTTTACAGCCCCGTGCAGCC	18cancers,cancer,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	10	4	25	16	12403529	+	11	73468492	-	8.0134	22.9138	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0125-02A	ENSG00000048471	ENSG00000054965	SNX29	FAM168A	CTGTAACCTAGGCAGGCATTATATTATTATTATTATTATTATTATTATTA*TTTTAAATTTTATTGGAACTCACATTTTAAAAAGAAATAAAATTTAAAAT	18cancers,cancer,tcga-cancer	BOWTIE+STAR	intronic/UTR	0	10	1	23	16	12045639	+	11	73401159	-	8.0134	22.9138	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0125-02A	ENSG00000137714	ENSG00000189339	FDX1	SLC35E2B	GATGAGGAGAATGACATGCTCGATCTGGCATATGGACTAACAGACAG*GACGTCCCAGTGATCGGGAGGAGTGGGAAGAGCTTCAGCTACAACCA	m2,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	5	7	28	11	110457047	+	1	1668472	-	6.7472	9.0747	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0125-02A	ENSG00000259081	ENSG00000009830	AF111169.4	POMT2	GCATCCAGACCCGGAAAGGACCTAGTTTCAGCCTGGCACCTCCCAAG*GGGAACAGTGGCCTCAAACCCAAGGACAATGAGTTCACGTCCAAACC	antisense,exon-exon	BOWTIE;BOWTIE+STAR	exonic(no-known-CDS)/CDS(truncated)	0	4	4	23	14	76781400	-	14	77280463	-	0.1808	4.5133	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0125-02A	ENSG00000146648	ENSG00000115461	EGFR	IGFBP5	GGCGCTGCCCACCCGCCGAGACTGCACTGTTTAGGGAAGCTGAGGAAGGA*CGAGGGACAGGGGTTTCACCAGCCAGCAACCTGGGCCTTGTACTGTCTGT	oncogene,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	3	1	18	7	55019859	+	2	216672969	-	279.261	833.9899	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0125-02A	ENSG00000146648	ENSG00000115461	EGFR	IGFBP5	CTGCTTGAGGGGTGCTGAGCAAAGCCCTGCCTCTTACAGGATGAAGGTGC*GTGGCATCTGCTGGTGCGTGGACAAGTACGGGATGAAGCTGCCAGGCATG	oncogene,cancer,tumor	BOWTIE+STAR	intronic/CDS(truncated)	0	3	1	15	7	55022231	+	2	216676857	-	279.261	833.9899	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0125-02A	ENSG00000146648	ENSG00000115461	EGFR	IGFBP5	TAATAGCAGCAGCAGCCTGTGAAACATTGACAAGACCTGGAGTTGGAAGA*GACGAGGGACAGGGGTTTCACCAGCCAGCAACCTGGGCCTTGTACTGTCT	oncogene,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	3	1	14	7	55070583	+	2	216672971	-	279.261	833.9899	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0125-02A	ENSG00000091129	ENSG00000075624	NRCAM	ACTB	ACGGAGCCCTCTCATCTCCTTTTTGGTTTTGTTTTTTTGTTTGTTTTTTG*TTTTTTTTTTTTTTTGGCTTGACTCAGGATTTAAAAACTGGAACGGTGAA	cancer	BOWTIE+STAR	intronic/UTR	0	2	3	19	7	108415882	-	7	5527638	-	89.7232	2202.1531	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0125-02A	ENSG00000091129	ENSG00000075624	NRCAM	ACTB	TTATTTTATTCTACGGCCTTCAGGCCTCCGTTGTTTTTTGTTTTGTTTTT*TTTTTTTTTTTTTTTTGGCTTGACTCAGGATTTAAAAACTGGAACGGTGA	cancer	BOWTIE+STAR	intronic/UTR	0	2	1	17	7	108437589	-	7	5527639	-	89.7232	2202.1531	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-02-2483-01A	ENSG00000107902	ENSG00000203780	LHPP	FANK1	CAGCGGTGTGGAATGAGAGCGCTGCAGGTGCGCACCGGGAAGTTCAG*AAATCATGCCACCCTCAAAGCCTCATCCACCTGTCGTGGGCAAAGTG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	57	21	29	10	124517271	+	10	125980161	+	7.0881	11.7589	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-02-2483-01A	ENSG00000107902	ENSG00000203780	LHPP	FANK1	CCAGACCCAAGAATCGCCCGCCTCTCCAAGACCATCCCTGGCTGCTG*GGGATATGCAACGAAGCATGTTGTTGAAGGTCTGGAACCAAGGACGC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE;BOWTIE+STAR	UTR/CDS(truncated)	0	57	20	30	10	124546189	+	10	125988551	+	7.0881	11.7589	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-02-2483-01A	ENSG00000107902	ENSG00000203780	LHPP	FANK1	CCAGACCCAAGAATCGCCCGCCTCTCCAAGACCATCCCTGGCTGCTG*AAATCATGCCACCCTCAAAGCCTCATCCACCTGTCGTGGGCAAAGTG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	57	16	29	10	124546189	+	10	125980161	+	7.0881	11.7589	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-02-2483-01A	ENSG00000107902	ENSG00000203780	LHPP	FANK1	AGCAGGGTAGGAGGGTTGTTGGCACCTGCTGTGGCCGGGGCCGTGCCAGG*GGATATGCAACGAAGCATGTTGTTGAAGGTCTGGAACCAAGGACGCTGTA	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BOWTIE2	intronic/CDS(truncated)	0	57	11	38	10	124546242	+	10	125988552	+	7.0881	11.7589	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-02-2483-01A	ENSG00000107902	ENSG00000203780	LHPP	FANK1	CAGCGGTGTGGAATGAGAGCGCTGCAGGTGCGCACCGGGAAGTTCAG*GGGATATGCAACGAAGCATGTTGTTGAAGGTCTGGAACCAAGGACGC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	57	7	27	10	124517271	+	10	125988551	+	7.0881	11.7589	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-02-2483-01A	ENSG00000107902	ENSG00000203780	LHPP	FANK1	GAGCAGGGTAGGAGGGTTGTTGGCACCTGCTGTGGCCGGGGCCGTGCCAG*AAATCATGCCACCCTCAAAGCCTCATCCACCTGTCGTGGGCAAAGTGACT	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	intronic/CDS(truncated)	0	57	5	33	10	124546241	+	10	125980161	+	7.0881	11.7589	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-02-2483-01A	ENSG00000107902	ENSG00000203780	LHPP	FANK1	AGTTTTTCAAGTCTGCCCTGCAAGCGATAGGAGTGGAAGCCCACCAG*AAATCATGCCACCCTCAAAGCCTCATCCACCTGTCGTGGGCAAAGTG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	57	4	30	10	124498128	+	10	125980161	+	7.0881	11.7589	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-02-2483-01A	ENSG00000107902	ENSG00000203780	LHPP	FANK1	AGACACTCCCTGAAGCGCGTTCCCCAGGAGCTGGAAGGGGGATAACGCAG*AAATCATGCCACCCTCAAAGCCTCATCCACCTGTCGTGGGCAAAGTGACT	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	intronic/CDS(truncated)	0	57	1	34	10	124526264	+	10	125980161	+	7.0881	11.7589	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-02-2483-01A	ENSG00000148219	ENSG00000242173	ASTN2	ARHGDIG	CAGTCTGGGACATCCAGGGGAAGAGAAGGTGGACTTTGAGAAGAAAG*ACCCAAGCCTGCCCAATGTGCAGGTGACCAGGCTGACACTCCTGTCG	known,tcga,cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	39	25	30	9	117214358	-	16	282025	+	13.9561	7.8852	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-02-2483-01A	ENSG00000148219	ENSG00000242173	ASTN2	ARHGDIG	CAGTCTGGGACATCCAGGGGAAGAGAAGGTGGACTTTGAGAAGAAAG*TCCTCCTGGCTGACAAGGAGGGTGGGCCGCCGGCAGTGGACGAGGTG	known,tcga,cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	39	15	29	9	117214358	-	16	281746	+	13.9561	7.8852	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-02-2483-01A	ENSG00000150760	ENSG00000166171	DOCK1	DPCD	CACCAGGAAACTGACCTCGGGGTTGCGGCGACCTTTTGGAGTGGCTG*GAATCTTTGCAAGTACTTTTGATGATGCATCAGCATGAATTTTCTGC	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE;BOWTIE+STAR	CDS(truncated)/UTR	0	17	15	28	10	127000307	+	10	101587276	+	14.8481	84.9678	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-02-2483-01A	ENSG00000150760	ENSG00000166171	DOCK1	DPCD	CAACACCAGGAAACTGACCTCGGGGTTGCGGCGACCTTTTGGAGTGGCTG*GACTGGAACTTCTGAGGTTCTCCCTCTGAGGGGGCCCCCAGACCTGTGCT	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(truncated)/UTR	0	17	2	30	10	127000307	+	10	101580158	+	14.8481	84.9678	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-02-2483-01A	ENSG00000150760	ENSG00000166171	DOCK1	DPCD	TTGTGTCATAAGTTCCTACGAATGCGTAGTTATATTTCTTAAAGATGAAA*CTGTTACAACTCAGGCTGGAGTGCAGTGGTGTAATCTCAGCTCATTGGAA	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	intronic/intronic	0	17	1	29	10	127002357	+	10	101576349	+	14.8481	84.9678	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-02-2483-01A	ENSG00000150760	ENSG00000166171	DOCK1	DPCD	TAGTCTCTCACTGGGTAGCTTCACCATCCTAAAAGTCCTCTGTGCTCCGC*CTTCCTGCCGAAGACTGTCAAGGAGGCGGCTGAAGATACCCCGGTGGGAC	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/UTR	0	17	1	18	10	127001609	+	10	101580248	+	14.8481	84.9678	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-02-2483-01A	ENSG00000150760	ENSG00000166171	DOCK1	DPCD	CACCAGGAAACTGACCTCGGGGTTGCGGCGACCTTTTGGAGTGGCTG*GGAGAAGGAAGGTTCACTATTTATTCCCAGACGGCAAGGAAATGGCT	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	17	1	13	10	127000307	+	10	101594658	+	14.8481	84.9678	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-02-2483-01A	ENSG00000100906	ENSG00000125107	NFKBIA	CNOT1	GGACTGCCCTTCACCTCGCAGTGGACCTGCAAAATCCTGACCTGGTGTCA*CTCCTGTCTTATGTGGGCACGTTCCAAAGTTTAAATGCATTTTTTTGACT	cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	2	1	23	14	35402598	-	16	58520811	-	31.699	8.4554	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-27-2523-01A	ENSG00000130165	ENSG00000196365	ELOF1	LONP1	GGGGACTGTTTCCTGACATCCTGGACAAGGGAAGCCCACTAGAGGCTGGA*GTGGTCCTGTTTCAGGGCCTTTGCACGGGCTGTGTCCTGGGCCTGGAACA	oncogene,18cancers,cancer,tumor	BOWTIE+STAR	UTR/intronic	0	13	1	14	19	11553311	-	19	5697451	-	19.0399	20.5596	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-27-2523-01A	ENSG00000130165	ENSG00000196365	ELOF1	LONP1	CACCAGCACCGTGCCCATCTCAACTGGACTTCCCGCTCTCCTTCTCCACC*GTGCCCAGCTGAACTTATTCTTAAAGCAAGTGCCCCGGACCTCCAGTGGG	oncogene,18cancers,cancer,tumor	BOWTIE+STAR	UTR/intronic	0	13	1	14	19	11553240	-	19	5709637	-	19.0399	20.5596	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000196365	ENSG00000130165	LONP1	ELOF1	CCCCTCCGTTCTGCAGAGCGACAGATGCCCCTTGCTCCCGGTGCCTGAGC*CAGGCCCACTCTGCCATGACATGTCTTCCCTGGTTATCCCGCCACCTCCA	oncogene,18cancers,cancer,tumor	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	UTR/UTR	0	13	20	36	19	5717531	-	19	11552046	-	20.5596	19.0399	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000146648	ENSG00000132434	EGFR	LANCL2	AGGTCCCCACTGCAAACCGATACCCAGCTTAGACAGCAGTTCTGCAGTCG*AGGTGGTGTCTATCTTGTATATCAGAAAGATTATCTAGGGTCTATCCTAG	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	intronic/UTR	0	3	1	17	7	55112182	+	7	55431712	+	48.2433	728.6396	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000146648	ENSG00000132434	EGFR	LANCL2	AGCTAACCATCACCCCCAGGACTGACCTCTTCCTCCTCGCTGCCAGATGA*TTGGCAGCGAGGTTTGCTGCGGAAGGGCTACGGGATATGCCATGGGACTG	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	UTR/CDS(truncated)	0	3	1	16	7	55170731	+	7	55425307	+	48.2433	728.6396	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000146648	ENSG00000132434	EGFR	LANCL2	TGTGTGAGTGTTCATGATGTGTGTACATCTGTGTATGTGTGTGTGTGTAT*GTGTGGGGCTGGCACCCGAAATGTGTGACATTCAGCTTCTAAACGATGCC	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+BLAT	UTR/UTR	0	3	1	15	7	55202956	+	7	55432728	+	48.2433	728.6396	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000146648	ENSG00000132434	EGFR	LANCL2	CAATCGTCAGCTTTTCTGTTTGAAATCTAAATTCTTCCTGACTGCAGGGG*TGGGCTTTGCAGGCAGTCCAGCAGCCCACACCTGCAGGCAGGATGCTGTC	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	intronic/UTR	0	3	1	15	7	55150503	+	7	55432903	+	48.2433	728.6396	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000146648	ENSG00000132434	EGFR	LANCL2	ACTTTTTGAATAAATAAATAAAAGCACAAGTACAGTTTTTTTAAAATACT*CCACCTGGGTTGACACCTTCCTACTTATCCACTAGATGTCATCAGAGGTG	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	intronic/UTR	0	3	1	15	7	55140126	+	7	55433348	+	48.2433	728.6396	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000146648	ENSG00000132434	EGFR	LANCL2	CTCAGCACCTCCCCTCAGGCAGAAAAGAATCATCTGTGGAGCTTCAAAAG*TTTTGCAGCTCCAGAGATCGGTTGTCTGCCAAGAATCAGACCTTCCTGAT	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	UTR/CDS(truncated)	0	3	1	15	7	55209124	+	7	55399959	+	48.2433	728.6396	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000146648	ENSG00000132434	EGFR	LANCL2	CTTTATTCCATGGCAACATGGGTATACACATCCCACCGGCTGTTTCAGTG*AGTATTGATTATGTGCGCCACAAAAAATTCCGATCTGGGAATTACCCATC	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	intronic/CDS(truncated)	0	3	1	15	7	55070994	+	7	55411955	+	48.2433	728.6396	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000146648	ENSG00000132434	EGFR	LANCL2	CTCAATTACACAGAAGTTTCAGATTATGTAACAGATGCTGTGCTGGGTTA*TGCTTTGCTGAAGACCTCACACGATGTCCAATCTCATCCAAATAACATTG	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	intronic/UTR	0	3	1	15	7	55099299	+	7	55432973	+	48.2433	728.6396	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000146648	ENSG00000132434	EGFR	LANCL2	ATTTCCTTGCCTGGGGGCTGTAAAACCTTACAGAACAGAAATCCTTGCCT*ACTTGGCATAGCAGGTCAGCAAGGGATGTCTCAGCCAAGACCTGAGGGAC	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	3	1	14	7	55209660	+	7	55426627	+	48.2433	728.6396	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000146648	ENSG00000132434	EGFR	LANCL2	TAGTACAGACAGGGTTTCACCATGTTGGCCAGGCTTGTCTTGATCTCCTG*CACAGCACTCAGTAGAGGTCCTGCCTCCCCATTTCTCAAGGGAAGCCAGT	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	intronic/UTR	0	3	1	14	7	55169329	+	7	55433063	+	48.2433	728.6396	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000146648	ENSG00000132434	EGFR	LANCL2	AGCAGCCTGGACATCCCTGTTGGTGTTTCCAGCCCTGTCCTCTCCTGAGT*GCTGAGGGTAGCTGCTTTGCTGAAGACCTCACACGATGTCCAATCTCATC	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	intronic/UTR	0	3	1	14	7	55145305	+	7	55432961	+	48.2433	728.6396	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000146648	ENSG00000132434	EGFR	LANCL2	ATACAGGTCCCTCAGAGCAGGTGACTGAGTGTGTATCCTGTCTGGAGCAT*AAAGCCACCAGATTGCTTAGTGCCTGACACAGAAACAACTGGGAATCCTG	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	intronic/UTR	0	3	1	14	7	55198380	+	7	55431359	+	48.2433	728.6396	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000146648	ENSG00000132434	EGFR	LANCL2	ACTGTGAGAGCACAGAGCAGGGAGGTTGGGTCCTGCCTGAGGAGACCTGG*TCAGCCTCCTGTGTAGCTGGGACCACAGGCACATGCCACCACACCTGGCT	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	3	1	14	7	55207567	+	7	55392466	+	48.2433	728.6396	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000146648	ENSG00000132434	EGFR	LANCL2	ATACACACACACACACAAATATGGCCAAGAAATAAAGTAAAATGTTATTT*GGATGCTGTCGTCAATGAGCTGAGGGTAGCTGCTTTGCTGAAGACCTCAC	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	intronic/UTR	0	3	1	14	7	55149434	+	7	55432943	+	48.2433	728.6396	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000146648	ENSG00000132434	EGFR	LANCL2	TTGCACTTGTGTAGGATGAAGCTGGTGGGTGATGGGAACTCAGCACCTCC*TATTTATTGCAACATTGTCCCATTCTTGTGAAGTTAAAGTTATCTCTTCT	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	3	1	14	7	55209086	+	7	55391731	+	48.2433	728.6396	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000146648	ENSG00000132434	EGFR	LANCL2	GCTGCAGTGACATCACCTGAGGAGCTTTTAAAAGCTTGAAGCCCAGCTAC*CCTAGATATGTTATTTATTTACATTTTCCAATTATGTATTGCCAGTATAT	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	3	1	14	7	55210433	+	7	55418121	+	48.2433	728.6396	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	GATGAGCTGCTTTATGGACGGGCAGGTTATCTGTATGCCTTACTGTACCT*CTCTCTGTGATCAGGTGCTGCCCTCCCTGGCAGGAGGACTGCAGACAGGA	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/intronic	0	3	2	16	7	55400055	+	7	55120151	+	728.6396	48.2433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-27-2523-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	ACATCAAAACATAACACATCACAGCACTCAGTAGAGGTCCTGCCTCCCCA*CTCACCACACCAAAAAAAGGTATGTGCAGTAATACAGTCATTAATTAGCT	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	3	2	15	7	55433093	+	7	55080695	+	728.6396	48.2433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	CCGGCTGGTGCACTGGTGCCACGGCGCCCCGGGGGTCATCCACATGCTCA*TGCAGGCGAGATGGGAAGTGCAGCCACTGAGAACTCACAGTAGAGCGTGT	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/intronic	0	3	1	21	7	55412075	+	7	55093979	+	728.6396	48.2433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	TTTGGAATGAATGCATTTCCTATTTTTTGTCTACTTTTGGGTGATAAAAA*GTAGGAAATGCATTTCTTCATAGCTAAGTGTACCTCCTTGTGAAATATCT	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	3	1	19	7	55432356	+	7	55123508	+	728.6396	48.2433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	CGGAGCACACGGGTGCCGCATTCCTGACAGACCCTATTCGCTCTTTGAAG*GGCCAGGACTGGAGTGATGGTTGAGACAGGCACGCACTGGGTCTTGTCTG	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/intronic	0	3	1	18	7	55428447	+	7	55079493	+	728.6396	48.2433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	AGAAGGGCTGAAGACAGCTGATCCCCATGACTGCTCTGCTTATACTGGCT*GCACATGGCTGATCCCCACTGAGTGTTCTTTTCCTCCTTTGATCCCCTTT	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/intronic	0	3	1	18	7	55391904	+	7	55184210	+	728.6396	48.2433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	TTCCAGATGAGAATGAGGGAGCGACCACTCCAAGGACGGACAGGACCAGC*TCATGCCCTTCGGCTGCCTCCTGGACTATGTCCGGGAACACAAAGACAAT	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	UTR/CDS(truncated)	0	3	1	17	7	55431844	+	7	55181384	+	728.6396	48.2433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	GGGGCGTGCTGGGGTGGTTTGGGAGTGCACAGCTGAACGCTTCCCGTTTG*GGGCTCCACAGCTGAAAATGCAGAATACCTAAGGGTCGCGCCACAAAGCA	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	UTR/CDS(truncated)	0	3	1	16	7	55431903	+	7	55205548	+	728.6396	48.2433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	AGGGGCGTGCTGGGGTGGTTTGGGAGTGCACAGCTGAACGCTTCCCGTTT*GGTATTTCACAGCTGGTGCGGACCCAGAAAGACTTCTGCTTTTGCCCCAA	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	3	1	16	7	55431902	+	7	55182090	+	728.6396	48.2433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	CAGCCTTTTCTGTGGCACCTTCCAGATGAGAATGAGGGAGCGACCACTCC*CAAACCAGCCCAGCCCTCCCAGCCTGCATCATCGTGGTCCTGTAGGGGCT	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	3	1	16	7	55431825	+	7	55159130	+	728.6396	48.2433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-27-2523-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	TTTATCAACATTATAAGTTACTGTTCTAAGAAAAGTAAATACAGTTCCAG*AACATTTTCCCAGGTAGTATTTTTCCTCATGTAAAACAACAGCAATTTAA	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	3	1	16	7	55432210	+	7	55081099	+	728.6396	48.2433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-27-2523-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	AGGCTTCAGGTGCTTTGTGTAGAGTCCAGGGCAGCTGGAGCTTTGTTGGG*AAAGCTTCCTTTTGGCCACTATACTACTTAGAAATGCCCTGCAAAAGGTG	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	3	1	15	7	55432029	+	7	55080975	+	728.6396	48.2433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	AAATCATCCTGATCCTATTTTACCTGGCCTCCAGGGCCTGTTGATGGGCT*ACCTGCAAAGTCCATGCCTGGGCCAGTGCAGCATGTGTCCTCAATGGGCT	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	3	1	15	7	55432908	+	7	55122362	+	728.6396	48.2433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	TCCAATCTCATCCAAATAACATTGTTCCCATCCTCCCCACCCACCACATC*CTCCCCACCCATGGCTCCCTCACGCTGCAGCAGAGGCCCTGCCACAGCAC	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	3	1	15	7	55433048	+	7	55096713	+	728.6396	48.2433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	CCCTTATTTATAGATATGAGAAACATAATGTTCTAACCAACAACATTATG*TATCTAATATCTATATATCTAATATGTAGTTTATTAGCTATCTAATATCT	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	3	1	15	7	55432413	+	7	55203862	+	728.6396	48.2433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	AGCAGTGACTAAGCACTGGCAGTTCCAGAACATTTACCCAGGTATATGTT*CTGGAACTACCAGACCATGAGCCTGAATTTTTTGTTTAAAAATCATATCC	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	3	1	14	7	55432138	+	7	55194852	+	728.6396	48.2433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-27-2523-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	GGGCGTGCTGGGGTGGTTTGGGAGTGCACAGCTGAACGCTTCCCGTTTGG*GGGTTTACAGCTGGCCCCCTGGCCTGGTTTGTGAACATAAAACAGAAACA	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	3	1	14	7	55431904	+	7	55074418	+	728.6396	48.2433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-27-2523-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	ACGATGTCCAATCTCATCCAAATAACATTGTTCCCATCCTCCCCACCCAC*CCCGGCTAATGATAGCTCGGCCTGCCCCGGCGTCAGCCGCTCCTGGCAGG	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	3	1	14	7	55433042	+	7	55092739	+	728.6396	48.2433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	AAACGATGCCTGGAGAGTCTGTTTGCTGCAGACACCCTTGCTCCTGAGTC*TGTTTACTGCAGAGTGACCCTGCTCAAAGCTGTGGTCACCCAAGGCTTTG	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	3	1	14	7	55432817	+	7	55100555	+	728.6396	48.2433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	CAACATTTTCTAACAGCACCCTCATCAATATAAAATATGACTTCTTCACA*ACAGAGAACCTCTAGTGTTTGTTCAATAAATATATGAATGGATAGAGGGA	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	3	1	14	7	55431524	+	7	55159713	+	728.6396	48.2433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	TTAAGCAATGAAACAGACCGGCTGGTGCACTGGTGCCACGGCGCCCCGGG*CTCCTTGGCACCAGCTGGTATTCATCCTCAATGCTAGCTAGAGTTGAAAT	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/intronic	0	3	1	14	7	55412058	+	7	55059214	+	728.6396	48.2433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	CAGACACCGTCACAGGCCCCTCTGGTTAGACTAGCATGAGTGACCGAAGC*AGACACACTCACAGAGACACACAGATACACACAGGCACACACACAGAGAG	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	3	1	14	7	55431467	+	7	55095770	+	728.6396	48.2433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	TATGTTACTAAAACAGGCTCCACCTCAGTTTATCAACATTATAAGTTACT*AAAACAGGCTCTGCGGCACAATATTGGCAAGTGAAATTTTGTAAACCGGC	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	3	1	14	7	55432182	+	7	55092175	+	728.6396	48.2433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	AACATTATAAGTTACTGTTCTAAGAAAAGTAAATACAGTTCCAGATGGGT*GTCATTCTGTCAATGTTCATGTTTAATGTCATCAGTGGAACACTCCCACT	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	3	1	14	7	55432216	+	7	55145927	+	728.6396	48.2433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	TCAGTAGAGGTCCTGCCTCCCCATTTCTCAAGGGAAGCCAGTAGGCAACA*TTGGTGGCTGCTCTTAGCCAAACAGCTGAGGCCTTTGCATCCCTGGAGAA	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	3	1	14	7	55433120	+	7	55198905	+	728.6396	48.2433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	AAATCATCCTGATCCTATTTTACCTGGCCTCCAGGGCCTGTTGATGGGCT*GCTGGCCTGTCTGCGCCTCGTCTCCCGACTGTGGAGTGTGTTCTGCCCCT	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	3	1	14	7	55432908	+	7	55184101	+	728.6396	48.2433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	CCTGGCTGTTGGAGCTGTGATTTATCACAAACTCAGAAGTGACTGTGAGT*TTGTGTTTAATCACATGAAGGATATTTGCATTGTTTTCCAACTGATGCCA	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/intronic	0	3	1	14	7	55398611	+	7	55085176	+	728.6396	48.2433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	ACCAAAAGCCACCAGATTGCTTAGTGCCTGACACAGAAACAACTGGGAAT*TTTGGTTGTCTTTTTTTTTTTGAAAGAGGGGCTTTTATGCTTTTTTCCTA	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	3	1	14	7	55431404	+	7	55132019	+	728.6396	48.2433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	TAAGGCTTGTGTCATGAAAGACAAGAGGCCTCTCTTAACAGCCCAGTCCT*CCCCCCACAGACAAGTAAACCACATTCTCTTCACATTCCCAATGTTTTGT	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	3	1	14	7	55432614	+	7	55113520	+	728.6396	48.2433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2523-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	ATATTGACAAATGAGGGAACAGGTGGTGTCTATCTTGTATATCAGAAAGA*CAGCACCTGCTCCCTCTGCAAGCCCAGCCCCCTTCAGCAAGGGCAGTGAC	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	3	1	14	7	55431741	+	7	55162656	+	728.6396	48.2433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0190-02A	ENSG00000142657	ENSG00000171735	PGD	CAMTA1	TCATGGGCCAGAACTTAATTCTGAACATGAATGACCACGGCTTTGTG*ACCACAGAATGGCTCAATGATACTCTACAACAGGAAGAAAGTGAAAT	known,tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	17	13	26	1	10399704	+	1	7249491	+	30.3894	2.1983	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0190-02A	ENSG00000142657	ENSG00000171735	PGD	CAMTA1	AAGAGATGGTCTCCAAGCTGAAGAAGCCCCGGCGGATCATCCTCCTGGTG*CAAGCCCAGTCCCCGCACCTCCCTCCTCTCCTTCCCTGGGCAAATTCTGG	known,tcga,18cancers,chimerdb3seq,cancer,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	17	1	15	1	10400533	+	1	7448124	+	30.3894	2.1983	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0190-02A	ENSG00000142657	ENSG00000171735	PGD	CAMTA1	CTCCTGGTGAAGGCTGGGCAAGCTGTGGATGATTTCATCGAGAAATTGGT*CACCAGTATACACCACTCTGGAGACCAGCTCTAGCCACTTGGCAGGGCTC	known,tcga,18cancers,chimerdb3seq,cancer,tcga-cancer	BOWTIE+STAR	intronic/intronic	0	17	1	14	1	10400574	+	1	7456329	+	30.3894	2.1983	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0190-02A	ENSG00000105229	ENSG00000156689	PIAS4	GLYATL2	GAGGCTGAAGACCATTGGGGTAAAGCACCCGGAGCTGTGCAAGGCACTGG*TCCGTAGAGTATTAGCTACAGAAACCTTTCCATTGCCATACTGAGAAACT	18cancers	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/UTR	0	3	3	34	19	4029036	+	11	58844524	-	5.5554	1.688	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0190-02A	ENSG00000187017	ENSG00000227634	ESPN	LINC01714	AAAGGAGACTTCCCCTCCCTGAGGCTTCTCGTCGAGCACTACCCTGA*ATGAGGATGTCAAGACTTGGAGTAGGTGACAGTTGGCCTTGGGCTTC	lincrna,exon-exon	BOWTIE;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	2	5	26	1	6428419	+	1	8208667	+	0.0685	0.3679	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0190-02A	ENSG00000107186	ENSG00000106278	MPDZ	PTPRZ1	GCACTGGTCCTGACAATTTTTATGCTGTGTTCAGCCGGGTCTTCAAAACT*TAAGTATTATTTCAAATTGTCGTTTAAAAAAATGTGTAAGTTTGCGTTCA	NA	BOWTIE+STAR	UTR/intronic	0	2	1	14	9	13106856	-	7	122001158	+	19.0614	16.7208	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0190-02A	ENSG00000071564	ENSG00000100345	TCF3	MYH9	GGCTCTTTGATAACGTTTGGAGGCGCCTGTCTTTCCACCTGCGCAGGGAG*GGTGGCCGACATGAAAAAGAAGATGGAGGACAGTGTGGGGTGCCTGGAAA	oncogene,cancer,tumor	BOWTIE+STAR	intronic/intronic	0	2	1	15	19	1640106	-	22	36292235	-	22.0133	149.1753	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0190-02A	ENSG00000071564	ENSG00000100345	TCF3	MYH9	CCCGGCCCGGGCGCCGGAGTTTGGGGTGGGGAGCGCGCGGGAGGGACGTC*AGAATAGCTGAGTTCACCACCAACCTCACAGAAGAGGAGGAGAAATCTAA	oncogene,cancer,tumor	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	14	19	1651869	-	22	36299021	-	22.0133	149.1753	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000136897	ENSG00000023318	MRPL50	ERP44	TGGACAGTCTCAGGGACACCATGTAGAGAATTTTGGTCTCGATTCAG*GTAACTTGGGTTTTTACTCCTGTAACAACTGAAATAACAAGTCTTGA	known,ribosomal,tcga,18cancers,chimerdb3seq,m304,tcga-cancer,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	313	35	30	9	101398501	-	9	100060172	-	7.0191	98.8783	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000136897	ENSG00000023318	MRPL50	ERP44	TGGACAGTCTCAGGGACACCATGTAGAGAATTTTGGTCTCGATTCAG*GTGTCGTTTCAGTCAGATGTTGCATCCAATTTTTGAGGAAGCTTCCG	known,ribosomal,tcga,18cancers,chimerdb3seq,m304,tcga-cancer,exon-exon	BOWTIE	in-frame	0	313	2	26	9	101398501	-	9	100052532	-	7.0191	98.8783	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000136897	ENSG00000023318	MRPL50	ERP44	TGGACAGTCTCAGGGACACCATGTAGAGAATTTTGGTCTCGATTCAG*ACAATGCTGATGTTGCTTTAGTAAATTTTTATGCTGACTGGTGTCGT	known,ribosomal,tcga,18cancers,chimerdb3seq,m304,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	313	2	23	9	101398501	-	9	100057859	-	7.0191	98.8783	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000136897	ENSG00000023318	MRPL50	ERP44	ATGTGGACAGTCTCAGGGACACCATGTAGAGAATTTTGGTCTCGATTCAG*TGTAAAGTGTATTTCTTGCTGTGGATCATGGTCATAAAAAGTTTGAAAAG	known,ribosomal,tcga,18cancers,chimerdb3seq,m304,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	313	1	20	9	101398501	-	9	100073838	-	7.0191	98.8783	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000136897	ENSG00000023318	MRPL50	ERP44	ATGTGGACAGTCTCAGGGACACCATGTAGAGAATTTTGGTCTCGATTCAG*AAAACTCCAGCAGATTGTCCTGTAATCGCTATTGACAGCTTTAGGCATAT	known,ribosomal,tcga,18cancers,chimerdb3seq,m304,tcga-cancer	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	out-of-frame	0	313	1	20	9	101398501	-	9	100006585	-	7.0191	98.8783	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-06-0744-01A	ENSG00000280890	ENSG00000132432	AC073324.2	SEC61G	CTGCCCTCCCTTCTCTCTACAATAATGCATTTGGAATTTTTAGTTGGGTG*GGCAGTCATGGATCAGGTAATGCAGTTTGTTGAGCCAAGTCGGCAGTTTG	lincrna	BOWTIE+STAR	intronic/intronic	0	207	1	15	7	55250582	-	7	54757595	-	1383.7173	2729.0488	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000132432	ENSG00000280890	SEC61G	AC073324.2	TGGTGAACAAGTGTGAGGGTGTGAGAAACTCACAGAATACAAATTTGCCT*CACAACGAGCGCAAGCCTGGCATCCGTCCGGCAAGACTGAACACCTGCGG	lincrna	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	UTR/intronic	0	207	69	37	7	54752326	-	7	55240152	-	2729.0488	1383.7173	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000132432	ENSG00000280890	SEC61G	AC073324.2	TGGTGAACAAGTGTGAGGGTGTGAGAAACTCACAGAATACAAATTTGCCT*GTGTGTAAAAATCGCTCCAGTGGTGAATTGGAAACTCGCAGTGCCAGGAA	lincrna	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	UTR/exonic(no-known-CDS)	0	207	64	38	7	54752326	-	7	55238666	-	2729.0488	1383.7173	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000132432	ENSG00000280890	SEC61G	AC073324.2	TGGTGAACAAGTGTGAGGGTGTGAGAAACTCACAGAATACAAATTTGCCT*GCTTGCAGCAGGAGGGCGGAGCAGATTGATCTGTTGACGGTGGGATTCTC	lincrna	BOWTIE+BLAT;BOWTIE+STAR	UTR/intronic	0	207	48	38	7	54752326	-	7	55240214	-	2729.0488	1383.7173	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000132432	ENSG00000280890	SEC61G	AC073324.2	GGCTTCTTTGTGAAATTGATCCATATTCCTATTAATAACATCATTGT*GTGTGTAAAAATCGCTCCAGTGGTGAATTGGAAACTCGCAGTGCCAG	lincrna,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	207	31	29	7	54755779	-	7	55238666	-	2729.0488	1383.7173	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000132432	ENSG00000280890	SEC61G	AC073324.2	GGACTCCATTCGGCTGGTTAAAAGATGCACTAAACCTGATAGAAAAG*GTGTGTAAAAATCGCTCCAGTGGTGAATTGGAAACTCGCAGTGCCAG	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	207	10	28	7	54757495	-	7	55238666	-	2729.0488	1383.7173	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000132432	ENSG00000280890	SEC61G	AC073324.2	ATTGGCTTCTTTGTGAAATTGATCCATATTCCTATTAATAACATCATTGT*CACAACGAGCGCAAGCCTGGCATCCGTCCGGCAAGACTGAACACCTGCGG	lincrna	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/intronic	0	207	4	34	7	54755779	-	7	55240152	-	2729.0488	1383.7173	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000132432	ENSG00000280890	SEC61G	AC073324.2	ATTGGCTTCTTTGTGAAATTGATCCATATTCCTATTAATAACATCATTGT*GCTTGCAGCAGGAGGGCGGAGCAGATTGATCTGTTGACGGTGGGATTCTC	lincrna	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	207	3	35	7	54755779	-	7	55240214	-	2729.0488	1383.7173	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000132432	ENSG00000280890	SEC61G	AC073324.2	AGCTCCAGTGCTACGTGTCCCTGGCATTTTAGGTGTCGGTTGGGTAG*GTGTGTAAAAATCGCTCCAGTGGTGAATTGGAAACTCGCAGTGCCAG	lincrna,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	207	3	29	7	54759158	-	7	55238666	-	2729.0488	1383.7173	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000132432	ENSG00000280890	SEC61G	AC073324.2	AAAGGACTCCATTCGGCTGGTTAAAAGATGCACTAAACCTGATAGAAAAG*GCTTGCAGCAGGAGGGCGGAGCAGATTGATCTGTTGACGGTGGGATTCTC	lincrna	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	207	2	36	7	54757495	-	7	55240214	-	2729.0488	1383.7173	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000132432	ENSG00000280890	SEC61G	AC073324.2	TGGTGAACAAGTGTGAGGGTGTGAGAAACTCACAGAATACAAATTTGCCT*AATATGGACCCTGTAATATTTACAGATTGATGAAGTATGGTTTGCAATAT	lincrna	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	UTR/intronic	0	207	2	32	7	54752326	-	7	55239430	-	2729.0488	1383.7173	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000132432	ENSG00000280890	SEC61G	AC073324.2	CATTTTGGAAGAGAGTTTTTCATCTTAGAGATTGGTGAACAAGTGTGAGG*GCTTGCAGCAGGAGGGCGGAGCAGATTGATCTGTTGACGGTGGGATTCTC	lincrna	BOWTIE+BLAT;BOWTIE+STAR	UTR/intronic	0	207	1	36	7	54752358	-	7	55240214	-	2729.0488	1383.7173	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000132432	ENSG00000280890	SEC61G	AC073324.2	AAAGGACTCCATTCGGCTGGTTAAAAGATGCACTAAACCTGATAGAAAAG*CACAACGAGCGCAAGCCTGGCATCCGTCCGGCAAGACTGAACACCTGCGG	lincrna	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/intronic	0	207	1	31	7	54757495	-	7	55240152	-	2729.0488	1383.7173	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000132432	ENSG00000280890	SEC61G	AC073324.2	CATTTTGGAAGAGAGTTTTTCATCTTAGAGATTGGTGAACAAGTGTGAGG*GTGTGTAAAAATCGCTCCAGTGGTGAATTGGAAACTCGCAGTGCCAGGAA	lincrna	BOWTIE+BLAT;BOWTIE+STAR	UTR/exonic(no-known-CDS)	0	207	1	29	7	54752358	-	7	55238666	-	2729.0488	1383.7173	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000132432	ENSG00000280890	SEC61G	AC073324.2	TTTTTTCCTTTCAAGATGTTTTCTATTTCTAAATTAAAGTAATTTCAAAG*CTTGCAGCAGGAGGGCGGAGCAGATTGATCTGTTGACGGTGGGATTCTCA	lincrna	BOWTIE+BOWTIE2	UTR/intronic	0	207	1	22	7	54752257	-	7	55240213	-	2729.0488	1383.7173	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000234707	ENSG00000146648	AC074351.1	EGFR	GCAAAAGATCTGAACAGACATTGCATAAAAGAAGATACACAGATGGCAAA*CTCTTTTAATTATTACTAGTTTAATGTATGTTTTGCTTAGTTAAGGAAAA	antisense,oncogene,cancer,tumor	BOWTIE+BOWTIE2	intronic/intronic	0	33	1	33	7	54763608	+	7	55053170	+	16.2988	1053.1268	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000146648	ENSG00000234707	EGFR	AC074351.1	GCTGGCTGCGCTCTGCCCGGCGAGTCGGGCTCTGGAGGAAAAGAAAG*TCAGAAGATTGAACATGTTGTAACTGTAGAAAGCCCGTCATCCTTGT	antisense,oncogene,cancer,tumor,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	33	11	29	7	55019365	+	7	54804666	+	1053.1268	16.2988	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000146648	ENSG00000234707	EGFR	AC074351.1	GCTGGCTGCGCTCTGCCCGGCGAGTCGGGCTCTGGAGGAAAAGAAAG*GTCAGTCAGGATCTTTGATTTTGGAGCACAAGCCTTCTGCGTGCTAC	antisense,oncogene,cancer,tumor,exon-exon	BOWTIE;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	33	5	23	7	55019365	+	7	54783108	+	1053.1268	16.2988	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000146648	ENSG00000234707	EGFR	AC074351.1	GCAGACGCCGGCCATGTGTGCCACCTGTGCCATCCAAACTGCACCTACGG*ATGTTTTGTCAAGCCATCACAGACGGATGTGCATTTTCTTCCCGAGAACA	antisense,oncogene,cancer,tumor	BOWTIE+BLAT	CDS(truncated)/intronic	0	33	1	33	7	55165437	+	7	54795449	+	1053.1268	16.2988	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000146648	ENSG00000234707	EGFR	AC074351.1	CTCCATGCCTTTGAGAACCTAGAAATCATACGCGGCAGGACCAAGCAACA*GACTTTGCGTGTGACCACTGCACCTCCAGGAAGGCCAGGTGCACATCGCT	antisense,oncogene,cancer,tumor	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	33	1	26	7	55157753	+	7	54782592	+	1053.1268	16.2988	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000146648	ENSG00000234707	EGFR	AC074351.1	TACTAGTACCATGCTGTTTTGGTTACTGTATCCCTGTAGTTTAAAGTCAG*GGCTACAGTAACCAAAACAGCATGGTACTAGTACAAAAACAGACACATAG	antisense,oncogene,cancer,tumor	BOWTIE+STAR	intronic/intronic	0	33	1	21	7	55196935	+	7	54792976	+	1053.1268	16.2988	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000146648	ENSG00000234707	EGFR	AC074351.1	TGATGCAAATAAAACCGGACTGAAGGAGCTGCCCATGAGAAATTTACAGG*AAGATTGAACATGTTGTAACTGTAGAAAGCCCGTCATCCTTGTGTATGCA	antisense,oncogene,cancer,tumor	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	33	1	20	7	55143488	+	7	54804670	+	1053.1268	16.2988	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000146648	ENSG00000234707	EGFR	AC074351.1	GCTGCTGGCTGCGCTCTGCCCGGCGAGTCGGGCTCTGGAGGAAAAGAAAG*CTCATGACCAGCTCGTGAAAAAGATCACTACACAGCGTGGCAGAATTGCG	antisense,oncogene,cancer,tumor	BOWTIE+STAR	CDS(truncated)/intronic	0	33	1	16	7	55019365	+	7	54799275	+	1053.1268	16.2988	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000178966	ENSG00000136874	RMI1	STX17	CGCTGCCCAGGGACCGATGTTGCGCGAGGAAAATGCGGGACGCCCAG*TATCAAAGGTGCAGAATCTGGGACAAGTTGCATGAAGAGCATATCAA	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE;BOWTIE+STAR	UTR/CDS(truncated)	0	24	16	27	9	83980891	+	9	99928778	+	3.8353	32.1487	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000178966	ENSG00000136874	RMI1	STX17	GAGCAGAGGCATGATCACATCTCACTGCAGCCTTGTCCTCCTAGGCTCAG*TATCAAAGGTGCAGAATCTGGGACAAGTTGCATGAAGAGCATATCAATGC	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	intronic/CDS(truncated)	0	24	2	22	9	83988404	+	9	99928778	+	3.8353	32.1487	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000178966	ENSG00000136874	RMI1	STX17	CCCGCCCCGGGCTGTGGTCTGTGGGCTGTGGGACGAGCTGCGGCGCG*TATCAAAGGTGCAGAATCTGGGACAAGTTGCATGAAGAGCATATCAA	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	24	2	15	9	83981004	+	9	99928778	+	3.8353	32.1487	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000280890	ENSG00000146648	AC073324.2	EGFR	AACCCTCCAGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTG*GGAGGCCTCACAGGAGGATGACCAGGTCTCAGTCAGCGGGGAGGTGGAAA	lincrna,oncogene,cancer,tumor	BOWTIE+BLAT	intronic/UTR	0	23	1	29	7	55251125	-	7	55207571	+	1383.7173	1053.1268	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000280890	ENSG00000146648	AC073324.2	EGFR	TTTCCTCAATGTGGGAAAAGCAGAGCTCTTTCCCCAAACACACAACACAG*ACAGACACGTACACACACTACAGACATGTATGCACACATACACACACACC	lincrna,oncogene,cancer,tumor	BOWTIE+STAR	intronic/intronic	0	23	1	14	7	55247860	-	7	55203426	+	1383.7173	1053.1268	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000280890	ENSG00000146648	AC073324.2	EGFR	ACTTGGGCTCAGTGAAGCAGATTAATAAAGCAATGGGGCATCTCTGGCTG*TCAGCAGCAGCCAGTCTCCAGTGTCCAAGCCAGGTGCTCCCTCCAGCATC	lincrna,oncogene,cancer,tumor	BOWTIE+STAR	exonic(no-known-CDS)/CDS(truncated)	0	23	1	14	7	55237301	-	7	55202676	+	1383.7173	1053.1268	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000146648	ENSG00000280890	EGFR	AC073324.2	GACGCCGGCCATGTGTGCCACCTGTGCCATCCAAACTGCACCTACGG*GTGTGTAAAAATCGCTCCAGTGGTGAATTGGAAACTCGCAGTGCCAG	lincrna,oncogene,cancer,tumor,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	23	15	29	7	55165437	+	7	55238666	-	1053.1268	1383.7173	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000146648	ENSG00000280890	EGFR	AC073324.2	CATGCCTTTGAGAACCTAGAAATCATACGCGGCAGGACCAAGCAACA*GTGTGTAAAAATCGCTCCAGTGGTGAATTGGAAACTCGCAGTGCCAG	lincrna,oncogene,cancer,tumor,exon-exon	BOWTIE;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	23	7	29	7	55157753	+	7	55238666	-	1053.1268	1383.7173	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000146648	ENSG00000280890	EGFR	AC073324.2	GCTGGCTGCGCTCTGCCCGGCGAGTCGGGCTCTGGAGGAAAAGAAAG*GTGTGTAAAAATCGCTCCAGTGGTGAATTGGAAACTCGCAGTGCCAG	lincrna,oncogene,cancer,tumor,exon-exon	BOWTIE;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	23	2	27	7	55019365	+	7	55238666	-	1053.1268	1383.7173	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000146648	ENSG00000280890	EGFR	AC073324.2	GTCTAAACCAGTAGCTCTTAACTGAGACAATCCTGTCCTCATCTCACCTG*AGGACAGGTGCAGGCGATTGCTTTCACCTTCTAACTTTAGAATCTGGAGA	lincrna,oncogene,cancer,tumor	BOWTIE+STAR	intronic/exonic(no-known-CDS)	0	23	1	16	7	55043264	+	7	55237564	-	1053.1268	1383.7173	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000146648	ENSG00000023318	EGFR	ERP44	GCTGGCTGCGCTCTGCCCGGCGAGTCGGGCTCTGGAGGAAAAGAAAG*CTGACATAGCCCAGAGATACAGGATAAGCAAATACCCAACCCTCAAA	known,oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	in-frame	0	16	17	30	7	55019365	+	9	100022226	-	1053.1268	98.8783	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000146648	ENSG00000023318	EGFR	ERP44	GCTGGCTGCGCTCTGCCCGGCGAGTCGGGCTCTGGAGGAAAAGAAAG*CGCAGCAAAAGAAATATCATTGGATATTTTGAGCAAAAGGACTCGGA	known,oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	16	4	22	7	55019365	+	9	100020731	-	1053.1268	98.8783	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000146648	ENSG00000023318	EGFR	ERP44	TGTCCAGCCCACCTGTGTCAACAGCACATTCGACAGCCCTGCCCACTGGG*CTGGTAAAACCCAGTGCCAGAAAGGCTTCTGTGGCCCCAGACTCCAGGCT	known,oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	16	1	19	7	55205456	+	9	100004555	-	1053.1268	98.8783	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000146648	ENSG00000023318	EGFR	ERP44	TTCATCATACATGTTTAAAAACCTAGTTAAATAGTAGTTAAACTGACTGC*TGTCGTTTCAGTCAGATGTTGCATCCAATTTTTGAGGAAGCTTCCGATGT	known,oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	16	1	15	7	55195151	+	9	100052531	-	1053.1268	98.8783	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000146648	ENSG00000023318	EGFR	ERP44	TCTCTTCCTTTTATTCTTTGCCCTTGGCTTTTGGAGGTTTTGGGTTTTCT*ATCTTTTCCTCCAGCCCCCCTTCTGAGAGCTCATATTCCATTTTAACCTC	known,oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+STAR	intronic/intronic	0	16	1	14	7	55161770	+	9	100022860	-	1053.1268	98.8783	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000146648	ENSG00000023318	EGFR	ERP44	AACCCATTCTTACATGAATGGCATTAATCCATTCCTTAGGGCACAGCTCT*CTGACATAGCCCAGAGATACAGGATAAGCAAATACCCAACCCTCAAATTG	known,oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	16	1	14	7	55139045	+	9	100022226	-	1053.1268	98.8783	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000146648	ENSG00000023318	EGFR	ERP44	CATCGCCACTGGGATGGTGGGGGCCCTCCTCTTGCTGCTGGTGGTGGCCC*TTCTCTTGCTGCTGGTTATTCAGGCCAAAGGGCTCTTCAGTAAGCAGGTG	known,oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	16	1	14	7	55173047	+	9	100037843	-	1053.1268	98.8783	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000023318	ENSG00000146648	ERP44	EGFR	CAGCCTAGGTGACAGAACAAGACCTTGTCTCAAAAAAAAAAAAAAAAAAA*GGAATCCTATGACCTGATTTGGCCACAAAAATAATCTTGCTGTACAATAC	known,oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+BOWTIE2	intronic/UTR	0	16	1	33	9	100071094	-	7	55211245	+	98.8783	1053.1268	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000023318	ENSG00000146648	ERP44	EGFR	GCTTTTTGGCCATTTGTATGTCTTTTGAGAAATGTTTGTTGAGATGCCAT*GACCCCCACAGCACTGCAGTGGGCAACCCCGAGTATCTCAACACTGTCCA	known,oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	16	1	14	9	100029356	-	7	55205363	+	98.8783	1053.1268	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000023318	ENSG00000146648	ERP44	EGFR	AGTTAGAGAACTTTTTTGTTTTTTAGTTCTGTTTTTTAGAAAAATGAGTT*TCAAAATTTGAAACTGAAATCTTTGTTTAAAAGGGTTAAGTTGAGGCAAG	known,oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+STAR	intronic/UTR	0	16	1	14	9	100072473	-	7	55209868	+	98.8783	1053.1268	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000164970	ENSG00000130997	FAM219A	POLN	TCGACCGGTTCCAGGTGCCCACCGCGCACTCGGAGATGCAGCCGCTG*GAAGGATGTGCCCGTGGAACAGGTGACACACGCAGACAGAGAGCAAA	known,18cancers,exon-exon	BOWTIE	out-of-frame	0	4	9	28	9	34458204	-	4	2095933	-	16.2356	9.5319	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0744-01A	ENSG00000164970	ENSG00000130997	FAM219A	POLN	TCGACCGGTTCCAGGTGCCCACCGCGCACTCGGAGATGCAGCCGCTG*GCTGTGTGGTGTCCATCATGGGCAGAAGGAGACCCCTGCCAAGGATT	known,18cancers,exon-exon	BOWTIE	in-frame	0	4	1	13	9	34458204	-	4	2081743	-	16.2356	9.5319	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0211-02A	ENSG00000107338	ENSG00000174482	SHB	LINGO2	GAGTGCTGGCTACATGGAGCCCTATGAGGCACAGAGGATCATGACAG*ACCCGTGACCAAGGTGTAGACTAAGAAGTGGAGTCATGCTTCACACG	18cancers,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	4	3	29	9	38016011	-	9	27950706	-	1.4676	2.0887	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-06-0211-02A	ENSG00000132434	ENSG00000154997	LANCL2	SEPT14	GCCACGGCGCCCCGGGGGTCATCCACATGCTCATGCAGGCGTACAAG*GGGCTGTTACCCTTTGCTGTGGTAGGGAGTACAGATGAAGTGAAAGT	known,tcga,exon-exon	BOWTIE	in-frame	0	1	2	26	7	55412089	+	7	55819223	-	152.4196	0.1056	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-15-1444-01A	ENSG00000138162	ENSG00000177640	TACC2	CASC2	CAGCCAGCCCCAGCCAGCGACCTGAACCTGGAGGCTTCCGAGGCAAT*AGCCAGAAAATGCATGACACAGGAGAAGATGTACCCTCATCTGTTCA	antisense,18cancers,exon-exon	BOWTIE;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	3	3	23	10	122163992	+	10	118206522	+	1.1467	1.1301	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-15-1444-01A	ENSG00000138162	ENSG00000177640	TACC2	CASC2	CAGCCAGCCCCAGCCAGCGACCTGAACCTGGAGGCTTCCGAGGCAAT*GAAAATTAAGGAAGTTTTTCAAAGAACCCTATTCCGAGTAAGAAGTG	antisense,18cancers,exon-exon	BOWTIE;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	3	3	22	10	122163992	+	10	118052131	+	1.1467	1.1301	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0686-01A	ENSG00000237686	ENSG00000135678	AL109615.3	CPM	CGAGTCTGGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCACGATCTCGGCT*CGCTTGAACCTGGGAGGCAGAGGTTGCAGTGAGCCGGGATTGCGCCATTG	antisense	BOWTIE+BLAT	intronic/UTR	0	2	1	22	6	44026464	-	12	68854960	-	23.753	456.8681	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0686-01A	ENSG00000237686	ENSG00000135678	AL109615.3	CPM	AGTGGGGAGGCAGCTCTGAATCGAGAGAACTGGCCTCAAGCAGATGATGG*CCTCCAACCCATCATGTGGAGATACTCATCCTGTTCCCCCTAGAGCTGCT	antisense	BOWTIE+STAR	intronic/UTR	0	2	1	14	6	44012035	-	12	68855332	-	23.753	456.8681	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0686-01A	ENSG00000135678	ENSG00000237686	CPM	AL109615.3	GAACTTTCCTAATGGTGTTACAAATGGATACTCTTGGTATCCACTCCAAG*AAAGAAGCTGGAAGCTCAAGCCTGACTATAGGACCAGCACAGCCCCTGGC	antisense	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/intronic	0	2	3	34	12	68869325	-	6	44021472	-	456.8681	23.753	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0686-01A	ENSG00000135678	ENSG00000237686	CPM	AL109615.3	CTTTCCTAATGGTGTTACAAATGGATACTCTTGGTATCCACTCCAAG*AAACACTCTGTCTTCCTGCTTTGAGGACAGCTGAAGTCTTGCCACTT	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	2	2	26	12	68869325	-	6	44001116	-	456.8681	23.753	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0686-01A	ENSG00000135678	ENSG00000237686	CPM	AL109615.3	CCTCCCGGGTTCAAGCAATTCTCCTGTCTCAGCCTCCCGAGTACCTGGGA*CAGGAGAATTGCTTGAACCCGGGAGGCAGAGGTTGCAGTGAGCCAAGATC	antisense	BOWTIE+BLAT	UTR/intronic	0	2	1	37	12	68851492	-	6	44055858	-	456.8681	23.753	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0686-01A	ENSG00000135678	ENSG00000237686	CPM	AL109615.3	CTGGGAGTCATCCTTGATACTTTCTCTTCCTCCTTAATCCTGTGTATTCA*CCATGTTGGCCAGGCTGGTCTTGAACTCCTGACCTCAGGTGATCCACCCG	antisense	BOWTIE+BLAT	UTR/intronic	0	2	1	19	12	68855183	-	6	44012919	-	456.8681	23.753	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0686-01A	ENSG00000135678	ENSG00000237686	CPM	AL109615.3	ATGAATTCTGCTCTCTGCTCTCTATGGTTGTCAACACTGCAGAGTTGAGG*GTTTCTTTCTTTCCTGTTGAGCCTTCCCTGTAGGGGTGGATGCCCTGGGC	antisense	BOWTIE+STAR	UTR/intronic	0	2	1	19	12	68854795	-	6	44059388	-	456.8681	23.753	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0686-01A	ENSG00000135678	ENSG00000237686	CPM	AL109615.3	GCTGCAACAGCTTACTGGTCCCTTGCTCCCAGCCTTCTCCTCTTCAGTCC*CAAGAGCTGTGTGGCTCTGTATAGGACTAGGATATAAAGCATTGTGTGTC	antisense	BOWTIE+STAR	UTR/intronic	0	2	1	14	12	68854725	-	6	44053191	-	456.8681	23.753	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0686-01A	ENSG00000135678	ENSG00000237686	CPM	AL109615.3	GCCACTTGAAACAAAAGTCAACAACTGGTTGTAGTTCATAAACACAGAGC*ATTTGGGAAGGGGAGAGAAATGGGGACTCATTCTACAGACCCCCAAACAT	antisense	BOWTIE+STAR	UTR/intronic	0	2	1	14	12	68854647	-	6	44000180	-	456.8681	23.753	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0686-01A	ENSG00000135678	ENSG00000237686	CPM	AL109615.3	CAACACTGCAGAGTTGAGGCCTCATATCTCACCTGCACTGCTGCAACAGC*AAAGGACCAGTGAGACTAAAAGGCAAGGGAGATAAAACTGGAAAGTAGGC	antisense	BOWTIE+STAR	UTR/intronic	0	2	1	14	12	68854764	-	6	44049122	-	456.8681	23.753	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0686-01A	ENSG00000135678	ENSG00000237686	CPM	AL109615.3	AGCCGTTTCCCTAGCTTTTGGCACCTGGATGCCACAGTCCTCCATTAGGC*CTGTATCTTCTTGGTCCGTCCTAATGTTCCTGAACTGGAAGCTCCCTGCA	antisense	BOWTIE+STAR	UTR/intronic	0	2	1	14	12	68855431	-	6	44057960	-	456.8681	23.753	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0686-01A	ENSG00000135678	ENSG00000112759	CPM	SLC29A1	AAAATGGGACCCCACCCCCACTGTGCGTGTGTGTGTGTTTGTGTGTGTGT*GGGTGGCTAGGAGCTGGGTCTGACCGTTGTATGGTTTGACCTGATATACT	cancer	BOWTIE+STAR	intronic/UTR	0	2	1	28	12	68883010	-	6	44233906	+	456.8681	2548.3419	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0686-01A	ENSG00000135678	ENSG00000112759	CPM	SLC29A1	AAAATGGGACCCCACCCCCACTGTGCGTGTGTGTGTGTTTGTGTGTGTGT*GTCCGTGTCTGTCAGACTGTCTGCCTGTCCTGGGGTGGCTAGGAGCTGGG	cancer	BOWTIE+BLAT;BOWTIE+STAR	intronic/UTR	0	2	1	23	12	68883010	-	6	44233874	+	456.8681	2548.3419	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0686-01A	ENSG00000135679	ENSG00000112759	MDM2	SLC29A1	CATCTGTGAGTGAGAACAGGTGTCACCTTGAAGGTGGGAGTGATCAAAAG*GGCAGCCTGTTTGGTCTGGCTGGCCTTCTGCCTGCCAGCTACACGGCCCC	oncogene,cancer,tumor	BOWTIE+STAR	in-frame	0	2	1	18	12	68824430	+	6	44230367	+	156.0284	2548.3419	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0686-01A	ENSG00000112759	ENSG00000135678	SLC29A1	CPM	AGCGAGAGCGCGCGGATCTCAGCGCGGGAGCAGTGCTTCTGCGGCAG*AACATGGACTTCCCGTGCCTCTGGCTAGGGCTGTTGCTGCCTTTGGT	cancer,exon-exon	BOWTIE	UTR/UTR	0	2	2	24	6	44223641	+	12	68932840	-	2548.3419	456.8681	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0686-01A	ENSG00000112759	ENSG00000135678	SLC29A1	CPM	TTTCCGTCCCCCACCAAGTCCGGATGCTCACTCCAAAGTCTCAGCAG*AACATGGACTTCCCGTGCCTCTGGCTAGGGCTGTTGCTGCCTTTGGT	cancer,exon-exon	BOWTIE;BOWTIE+STAR	UTR/UTR	0	2	2	22	6	44219782	+	12	68932840	-	2548.3419	456.8681	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0686-01A	ENSG00000112759	ENSG00000135678	SLC29A1	CPM	TCAGTCTCCAACTCTCAGCCCACCAATGAAAGCCACTCTATCAAAGCCAT*CTAAAAAATATCTTAGGTTTTACAATAGTGATATTATCCCTCTGAGCAAT	cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	16	6	44231451	+	12	68878437	-	2548.3419	456.8681	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0686-01A	ENSG00000112759	ENSG00000135678	SLC29A1	CPM	ATGTGCCATGCTGCCCCTGCTGTTATTCACCTACCTCAACTCCTTCCTGC*GTCAGAATCTCCTTCCACACCTCTTCTCCTCTTGAGCATCTTCCAGTAAC	cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	15	6	44229784	+	12	68922121	-	2548.3419	456.8681	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0686-01A	ENSG00000112759	ENSG00000135678	SLC29A1	CPM	GCTGCCTTTGCCTTCTCCAACGGCTACCTCGCCAGCCTCTGCATGTGCTT*CACTTTCTTGGGCCTCCACGAGAAAAATTCTATTCAATTAGTCGTGGGCT	cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	14	6	44232997	+	12	68934324	-	2548.3419	456.8681	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0686-01A	ENSG00000112759	ENSG00000135678	SLC29A1	CPM	CAGGTGCCTTCAGAGGCTCTCTGATTTAAATAAACCTTTCTTGTTTTTTT*AACAAAAAAAAAAACGGCCAGGCGCAGTGGCTCACACCTGTAATCCCAGC	cancer	BOWTIE+STAR	UTR/intronic	0	2	1	14	6	44234141	+	12	68849404	-	2548.3419	456.8681	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0686-01A	ENSG00000112759	ENSG00000137216	SLC29A1	TMEM63B	GTGCCGCTGACTGCGCTGGCGGAGGGGTATGGGGATGGGGATGGGGATGG*GCCCCCATCATCCTCATCCCAAGATGAGGAGTTGCTGATGCCACCCGACG	cancer,10K<gap<100K	BOWTIE+BOWTIE2;BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	26	6	44224025	+	6	44154769	+	2548.3419	676.3291	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0686-01A	ENSG00000137216	ENSG00000112759	TMEM63B	SLC29A1	TTTTTTTGTTCTTTTTTGTTTTTTTCCTTTAAAATAAAAACAAAGAAAAG*GTCTCAAAAAAAAAAAAAAAAAGAAAAAATCTGAGACCTGAGGCTTTCCC	cancer,10K<gap<100K	BOWTIE+STAR	UTR/intronic	0	2	1	15	6	44155513	+	6	44225503	+	676.3291	2548.3419	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0686-01A	ENSG00000137216	ENSG00000112759	TMEM63B	SLC29A1	CCCCCACCCCTCACATCCCCTGGCTCCACTGGGGTCAAGCCTCAGAAGGC*GTGTCTGTGTGTCTGCGTCCGTGTCTGTCAGACTGTCTGCCTGTCCTGGG	cancer,10K<gap<100K	BOWTIE+STAR	intronic/UTR	0	2	1	15	6	44141004	+	6	44233858	+	676.3291	2548.3419	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-41-5651-01A	ENSG00000135506	ENSG00000155980	OS9	KIF5A	GGTCCAAGTGCGACCTTAATGGGAGGCCCCGGGAGGCCGAGGTTCGG*GGTTGTACTGAACGCTTTGTGTCCAGCCCGGAGGAGATTCTGGATGT	known,tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	47	21	29	12	57696373	+	12	57567126	+	531.9381	95.1041	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-41-5651-01A	ENSG00000123297	ENSG00000139269	TSFM	INHBE	TGGGCCTGACAGAGAAGGCTCACTCAAGGATCAGTTGGCTTTAGCAATTG*CCTTCCTGAGTCCCAGACAATAGAAGACAGGTGGCTGTACCCTTGGCCAA	known,18cancers,cancer	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(complete)/UTR	0	11	12	37	12	57793073	+	12	57455368	+	3.0035	9.2247	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-41-5651-01A	ENSG00000123297	ENSG00000139269	TSFM	INHBE	GCCTGACAGAGAAGGCTCACTCAAGGATCAGTTGGCTTTAGCAATTG*ACTCCACTTCAGCCTACAGCTCCCTGCTCACTTTTCACCTGTCCACT	known,18cancers,cancer,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	11	10	28	12	57793073	+	12	57456094	+	3.0035	9.2247	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-41-5651-01A	ENSG00000123297	ENSG00000139269	TSFM	INHBE	GCCTGACAGAGAAGGCTCACTCAAGGATCAGTTGGCTTTAGCAATTG*GCAGCGCTGACCAGAGCCCTCCGGAGACTACAGCCAGGGAGTGTGGC	known,18cancers,cancer,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	11	5	28	12	57793073	+	12	57455744	+	3.0035	9.2247	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-41-5651-01A	ENSG00000123297	ENSG00000139269	TSFM	INHBE	TGGGCCTGACAGAGAAGGCTCACTCAAGGATCAGTTGGCTTTAGCAATTG*GCCTGAAGGGTGGTGCGGTGGCTCACGCCTGTAACCTCAGCACTTTAGGA	known,18cancers,cancer	BOWTIE+STAR	CDS(complete)/intronic	0	11	2	18	12	57793073	+	12	57454129	+	3.0035	9.2247	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-41-5651-01A	ENSG00000123297	ENSG00000139269	TSFM	INHBE	TGGGCCTGACAGAGAAGGCTCACTCAAGGATCAGTTGGCTTTAGCAATTG*CAATCAGACTCAACAGACGGAGCAACTGCCATCCGAGGCTCCTGAACCAG	known,18cancers,cancer	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(complete)/UTR	0	11	1	36	12	57793073	+	12	57455470	+	3.0035	9.2247	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-41-5651-01A	ENSG00000135454	ENSG00000244390	B4GALNT1	AC068305.1	GGGGGCAATCTGGGGGTAATGGCATTTCTCACAAAGTCCACTCGGCTGAT*GCTCCGGGTGAAGAATGGAAGGGCTACGTTGTTTGAATAAATGATGGGAA	pseudogene,m9	BOWTIE+BLAT;BOWTIE+STAR	UTR/exonic(no-known-CDS)	0	10	18	38	12	57624081	-	12	59020286	+	86.0085	1.8709	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	processed_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-41-5651-01A	ENSG00000038532	ENSG00000153066	CLEC16A	TXNDC11	TGTCTGAGATGTACGCTAAGACTGAACAGGATATTCAGAGAAGTTCT*GATTGACGTGTCTCAGAATGACCTTCCTTGGGAATTTATGGTCGATC	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	10	8	27	16	10982991	+	16	11684245	-	2.7627	6.5772	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-41-5651-01A	ENSG00000038532	ENSG00000153066	CLEC16A	TXNDC11	ATTGGGAGCCATGTGATCGAACTCGATGACTGCGTGCAGACTGATGAGGA*GATTGACGTGTCTCAGAATGACCTTCCTTGGGAATTTATGGTCGATCGTC	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE+STAR	in-frame	0	10	1	19	16	10973061	+	16	11684245	-	2.7627	6.5772	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-41-5651-01A	ENSG00000135454	ENSG00000123297	B4GALNT1	TSFM	TTTCCCTTGCCTGTGAGTAAAGCATACTAGGAGTTATGTTTGCTGGGGGA*GTAGGTGGTGTCATCTCTATTTTAAAGGTGAGGAAACAAAGGCTTGATAA	known,18cancers,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	UTR/intronic	0	6	17	37	12	57624210	-	12	57795442	+	86.0085	3.0035	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-41-5651-01A	ENSG00000135454	ENSG00000123297	B4GALNT1	TSFM	GCCTGCCTCCTTGTCCCTGCCAGGAATTTCCAACAAACCCCACCACCCTG*AAAACTGGGAGAAAACATGATTCTTAAACGAGCTGCATGGGTGAAGGTGC	known,18cancers,tcga-cancer	BOWTIE+BOWTIE2	UTR/CDS(truncated)	0	6	4	33	12	57626661	-	12	57796178	+	86.0085	3.0035	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-41-5651-01A	ENSG00000135454	ENSG00000123297	B4GALNT1	TSFM	CTTCCTTTTCAGAACCTGATGCCCAGTAGGGGTTGTCCTGGTGACACCCC*CTACTGGCTATCAGGATTGTTGTAAAGATCAAAAAGATGATGTGTATGGA	known,18cancers,tcga-cancer	BOWTIE+STAR	UTR/intronic	0	6	1	14	12	57626569	-	12	57801864	+	86.0085	3.0035	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-41-5651-01A	ENSG00000257921	ENSG00000037897	AC025165.3	METTL1	TCTAGTGAGGGAGACAGAGGACGATGTCATAGAACAAGAACTCTGGCGAG*TGGAACTGTCACCGCTGTTCCCAGACACACTTATTCTGGGTCTGGAGATC	NA	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	intronic/CDS(truncated)	0	3	2	22	12	57774688	+	12	57769956	-	0	110.8976	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-41-5651-01A	ENSG00000257921	ENSG00000037897	AC025165.3	METTL1	CGAACTGGGTGCGGGGACAGGCATCGTGGGGATCTTGGCAGCGCTGCAGG*CTGACAAAGATGTTCTTCCTCTTCCCCGACCCACATTTCAAGCGGACAAA	exon-exon	BOWTIE+BLAT;BOWTIE+STAR	CDS(no-known-start-or-end)/CDS(truncated)	0	3	1	19	12	57773128	+	12	57769678	-	0	110.8976	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-41-5651-01A	ENSG00000075213	ENSG00000257259	SEMA3A	LINC02388	CTATCAGAATGGGAAGAACAATGTGCCAAGGCTGAAATTATCCTACAAAG*ACTCTCACTCTATTACCCAGGCTGGAGTGCGGTGGCATGATCTCGGCTCA	lincrna	BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/intronic	0	3	2	24	7	84194475	-	12	58571452	-	1.631	0.7765	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000257747	ENSG00000165966	LINC02426	PDZRN4	TTTGAACAACTTATGTAAGGTCATCTTGGGTTATGATTGTCCCTCTCAGG*GCCCAGAACACAGCAGTGTTTTGCAGGTTTAACACATCCACTCTTACCTT	lincrna	BOWTIE+STAR	intronic/intronic	0	106	1	14	12	81954481	+	12	41467605	+	20.6692	23.4855	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000166889	ENSG00000109927	PATL1	TECTA	AGAGATTGATCAATTCAATGATGATACATTTGGGTCAGGTGCAGTTG*GTGTCAGAACCTCAAAGATAACACCATTGGCATCGAGGAGAATGCAG	known,tcga,18cancers,chimerdb3seq,cancer,m63,tcga-cancer,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	77	31	29	11	59666853	-	11	121187832	+	14.2564	7.8476	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000135678	ENSG00000165966	CPM	PDZRN4	GGAGCAGTGGCTCACACCTTGTAATCCCAGCACTTTGGGAGGCCAAG*GAGGTCGAGTTGTGTCGTGTTAGCAGTCAAGAGAAGCTGGGCCTGAC	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	7	5	29	12	68855981	-	12	41552656	+	19.6601	23.4855	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000135678	ENSG00000165966	CPM	PDZRN4	AGAAAAATGTGGGAGTGAAATGGTATTTAGAAAGCAGCAGTCAGGCACGG*TGGCTCACGCCTGTAATCCCAGCACCTTGGGAGGCCGAAGCAGGCAGATC	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	UTR/intronic	0	7	1	36	12	68852850	-	12	41435519	+	19.6601	23.4855	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000135678	ENSG00000165966	CPM	PDZRN4	CCTCCCGAGTACCTGGGACTACCGGTGCCTGTCTCCACGCCCGGCTAATT*TTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGG	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	UTR/intronic	0	7	1	29	12	68851460	-	12	41541621	+	19.6601	23.4855	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000135678	ENSG00000165966	CPM	PDZRN4	CTCGCGTCCCACTGCCCACAGGACACATCCACCTGGATGTGACTCACAGG*AGGTCGAGTTGTGTCGTGTTAGCAGTCAAGAGAAGCTGGGCCTGACAGTC	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BOWTIE2	UTR/CDS(truncated)	0	7	1	23	12	68855335	-	12	41552657	+	19.6601	23.4855	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000135678	ENSG00000165966	CPM	PDZRN4	GGTACCATGACCACACTTTGAGAACCTCTGCCTTATGAAGTTTCCAAAGA*CAATGGGAAGGATCTTTCAAAGGCCACTCATGAAGAGGCAGTGGAAGCTT	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	7	1	22	12	68891565	-	12	41506458	+	19.6601	23.4855	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000165966	ENSG00000135678	PDZRN4	CPM	TTGCTGCCAAAGACGGCCGGATTCGAGAAGGGGATCGGATTTTGCAA*AACATGGACTTCCCGTGCCTCTGGCTAGGGCTGTTGCTGCCTTTGGT	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	7	4	29	12	41555760	+	12	68932840	-	23.4855	19.6601	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000165966	ENSG00000135678	PDZRN4	CPM	GCATTGCTGCCAAAGACGGCCGGATTCGAGAAGGGGATCGGATTTTGCAA*AGTCTCGCTCTGTCACCCAGGCTGGAGTGCAATGGTGCGATCCCAGCTCA	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	7	2	31	12	41555760	+	12	68916880	-	23.4855	19.6601	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000165966	ENSG00000135678	PDZRN4	CPM	TCTTCCCACTCCTCCCACCCCTGGAGCAGGAAAAGAAAAAAAAAAAGAAA*AACTCTGGTGAGCAGATTTCTTTCCTTTCTTCCTTCCTTCTCCTCTTCCT	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/UTR	0	7	2	20	12	41402090	+	12	68853888	-	23.4855	19.6601	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000165966	ENSG00000135678	PDZRN4	CPM	ATTGCTGCCAAAGACGGCCGGATTCGAGAAGGGGATCGGATTTTGCAAGT*CACATTCAGTTTCTTTATCTGTAAAATGGAGACCACCCCCCGCCACGCTG	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/UTR	0	7	2	15	12	41555762	+	12	68852506	-	23.4855	19.6601	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000165966	ENSG00000135678	PDZRN4	CPM	AGCATTGCTGCCAAAGACGGCCGGATTCGAGAAGGGGATCGGATTTTGCA*AAGTCTCGCTCTGTCACCCAGGCTGGAGTGCAGTGGTGGGATCTCGGCTC	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BOWTIE2	CDS(truncated)/intronic	0	7	1	33	12	41555759	+	12	68850279	-	23.4855	19.6601	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000165966	ENSG00000135678	PDZRN4	CPM	GCATTGCTGCCAAAGACGGCCGGATTCGAGAAGGGGATCGGATTTTGCAA*ACTGTTGGGCGGGAGCTGCTGCTCCATCTGATTGACTATCTCGTAACCAG	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE+STAR	in-frame	0	7	1	18	12	41555760	+	12	68871956	-	23.4855	19.6601	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000165966	ENSG00000135678	PDZRN4	CPM	AATACACCATTCCCTTGCTATTGCAGTTTATTTTCAACCTCAATTATTTA*GAATTCTGCTCTCTGCTCTCTATGGTTGTCAACACTGCAGAGTTGAGGCC	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/UTR	0	7	1	17	12	41249648	+	12	68854842	-	23.4855	19.6601	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000135679	ENSG00000165966	MDM2	PDZRN4	CAAGAAGATGTGAAAGAGTTTGAAAGGGAAGAAACCCAAGACAAAGAAGA*TATCAAAGAGTTTGAAAGCCAGTGATGGAAGAAACATGATGGGTATGAAA	oncogene,18cancers,cancer,tumor	BOWTIE+STAR	CDS(truncated)/intronic	0	4	2	18	12	68839644	+	12	41515164	+	415.4333	23.4855	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000135679	ENSG00000165966	MDM2	PDZRN4	CCTTCTGGGTTCAAGCTATTCTCCTGCCTCAGCCTTCCAAGTAACTGGGA*AGGCTGAGGCAGGAGAATAGCTTGAACCCAGGAGGCGGAGGTTGCAGTGA	oncogene,18cancers,cancer,tumor	BOWTIE+BLAT;BOWTIE+STAR	UTR/intronic	0	4	1	31	12	68840981	+	12	41416553	+	415.4333	23.4855	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000135679	ENSG00000165966	MDM2	PDZRN4	TGTGTGAAAGATTTAGTTTTTTGTTTTTTTGTTTGTTTGTTTGTTTGTTT*CGGAATCTCTGTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCAGC	oncogene,18cancers,cancer,tumor	BOWTIE+STAR	UTR/intronic	0	4	1	31	12	68840529	+	12	41384025	+	415.4333	23.4855	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000135679	ENSG00000165966	MDM2	PDZRN4	CCTCAGCCTCCCAATTAGCTTGGCCTACAGTCATCTGCCACCACACCTGG*CTATTCGGGAGGCTGAGGCAGGAGAATGGTGTAAACCTGGGAGGCGGAGC	oncogene,18cancers,cancer,tumor	BOWTIE+BLAT	UTR/intronic	0	4	1	30	12	68840307	+	12	41346349	+	415.4333	23.4855	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000135679	ENSG00000165966	MDM2	PDZRN4	TGGGATTACAGGCATGCACCACCATGCCCAGCTAATTTTTGTATTTTTAG*TGGTGAAACCCTGTCTCCACTAAAAATACAAAAATTAGCTGAGCATGGTG	oncogene,18cancers,cancer,tumor	BOWTIE+STAR	UTR/intronic	0	4	1	27	12	68840687	+	12	41263504	+	415.4333	23.4855	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000135679	ENSG00000165966	MDM2	PDZRN4	ACTATATTGGCCAGGCTGGTCTCGAACTCCTGACCTCATGATCCGCCTGC*CACCATGCCCAGCTAATTTTTGTATTTTTAATAGAGACAGGGTTTCACCA	oncogene,18cancers,cancer,tumor	BOWTIE+STAR	UTR/intronic	0	4	1	24	12	68848959	+	12	41568956	+	415.4333	23.4855	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000135679	ENSG00000165966	MDM2	PDZRN4	TGCCTCAGCCTCCCAGTAGTTGGAATTACAGGCGCATGCCACCATGCATG*GCTGAGGCAGGAGAATCATTGAACCTGGGAGGCGGAGGTTATGGTGAGCT	oncogene,18cancers,cancer,tumor	BOWTIE+BLAT	UTR/intronic	0	4	1	20	12	68849570	+	12	41504167	+	415.4333	23.4855	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000135679	ENSG00000165966	MDM2	PDZRN4	CTTTATTTTTCGAGCCTAGCAATGATCTAGAAGCAGATGTTATCTCAGTG*ATATTAGAAGAGAGTAGTGTGTATCTGTTCATTATATGGCAGAAATTGTG	oncogene,18cancers,cancer,tumor	BOWTIE+STAR	UTR/intronic	0	4	1	20	12	68843070	+	12	41422258	+	415.4333	23.4855	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000135679	ENSG00000165966	MDM2	PDZRN4	GTTGTGAAAGAAGCAGTAGCAGTGAATCTACAGGGACGCCATCGAATCCG*ACACTACTGAAATACCTGAATCCATGGTGGAGAGCAGATCTCCCAAGACA	oncogene,18cancers,cancer,tumor	BOWTIE+STAR	CDS(truncated)/intronic	0	4	1	19	12	68828931	+	12	41274623	+	415.4333	23.4855	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000135679	ENSG00000165966	MDM2	PDZRN4	AGGGGAGAGTGATACAGATTCATTTGAAGAAGATCCTGAAATTTCCTTAG*CTTACTAGTTTAAAGTTATTTTTACTAGCAACAACCAAAATGTTAAAGTA	oncogene,18cancers,cancer,tumor	BOWTIE+STAR	CDS(truncated)/intronic	0	4	1	18	12	68836747	+	12	41472882	+	415.4333	23.4855	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000135679	ENSG00000165966	MDM2	PDZRN4	CTAAAAATACAAAAATTAGCCAGGCGTCATGGCATGTGCCTGTTAATTCC*GGCTACTCGGGAGGCTGAGGCAGGAGAATAGCTTGAACCCAGGAGGCGGA	oncogene,18cancers,cancer,tumor	BOWTIE+STAR	UTR/intronic	0	4	1	17	12	68850170	+	12	41416542	+	415.4333	23.4855	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000135679	ENSG00000165966	MDM2	PDZRN4	CTCTCTCTCTCTCTCTCTGTCTGTCTCAATAAATGGCCAAAGGGATTAGT*GGTTTGCTTGTGGACAATTTGAGACATGGGAACATTCACGTGGAAGCGTC	oncogene,18cancers,cancer,tumor	BOWTIE+STAR	UTR/intronic	0	4	1	16	12	68843748	+	12	41523356	+	415.4333	23.4855	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000135679	ENSG00000165966	MDM2	PDZRN4	TTTGGAGGTCCTCGAAGCATTATTTGGAGTTGATAATACTTCAGCTTCAA*CCAAGCAGAATTTCTTAAATTGAATACTTAAGTTTATTAAATTGCATGAT	oncogene,18cancers,cancer,tumor	BOWTIE+STAR	UTR/intronic	0	4	1	16	12	68843875	+	12	41516895	+	415.4333	23.4855	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000135679	ENSG00000165966	MDM2	PDZRN4	AATGTTTTTTAGGTTTTCTTGATTTAACAATAGAGACAGGGTCTCCCTGT*GCAACACAGGGAGACCCAGTATCTACAAAAAATAAAAAATAAAAAAAATT	oncogene,18cancers,cancer,tumor	BOWTIE+STAR	UTR/intronic	0	4	1	16	12	68841298	+	12	41254897	+	415.4333	23.4855	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000135679	ENSG00000165966	MDM2	PDZRN4	TTACTAATGGTACATTGTTGCTTCAAAACTCTCTCTCTCTCTCTCTGTCT*GTCTTGATGTATGGCTCATTATGAATAGCAGCTTTTTTTTTTTTTACTTT	oncogene,18cancers,cancer,tumor	BOWTIE+STAR	UTR/intronic	0	4	1	16	12	68843720	+	12	41516739	+	415.4333	23.4855	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000135679	ENSG00000165966	MDM2	PDZRN4	TGTTCTTGCTACAAATAAATGATATTTGAGCTGATGGGTGTGCTAATTAC*AAATATTTATCCGTTGTTTCTTATTTCTCACTTTGCTAATGAAAAGTCTT	oncogene,18cancers,cancer,tumor	BOWTIE+STAR	UTR/intronic	0	4	1	16	12	68843393	+	12	41370396	+	415.4333	23.4855	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000135679	ENSG00000165966	MDM2	PDZRN4	GTACTAATCCCTTTGGCCATTTATTGAGAGAGAGAGAGAGAGAGAGTAGG*ATGACTATAGTTAATAATACTATACTATATAGTTTCAAATAGCTAGAAGG	oncogene,18cancers,cancer,tumor	BOWTIE+STAR	UTR/intronic	0	4	1	15	12	68843320	+	12	41413464	+	415.4333	23.4855	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000135679	ENSG00000165966	MDM2	PDZRN4	AGTTATTAAAGTCTGTTGGTGCACAAAAAGACACTTATACTATGAAAGAG*CACTTTCAGATGCTTTCCTCCATTTCCTCAATCATCAAATAAAGACATGT	oncogene,18cancers,cancer,tumor	BOWTIE+STAR	CDS(truncated)/intronic	0	4	1	15	12	68813628	+	12	41433209	+	415.4333	23.4855	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000165966	ENSG00000135679	PDZRN4	MDM2	GTGAGCCGAGATCCCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGAC*TTCGTCCCAAAAAAAAAAAAAAAAGCTGCAAATTTAAACGTTGAAGTCTA	oncogene,18cancers,cancer,tumor	BOWTIE+BOWTIE2	intronic/UTR	0	4	1	33	12	41266302	+	12	68850278	+	23.4855	415.4333	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000165966	ENSG00000135679	PDZRN4	MDM2	CCCAGGAGTGCAATGGCATGATCTCAGCTCACTGCAACCTCTGTCTCCCA*GGTTCAAGCTATTCTCCTGCCTCAGCCTTCCAAGTAACTGGGATTACAGG	oncogene,18cancers,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	4	1	23	12	41421292	+	12	68840939	+	23.4855	415.4333	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000165966	ENSG00000135679	PDZRN4	MDM2	CTGATAAAACAGACTTTAAACCAACAAAGATTTAAAAAGACAAAGAAGAG*TGTGTTGAGGAAAATGATGATAAAATTACACAAGCTTCACAATCACAAGA	oncogene,18cancers,cancer,tumor	BOWTIE+STAR	intronic/CDS(truncated)	0	4	1	15	12	41282278	+	12	68839493	+	23.4855	415.4333	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000165966	ENSG00000135679	PDZRN4	MDM2	CATCAAAGCATTCTTTGCTCATGAAACTCTGCTCATGAAACTCTTTTTTT*TGGAGGTCCTCCAAGCATTATTTGGAGTTGATAATACTTCAGCTACAACC	oncogene,18cancers,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	4	1	14	12	41267061	+	12	68843759	+	23.4855	415.4333	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000165966	ENSG00000135679	PDZRN4	MDM2	TTCTACCAACCAAACAAATGACAAGCACAAAAGCAACAGCATAAAACAAC*ACCCATTGTATGTGAAACAGTACATACACCATATTTACAATTATGTATTT	oncogene,18cancers,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	4	1	14	12	41461179	+	12	68843409	+	23.4855	415.4333	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000165966	ENSG00000135679	PDZRN4	MDM2	TCTTGTGCTTTCAAAGTTCTCTCTTTGTCTTTCACTTTTGGCAATTTTAT*GAGAGAGAGAGAGAGAGAGTAGGGTGACTATAGTTAATGTATTGAATGTT	oncogene,18cancers,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	4	1	14	12	41381174	+	12	68843298	+	23.4855	415.4333	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5132-01A	ENSG00000165966	ENSG00000135679	PDZRN4	MDM2	GGATCACTTAAGGCCAAGAGTTCTAGACTAGCCTAGGCAACACAGGGAGA*CCCTGTGTTGCCCAGGCTGGTCTCGAACTCCTGGGCTCAAGAGATCCTCC	oncogene,18cancers,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	4	1	14	12	41254910	+	12	68841293	+	23.4855	415.4333	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0125-01A	ENSG00000117713	ENSG00000092098	ARID1A	RNF31	TCTATCGCCTCTATGTGTCTGTGAAGGAGATTGGTGGATTGACTCAG*ATGCAGGCCCTGACTTCCTGTGAGTGCACCATCTGTCCTGACTGCTT	known,tcga,cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	28	26	29	1	26767999	+	14	24155157	+	7.2839	0.2923	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0125-01A	ENSG00000117713	ENSG00000259529	ARID1A	AL136295.5	ACCTCTATCGCCTCTATGTGTCTGTGAAGGAGATTGGTGGATTGACTCAG*ATGCAGGCCCTGACTTCCTGTGAGTGCACCATCTGTCCTGACTGCTTCCG	cancer,exon-exon	BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	26	4	19	1	26767999	+	14	24155157	+	7.2839	0.4675	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0125-01A	ENSG00000117713	ENSG00000259529	ARID1A	AL136295.5	TCTGTCTCTAAATAAATAAGACCCTGAACACCCGGACCATCAGGACAGTG*AGTTTATAAATGTTTCCGTATATATCTCTAAAATGTAAAACTTTATTTAT	cancer	BOWTIE+STAR	UTR/intronic	0	26	1	16	1	26770254	+	14	24152369	+	7.2839	0.4675	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0125-01A	ENSG00000272368	ENSG00000123352	AC074032.1	SPATS2	TGCCTGCCTGAGGAGGCCTCGGTTGGATGCGAAGGAGCTGCAGCATCCAG*AATCTCCCTGGAAAAGGAGACATGAATGTCTGCAATGATACTTCCTGACA	antisense,exon-exon	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	exonic(no-known-CDS)/UTR	0	6	1	18	12	50112301	+	12	49460770	+	0.9575	6.578	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0125-01A	ENSG00000259081	ENSG00000009830	AF111169.4	POMT2	GCATCCAGACCCGGAAAGGACCTAGTTTCAGCCTGGCACCTCCCAAG*GGGAACAGTGGCCTCAAACCCAAGGACAATGAGTTCACGTCCAAACC	antisense,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	4	4	26	14	76781400	-	14	77280463	-	0.8561	8.7819	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0125-01A	ENSG00000130175	ENSG00000196632	PRKCSH	WNK3	GCCGAGGCTGGAATGTGGAATGCAATGGCGCGATCTCGGCTCACTGCAAC*CTCCCCCTCCTGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGC	cancer	BOWTIE+STAR	UTR/UTR	0	2	1	22	19	11449926	+	X	54197660	-	67.2665	2.8479	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0125-01A	ENSG00000196632	ENSG00000130175	WNK3	PRKCSH	GCTACTTGGGAGGCCGAGGCAGGAGAATCGCTTAAGCCCAGGAGGTGGAG*GTTGGAGTGAGCCAAGATCATGCTACTGCACTCTCCAGCCTGGGCTACAG	cancer	BOWTIE+STAR	intronic/intronic	0	2	4	27	X	54236192	-	19	11450413	+	2.8479	67.2665	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0125-01A	ENSG00000196632	ENSG00000130175	WNK3	PRKCSH	GCTACTCAGAAGGCTGAGGCAGGAGAATTGCTTGAACCCGGGAGGTGGAG*GTTGGAGTGAGCCAAGATCATGCTACTGCACTCTCCAGCCTGGGCTACAG	cancer	BOWTIE+STAR	intronic/intronic	0	2	4	27	X	54320979	-	19	11450413	+	2.8479	67.2665	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0125-01A	ENSG00000196632	ENSG00000130175	WNK3	PRKCSH	GCTACTCTGGAGGCTGAGGCAGGAGAATTGCTTGAACCCGGGAGGTGGAG*GTTGGAGTGAGCCAAGATCATGCTACTGCACTCTCCAGCCTGGGCTACAG	cancer	BOWTIE+STAR	intronic/intronic	0	2	4	27	X	54348259	-	19	11450413	+	2.8479	67.2665	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0125-01A	ENSG00000196632	ENSG00000130175	WNK3	PRKCSH	ACTACTCGGGAGGCTGAGACAGGAGAATCGCTTGAACCCAGGAGGCGGAG*GTTGGAGTGAGCCAAGATCATGCTACTGCACTCTCCAGCCTGGGCTACAG	cancer	BOWTIE+STAR	intronic/intronic	0	2	2	25	X	54255062	-	19	11450413	+	2.8479	67.2665	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0125-01A	ENSG00000196632	ENSG00000130175	WNK3	PRKCSH	CTGCAACCTCCACCTCCTGGGTTCCAGTGATTCTTGTGCCTCAGCCTCCC*AAAGTGCTGGGATTACAGGCTTGAGCTACCATGTCTGGCCATCCCCTGCT	cancer	BOWTIE+BOWTIE2	intronic/intronic	0	2	1	37	X	54258171	-	19	11450104	+	2.8479	67.2665	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0125-01A	ENSG00000196632	ENSG00000130175	WNK3	PRKCSH	GCCTCCTGGGTTCAAGCGATTCTCCCACCTCAGCCTCCCAAGTAGCTGGG*ACTACAGGCAAACATCACCATGTCCAGCTGTCCCCAGCTTTCTAATCTGG	cancer	BOWTIE+BOWTIE2	intronic/UTR	0	2	1	35	X	54290158	-	19	11450579	+	2.8479	67.2665	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0125-01A	ENSG00000196632	ENSG00000130175	WNK3	PRKCSH	GCAGGAGAATTGCTCGAACCTGGGAGGTGGAGGTTGCAGTGAGCCGAGAT*CATGCTACTGCACTCTCCAGCCTGGGCTACAGAGTGAGACTCTCAAAAAA	cancer	BOWTIE+BOWTIE2	intronic/UTR	0	2	1	34	X	54299924	-	19	11450431	+	2.8479	67.2665	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0125-01A	ENSG00000196632	ENSG00000130175	WNK3	PRKCSH	TCTCCCTTTGTTCCCCAGGCTGGAGTGCAGTGGCACAATCTCGGCTCACT*CTGCAACCTCTACCTCCCGGGTTCAAACAATTGTCTTGTCTCAGCCTCCC	cancer	BOWTIE+STAR	intronic/UTR	0	2	1	31	X	54345183	-	19	11449618	+	2.8479	67.2665	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0125-01A	ENSG00000196632	ENSG00000130175	WNK3	PRKCSH	TGCCATGTTAGCCAGGCTGGTCTCGAACTCCTGACCTCAGATGATCCACC*TGTCTCAGCCTCCCAAGTAGCTGGGATTACAGGTGTGCACCACCATGCCT	cancer	BOWTIE+STAR	intronic/UTR	0	2	1	29	X	54351684	-	19	11449654	+	2.8479	67.2665	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0125-01A	ENSG00000196632	ENSG00000130175	WNK3	PRKCSH	GATCTTGGCTCACTGCAGCCTCCACCTCCTGGGTTCAAGCGATTCTCCTG*CCTCAGCCTCCCAAAGTGCTGGGATTACAGGCTTGAGCTACCATGTCTGG	cancer	BOWTIE+STAR	intronic/intronic	0	2	1	27	X	54257695	-	19	11450092	+	2.8479	67.2665	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0125-01A	ENSG00000196632	ENSG00000130175	WNK3	PRKCSH	TGGGCTCAAGTGATTCTCATGTCTCAGCCTCCCAAGTAGCTGGGATTACA*GAACCTCAAGAAGGCATGAAGCCAGCCCCTGCAGTGCCGTCCACCCGCCC	cancer	BOWTIE+BOWTIE2	intronic/UTR	0	2	1	26	X	54314069	-	19	11450645	+	2.8479	67.2665	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0125-01A	ENSG00000196632	ENSG00000130175	WNK3	PRKCSH	CGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGC*CTCCTGGGTGCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAATTGGGAC	cancer	BOWTIE+STAR	intronic/UTR	0	2	1	23	X	54291243	-	19	11449933	+	2.8479	67.2665	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0125-01A	ENSG00000196632	ENSG00000130175	WNK3	PRKCSH	CACCCAGGCTGGAGTGCAGTGGCACGATCTCGGCTCACTGCAACCTCCGC*CTCCTGGGTGCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAATTGGGAC	cancer	BOWTIE+STAR	intronic/UTR	0	2	1	23	X	54349268	-	19	11449933	+	2.8479	67.2665	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0125-01A	ENSG00000196632	ENSG00000130175	WNK3	PRKCSH	GGGTTCCAGTGATTCTTGTGCCTCAGCCTCCCAAGTAGCTGGGATTACAG*AACCTCAAGAAGGCATGAAGCCAGCCCCTGCAGTGCCGTCCACCCGCCCC	cancer	BOWTIE+BLAT	intronic/UTR	0	2	1	22	X	54258153	-	19	11450646	+	2.8479	67.2665	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0125-01A	ENSG00000196632	ENSG00000130175	WNK3	PRKCSH	ACAAAATTTAGCCAGGTGTGGTGATGTACGCCTGTAATCCCAGCTACTTG*GGATTACAGGTGTGCACCACCATGCCTGGCTAATTTTTAGTAGAGATGGG	cancer	BOWTIE+BLAT	intronic/UTR	0	2	1	20	X	54258458	-	19	11449677	+	2.8479	67.2665	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-2557-01A	ENSG00000127995	ENSG00000188730	CASD1	VWC2	CTTTTGTAAAAATAATTAATCCCCAATTCAAAGAAGAAGGAAATAAG*GTCCAAACTGCTTTGCAGAAACCGCGGTGATCCCTGCTGGCAGAGAA	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	24	21	29	7	94518323	+	7	49912034	+	15.1628	3.8806	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-2557-01A	ENSG00000127995	ENSG00000188730	CASD1	VWC2	AAAGTTTGGCAACCTCACAGTTGTATGATGCATAAATACAAAATCAG*GTCCAAACTGCTTTGCAGAAACCGCGGTGATCCCTGCTGGCAGAGAA	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	24	3	26	7	94517656	+	7	49912034	+	15.1628	3.8806	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-2557-01A	ENSG00000173960	ENSG00000146729	UBXN2A	NIPSNAP2	TTGGCCAATGGAAAAAGGATTGTCCAGAAATTTAACATTACTCATAG*CTTACAGGGATCTTCAGACCAGGGAAGACATACGGAATGCAGCATGG	known,18cancers,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	10	12	26	2	23984831	+	7	55997366	+	4.2115	284.3861	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-2557-01A	ENSG00000173960	ENSG00000146729	UBXN2A	NIPSNAP2	GCACTGATTTTTGATAGACTAAGTGGAAAATTTGCAGAGAAATGATGGTT*CTTACAGGGATCTTCAGACCAGGGAAGACATACGGAATGCAGCATGGCAC	known,18cancers	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	UTR/CDS(truncated)	0	10	3	26	2	23999910	+	7	55997366	+	4.2115	284.3861	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-2557-01A	ENSG00000173960	ENSG00000146729	UBXN2A	NIPSNAP2	ACCTGGCACGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAG*CTTACAGGGATCTTCAGACCAGGGAAGACATACGGAATGCAGCATGGCAC	known,18cancers	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	10	1	29	2	23987547	+	7	55997366	+	4.2115	284.3861	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-2557-01A	ENSG00000173960	ENSG00000146729	UBXN2A	NIPSNAP2	ACCTTTCCCAACACTGACACTAAGAGTGGGGAGCGGTGGGTGGGGGTGCA*TGACCTCAGACACTCTCTGGCTAATATTTTAATAAGCTCACAGCAGATAA	known,18cancers	BOWTIE+STAR	intronic/UTR	0	10	1	15	2	23932561	+	7	55999850	+	4.2115	284.3861	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-2557-01A	ENSG00000173960	ENSG00000146729	UBXN2A	NIPSNAP2	ACATATGTACCACCTACCTCAAAACATAGATTCTTATCAGTATACCTTAT*AACACCCCGTGTTGTCCAGTATACCTTATAACACTGAGCCACTTCTCCCC	known,18cancers	BOWTIE+STAR	intronic/UTR	0	10	1	14	2	23987302	+	7	55999288	+	4.2115	284.3861	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-2557-01A	ENSG00000132434	ENSG00000127980	LANCL2	PEX1	GAAGACAGCTGATCCCCATGACTGCTCTGCTTATACTGGCTGGACAG*AATCAAGCTATAGAAGTGGTCTGGAGTCACCAGCCTGCATTCTTGAG	18cancers,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	4	7	29	7	55391910	+	7	92522245	-	104.0409	5.3524	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-2557-01A	ENSG00000127914	ENSG00000105854	AKAP9	PON2	ACACTCAAGGCACAGCATAAACACCTAAAAGAATTGGAGGCTTTCAG*AAGCTGGCTCTGAAGATATTGACATACTTCCCAATGGTCTGGCTTTT	known,oncogene,18cancers,cancer,exon-exon	BOWTIE	out-of-frame	0	3	6	29	7	92093316	+	7	95416297	-	2.8058	103.2306	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-2557-01A	ENSG00000127914	ENSG00000105854	AKAP9	PON2	AGTATTACATATTTATGGTAGAATACAGAAAAGAATAGAGTGAAAATCAT*TTCTTTAAAATGCCAAGCAAGGGACAGAAAAGAAAGCTGCTTTCGAATAA	known,oncogene,18cancers,cancer	BOWTIE+STAR	UTR/UTR	0	3	1	15	7	92092039	+	7	95405144	-	2.8058	103.2306	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-2557-01A	ENSG00000127914	ENSG00000105854	AKAP9	PON2	GAAAATTACTCTGAAAAGAGAACAAGAGAGTGAGAAACCAAGCCAAG*AAGCTGGCTCTGAAGATATTGACATACTTCCCAATGGTCTGGCTTTT	known,oncogene,18cancers,cancer,exon-exon	BOWTIE	in-frame	0	3	1	13	7	92089529	+	7	95416297	-	2.8058	103.2306	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0210-01A	ENSG00000163531	ENSG00000188783	NFASC	PRELP	GCGGACAGCTCGGACAGCGCCCAGGGCCGGAGCCCGAGCCCTTGGAG*GTGCATCACCTGGATCATGAGGTCACCCCTCTGCTGGCTCCTCCCAC	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	UTR/UTR	0	38	27	30	1	204828782	+	1	203483169	+	4.0102	58.0384	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-06-0210-01A	ENSG00000163531	ENSG00000188783	NFASC	PRELP	TCAAAACCAGCCTGGCCAACATGGTAAAACCCTGTCTCTACTAAAATACA*AAAAAAATTAGCCAGGCATAGTGGCGCGCGCCTATAATCCCAGCTACTGG	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/UTR	0	38	4	25	1	204845296	+	1	203488365	+	4.0102	58.0384	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-06-0210-01A	ENSG00000163531	ENSG00000188783	NFASC	PRELP	GAGATGGGGGTTTCACCATGTTGGCCAGGCTGGTCTTGAACTCCTGACCT*ACATAGTGAAACCCCTTGTTTACTCAAAATACAAAAATTGGCTGGGTGCG	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BOWTIE2	intronic/UTR	0	38	1	34	1	204835461	+	1	203489771	+	4.0102	58.0384	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-06-0210-01A	ENSG00000106603	ENSG00000002746	COA1	HECW1	AAGAACTCGTCATGCTCTTTGTAGCGTGGTGCTTCTGTTGCTCACAG*GTTCAGGTTTAGCGGTCGCATCCTGGGTCTGGCTCTGATCCATCAGT	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE;BOWTIE+STAR	UTR/CDS(truncated)	0	12	13	28	7	43729429	-	7	43541163	+	4.0547	0.9109	FALSE	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0210-01A	ENSG00000002746	ENSG00000106603	HECW1	COA1	CTCACCGACAGCACCTCCAGAGGCTCCGAAGTTACAGCGCTGGAGAG*TTGCACCTGGACTTGATATGAAAGTAACCATCAGAAAATCAACAGAG	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	12	3	29	7	43479744	+	7	43609641	-	0.9109	4.0547	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0210-01A	ENSG00000002746	ENSG00000106603	HECW1	COA1	CTCACCGACAGCACCTCCAGAGGCTCCGAAGTTACAGCGCTGGAGAG*AAACACAACTGGTTTTGAGAATCCATCCCTTCTTCACTCAGTCCACG	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	12	3	28	7	43479744	+	7	43609495	-	0.9109	4.0547	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0210-01A	ENSG00000002746	ENSG00000106603	HECW1	COA1	TGAGATGAAATCTATTCCTGGTGAAGATACTGTGAACATTGTTGAAATGA*CAAGAGAACTAGAAGTGGAGGGGCCTAGAGATGTGACCGAATTGCTGTAA	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/UTR	0	12	1	37	7	43129077	+	7	43632330	-	0.9109	4.0547	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0210-01A	ENSG00000131165	ENSG00000204991	CHMP1A	SPIRE2	TAGACGCAGTGGCCTCCAAGGTGCAGACAGCTGTGACTATGAAGGGG*GGTTTGGCTCTCTGCCCTGCATCCTCAACGCCTGCTCCGGAGATGCC	18cancers,exon-exon	BOWTIE	out-of-frame	0	5	9	29	16	89649351	-	16	89858338	+	13.9539	1.713	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0210-01A	ENSG00000075785	ENSG00000156508	RAB7A	EEF1A1	AGATTCATGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAG*GCGCCTGCCTCTCCAGGATGTCTACAAAATTGGTGGTAAGTTGGCTGTAA	oncogene,cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	36	3	128730372	+	6	73518732	-	52.4328	903.7108	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0210-01A	ENSG00000075785	ENSG00000156508	RAB7A	EEF1A1	GGGTTCACACCATTCTCCTGCCTCAGCATCCCGAGTAGCTGGGACTACAG*GCGCCTGCCTCTCCAGGATGTCTACAAAATTGGTGGTAAGTTGGCTGTAA	oncogene,cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	36	3	128745016	+	6	73518732	-	52.4328	903.7108	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0210-01A	ENSG00000075785	ENSG00000156508	RAB7A	EEF1A1	ACTTAACTCATGGGGCCTGGAGTCTCTGTTTTGGTGATGGCATCACTGCT*AAGGTGATTATCCTGAACCATCCAGGCCAAATAAGCGCCGGCTATGCCCC	oncogene,cancer	BOWTIE+STAR	intronic/UTR	0	2	1	15	3	128730846	+	6	73518267	-	52.4328	903.7108	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0210-01A	ENSG00000075785	ENSG00000156508	RAB7A	EEF1A1	GGCTCCCGCCTGCAATCAATCCCATCACTTTGGGAGGCCGCCGAGATGGG*AAGGGCTCCTTCAAGTATGCCTGGGTCTTGGATAAACTGAAAGCTGAGCG	oncogene,cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	15	3	128740153	+	6	73519510	-	52.4328	903.7108	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0210-01A	ENSG00000186153	ENSG00000137872	WWOX	SEMA6D	TGAGATCGCACTACTTCATTCCAGCCTGGGCAACAGAGAGAAACTGTGTC*AAAACAAACAAACAAACAAAAATAGAAGACAAAAGAAAGACATATGAAAG	cancer,tumor	BOWTIE+STAR	intronic/UTR	0	2	1	20	16	78694210	+	15	47772867	+	3.4731	23.6509	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0210-01A	ENSG00000186153	ENSG00000137872	WWOX	SEMA6D	TGGCTTTGATGTATGTATATGTGGGCAGGAATGTGTGTGCGTGTGTGTGT*GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTCTGTACCCACTAGGA	cancer,tumor	BOWTIE+STAR	intronic/UTR	0	2	1	19	16	78813588	+	15	47772358	+	3.4731	23.6509	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0190-01A	ENSG00000142657	ENSG00000171735	PGD	CAMTA1	TCATGGGCCAGAACTTAATTCTGAACATGAATGACCACGGCTTTGTG*ACCACAGAATGGCTCAATGATACTCTACAACAGGAAGAAAGTGAAAT	known,tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	7	8	29	1	10399704	+	1	7249491	+	34.8523	2.8087	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0190-01A	ENSG00000240498	ENSG00000259678	CDKN2B-AS1	AC066613.2	GGCGCTGGCGCTGCCGGAGCTGTCGACCCGGCCTGGCGCCGGACTAG*GAAAGAATGGAAACGGCCTCTCACAGCAGAGAACTGGTCACTGCGCA	antisense,exon-exon	BOWTIE	exonic(no-known-CDS)/exonic(no-known-CDS)	0	2	3	26	9	21995161	+	15	51448458	+	0.0142	0.1726	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	antisense_RNA	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0190-01A	ENSG00000105229	ENSG00000156689	PIAS4	GLYATL2	GAGGCTGAAGACCATTGGGGTAAAGCACCCGGAGCTGTGCAAGGCACTGG*TCCGTAGAGTATTAGCTACAGAAACCTTTCCATTGCCATACTGAGAAACT	18cancers	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/UTR	0	2	4	36	19	4029036	+	11	58844524	-	6.7345	1.6083	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2620-01A	ENSG00000126461	ENSG00000007255	SCAF1	TRAPPC6A	GCCCAGCCTGCTGCCCCGTCTCAGGGCCTGGAGGACGGGCAAAACGG*GGACAGAAGATGAGCCTGTCGGTCCTGGAGGGTATGGGGTTCCGTGT	known,tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	25	12	28	19	49646830	+	19	45165194	-	24.3996	30.1838	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-19-2620-01A	ENSG00000126461	ENSG00000007255	SCAF1	TRAPPC6A	GCCCAGCCTGCTGCCCCGTCTCAGGGCCTGGAGGACGGGCAAAACGG*GCTGCCCCGGGAGACGCTGGCCTTCAGGGAGGAGCTGGATGTCCTCA	known,tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	25	12	28	19	49646830	+	19	45164970	-	24.3996	30.1838	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-19-2620-01A	ENSG00000170088	ENSG00000164168	TMEM192	TMEM184C	ATCAACAAGGCATCTCAAGAGACTTGCGTTGATGATACAGTCCTCTG*GCCTTAACCCCGAAACTGACTATACTGGAGAAGGAAAGGCCGTGTAA	18cancers,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	23	18	30	4	165100628	-	4	147671867	+	2.7165	9.9901	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-19-2620-01A	ENSG00000274070	ENSG00000085563	CASTOR2	ABCB1	TTCACCTACGGCCTGATCAAACTTGCCTTCCTGTCCTCCAAGACCAG*ATCGCTACTGAAGCAATAGAAAACTTCCGAACCGTTGTTTCTTTGAC	cancer,m13,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	15	9	29	7	74965098	+	7	87520876	-	7.9464	7.688	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2620-01A	ENSG00000274070	ENSG00000085563	CASTOR2	ABCB1	TTCACCTACGGCCTGATCAAACTTGCCTTCCTGTCCTCCAAGACCAG*AGTATTTTCAGCTGTTGTCTTTGGTGCCATGGCCGTGGGGCAAGTCA	cancer,m13,exon-exon	BOWTIE	in-frame	0	15	3	26	7	74965098	+	7	87516665	-	7.9464	7.688	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2620-01A	ENSG00000274070	ENSG00000085563	CASTOR2	ABCB1	CTGTTCACCTACGGCCTGATCAAACTTGCCTTCCTGTCCTCCAAGACCAG*TTAATGATTATTCTGCAAGTATATAAACACAAGCAGAACATAATAAAACA	cancer,m13	BOWTIE+STAR	CDS(truncated)/intronic	0	15	1	14	7	74965098	+	7	87513418	-	7.9464	7.688	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2620-01A	ENSG00000174469	ENSG00000197081	CNTNAP2	IGF2R	ATGGGTGTCACACTGGAAAATTCCACCAGAATAAAAAGCTAAACAAGGCA*TGAAAGTTCACTCGGGCAGGGGAGCTGGGGCAGAGAGCTCCCACCCAGTG	cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	16	7	147814256	+	6	160104864	+	3.7389	2.1469	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2620-01A	ENSG00000197081	ENSG00000174469	IGF2R	CNTNAP2	CCGGGGTCCACGCAGGCCCAGGCCGCCCCGTTCCCCGAGCTGTGCAG*CTCGATCATTATCCTTCTGTGAGTTACCATCTGCCAAGTTCATCCGA	cancer,exon-exon	BOWTIE;BOWTIE+BOWTIE2;BOWTIE+STAR	out-of-frame	0	2	6	25	6	159969395	+	7	148267033	+	2.1469	3.7389	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2620-01A	ENSG00000164880	ENSG00000120885	INTS1	CLU	CGGCCTCTCTCTGCCCCAGTTCCTGGCCATGGTGTTCCAGGACCTGCTGA*GCCTCACTTCTTCTTTCCCAAGTCCCGCATCGTCCGCAGCTTGATGCCCT	oncogene,cancer	BOWTIE+STAR	out-of-frame	0	2	3	15	7	1497284	-	8	27605108	-	12.3965	3345.0219	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2620-01A	ENSG00000164880	ENSG00000120885	INTS1	CLU	CCGACTGAGCCGCTCCCGGGCGGCTGGGAGGCGGGGTCCCTGCAGCTCCT*TCTCCAGGAAGAACCCTAAATTTATGGAGACCGTGGCGGAGAAAGCGCTG	oncogene,cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	16	7	1504138	-	8	27598532	-	12.3965	3345.0219	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0221-02A	ENSG00000231074	ENSG00000065559	HCG18	MAP2K4	ATGCTCTAGCTTGGGTTAAGGGATTTGGAATTGCACTTGTTTCAGAG*GGTGACTGTTGGATCTGTATGGAACTCATGTCTACCTCGTTTGATAA	antisense,cancer,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	11	3	25	6	30314269	-	17	12107790	+	2.7023	15.8737	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0221-02A	ENSG00000065559	ENSG00000231074	MAP2K4	HCG18	GTGATTGCCCATACATTGTTCAGTTTTATGGTGCACTCTTCAGAGAG*AGCTCCCTCTTTGCCCACTAGCAGGGCATTAGCTGGTGCTGAAGACA	antisense,cancer,exon-exon	BOWTIE;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	11	3	28	17	12095694	+	6	30296237	-	15.8737	2.7023	TRUE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0221-02A	ENSG00000172554	ENSG00000171853	SNTG2	TRAPPC12	CATGGCTTCACCCAGAACAACTTCCAGTCCTGAAGGCTCTATTCATG*ATCCTGGCCAATTTGGAGCAAGGCTTAGCAGAAGACGGCGGCATGAG	exon-exon	BOWTIE	UTR/CDS(truncated)	0	3	2	19	2	1210679	+	2	3457621	+	0.4959	10.8964	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0221-02A	ENSG00000172554	ENSG00000171853	SNTG2	TRAPPC12	TCTGTACAGGCCCCATCGTCACCTTCCTCGCCCATAGCTAAGGACCCGAG*ATCCTGGCCAATTTGGAGCAAGGCTTAGCAGAAGACGGCGGCATGAGCAG	NA	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	out-of-frame	0	3	1	24	2	1209143	+	2	3457621	+	0.4959	10.8964	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0221-02A	ENSG00000172554	ENSG00000171853	SNTG2	TRAPPC12	CCCTCTTTGACAGCGGTTTGCATCTGAACGGAAACTCCAGTACCACA*ATCCTGGCCAATTTGGAGCAAGGCTTAGCAGAAGACGGCGGCATGAG	exon-exon	BOWTIE	in-frame	0	3	1	14	2	1173183	+	2	3457621	+	0.4959	10.8964	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-02-2485-01A	ENSG00000258231	ENSG00000166986	AC020637.1	MARS	GGGTGGGGATGACTTAATCACACGATCCCTTTAAAGGACAGAGTTTTCTC*CTGCTGTACATTCGGCCTGAGGGCCAGGACAGTGCTTTCTCCTGGACGGA	lincrna,cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	169	1	15	12	58588149	+	12	57512858	+	64.524	257.1873	FALSE	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-02-2485-01A	ENSG00000179912	ENSG00000258231	R3HDM2	AC020637.1	CCCCTGGCTCTGAGCAGTACCAGATGCCTCAGTCTCCCTCTCCCTGCAGT*ACCAAATACCTCAGGGGTTAACGGAGAAAAAATAGGAAATGACCAGACTT	lincrna	BOWTIE+STAR	CDS(truncated)/intronic	0	20	1	14	12	57266759	-	12	58639240	+	37.2001	64.524	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-02-2485-01A	ENSG00000166986	ENSG00000179912	MARS	R3HDM2	AACATTTCGTTTGATATTTTTGGTCGCACCACCACTCCACAGCAGACCAA*GTTGGAGTGCAATGGCGTGATATCAGCTCACTGCAACCTCTGCCTCCCGG	18cancers,cancer	BOWTIE+BLAT	CDS(truncated)/intronic	0	10	1	17	12	57498623	+	12	57381203	-	257.1873	37.2001	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-02-2485-01A	ENSG00000179912	ENSG00000166986	R3HDM2	MARS	GCGGCGGGCGGAGACGTGGGCGCCCTCCCCGCCAAGGCCCGTGCGAG*AAGCCTCAGTGTAAAGTCTGCCGATCATGCCCTGTGGTGCAGTCGAG	18cancers,cancer,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	10	22	30	12	57430720	-	12	57504225	+	37.2001	257.1873	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-02-2485-01A	ENSG00000123427	ENSG00000139269	EEF1AKMT3	INHBE	ACTGGGTGCGGGGACAGGCATCGTGGGGATCTTGGCAGCGCTGCAGG*ACTCCACTTCAGCCTACAGCTCCCTGCTCACTTTTCACCTGTCCACT	18cancers,cancer,exon-exon	BOWTIE	in-frame	0	9	7	29	12	57773128	+	12	57456094	+	22.789	6.7505	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-02-2485-01A	ENSG00000123427	ENSG00000139269	EEF1AKMT3	INHBE	ACTGGGTGCGGGGACAGGCATCGTGGGGATCTTGGCAGCGCTGCAGG*GCAGCGCTGACCAGAGCCCTCCGGAGACTACAGCCAGGGAGTGTGGC	18cancers,cancer,exon-exon	BOWTIE	out-of-frame	0	9	4	27	12	57773128	+	12	57455744	+	22.789	6.7505	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-02-2485-01A	ENSG00000123427	ENSG00000139269	EEF1AKMT3	INHBE	CGAACTGGGTGCGGGGACAGGCATCGTGGGGATCTTGGCAGCGCTGCAGG*GCCTGAAGGGTGGTGCGGTGGCTCACGCCTGTAACCTCAGCACTTTAGGA	18cancers,cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	9	1	24	12	57773128	+	12	57454129	+	22.789	6.7505	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-02-2485-01A	ENSG00000257921	ENSG00000139269	AC025165.3	INHBE	CGAACTGGGTGCGGGGACAGGCATCGTGGGGATCTTGGCAGCGCTGCAGG*GCAGCGCTGACCAGAGCCCTCCGGAGACTACAGCCAGGGAGTGTGGCTCC	cancer,exon-exon	BOWTIE+BLAT;BOWTIE+STAR	CDS(no-known-start-or-end)/CDS(truncated)	0	6	1	21	12	57773128	+	12	57455744	+	0	6.7505	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-02-2485-01A	ENSG00000257921	ENSG00000139269	AC025165.3	INHBE	CGAACTGGGTGCGGGGACAGGCATCGTGGGGATCTTGGCAGCGCTGCAGG*ACTCCACTTCAGCCTACAGCTCCCTGCTCACTTTTCACCTGTCCACTCCT	cancer,exon-exon	BOWTIE+STAR	CDS(no-known-start-or-end)/CDS(truncated)	0	6	1	14	12	57773128	+	12	57456094	+	0	6.7505	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-02-2485-01A	ENSG00000139263	ENSG00000037897	LRIG3	METTL1	AAACACAGTCGGCAATAAAAGGTTCCAATTTGAGTTTCATCTGCTCAGCT*GTAGAGAAACCCCGGACTGGGATCATGGCAGCCGAGACTCGGAACGTGGC	NA	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	2	4	27	12	58880816	-	12	57772107	-	28.0263	51.5453	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-02-2485-01A	ENSG00000139263	ENSG00000037897	LRIG3	METTL1	TTTCATTTCATTTCCCTCTGTTTACAGGTGAGAAAATTAAGGTTCACAAA*CAGTGGAACTGTCACCGCTGTTCCCAGACACACTTATTCTGGGTCTGGAG	NA	BOWTIE+STAR	intronic/intronic	0	2	1	14	12	58898265	-	12	57769959	-	28.0263	51.5453	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-14-1823-01A	ENSG00000127989	ENSG00000154978	MTERF1	VOPP1	CAGAGGCGGAAGTAAAAGCGAACTACAGTGGATGGGTGCAGTTCAGG*GAGCCCAGCAGCCGGGGCCGCCCTATTACACCGACCCAGGAGGACCG	m5,exon-exon	BOWTIE;BOWTIE+STAR	UTR/CDS(truncated)	0	27	11	30	7	91880657	-	7	55473045	-	106.602	56.5276	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-14-1823-01A	ENSG00000127989	ENSG00000154978	MTERF1	VOPP1	ACTAGCAAGCCAACAGGTGAAGTTTCGACACACCTCCTTTAATAAAG*GAGCCCAGCAGCCGGGGCCGCCCTATTACACCGACCCAGGAGGACCG	m5,exon-exon	BOWTIE	UTR/CDS(truncated)	0	27	11	29	7	91827415	-	7	55473045	-	106.602	56.5276	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-14-1823-01A	ENSG00000127989	ENSG00000154978	MTERF1	VOPP1	TCCAGCCTTTCTGGAGGGATGCAGAGCCTTTCCTTAGGACAAACAAG*GAGCCCAGCAGCCGGGGCCGCCCTATTACACCGACCCAGGAGGACCG	m5,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	27	10	25	7	91880055	-	7	55473045	-	106.602	56.5276	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-14-1823-01A	ENSG00000127989	ENSG00000154978	MTERF1	VOPP1	ATGTGAAGATGGAATGAAGATCACAAAGCTTTGTCCTTCAAAGAGAAGAG*GAGCCCAGCAGCCGGGGCCGCCCTATTACACCGACCCAGGAGGACCGGGG	m5	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	27	1	35	7	91731530	-	7	55473045	-	106.602	56.5276	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-14-1823-01A	ENSG00000127989	ENSG00000154978	MTERF1	VOPP1	CTCTACAGTTTGGCTCTCATGAAGCCTCATCCCTGAGCACCCACATCCAG*GAGCCCAGCAGCCGGGGCCGCCCTATTACACCGACCCAGGAGGACCGGGG	m5	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	27	1	20	7	91824134	-	7	55473045	-	106.602	56.5276	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-14-1823-01A	ENSG00000154978	ENSG00000127989	VOPP1	MTERF1	CTTTTTGATAGCAAATTATGTTAAGAGACAGTGATGGCTAGGGCTCAACA*TAATTTGCTATTAAAATGTTGCAATTTCAGTTTTAGACAGTTGAGCTATA	m5	BOWTIE+STAR	UTR/intronic	0	27	1	18	7	55470951	-	7	91789847	-	56.5276	106.602	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-14-1823-01A	ENSG00000154978	ENSG00000127989	VOPP1	MTERF1	AATGAACAGAATAAGTTATCAGACTATGATTTCAGTAAGGGATGAAGTGG*GGGAGGCAAAAGAGGAGGTCAGAGTGATCCTGTATAAGAAAGACAACTAC	m5	BOWTIE+STAR	intronic/UTR	0	27	1	14	7	55494574	-	7	91873421	-	56.5276	106.602	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-14-1823-01A	ENSG00000154978	ENSG00000127989	VOPP1	MTERF1	TCTGAAGGGTGCTTTCAAAACGGGGCACATCTGGCTGGGAAGTCACATGG*TCAGTGATGTTGAGCTTTTTTTCATATGTTTCTTGGCCACATAAATGTCT	m5	BOWTIE+STAR	UTR/intronic	0	27	1	14	7	55471876	-	7	91758360	-	56.5276	106.602	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-14-1823-01A	ENSG00000280890	ENSG00000105810	AC073324.2	CDK6	TCCCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAA*AAAAAAAAAAAAAAGTGTGTAAGCTTTAGACTTCACAAACCAGAGATTGC	lincrna,oncogene,cancer	BOWTIE+STAR	intronic/intronic	0	2	1	37	7	55250882	-	7	92701423	-	1.1358	62.2987	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-14-1823-01A	ENSG00000140262	ENSG00000131095	TCF12	GFAP	ATTTTGTATTTTTAGTGGAGATGGGGTTTTGCCATGTTGCCCAGGCTGGT*CTTGAACTCCTGGGCTCAAGCAGTCTACCCACCTCAGCCTCCTGTGTAGC	cancer	BOWTIE+BLAT	intronic/UTR	0	2	1	25	15	57009327	+	17	44906792	-	18.6608	1320.2584	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-14-1823-01A	ENSG00000140262	ENSG00000131095	TCF12	GFAP	TTCCAGCTGCCTTTTCCTCCCAGAACTCTAATTTCTGTCCCCTCCATTCA*AGCCCAGGAGGACTGCCCCGTGCAGACTGGAGGGGACGCTGGTAGAGATG	cancer	BOWTIE+STAR	intronic/UTR	0	2	1	14	15	56947462	+	17	44906419	-	18.6608	1320.2584	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-14-1402-02A	ENSG00000105968	ENSG00000236197	H2AFV	AC002429.2	CCGTGGTGATGAAGAGTTGGATTCTCTTATCAAGGCTACCATAGCTGGGG*TTCAAATTCTGGATGAGAATTCGCTTCTGCAAATTAGAAGCAATTCATCT	m65	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	in-frame	0	104	15	36	7	44835532	-	7	95036781	-	40.6564	11.735900000000001	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-14-1402-02A	ENSG00000105968	ENSG00000236197	H2AFV	AC002429.2	TGATGAAGAGTTGGATTCTCTTATCAAGGCTACCATAGCTGGGGGTG*AGTACTTTAAAGCAAATCCCAGACAATATGCGAATACTTCAGTATGT	m65,exon-exon	BOWTIE;BOWTIE+STAR	CDS(truncated)/UTR	0	104	14	28	7	44835529	-	7	95037111	-	40.6564	11.735900000000001	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-14-1402-02A	ENSG00000105968	ENSG00000236197	H2AFV	AC002429.2	TGATGAAGAGTTGGATTCTCTTATCAAGGCTACCATAGCTGGGGGTG*TTCAAATTCTGGATGAGAATTCGCTTCTGCAAATTAGAAGCAATTCA	m65,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	104	10	30	7	44835529	-	7	95036781	-	40.6564	11.735900000000001	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-14-1402-02A	ENSG00000105968	ENSG00000236197	H2AFV	AC002429.2	GGTGATGAAGAGTTGGATTCTCTTATCAAGGCTACCATAGCTGGGGGTGG*AAATGAAGAATTACTAAATCATAAGAGACTCCTATCAATGGAGAAGGCAC	m65	BOWTIE+BOWTIE2	CDS(truncated)/intronic	0	104	1	32	7	44835528	-	7	95077891	-	40.6564	11.735900000000001	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-14-1402-02A	ENSG00000105968	ENSG00000236197	H2AFV	AC002429.2	TGGTGATGAAGAGTTGGATTCTCTTATCAAGGCTACCATAGCTGGGGGTG*ATGTAGTCTCCCTCTGTCGCCCAGGCTGGAGTACAGTGGCATGATCTTGG	m65	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	104	1	31	7	44835529	-	7	95039554	-	40.6564	11.735900000000001	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-14-1402-02A	ENSG00000105968	ENSG00000236197	H2AFV	AC002429.2	TGGTGATGAAGAGTTGGATTCTCTTATCAAGGCTACCATAGCTGGGGGTG*GTTGCAAGCTTCAGTTAAAAGACACTGCTTACAGCATGATCTTATTAAGA	m65	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	104	1	30	7	44835529	-	7	95036092	-	40.6564	11.735900000000001	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-14-1402-02A	ENSG00000114127	ENSG00000185420	XRN1	SMYD3	TCTCAGAGCGGTATCCCTGTCTCAGCGAAGTGGTGAAAGAGCATCAG*GTGATCTGCAACTCTTTCACCATCTGTAATGCGGAGATGCAGGAAGT	known,18cancers,cancer,tumor,tcga-cancer,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	39	15	29	3	142447870	-	1	245929937	-	3.0611	7.3171	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-14-1402-02A	ENSG00000104870	ENSG00000105552	FCGRT	BCAT2	CCTGCGGGAGCACCTGGAGAGGGGCCGCGGAAACCTGGAGTGGAAGG*CTGTTTGAGGGCATGAAGGCGTTCAAAGGCAAAGACCAGCAGGTGCG	18cancers,tcga-cancer,exon-exon	BOWTIE	in-frame	0	6	5	28	19	49514486	+	19	48800297	-	43.7548	7.9284	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-14-1402-02A	ENSG00000198858	ENSG00000182087	R3HDM4	TMEM259	TATTATCTCCACTCAGAGGCCATACCCATCTCTACCGAGGTGATTTGTAT*AGCAGCCTGGCCCTGGTCACCTCCTGGCTCTTCATCCAGGTGAGGCCTGG	10K<gap<100K	BOWTIE+BLAT	intronic/CDS(truncated)	0	6	1	34	19	910728	-	19	1011134	-	19.593	22.2543	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-14-1402-02A	ENSG00000146477	ENSG00000175048	SLC22A3	ZDHHC14	CAGTTAGCCATCACGCTGCCCAGCTTTCTCTTCCTCCTTTATTACTG*CTGTCCGTACCTGGCGGTGAAAATCACCCCTGCCATCCCTGCAGTCG	18cancers,cancer,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	4	4	27	6	160408921	+	6	157542585	+	1.6254	1.3461	FALSE	TRUE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-14-1402-02A	ENSG00000146477	ENSG00000175048	SLC22A3	ZDHHC14	GCAAGGTGTATTTGGAAAGGGGACGTGGATGACTTGCTACGTGATTG*CTGTCCGTACCTGGCGGTGAAAATCACCCCTGCCATCCCTGCAGTCG	18cancers,cancer,exon-exon	BOWTIE	out-of-frame	0	4	2	27	6	160407195	+	6	157542585	+	1.6254	1.3461	FALSE	TRUE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-14-1402-02A	ENSG00000146477	ENSG00000175048	SLC22A3	ZDHHC14	CCTGCAAGGTGTATTTGGAAAGGGGACGTGGATGACTTGCTACGTGATTG*ATATCGCAAACGGCACCAGTTCAGGGGGGTACCGCCCGCCTCCCAGAACC	18cancers,cancer,exon-exon	BOWTIE+STAR	in-frame	0	4	1	18	6	160407195	+	6	157592988	+	1.6254	1.3461	FALSE	TRUE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-14-1402-02A	ENSG00000132434	ENSG00000154978	LANCL2	VOPP1	GGCAGGTTATCTGTATGCCTTACTGTACCTGAACACAGAGATAGGTCCAG*TAAAGCATACAGAAAAGCTGAAAAAAAATTACCGTGAACACTCATAAACC	known,m2	BOWTIE+STAR	CDS(truncated)/intronic	0	3	1	16	7	55400075	+	7	55469112	-	193.4004	164.8222	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-14-1402-02A	ENSG00000132434	ENSG00000154978	LANCL2	VOPP1	TGTACCTGAACACAGAGATAGGTCCAGGCACCGTGTGTGAGTCAGCTATT*AAGTGATAGTCAATGAGAATTCACAGATGGGTTGGACAAAGGTGCTACCC	known,m2	BOWTIE+STAR	CDS(truncated)/UTR	0	3	1	14	7	55400098	+	7	55493128	-	193.4004	164.8222	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-14-1402-02A	ENSG00000112541	ENSG00000135747	PDE10A	ZNF670-ZNF695	TAATGCGAGCTGCTTCCGAAGGCTGACCGAGTGCTTCCTGAGCCCCA*GGTCCAGTCGTCGACCATCGAGCTGCTTTGAAGACCCTGCGGAGGTT	exon-exon	BOWTIE	CDS(truncated)/UTR	0	3	4	29	6	165661947	-	1	246945827	-	0.1172	0.0091	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-14-1402-02A	ENSG00000112541	ENSG00000197472	PDE10A	ZNF695	TAATAATGCGAGCTGCTTCCGAAGGCTGACCGAGTGCTTCCTGAGCCCCA*GGTCCAGTCGTCGACCATCGAGCTGCTTTGAAGACCCTGCGGAGGTTCCG	tcga-cancer,exon-exon	BOWTIE+STAR	out-of-frame	0	3	1	17	6	165661947	-	1	246945827	-	0.1172	0.0155	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-14-1402-02A	ENSG00000154978	ENSG00000132434	VOPP1	LANCL2	GAGATTTCTATATCTTTTTGAACCTAAATTTTCCGTCTTTGTCCATTTTT*GCTGCCCGCTGTTGTACCAGTGGCACCGGAAGCAGTACGTTGGAGCAGCC	known,m2	BOWTIE+STAR	intronic/CDS(truncated)	0	3	1	15	7	55443166	-	7	55401235	+	164.8222	193.4004	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-14-1402-02A	ENSG00000154978	ENSG00000234707	VOPP1	AC074351.1	GCGCCAGCCTGCGAAGGTGGCGGCGCTGCTGCTCGGGCTGCTCTTGGAGG*ACTTTGCGTGTGACCACTGCACCTCCAGGAAGGCCAGGTGCACATCGCTT	antisense	BOWTIE+BOWTIE2	intronic/intronic	0	2	1	32	7	55572270	-	7	54782593	+	164.8222	6.2975	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-14-1402-02A	ENSG00000018607	ENSG00000267173	ZNF806	AC245748.1	CTGTACCAAGACGTGATGCTGGAAAACTTCAGGAACTTCATCTCAGTGGG*GTCTTGCTGTGTCACCCAGGTGGCTGGAGTGCAGTGGCCTGATCATTGCT	pseudogene	BOWTIE+BOWTIE2	exonic(no-known-CDS)/intronic	0	2	1	35	2	132312996	+	19	44384991	-	0.107	0	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	unprocessed_pseudogene	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-14-1034-01A	ENSG00000105701	ENSG00000105143	FKBP8	SLC1A6	CCATCCCCATCCTGAGGGCAGCCCTGAAGCTGGAACCTTCCAACAAG*TGACCGGCTTCGCACAATGACCAACGTACTGGGGGACTCAATTGGAG	known,tcga,18cancers,chimerdb3seq,m67,tcga-cancer,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	86	29	29	19	18533270	-	19	14950390	-	113.3058	1.5561	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-14-1034-01A	ENSG00000105701	ENSG00000105143	FKBP8	SLC1A6	TGGAGCACCAGCCAGACAACATCAAGGCTCTCTTCCGCAAGGGCAAG*TGACCGGCTTCGCACAATGACCAACGTACTGGGGGACTCAATTGGAG	known,tcga,18cancers,chimerdb3seq,m67,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	86	5	24	19	18537601	-	19	14950390	-	113.3058	1.5561	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-14-1034-01A	ENSG00000105143	ENSG00000105701	SLC1A6	FKBP8	TGGGGAGTTGAGGAGGGCAAGGAAGATCCCAGAAAAGCCAGTGGCAGCAA*CCCCAACTCCCCCAGGCTCCCTGTCCACTGCCCTCCCTGGTCTGGCCCCC	known,tcga,18cancers,chimerdb3seq,m67,tcga-cancer	BOWTIE+STAR	UTR/UTR	0	86	1	14	19	14976839	-	19	18532116	-	1.5561	113.3058	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-14-1034-01A	ENSG00000161960	ENSG00000173868	EIF4A1	PHOSPHO1	CCACCCAGGCCTTGGTCCTAGCACCCACTCGAGAATTGGCTCAGCAG*GACGGCAGGATGGCCGCGCAGGGCGCGCCGCGCTTCCTCCTGACCTT	known,tcga,18cancers,chimerdb3seq,m63,tcga-cancer,exon-exon	BOWTIE	in-frame	0	64	21	30	17	7575258	+	17	49225004	-	0.0727	35.9734	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-14-1034-01A	ENSG00000161960	ENSG00000173868	EIF4A1	PHOSPHO1	CCACCCAGGCCTTGGTCCTAGCACCCACTCGAGAATTGGCTCAGCAG*GTGTTGGATGTGCCAGCGCCTCTGGCCGTGGCCCGCTAACCAGCCTC	known,tcga,18cancers,chimerdb3seq,m63,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/CDS(no-known-start-or-end)	0	64	19	30	17	7575258	+	17	49225131	-	0.0727	35.9734	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-14-1034-01A	ENSG00000161960	ENSG00000173868	EIF4A1	PHOSPHO1	TAAAAGCTATTTCTTACCCAAACGTAACCATTGCTTCCTCCACCCATTTC*CTTGGGTCCTCCTCAGGTGTTGGATGTGCCAGCGCCTCTGGCCGTGGCCC	known,tcga,18cancers,chimerdb3seq,m63,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	UTR/intronic	0	64	2	23	17	7575449	+	17	49225147	-	0.0727	35.9734	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-14-1034-01A	ENSG00000173868	ENSG00000277957	PHOSPHO1	SENP3-EIF4A1	CCTGCCGCGCCCCCTCTCGCTTGCCCCCTCCTCCTCCTCCTCCTGCTGCT*GCTCAATCTCTGGGGGCTGAGGAGCAGCAGGAGGGGGGAGGGAAGGGAGC	m59	BOWTIE+STAR	CDS(truncated)/UTR	0	60	1	16	17	49225022	-	17	7578518	+	35.9734	0	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-14-1034-01A	ENSG00000277957	ENSG00000173868	SENP3-EIF4A1	PHOSPHO1	AAGCCACCCAGGCCTTGGTCCTAGCACCCACTCGAGAATTGGCTCAGCAG*GACGGCAGGATGGCCGCGCAGGGCGCGCCGCGCTTCCTCCTGACCTTCGA	m59,exon-exon	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	60	5	21	17	7575258	+	17	49225004	-	0	35.9734	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-14-1034-01A	ENSG00000277957	ENSG00000173868	SENP3-EIF4A1	PHOSPHO1	AAGCCACCCAGGCCTTGGTCCTAGCACCCACTCGAGAATTGGCTCAGCAG*GTGTTGGATGTGCCAGCGCCTCTGGCCGTGGCCCGCTAACCAGCCTCTCC	m59,exon-exon	BOWTIE+STAR	UTR/CDS(no-known-start-or-end)	0	60	2	17	17	7575258	+	17	49225131	-	0	35.9734	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-14-1034-01A	ENSG00000277957	ENSG00000173868	SENP3-EIF4A1	PHOSPHO1	TAAAAGCTATTTCTTACCCAAACGTAACCATTGCTTCCTCCACCCATTTC*CTTGGGTCCTCCTCAGGTGTTGGATGTGCCAGCGCCTCTGGCCGTGGCCC	m59	BOWTIE+BLAT;BOWTIE+STAR	intronic/intronic	0	60	1	25	17	7575449	+	17	49225147	-	0	35.9734	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-14-1034-01A	ENSG00000175899	ENSG00000091129	A2M	NRCAM	TGTTTTACCTACCGGGGACGTGATTGGGGATTCTGCAAAATATGATGTTG*GCCAGACATTGTTCTAAAACAAAATAGTCAAAAATCTCTGTGGTAATGGA	cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	14	12	9099401	-	7	108188545	-	825.5957	144.4822	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-14-1034-01A	ENSG00000171094	ENSG00000054118	ALK	THRAP3	TAACTGGGACTACAGGCATCTGCCACCACACCCGGCTAATTTTTTGTATT*TTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTC	oncogene,cancer,tumor	BOWTIE+BLAT	intronic/intronic	0	2	1	35	2	29445662	-	1	36292448	+	2.0728	37.8726	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-14-1034-01A	ENSG00000171094	ENSG00000054118	ALK	THRAP3	GATCTTACCTTAGCCTAACTATCTTCTTTCCTCACAAGATGCCTAAGGAA*CACAGGAAGCATCGGAGAGCAAGAGACAGGTCCAGATCCTCCTCCTCTTC	oncogene,cancer,tumor	BOWTIE+STAR	intronic/intronic	0	2	1	15	2	29869323	-	1	36300881	+	2.0728	37.8726	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-14-1034-01A	ENSG00000171094	ENSG00000054118	ALK	THRAP3	CGTGGAAAACCTGCGCGCTGTTCCCAGCCAGCGTGTTGGGTATGCAAGGC*ACACAGGCTTGGGTGATGGAAAAATGAAATCTGATTCTTTTGCTCCCAAA	oncogene,cancer,tumor	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	14	2	29818477	-	1	36289158	+	2.0728	37.8726	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-14-1034-01A	ENSG00000091129	ENSG00000175899	NRCAM	A2M	AAACCAAGTACAGTAGTAGTATGTTTGCTCAGGACAAGGAAGTCTGGTGG*TAGACATCCTTGAAATACAATATTCTCCCAGAAAAGGAAGAGTTCCCCTT	cancer	BOWTIE+STAR	intronic/intronic	0	2	2	16	7	108290358	-	12	9072489	-	144.4822	825.5957	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-14-1034-01A	ENSG00000091129	ENSG00000175899	NRCAM	A2M	ACCGCTTCTGACCTTTGGGTGAATAAATTTTTGGAAGTGTGCAGCTGGCA*GCCTCTCTCCGAGCCTTCCAGCCCTTCTTTGTGGAGCTCACAATGCCTTA	cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	16	7	108440725	-	12	9091320	-	144.4822	825.5957	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-14-1034-01A	ENSG00000091129	ENSG00000175899	NRCAM	A2M	TAGATGGTTGGATTTAGTGACCTTCCAGGCTCCTTCTGTCTCCCAAAATT*GAGACATATTAGGCTCTGCCATGCAAAACACACAAAATCTTCTCCAGATG	cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	16	7	108402526	-	12	9079815	-	144.4822	825.5957	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-14-1034-01A	ENSG00000091129	ENSG00000175899	NRCAM	A2M	ACCAAATAGAAAAATAAGCATGTTAACTTTATTCTTAGCAAGTTCCAGGT*GGACTGGGAAGGCTGCACAGGTGACTATCCAGTCTTCAGGGACATTTTCC	cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	14	7	108282452	-	12	9072816	-	144.4822	825.5957	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-14-1034-01A	ENSG00000091129	ENSG00000175899	NRCAM	A2M	ACTTGTCAAGCTCTGAACATACCTTGTTGTTACCTACTCTGGGTCTTTGC*TCGATGAAGCACACATTACCCAAGCCCTCATATGGCTCTCCCAGAGGCAG	cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	14	7	108348302	-	12	9077804	-	144.4822	825.5957	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-14-1034-01A	ENSG00000091129	ENSG00000175899	NRCAM	A2M	TGAAAAATAAAATAAAACTTTTGAAGATAATTTTATGGAGTAAATAGGAC*CAAAATCTTCTCCAGATGCCCTATGGCTGTGGAGAGCAGAATATGGTCCT	cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	14	7	108365357	-	12	9079783	-	144.4822	825.5957	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-14-1034-01A	ENSG00000091129	ENSG00000175899	NRCAM	A2M	TTCTGAAGGCTCAGAAAGAGCAGTTGAAATGTGTTTGAAGAAAGACATCA*CTGGCCTATGCTTTTGCCCTGGCAGGTAACCAGGACAAGAGGAAGGAAGT	cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	14	7	108308689	-	12	9076840	-	144.4822	825.5957	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-14-1034-01A	ENSG00000091129	ENSG00000175899	NRCAM	A2M	AAACCAGAGCAGAAAGGCTGAAGATTCCAAAAACCAGAAGGCCTCTTCTC*TGCCTCTCTCCGAGCCTTCCAGCCCTTCTTTGTGGAGCTCACAATGCCTT	cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	14	7	108277807	-	12	9091321	-	144.4822	825.5957	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-14-1034-01A	ENSG00000091129	ENSG00000175899	NRCAM	A2M	CAGTTTTTATTTCTTATATTTCCCCAGGTTCTTGGCTCAAGGAAGATGTA*GGCTCTCCCAGAGGCAGAAGGACAATGGCTGTTTCAGGAGCTCTGGGTCA	cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	14	7	108383738	-	12	9077771	-	144.4822	825.5957	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-14-1034-01A	ENSG00000091129	ENSG00000175899	NRCAM	A2M	GCCCTTGGCTTCCCCAGGAAAATTGAAAGTGGAAGCTGGCTCCAGGCAGA*TATCCAGTCTTCAGGGACATTTTCCAGCAAATTCCAAGTGGACAACAACA	cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	14	7	108338057	-	12	9072791	-	144.4822	825.5957	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-14-1034-01A	ENSG00000145675	ENSG00000115919	PIK3R1	KYNU	TAGCATTAGCTGCCCAGGATGCTGCTATATATATATATATATATATATAT*ATATATATATATATATATATATGTGTGTGTGTGTGTGTGTATATATATAT	oncogene,cancer	BOWTIE+BLAT	UTR/UTR	0	2	1	34	5	68301367	+	2	143042610	+	17.7316	0.3669	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-14-1034-01A	ENSG00000131748	ENSG00000131095	STARD3	GFAP	ATCTCGGCTCACTGCAAGCTTCACCTCCTGGGTTCACGCCATTCTTCTGC*CTCAGCCTCCTGTGTAGCTGGGATTATAGATTGGAGCCACCATGCCCAGC	cancer	BOWTIE+BLAT;BOWTIE+STAR	intronic/UTR	0	2	1	23	17	39651677	+	17	44906760	-	12.0645	2049.5413	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-14-1034-01A	ENSG00000131748	ENSG00000131095	STARD3	GFAP	GAGGTCATTCAAGAATGAGGAAACAGGGCGCCCAGGCGATGGGCTGTGGT*GAGGCGCTGGCGCGGCTGGAGGAAGAGGGGCAGAGCCTCAAGGACGAGAT	cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	16	17	39642131	+	17	44911387	-	12.0645	2049.5413	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0171-02A	ENSG00000134313	ENSG00000187068	KIDINS220	C3ORF70	TTCATCTTTTACTGCAAAATGGTGCTAAAGTCAACTGCTCTGATAAG*GCAAATACATGTATCAGCCTATGACCCCTGTGGAACAGCTTCCAAGC	18cancers,tcga-cancer,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	7	13	28	2	8812395	-	3	185083563	-	12.2358	6.4274	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0171-02A	ENSG00000124802	ENSG00000251281	EEF1E1	AC034223.2	TGGGACTGAGTAAGGGGAATAAATACAGTGCTCAGGGCGAGCGACAG*GTCATTGTTGAGAGACAAAATGAGATCATGTCTGGGAAAATACTTCT	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	4	6	28	6	8102435	-	5	33011560	-	1.5794	1.7801	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0171-02A	ENSG00000124802	ENSG00000251281	EEF1E1	AC034223.2	TCAGTTTAAGTGTTACGACCCACAGTGAATGCGGGAAACATCACAAG*GTCATTGTTGAGAGACAAAATGAGATCATGTCTGGGAAAATACTTCT	lincrna,exon-exon	BOWTIE	CDS(no-known-start-or-end)/exonic(no-known-CDS)	0	4	3	26	6	8101765	-	5	33011560	-	1.5794	1.7801	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0171-02A	ENSG00000156931	ENSG00000143797	VPS8	MBOAT2	AACCAGGTTTTGCTTTTCAAATTTTTGAGGAGTCTTCTTGACCCAAG*TTACTGCTTTGTGTTTGCTCTGGGATACCTCACAGTGTGCCAAGTTA	18cancers,exon-exon	BOWTIE	in-frame	0	3	3	27	3	184940243	+	2	8908716	-	6.0146	5.9977	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0171-02A	ENSG00000156931	ENSG00000143797	VPS8	MBOAT2	TCCCATGCTTGCCTTCTGCAGAGGAGATGTTGTTCATTTTCTATTGGTAA*AGGAAGATTAATCTGTCGATAATACATAGAATGAATTAAAAGGAGCATGG	18cancers	BOWTIE+STAR	intronic/intronic	0	3	1	15	3	184855822	+	2	8873385	-	6.0146	5.9977	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2528-01A	ENSG00000133612	ENSG00000234336	AGAP3	JAZF1-AS1	TTTGGCGCTGCAGAACCAGATCCGGGAGCACGTCATCTCCATCGAGG*CCCTTCTACCGTGAAGGTGAGCCGTGAAGTCTATTGCCCAGGGATTG	antisense,18cancers,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	931	35	30	7	151087072	+	7	28240457	+	7.1771	219.0955	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2528-01A	ENSG00000133612	ENSG00000234336	AGAP3	JAZF1-AS1	CGATAACATGGAGTTATGGGCAGGGGCCTGTCCCTGACTTGGGCCTTAAG*CCCTTCTACCGTGAAGGTGAGCCGTGAAGTCTATTGCCCAGGGATTGGGG	antisense,18cancers	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	intronic/exonic(no-known-CDS)	0	931	1	30	7	151088124	+	7	28240457	+	7.1771	219.0955	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2528-01A	ENSG00000133612	ENSG00000234336	AGAP3	JAZF1-AS1	GGATTTGGCGCTGCAGAACCAGATCCGGGAGCACGTCATCTCCATCGAGG*TTTGTTTTCCCCCTTTCTCTTGCAGCCCTTCTACCGTGAAGGTGAGCCGT	antisense,18cancers	BOWTIE+STAR	CDS(truncated)/intronic	0	931	1	18	7	151087072	+	7	28240432	+	7.1771	219.0955	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2528-01A	ENSG00000133612	ENSG00000234336	AGAP3	JAZF1-AS1	GCTCTCCCTGTCGGGGGTCCTTGCGCGCTTGAGGACCAGGCCACGAG*CCCTTCTACCGTGAAGGTGAGCCGTGAAGTCTATTGCCCAGGGATTG	antisense,18cancers,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	931	1	14	7	151087204	+	7	28240457	+	7.1771	219.0955	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-27-2528-01A	ENSG00000106069	ENSG00000158457	CHN2	TSPAN33	AAGGCAACACACGTTCGCTGATGGTCTACATTCCAGCTGCACTAGCA*GTGATTTCCATGGTGATGGTGGCTGTGGGTGTCTACGCTCGGCTAAT	known,18cancers,exon-exon	BOWTIE;BOWTIE+STAR	CDS(no-known-start-or-end)/CDS(truncated)	0	138	31	30	7	29146960	+	7	129161679	+	0.0543	180.2547	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2528-01A	ENSG00000146592	ENSG00000055118	CREB5	KCNH2	TCCAGCTCTGTCATCACTCAGGCACCTTCCACCAACCGCCAGATCGG*GGAAGAATGACATCTTTGGGGAGCCTCTGAACCTGTATGCAAGGCCT	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	56	19	29	7	28570537	+	7	150949049	-	13.8773	67.8874	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-27-2528-01A	ENSG00000146592	ENSG00000055118	CREB5	KCNH2	AAAATCAGCATTGAAATCCACCGATGCAGGGATCACACAGTGGAGCTTGT*TGTTCTTGCTCATGTGCACCTTTGCGCTCATCGCGCACTGGCTAGCCTGC	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	intronic/CDS(truncated)	0	56	14	37	7	28587355	+	7	150951744	-	13.8773	67.8874	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-27-2528-01A	ENSG00000146592	ENSG00000055118	CREB5	KCNH2	TCCAGCTCTGTCATCACTCAGGCACCTTCCACCAACCGCCAGATCGG*GTGCTGAAGGGCTTCCCTGAGTGCCTGCAGGCTGACATCTGCCTGCA	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	56	4	22	7	28570537	+	7	150950420	-	13.8773	67.8874	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-27-2528-01A	ENSG00000146592	ENSG00000055118	CREB5	KCNH2	TGGAGCACGAGTTCAGGAAGGCTCAGGAAGAGGAGAGCAGCAAGCGG*GGAAGAATGACATCTTTGGGGAGCCTCTGAACCTGTATGCAAGGCCT	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	56	2	29	7	28507737	+	7	150949049	-	13.8773	67.8874	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-27-2528-01A	ENSG00000146592	ENSG00000055118	CREB5	KCNH2	CAGTCCAGCTCTGTCATCACTCAGGCACCTTCCACCAACCGCCAGATCGG*CAGCCTCACCAGTGTGGGCTTCGGCAACGTCTCTCCCAACACCAACTCAG	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	in-frame	0	56	1	25	7	28570537	+	7	150951533	-	13.8773	67.8874	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-27-2528-01A	ENSG00000055118	ENSG00000146592	KCNH2	CREB5	CCGCTACCACACACAGATGCTGCGGGTGCGGGAGTTCATCCGCTTCCACC*GTCACCCCCACCCCCTCCCAGAGGTCCTTGCAACAAAATCCAAATCCTAC	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	56	1	15	7	150951004	-	7	28697498	+	67.8874	13.8773	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-27-2528-01A	ENSG00000106477	ENSG00000146592	CEP41	CREB5	TTAAGATGTAAGCAGTTTACACAGTGGGATAAAAATGCTACTTTTCATAC*TTTGAAAAATGGTTTGAGACATTTTTACCGAACGCAAAATGCCATTGAGT	NA	BOWTIE+STAR	UTR/intronic	0	2	1	18	7	130419369	-	7	28698169	+	61.6766	13.8773	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-27-2528-01A	ENSG00000106477	ENSG00000146592	CEP41	CREB5	TGGAGATTTACCCCAGAAGACTTAAAAAAGATAGAATATTATCTGGAAGA*TCAGGAGGCCCTTGCATCTGCAGAGGAAGCTCACGCTGTCCTCCGCGAGG	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	14	7	130400065	-	7	28516948	+	61.6766	13.8773	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-27-2528-01A	ENSG00000106477	ENSG00000146592	CEP41	CREB5	CACCTGCAAGGCAAACCCTGGAAGTAAAGACTTTGTCTCACTTAGGCAAA*CCCTGTGAGTAAAGTAGACAGTCTATATGTGGAGACCCATATAAGGAGAT	NA	BOWTIE+STAR	UTR/intronic	0	2	1	14	7	130398868	-	7	28700988	+	61.6766	13.8773	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-27-2528-01A	ENSG00000106477	ENSG00000146592	CEP41	CREB5	CGCCGAGCCCTGAGCAGTTCATAAACAACGCAGGAGCAGGGGACTCCAGC*GGTGTTTATGTACTTGAGATTGGGTGGAGTCACCTGAGCCAGAAGTGAAT	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	14	7	130404581	-	7	28512256	+	61.6766	13.8773	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-27-2528-01A	ENSG00000115461	ENSG00000089169	IGFBP5	RPH3A	CGGGGCCGGCCCAGAGCCTGGGCTCCTTCGTGCACTGCGAGCCCTGCGAC*TAGGTGAAGATGGTGGATGGGTGGTCCTGACCGAGTGTCTCACTCAAGAT	cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	15	2	216694683	-	12	112706626	+	414.9203	15.9656	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-27-2528-01A	ENSG00000115461	ENSG00000089169	IGFBP5	RPH3A	TGTTAGGGTTTGGGGTTTTTTTGTTTTTGTTTTTGTTTTTTAATTTCTTG*TGTTTACCCCTGCCTTCCACTCCAGTGATGCATCTCAGAGCCTTGGGTCA	cancer	BOWTIE+STAR	UTR/intronic	0	2	1	15	2	216695323	-	12	112846704	+	414.9203	15.9656	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-2528-01A	ENSG00000089169	ENSG00000115461	RPH3A	IGFBP5	CATGAAGGGATGGGGGTAACACTGGGGCCTGTCGGGGGAGAGGTGACGGG*GGAGGAGGGACGAGGGACAGGGGTTTCACCAGCCAGCAACCTGGGCCTTG	cancer	BOWTIE+STAR	intronic/UTR	0	2	1	15	12	112639510	+	2	216672979	-	15.9656	414.9203	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-5411-01A	ENSG00000163531	ENSG00000198400	NFASC	NTRK1	GAAGGGCCCTGAGCCAGAGTCCGTCATCGGTTACTCCGGAGAAGATT*ACACTAACAGCACATCTGGAGACCCGGTGGAGAAGAAGGACGAAACA	known,oncogene,tcga,cell_lines,18cancers,chimerdb3pub,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	438	35	30	1	204982020	+	1	156874571	+	31.2604	64.8834	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-5411-01A	ENSG00000163531	ENSG00000198400	NFASC	NTRK1	ATGGACATATATGCCTGGCTTCCCAGACGGTGGTGGCCTCTCTGTCCCCA*GCTGCAGTCTCCTTCTCGCCGGTGGGTGAGTAGCCCAAGGTGGAGGGCAG	known,oncogene,tcga,cell_lines,18cancers,chimerdb3pub,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	intronic/UTR	0	438	4	38	1	204982697	+	1	156874376	+	31.2604	64.8834	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-5411-01A	ENSG00000163531	ENSG00000198400	NFASC	NTRK1	GGGTGGGCCAGAGGAGGGTCTGATTTCTGTGGTGAGTGAGAGACAGGATG*AGGGCAGGGACGAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTA	known,oncogene,tcga,cell_lines,18cancers,chimerdb3pub,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+STAR	intronic/UTR	0	438	1	15	1	204831491	+	1	156875688	+	31.2604	64.8834	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-06-5411-01A	ENSG00000198400	ENSG00000163531	NTRK1	NFASC	CTCCTTGTGCTCAACAAATGTGGACGGAGAAACAAGTTTGGGATCAACCG*CCCAGCACAGGAGGGGGCAAATGAGTGCCCTCTGAACATGTAGGCAGAGT	known,oncogene,tcga,cell_lines,18cancers,chimerdb3pub,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+STAR	intronic/intronic	0	438	1	15	1	156875009	+	1	204983774	+	64.8834	31.2604	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-5411-01A	ENSG00000058668	ENSG00000163531	ATP2B4	NFASC	AGGGAGAGTCCCGCCTGAAGAAACCTGGATCTTTGCTAGAAAGAGAG*GTTGATTGACTTATGTGCAATTTGGGACGCTGGAGTTTACCTTCCCT	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	UTR/UTR	0	7	11	26	1	203627219	+	1	204920632	+	123.5534	31.2604	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-06-5411-01A	ENSG00000283235	ENSG00000170089	AC139493.2	AC106795.1	TGGGGATGGCAAAGACGACATCCGGTGCGCCGAGGCTGCTCACAAAA*ATATTATCTGAAGCTTTAAAGCCTCCTGGAGTGAAAGCTAGTTCATA	pseudogene,exon-exon	BOWTIE	exonic(no-known-CDS)/exonic(no-known-CDS)	0	2	4	22	5	176199236	-	5	177950309	+	0.0826	4.0098	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	processed_transcript	transcribed_unprocessed_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-5411-01A	ENSG00000058668	ENSG00000236957	ATP2B4	AL139010.1	CGGAGGGAGAGTCCCGCCTGAAGAAACCTGGATCTTTGCTAGAAAGAGAG*GTAAGGACACAGCAAGAAAATGGTTGTCTATGAACCAGAAAGCAGGCCCT	pseudogene,exon-exon	BOWTIE+STAR	UTR/exonic(no-known-CDS)	0	2	1	16	1	203627219	+	1	157945656	+	123.5534	0.1435	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	transcribed_unprocessed_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0211-01B	ENSG00000146648	ENSG00000132434	EGFR	LANCL2	GCTGGCTGCGCTCTGCCCGGCGAGTCGGGCTCTGGAGGAAAAGAAAG*ATCATTCATAATTTCATAAGACGGATCCAGACCAAAATTAAAGATCT	known,oncogene,18cancers,cancer,tumor,100K<gap<200K,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	out-of-frame	0	1542	35	30	7	55019365	+	7	55391793	+	170.5763	216.0796	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0211-01B	ENSG00000146648	ENSG00000132434	EGFR	LANCL2	GCTGGCTGCGCTCTGCCCGGCGAGTCGGGCTCTGGAGGAAAAGAAAG*GCATAGCCCTTTTGTACCTGCAGTTGTACCGGGTCACATGTGACCAA	known,oncogene,18cancers,cancer,tumor,100K<gap<200K,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	1542	3	18	7	55019365	+	7	55398423	+	170.5763	216.0796	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0211-01B	ENSG00000146648	ENSG00000132434	EGFR	LANCL2	GCTGGCTGCGCTCTGCCCGGCGAGTCGGGCTCTGGAGGAAAAGAAAG*CCGGCAGCAAAAGTGGACCAAGAAACCTTGACAGAAATGGTGAAACC	known,oncogene,18cancers,cancer,tumor,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	1542	2	30	7	55019365	+	7	55411907	+	170.5763	216.0796	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0211-01B	ENSG00000146648	ENSG00000132434	EGFR	LANCL2	GGACATCTGGAATTGTTACAATATTGCCAAATATAGGAAAGAGGGAAAAG*ATCATTCATAATTTCATAAGACGGATCCAGACCAAAATTAAAGATCTTCT	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	intronic/CDS(truncated)	0	1542	1	30	7	55021144	+	7	55391793	+	170.5763	216.0796	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0211-01B	ENSG00000146648	ENSG00000132434	EGFR	LANCL2	GCTGCTGGCTGCGCTCTGCCCGGCGAGTCGGGCTCTGGAGGAAAAGAAAG*ACCAAAATTAAAGATCTTCTGCAGCAAATGGAAGAAGGGCTGAAGACAGC	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	out-of-frame	0	1542	1	24	7	55019365	+	7	55391823	+	170.5763	216.0796	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0211-01B	ENSG00000146648	ENSG00000132434	EGFR	LANCL2	GAAGGTTTAATTGCACAATTCCAACCTTGAGCTGCGCGGGTTCCAAGAGC*CAGATCATTCATAATTTCATAAGACGGATCCAGACCAAAATTAAAGATCT	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	intronic/intronic	0	1542	1	16	7	55020752	+	7	55391790	+	170.5763	216.0796	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0211-01B	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	AAGAAGGGCTGAAGACAGCTGATCCCCATGACTGCTCTGCTTATACTGGC*TGCAGACAGCTGATTCTTCTCCTCCCGCGGCTGAGCAGCCTCCTCCGAGC	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/intronic	0	1542	1	16	7	55391903	+	7	55101029	+	216.0796	170.5763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0211-01B	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	CCAAACCTACCTGCTCCGATCCCTGGATTACGTAAAAAGAACACTTCGGA*GCAGGGAGGTTGGGTCCTGCCTGAGGAGACCTGGAAGGGAGGCCTCACAG	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/UTR	0	1542	1	16	7	55398515	+	7	55207534	+	216.0796	170.5763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0211-01B	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	GCTCCTCTCCGTCGGGAGCAGGGCAAAGGCGCCAGGAACAGGGCAGAGGC*GCCAGGGCCAGGGCAGGGGCCACGGTTGCAGCCTGCATTCTTCTAAAGGG	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	1542	1	16	7	55365813	+	7	55075113	+	216.0796	170.5763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0211-01B	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	ATGAGCTGCTTTATGGACGGGCAGGTTATCTGTATGCCTTACTGTACCTG*CCCCTCCAAAAAGCAGAGGCATTCTTAAAAACACACATCTGCACATGTTC	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/intronic	0	1542	1	16	7	55400056	+	7	55125811	+	216.0796	170.5763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0211-01B	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	GATGAGCTGCTTTATGGACGGGCAGGTTATCTGTATGCCTTACTGTACCT*CTCTCTGTGATCAGGTGCTGCCCTCCCTGGCAGGAGGACTGCAGACAGGA	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/intronic	0	1542	1	15	7	55400055	+	7	55120151	+	216.0796	170.5763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0211-01B	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	CCGGGTCACATGTGACCAAACCTACCTGCTCCGATCCCTGGATTACGTAA*TCCAGGGATAGGAATATTAATAGCAAGCTTTTTGCCTGATATAGTCACTT	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/intronic	0	1542	1	14	7	55398500	+	7	55104980	+	216.0796	170.5763	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0211-01B	ENSG00000132434	ENSG00000154997	LANCL2	SEPT14	GCCACGGCGCCCCGGGGGTCATCCACATGCTCATGCAGGCGTACAAG*GGGCTGTTACCCTTTGCTGTGGTAGGGAGTACAGATGAAGTGAAAGT	known,tcga,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	485	35	30	7	55412089	+	7	55819223	-	216.0796	16.6792	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0211-01B	ENSG00000132434	ENSG00000154997	LANCL2	SEPT14	GGTGCCACGGCGCCCCGGGGGTCATCCACATGCTCATGCAGGCGTACAAG*AGTCTCACTCTTGTTTCTCAGACCGAGATGTAATGGCGCGATCTCAGCTC	known,tcga	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	485	1	18	7	55412089	+	7	55820933	-	216.0796	16.6792	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0211-01B	ENSG00000262583	ENSG00000166822	AC009163.5	TMEM170A	GTGTTATGTGCCCAGGGATTTTCCTGGACGGGATTGTGAAGTAGCGG*AGATGTGGTATGGTGTATTCCTGTGGGCACTGGTGTCTTCTCTCTTC	pseudogene,10K<gap<100K,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	3	3	25	16	75516203	-	16	75451839	-	0.6563	9.1622	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	transcribed_unprocessed_pseudogene	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0211-01B	ENSG00000186153	ENSG00000137872	WWOX	SEMA6D	TGCTGACTCAGTTCCTGGGTGGGGGCCAAAGGACTGGTTGGCAGGTCTGC*TCCCCATTAAGTCATGGGCATATCCCCAGTGCCATTGTTCTTCCAAATGC	cancer,tumor	BOWTIE+STAR	intronic/CDS(truncated)	0	3	1	15	16	78413805	+	15	47771012	+	3.5123	36.8502	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0211-01B	ENSG00000240184	ENSG00000106278	PCDHGC3	PTPRZ1	TGTTCTATAGGCAGGTGTTGGGTGCAGAGAGCGCCCCTCCCGGACAGGTA*CGCCCGCCACCACGCCTGGCTAATTTTTTGTATTTTTAGTAGAGACAGGG	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	16	5	141478549	+	7	121994439	+	111.9941	352.2686	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0211-01B	ENSG00000130340	ENSG00000146433	SNX9	TMEM181	CCAGCACAGCTCAGGCCAGTTCGTCGGCTGCCAGCAACAATCACCAG*GCTGGCGCCCATGCGGCTCTACACGCTCTCCAAGCGCCACTTTGTCC	exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	2	2	22	6	157875176	+	6	158573420	+	4.819	17.4849	FALSE	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5135-01A	ENSG00000118596	ENSG00000258231	SLC16A7	AC020637.1	GGGAACGGAGGGCTGCAGCGCCCACCCTGCGCCAGAGACCAGATAAA*TTCTCAAACAGTAGCTGCCACTTCTAGCTGGGAGAGAAATGAGAGCT	lincrna,exon-exon	BOWTIE;BOWTIE+STAR	UTR/exonic(no-known-CDS)	0	74	28	29	12	59596236	+	12	58812414	+	1.3053	8.6848	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5135-01A	ENSG00000118596	ENSG00000258231	SLC16A7	AC020637.1	GGGAACGGAGGGCTGCAGCGCCCACCCTGCGCCAGAGACCAGATAAA*AATAGAATGCAACTGAAGAAATGGCTGGTGCAATTCAGCAAGGTAAA	lincrna,exon-exon	BOWTIE;BOWTIE+STAR	UTR/exonic(no-known-CDS)	0	74	12	28	12	59596236	+	12	58805941	+	1.3053	8.6848	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5135-01A	ENSG00000118596	ENSG00000258231	SLC16A7	AC020637.1	GGGAACGGAGGGCTGCAGCGCCCACCCTGCGCCAGAGACCAGATAAA*GGCCTGAATTTTCTGCTCCTGAATTCAAACATTAAAATGTGTGGTAT	lincrna,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	74	3	28	12	59596236	+	12	58801260	+	1.3053	8.6848	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5135-01A	ENSG00000118596	ENSG00000258231	SLC16A7	AC020637.1	GGGAACGGAGGGCTGCAGCGCCCACCCTGCGCCAGAGACCAGATAAA*GTTTTGGTATCAGGATGATGCTGGCCTCATAAAATGAGTCAGGGAAG	lincrna,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	74	2	15	12	59596236	+	12	58800583	+	1.3053	8.6848	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5135-01A	ENSG00000118596	ENSG00000258231	SLC16A7	AC020637.1	ATGGCTAACCCCAGTCTGAACTCAGAGGGTTGCAAACTTTCCACAGACAG*GGCCTGAATTTTCTGCTCCTGAATTCAAAGTAAGTTTCCATAACCCTGAT	lincrna	BOWTIE+BLAT	intronic/exonic(no-known-CDS)	0	74	1	29	12	59597531	+	12	58801260	+	1.3053	8.6848	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5135-01A	ENSG00000118596	ENSG00000258231	SLC16A7	AC020637.1	ATGGCTAACCCCAGTCTGAACTCAGAGGGTTGCAAACTTTCCACAGACAG*TTCTCAAACAGTAGCTGCCACTTCTAGCTGGGAGAGAAATGAGAGCTCTG	lincrna	BOWTIE+BOWTIE2;BOWTIE+STAR	intronic/exonic(no-known-CDS)	0	74	1	29	12	59597531	+	12	58812414	+	1.3053	8.6848	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5135-01A	ENSG00000118596	ENSG00000258231	SLC16A7	AC020637.1	GGGAACGGAGGGCTGCAGCGCCCACCCTGCGCCAGAGACCAGATAAA*CTTTCTGTTTTTCTCATGCATGAGAAAAATGCATTTCAGCTGAAAAC	lincrna,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	74	1	14	12	59596236	+	12	58811922	+	1.3053	8.6848	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5135-01A	ENSG00000127314	ENSG00000245651	RAP1B	AC083805.1	GAGCGCGGGGCGACGCTGGCTGCAGGGACCCGGTGACAGCGTGAGAG*GAAGATAACTTTGGCAGCAGAATGGGAAGAAGATTGGATGGGAGAGA	lincrna,cancer,exon-exon	BOWTIE;BOWTIE+STAR	UTR/exonic(no-known-CDS)	0	50	23	29	12	68611043	+	12	57872088	-	2.4206	34.4644	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5135-01A	ENSG00000127314	ENSG00000245651	RAP1B	AC083805.1	GAGCGCGGGGCGACGCTGGCTGCAGGGACCCGGTGACAGCGTGAGAG*ATGGAGTTTTGCTCTTACGCCCAGGCTGGAATGAAGTGGCATGATCT	lincrna,cancer,exon-exon	BOWTIE;BOWTIE+STAR	UTR/exonic(no-known-CDS)	0	50	17	29	12	68611043	+	12	57872976	-	2.4206	34.4644	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5135-01A	ENSG00000127314	ENSG00000245651	RAP1B	AC083805.1	GAGCGCGGGGCGACGCTGGCTGCAGGGACCCGGTGACAGCGTGAGAG*AAATCAGAGCACCACAGCCAGCTCTAGCCCAGAGGGAAAGTAAGAGG	lincrna,cancer,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	50	13	29	12	68611043	+	12	57886696	-	2.4206	34.4644	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5135-01A	ENSG00000127314	ENSG00000245651	RAP1B	AC083805.1	GCGACGCTGGCTGCAGGGACCCGGTGACAGCGTGAGAGGTTCGCAGA*GAAGATAACTTTGGCAGCAGAATGGGAAGAAGATTGGATGGGAGAGA	lincrna,cancer,exon-exon	BOWTIE;BOWTIE+STAR	UTR/exonic(no-known-CDS)	0	50	13	29	12	68611052	+	12	57872088	-	2.4206	34.4644	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5135-01A	ENSG00000127314	ENSG00000245651	RAP1B	AC083805.1	GGGGAGCGCGGGGCGACGCTGGCTGCAGGGACCCGGTGACAGCGTGAGAG*GGCCTCTGGTCTTTCCCAAGCTGCCTGAGTAGAAGGAAACACACAGCTCC	lincrna,cancer	BOWTIE+BLAT;BOWTIE+STAR	UTR/exonic(no-known-CDS)	0	50	10	36	12	68611043	+	12	57893975	-	2.4206	34.4644	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5135-01A	ENSG00000127314	ENSG00000245651	RAP1B	AC083805.1	GCGACGCTGGCTGCAGGGACCCGGTGACAGCGTGAGAGGTTCGCAGA*ATGGAGTTTTGCTCTTACGCCCAGGCTGGAATGAAGTGGCATGATCT	lincrna,cancer,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	50	10	28	12	68611052	+	12	57872976	-	2.4206	34.4644	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5135-01A	ENSG00000127314	ENSG00000245651	RAP1B	AC083805.1	GGGGAGCGCGGGGCGACGCTGGCTGCAGGGACCCGGTGACAGCGTGAGAG*GCTGGAGTGCAATGGCATGATCTCGGCTCCCTGCAACCTCCACCTCCCAG	lincrna,cancer	BOWTIE+BLAT;BOWTIE+STAR	UTR/intronic	0	50	9	35	12	68611043	+	12	57880508	-	2.4206	34.4644	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5135-01A	ENSG00000127314	ENSG00000245651	RAP1B	AC083805.1	GGGGAGCGCGGGGCGACGCTGGCTGCAGGGACCCGGTGACAGCGTGAGAG*GTGCCTGCTACACCCAGGGAGGCCAGAAGAGGTGGACAGAAATAGTCTCC	lincrna,cancer	BOWTIE+BLAT;BOWTIE+STAR	UTR/intronic	0	50	6	38	12	68611043	+	12	57886776	-	2.4206	34.4644	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5135-01A	ENSG00000127314	ENSG00000245651	RAP1B	AC083805.1	GCGACGCTGGCTGCAGGGACCCGGTGACAGCGTGAGAGGTTCGCAGA*AAATCAGAGCACCACAGCCAGCTCTAGCCCAGAGGGAAAGTAAGAGG	lincrna,cancer,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	50	6	25	12	68611052	+	12	57886696	-	2.4206	34.4644	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5135-01A	ENSG00000127314	ENSG00000245651	RAP1B	AC083805.1	CAACAAAAGCTCCTCGATGGAACCATTTGATAGTGACAAGGATTGAA*GAAGATAACTTTGGCAGCAGAATGGGAAGAAGATTGGATGGGAGAGA	lincrna,cancer,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	50	3	23	12	68624873	+	12	57872088	-	2.4206	34.4644	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5135-01A	ENSG00000127314	ENSG00000245651	RAP1B	AC083805.1	GAGCGCGGGGCGACGCTGGCTGCAGGGACCCGGTGACAGCGTGAGAG*GTTTGTCTGCCAGTGGAGTCCATGTTTCCACCACTGTCCTACATGGC	lincrna,cancer,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	50	2	17	12	68611043	+	12	57870381	-	2.4206	34.4644	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5135-01A	ENSG00000127314	ENSG00000245651	RAP1B	AC083805.1	GGGGAGCGCGGGGCGACGCTGGCTGCAGGGACCCGGTGACAGCGTGAGAG*ACAGAGTCTCACTCGGTCACCCAGGCCAGAGTGTAGTAGTGCGATCTCGG	lincrna,cancer	BOWTIE+BLAT;BOWTIE+STAR	UTR/intronic	0	50	1	21	12	68611043	+	12	57871419	-	2.4206	34.4644	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-26-5135-01A	ENSG00000127314	ENSG00000175215	RAP1B	CTDSP2	ACCTTGTGATCTGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTGCAGGCG*GAGGACAGATAACTGATTTCCGTTCTTTTGACTGTGTTTTAAAATTCTCT	known,tcga,18cancers,chimerdb3seq,cancer,tcga-cancer	BOWTIE+STAR	intronic/UTR	0	10	1	15	12	68618368	+	12	57822860	-	2.4206	246.0813	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-26-5135-01A	ENSG00000134152	ENSG00000064419	KATNBL1	TNPO3	GTCAGCGCCGAGGCTGGGCTGAGGCGCCGCGGTACCATGAGGCGCCG*GGACAGCACTTGTCCTAGCCCGATTACCTTTGGATAAGATTACCGAA	18cancers,exon-exon	BOWTIE;BOWTIE+STAR	UTR/CDS(truncated)	0	4	4	23	15	34209951	-	7	128984259	-	1.9125	11.6049	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5135-01A	ENSG00000128052	ENSG00000251301	KDR	LINC02384	TCCCATTTCAAAGGAGAAGCAGAGCCATGTGGTCTCTCTGGTTGTGTATG*ACATGTGCCTTGGGAGCTTTGAGCTGACATGTTAGAAGTCAGTCTACATT	lincrna,cancer	BOWTIE+BLAT;BOWTIE+BOWTIE2	CDS(truncated)/intronic	0	3	4	31	4	55110403	-	12	68380747	-	13.1309	1.6439	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-26-5135-01A	ENSG00000128052	ENSG00000251301	KDR	LINC02384	GAGGAAGTATGTGACCCCAAATTCCATTATGACAACACAGCAGGAATCAG*CTTCTGAGTCGTGCTTCAGTTTTGACCAAAAATGGAACATTCTTATTGAT	lincrna,cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	3	1	14	4	55087607	-	12	68360628	-	13.1309	1.6439	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5135-01A	ENSG00000134853	ENSG00000127328	PDGFRA	RAB3IP	TACTCCATGTGTGGGACATTCATTGCGGAATAACATCGGAGGAGAAG*AAAATGTGCTCTCACTGGCCAGAGTAAGTCCTGTAAACACAGAATTA	known,oncogene,cancer,tumor,exon-exon	BOWTIE	UTR/CDS(truncated)	0	2	1	13	4	54229415	+	12	69812778	+	576.4191	5.5723	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5135-01A	ENSG00000127328	ENSG00000134853	RAB3IP	PDGFRA	CCTTTCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGAGAGA*GTGTGTGTGTGTTTTCAGCAAATTCCAGATTTGTTTCCTTTTGGCCTCCT	known,oncogene,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	2	1	18	12	69747337	+	4	54297660	+	5.5723	576.4191	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5135-01A	ENSG00000127328	ENSG00000134853	RAB3IP	PDGFRA	TTTTTTACATACATTCGATACATTCAGCAGGGACTCGTGAAACAGCAGGA*TGGACTTCCTGAAGAGTGACCATCCTGCTGTGGCACGCATGCGTGTGGAC	known,oncogene,cancer,tumor	BOWTIE+STAR	out-of-frame	0	2	1	15	12	69813031	+	4	54290332	+	5.5723	576.4191	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5135-01A	ENSG00000127328	ENSG00000134853	RAB3IP	PDGFRA	TTGTGCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGTGCTGCA*GGCACGAGATGTCAGAGGAACCTGAGTCATGCTCAGGCCCAAGCCCTGTT	known,oncogene,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	2	1	15	12	69773506	+	4	54281598	+	5.5723	576.4191	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5135-01A	ENSG00000127328	ENSG00000134853	RAB3IP	PDGFRA	GCACAACATGCAGGTTTGTTACATATGTATACATGGGCCATGTTGGTGTG*GTGCATGAAAAACCATTTTTGAACCTTAAAAGGTACTGGTACTATAGCAT	known,oncogene,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	2	1	15	12	69803587	+	4	54295763	+	5.5723	576.4191	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-26-5135-01A	ENSG00000127328	ENSG00000134853	RAB3IP	PDGFRA	TTGTTTTTTTCTTTTCCTTTCTTTTCCTCCCTATTGGGGTGTGACTGTAG*TTGAAATGAACTTTGTCAGTGTTGCCTCTTGCAATGCCTCAGTAGCATCT	known,oncogene,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	2	1	14	12	69767209	+	4	54295442	+	5.5723	576.4191	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0211-01A	ENSG00000146648	ENSG00000132434	EGFR	LANCL2	GCTGGCTGCGCTCTGCCCGGCGAGTCGGGCTCTGGAGGAAAAGAAAG*ATCATTCATAATTTCATAAGACGGATCCAGACCAAAATTAAAGATCT	known,oncogene,18cancers,cancer,tumor,100K<gap<200K,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	out-of-frame	0	676	35	30	7	55019365	+	7	55391793	+	131.7207	126.9668	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0211-01A	ENSG00000146648	ENSG00000132434	EGFR	LANCL2	GCTGGCTGCGCTCTGCCCGGCGAGTCGGGCTCTGGAGGAAAAGAAAG*GCATAGCCCTTTTGTACCTGCAGTTGTACCGGGTCACATGTGACCAA	known,oncogene,18cancers,cancer,tumor,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	676	2	28	7	55019365	+	7	55398423	+	131.7207	126.9668	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0211-01A	ENSG00000146648	ENSG00000132434	EGFR	LANCL2	GACTTTCTCAGCAACATGTCGATGGACTTCCAGAACCACCTGGGCAGCTG*GCAAAAGTGGACCAAGAAACCTTGACAGAAATGGTGAAACCCAGTATTGA	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	intronic/CDS(truncated)	0	676	1	16	7	55146741	+	7	55411913	+	131.7207	126.9668	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0211-01A	ENSG00000146648	ENSG00000132434	EGFR	LANCL2	GCTGCTGGCTGCGCTCTGCCCGGCGAGTCGGGCTCTGGAGGAAAAGAAAG*ATAATTCATAATTAATATCCTCAGGGAAATAAGAGAAGCTGTTGCATCCA	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/intronic	0	676	1	14	7	55019365	+	7	55408074	+	131.7207	126.9668	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0211-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	TATCTGTATGCCTTACTGTACCTGAACACAGAGATAGGTCCAGGCACCGT*AAGGCATACACTTAACCTCTTTAGGGTGTGAAACAGCTTTTACAAAAAGA	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/intronic	0	676	1	17	7	55400082	+	7	55030686	+	126.9668	131.7207	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0211-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	GCTCCAGAGATCGGTTGTCTGCCAAGAATCAGACCTTCCTGATGAGCTGC*CCTTCCATAAAACAGCTAAACTAGACGATCGTCAGACTCCTTCCAGCTGA	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/intronic	0	676	1	16	7	55400015	+	7	55029786	+	126.9668	131.7207	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0211-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	GCCTGGAAAACTCAACTTAAACGTACTTTAATCAGCAGGCAGAAGGGGAG*GGATGCATCCTATTGCACTCCAGCTGATGACACCAAAGCTTAGGTGTTTG	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	intronic/UTR	0	676	1	16	7	55379318	+	7	55208671	+	126.9668	131.7207	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0211-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	GATGAGCTGCTTTATGGACGGGCAGGTTATCTGTATGCCTTACTGTACCT*CTCTCTGTGATCAGGTGCTGCCCTCCCTGGCAGGAGGACTGCAGACAGGA	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/intronic	0	676	1	15	7	55400055	+	7	55120151	+	126.9668	131.7207	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0211-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	GGCTCCCATACAAGACAGGGGAGCAGAATCCCCAGGAAGTTGACAGGTGC*TGCCCTGGGACTTTCCAGCCTTCAGAACCACGAGCCAGACAAATTTCTTT	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	intronic/intronic	0	676	1	15	7	55409647	+	7	55051546	+	126.9668	131.7207	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0211-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	GACCAAGAAACCTTGACAGAAATGGTGAAACCCAGTATTGATTATGTGCG*AAATAGGAAGAGCCAGAGGGTTTCTTTGGTGTTATGGTTGTACAGCTTCC	known,oncogene,18cancers,cancer,tumor,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/intronic	0	676	1	14	7	55411971	+	7	55178204	+	126.9668	131.7207	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0211-01A	ENSG00000132434	ENSG00000154997	LANCL2	SEPT14	GCCACGGCGCCCCGGGGGTCATCCACATGCTCATGCAGGCGTACAAG*GGGCTGTTACCCTTTGCTGTGGTAGGGAGTACAGATGAAGTGAAAGT	known,tcga,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	271	35	30	7	55412089	+	7	55819223	-	126.9668	9.9918	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-1831-01A	ENSG00000150893	ENSG00000120662	FREM2	MTRF1	CAGAACTCCTTGCTGACTGTGGTGGCACCATTGGAACAGATGGACAG*GTGGATGTGAAATTGGACCCCAAGGATTTGCGAATAGATACATTTCG	known,18cancers,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	5	9	28	13	38864606	+	13	41234007	-	0.8554	4.6589	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-27-1831-01A	ENSG00000146648	ENSG00000234707	EGFR	AC074351.1	GCTGGCTGCGCTCTGCCCGGCGAGTCGGGCTCTGGAGGAAAAGAAAG*GTCAGTCAGGATCTTTGATTTTGGAGCACAAGCCTTCTGCGTGCTAC	antisense,oncogene,cancer,tumor,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	4	5	28	7	55019365	+	7	54783108	+	160.914	6.0622	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-1831-01A	ENSG00000146648	ENSG00000234707	EGFR	AC074351.1	GAATTCTCCAAAATGGCCCGAGACCCCCAGCGCTACCTTGTCATTCAGGT*TGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGAGGGCGGATC	antisense,oncogene,cancer,tumor	BOWTIE+BLAT;BOWTIE+STAR	UTR/intronic	0	4	4	31	7	55200415	+	7	54794746	+	160.914	6.0622	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-27-1831-01A	ENSG00000146648	ENSG00000234707	EGFR	AC074351.1	ATTGGCTCCCAGTACCTGCTCAACTGGTGTGTGCAGATCGCAAAGGTAAT*TAACTTAGAATCAATGAAAAAAGTGTACAACAAAAATTGTTGCTAGAAAA	antisense,oncogene,cancer,tumor	BOWTIE+STAR	intronic/intronic	0	4	1	15	7	55181483	+	7	54771219	+	160.914	6.0622	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-1831-01A	ENSG00000115977	ENSG00000198898	AAK1	CAPZA2	TACTATTTACAAAACAATTATGAACATACATAGAAATTTTGTAATTTACA*ACCAGTGAGCATATATATTTTAAAATACTTTCTTTGGATATTGTAATTCT	NA	BOWTIE+STAR	intronic/UTR	0	2	1	15	2	69559485	-	7	116918755	+	0.5418	106.5749	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-27-1831-01A	ENSG00000115977	ENSG00000198898	AAK1	CAPZA2	AGAGGTGTTATTTTAACAATTGTAAACTCATTTTGTCAAGCAGAAGACTG*CCTTTCAAGAAGGTTATTTAGCTAGCTTAGTGTTGAACTAAATTTTTTTT	NA	BOWTIE+STAR	intronic/UTR	0	2	1	14	2	69570288	-	7	116918402	+	0.5418	106.5749	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-5960-01A	ENSG00000112297	ENSG00000112320	CRYBG1	SOBP	ACGCCGAGCTCCCTGAGAGCGCTGCCAGGGACGACGCGGTGTTCGACGAC*TTGGAGCAGAGGTCATTATTTATGAAGCCTCTTCACCTCCATCTTCGCAT	known,tcga,chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	10	1	14	6	106512467	+	6	107575972	+	15.2684	5.1844	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-5960-01A	ENSG00000112320	ENSG00000112297	SOBP	CRYBG1	TGCTAAGGAAACTCCAAGGCTTGCCTTCAAGAATAACTGCGAACTACTTG*GCCCGGGCGGCAGAGAGGACCGCGTCCCGGCAGTCGGAGCGGGAGGAGGA	known,tcga,chimerdb3seq,tcga-cancer	BOWTIE+BOWTIE2	intronic/UTR	0	10	1	37	6	107587176	+	6	106360852	+	5.1844	15.2684	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-19-5960-01A	ENSG00000184613	ENSG00000135506	NELL2	OS9	TCAGGTCCCGGGGCTGCATAATGGGACGAAAGCCTTTCTCTTTCAAG*TTCCTCTGTGACGAGGGTGCAGGTATCTCTGGGGACTACATCGATCG	known,18cancers,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	5	12	29	12	44875225	-	12	57715760	+	19.4711	621.4274	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-19-5960-01A	ENSG00000184613	ENSG00000135506	NELL2	OS9	GGTATTTAGCCTTTCACGTTAACAGTCACTTGTCCCCTAATGATAGGCAA*GCCCCTGCTGGCAGCCACCTTGAGACCTCACCGGGCCTGTGATATTTGCT	known,18cancers	BOWTIE+STAR	intronic/UTR	0	5	2	21	12	44889576	-	12	57721079	+	19.4711	621.4274	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-19-5960-01A	ENSG00000184613	ENSG00000135506	NELL2	OS9	CTTGGCTGCTGATCTCAGGTAAGGCTCTCGGCGGAGGAGGAGGCAGTCGC*TGGGAGAATTTGAGAAGGAACTGGAAGGGATCCTGCTTCCGTCAGACCGA	known,18cancers	BOWTIE+STAR	intronic/CDS(truncated)	0	5	1	18	12	44875475	-	12	57718309	+	19.4711	621.4274	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-19-5960-01A	ENSG00000112584	ENSG00000146426	FAM120B	TIAM2	ACTGAGGCACCCGGACCTCGTCAGGCCGCTGCAGATGACCATTCCAG*CTTCATCCAGGTCTTTAAAAGTCCTGAAGAATTCCTCCAGCAACGAG	exon-exon	BOWTIE	in-frame	0	2	2	26	6	170330550	+	6	155256484	+	125.8129	21.8091	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-5960-01A	ENSG00000112584	ENSG00000146426	FAM120B	TIAM2	CGTCTTTCCGATGAATCCAGCCAATGCCATCCAGTACACACGCGCAGGAC*TTCAGACTGCGTCTTGCTGGCCTCTACAGCTTTATGATTCTGGGAAAAGT	NA	BOWTIE+STAR	UTR/intronic	0	2	1	15	6	170290822	+	6	155024138	+	125.8129	21.8091	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-5960-01A	ENSG00000112584	ENSG00000146426	FAM120B	TIAM2	CACTGATTACCTAATCTATGACACTTGTCCCTACTTTTCAATTAGCGAGC*CCCTGGCCTTCTGCACGCCTCCCCTCGTTGTTACTCTTCCCATAGCCCTC	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	14	6	170317976	+	6	155229099	+	125.8129	21.8091	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-5960-01A	ENSG00000112584	ENSG00000146426	FAM120B	TIAM2	CGTTTATTGCGCAGGCCTTGTGCCTCCAAGGAAAATCCACCTCGCAGCTT*TGTGGTGACTCTTGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGC	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	14	6	170358306	+	6	155053903	+	125.8129	21.8091	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-5960-01A	ENSG00000184613	ENSG00000037897	NELL2	METTL1	CCTGGAGGCTTTGTTTTTTTTGTTTTTTTTTCATTCTTTTTTCTCTAATC*CCTGGTCACTGACTGCTTACTCTACCTTAGCTGGACCTCGTCTCCCAGGG	NA	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	17	12	44899049	-	12	57769007	-	19.4711	114.4546	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-5960-01A	ENSG00000084733	ENSG00000116754	RAB10	SRSF11	TGCACTCCAGCCTGGGGGACAAGAGCGAGGAAAAAAAAAGAGAAAAAAAA*GAAAGAAGACAAAGAAAAGAAACGTTCTAAAACACCACCAAAAAGTTACA	NA	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	17	2	26076955	+	1	70246827	+	53.5966	28.395	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-5960-01A	ENSG00000103091	ENSG00000144791	WDR59	LIMD1	GCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCAC*TTAAGGTCAGGAGTTAGAGACCAGCCTGACCAACATGGTGAAACACTGTC	cancer,tumor	BOWTIE+STAR	intronic/UTR	0	2	1	34	16	74946050	-	3	45680793	+	7.4761	3.1833	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0210-02A	ENSG00000131165	ENSG00000158545	CHMP1A	ZC3H18	TCCCGCGTAGACGCAGTGGCCTCCAAGGTGCAGACAGCTGTGACTATGAA*TCTGTGCCTGTCCCAGAGTCCCGCACAGGTTGGTGCTTACCCACATTTGG	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	23	1	16	16	89649355	-	16	88615429	+	14.5801	3.5509	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0210-02A	ENSG00000158545	ENSG00000131165	ZC3H18	CHMP1A	CTCCGACTCCAGGGGAGCCGTGGCCTCCTCTCCGCCCTAGCGCTGAG*GTGACCAAGAATATGGCCCAGGTGACCAAAGCCCTGGACAAGGCCCT	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	23	25	30	16	88570566	+	16	89647331	-	3.5509	14.5801	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0210-02A	ENSG00000158545	ENSG00000131165	ZC3H18	CHMP1A	CATACGTTATTTTAACAGCCTCACAGACTGAACAGTCAAGTGACCGCTGA*CTCCACGTCGGCGGCCTTTTCTCCACCGACCCCGCGCTGGGTCTCCACGT	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/intronic	0	23	3	23	16	88575454	+	16	89648279	-	3.5509	14.5801	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0210-02A	ENSG00000158545	ENSG00000131165	ZC3H18	CHMP1A	CATACGTTATTTTAACAGCCTCACAGACTGAACAGTCAAGTGACCGCTGA*CTCCACGTCGGCGGCCTTTTCTCCACCGACCCCGCGCTGGGTCTCCACGT	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/intronic	0	23	3	23	16	88575454	+	16	89648321	-	3.5509	14.5801	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0210-02A	ENSG00000158545	ENSG00000131165	ZC3H18	CHMP1A	CATACGTTATTTTAACAGCCTCACAGACTGAACAGTCAAGTGACCGCTGA*CTCCACGTCGGCGGCCTTTTCTCCACCGACCCCGCGCTGGGTCTCCACGT	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/intronic	0	23	3	23	16	88575454	+	16	89648195	-	3.5509	14.5801	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0210-02A	ENSG00000158545	ENSG00000131165	ZC3H18	CHMP1A	CATACGTTATTTTAACAGCCTCACAGACTGAACAGTCAAGTGACCGCTGA*CTCCACGTCGGCGGCCTTTTCTCCACCGACCCCGCGCTGGGTCTCCACGT	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/intronic	0	23	3	23	16	88575454	+	16	89648363	-	3.5509	14.5801	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0210-02A	ENSG00000158545	ENSG00000131165	ZC3H18	CHMP1A	CATACGTTATTTTAACAGCCTCACAGACTGAACAGTCAAGTGACCGCTGA*CTCCACGTCGGCGGCCTTTTCTCCACCGACCCCGCGCTGGGTCTCCACGT	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/intronic	0	23	3	23	16	88575454	+	16	89648237	-	3.5509	14.5801	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0210-02A	ENSG00000158545	ENSG00000131165	ZC3H18	CHMP1A	ATACGTTATTTTAACAGCCTCACAGACTGAACAGTCAAGTGACCGCTGAC*TCCACGTCGGCGGCCTTTTCTCCACGGACCCCGCGCTGGGTCTCCACGTC	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BOWTIE2	intronic/intronic	0	23	2	24	16	88575455	+	16	89647900	-	3.5509	14.5801	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-06-0210-02A	ENSG00000106603	ENSG00000002746	COA1	HECW1	AAGAACTCGTCATGCTCTTTGTAGCGTGGTGCTTCTGTTGCTCACAG*GTTCAGGTTTAGCGGTCGCATCCTGGGTCTGGCTCTGATCCATCAGT	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE;BOWTIE+STAR	UTR/CDS(truncated)	0	6	13	28	7	43729429	-	7	43541163	+	3.0485	0.8468	FALSE	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0210-02A	ENSG00000002746	ENSG00000106603	HECW1	COA1	CTCACCGACAGCACCTCCAGAGGCTCCGAAGTTACAGCGCTGGAGAG*TTGCACCTGGACTTGATATGAAAGTAACCATCAGAAAATCAACAGAG	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	6	3	20	7	43479744	+	7	43609641	-	0.8468	3.0485	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0210-02A	ENSG00000002746	ENSG00000106603	HECW1	COA1	CTCACCGACAGCACCTCCAGAGGCTCCGAAGTTACAGCGCTGGAGAG*AAACACAACTGGTTTTGAGAATCCATCCCTTCTTCACTCAGTCCACG	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	6	2	19	7	43479744	+	7	43609495	-	0.8468	3.0485	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-06-0210-02A	ENSG00000002746	ENSG00000106603	HECW1	COA1	TTATTTACCACTTTTTCAGAAGGAGTCCTGTGTATACTCTGAGAAACATA*ATCTCTACCATATGGCCACTGGGGTGGTGGCCCATCTCAGTGACAGACAC	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/UTR	0	6	1	14	7	43480945	+	7	43639536	-	0.8468	3.0485	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-19-2629-01A	ENSG00000151694	ENSG00000187736	ADAM17	NHEJ1	TGAACGATTTTGGGATTTCATTGACCAGCTGAGCATCAATACTTTTG*ATGGAAGAACTGGAGCAAGGCCTGTTGATGCAGCCATGGGCGTGGCT	18cancers,exon-exon	BOWTIE	out-of-frame	0	26	23	30	2	9493747	-	2	219158362	-	7.0897	0.3882	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2629-01A	ENSG00000151694	ENSG00000280537	ADAM17	AC068946.1	AATTGAACGATTTTGGGATTTCATTGACCAGCTGAGCATCAATACTTTTG*ATGGAAGAACTGGAGCAAGGCCTGTTGATGCAGCCATGGGCGTGGCTACA	exon-exon	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/UTR	0	25	5	36	2	9493747	-	2	219158362	-	7.0897	0.0041	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2629-01A	ENSG00000151694	ENSG00000280537	ADAM17	AC068946.1	GAGTGTTTTCAAGAACGCAGCAATAAAGTTTGTGGGAACTCGAGGGTGGA*CAGCTCACTGAAGCCTTGACCTCCTTGGCTCAAGTGATCCTTCCACCTCA	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	25	1	14	2	9505259	-	2	219148508	-	7.0897	0.0041	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-19-2629-01A	ENSG00000232973	ENSG00000255248	CYP1B1-AS1	MIR100HG	AAAGAAATGTCTTTTCGTGATGGCTTTTTTTATTTTTATTTTTATTTATT*TTTTATTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAAC	antisense,oncogene	BOWTIE+STAR	intronic/intergenic	0	5	1	24	2	38078411	+	11	121861351	-	0.0217	1.0979	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-19-2629-01A	ENSG00000166979	ENSG00000159200	EVA1C	RCAN1	TGTCCTGGTCTGCTCCAAAGAGATCTCAGCGCTCACCGACTTCTCTG*GCCAAATTTGAGTCCCTCTTTAGGACGTATGACAAGGACATCACCTT	m2,exon-exon	BOWTIE	out-of-frame	0	3	2	21	21	32413013	+	21	34523710	-	2.8021	23.4854	FALSE	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-32-1970-01A	ENSG00000106049	ENSG00000175600	HIBADH	SUGCT	AGTTGAGAAAATGGGAGCAGTTTTCATGGATGCCCCTGTTTCTGGTG*GTATTACACAATGGCCTCGTTATGGAGATGGAGCATCCAACTGTGGG	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	53	19	30	7	27629371	-	7	40749434	+	28.6577	3.3733	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-32-1970-01A	ENSG00000106049	ENSG00000175600	HIBADH	SUGCT	AGTTGAGAAAATGGGAGCAGTTTTCATGGATGCCCCTGTTTCTGGTG*AACGCTGTCTCTGGCTTCCAAAGCCTGCTGCATTCCTTGGCCCATGG	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	53	6	29	7	27629371	-	7	40684056	+	28.6577	3.3733	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-32-1970-01A	ENSG00000175600	ENSG00000106049	SUGCT	HIBADH	CACTGCAACCTCCGCTTCTCAGGTTCAAGTGATTCTCCTGCCTCTGCCTC*TGTTTTTATATTTTTTTCTTTCTTGTTCATTCTTACTACGTATTTTTTGA	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/UTR	0	53	1	14	7	40294669	+	7	27525613	-	3.3733	28.6577	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-32-1970-01A	ENSG00000175600	ENSG00000106049	SUGCT	HIBADH	CAGGCTGGTCTCAAATTCCTGGGCTCAAGTGATCCGCCTGCCTCTGCCTC*TGTTTTTATATTTTTTTCTTTCTTGTTCATTCTTACTACGTATTTTTTGA	known,tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/UTR	0	53	1	14	7	40136255	+	7	27525613	-	3.3733	28.6577	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-32-1970-01A	ENSG00000198131	ENSG00000196961	ZNF544	AP2A1	GGAGCAAGAAGAGGACCTGTGCAGGGCAGAGCAGGAGGCCCCCCGAG*GTAAGAGCAAAGAGGCGGAAATTAAGAGAATCAACAAGGAACTGGCC	known,tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	29	26	28	19	58246794	+	19	49781757	+	6.7232	15.788	FALSE	TRUE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-32-1970-01A	ENSG00000198131	ENSG00000196961	ZNF544	AP2A1	CCCAGGTTCAAGTGATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGATTA*CAGGTAAGAGCAAAGAGGCGGAAATTAAGAGAATCAACAAGGAACTGGCC	known,tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	UTR/intronic	0	29	1	21	19	58247401	+	19	49781754	+	6.7232	15.788	FALSE	TRUE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-32-1970-01A	ENSG00000283515	ENSG00000196961	AC020915.6	AP2A1	GCTGGAGCAAGAAGAGGACCTGTGCAGGGCAGAGCAGGAGGCCCCCCGAG*GTAAGAGCAAAGAGGCGGAAATTAAGAGAATCAACAAGGAACTGGCCAAC	exon-exon	BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	20	3	26	19	58246794	+	19	49781757	+	0.0056	15.788	FALSE	TRUE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-32-1970-01A	ENSG00000167554	ENSG00000006451	ZNF610	RALA	ATCGCTCGGCGACGGGTCCTGTCCCCGCTCGTTCTGCCTTGGGCCAG*GTATTTTTTGATTTAATGAGAGAAATTCGAGCGAGAAAGATGGAAGA	known,tcga,18cancers,chimerdb3seq,cancer,m12,tcga-cancer,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	20	21	30	19	52336506	+	7	39706123	+	1.1572	28.3138	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-32-1970-01A	ENSG00000153814	ENSG00000169169	JAZF1	CPT1C	CCCCACCCTGGCCGACCTCATCGAGCACATCGAGGACAACCACATCG*TTCACTCTGGCTACAGAATGCTTTCAGCTGGGCTACTCAACAGACGG	known,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	11	16	29	7	28180463	-	19	49708723	+	8.2978	11.0702	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-32-1970-01A	ENSG00000153814	ENSG00000169169	JAZF1	CPT1C	AGCAGTATGGATGGTTGATGACATATTTTGATGCCGGTTGTCTGGTTGAG*CTGGTTTGACAAATCCTTCACCCTAATCGTCTTCTCTAACGGGAAGCTGG	known,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	intronic/CDS(truncated)	0	11	6	34	7	28170643	-	19	49707518	+	8.2978	11.0702	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-32-1970-01A	ENSG00000153814	ENSG00000169169	JAZF1	CPT1C	CCCCACCCTGGCCGACCTCATCGAGCACATCGAGGACAACCACATCG*GCTGATGACCATGGTTATGGTGTTTCTTATATCTTCATGGGGGATGG	known,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	11	4	26	7	28180463	-	19	49712972	+	8.2978	11.0702	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-32-1970-01A	ENSG00000153814	ENSG00000169169	JAZF1	CPT1C	AGCAGTATGGATGGTTGATGACATATTTTGATGCCGGTTGTCTGGTTGAG*TTCACTCTGGCTACAGAATGCTTTCAGCTGGGCTACTCAACAGACGGCCA	known,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	intronic/CDS(truncated)	0	11	2	25	7	28170643	-	19	49708723	+	8.2978	11.0702	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-32-1970-01A	ENSG00000153814	ENSG00000169169	JAZF1	CPT1C	GAGGTAGAAATGTTTCTGAATGTGTCAAGGCTTCTGAAGAAAACACTTAG*CTGGTTTGACAAATCCTTCACCCTAATCGTCTTCTCTAACGGGAAGCTGG	known,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	intronic/CDS(truncated)	0	11	1	35	7	28170596	-	19	49707518	+	8.2978	11.0702	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-32-1970-01A	ENSG00000153814	ENSG00000169169	JAZF1	CPT1C	GAGGTAGAAATGTTTCTGAATGTGTCAAGGCTTCTGAAGAAAACACTTAG*GACCCACAGTGCCTCGCCCTGTTCCGCGTGGCAGTGGACAAGCACCAGGC	known,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	11	1	30	7	28170596	-	19	49711809	+	8.2978	11.0702	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-32-1970-01A	ENSG00000077684	ENSG00000250503	JADE1	AC093831.1	GTCTGGACCTGTGGAATGGAGTGGTCATGGGGCCCTGCGGGGCAGACCAG*AAAGGTCATTTAAAACCACGTGAAACCATATGTTAAAGAAGAAACTGATG	lincrna	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	intronic/exonic(no-known-CDS)	0	10	14	36	4	128847552	+	4	130881347	-	3.6384	1.0739	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-32-1970-01A	ENSG00000077684	ENSG00000250503	JADE1	AC093831.1	GTCCAGGTGCCTGTGAGCCCGGGGACCATCCCTCAGCCTGTGGCCAG*AAAGGTCATTTAAAACCACGTGAAACCATATGTTAAAGAAGAAACTG	lincrna,exon-exon	BOWTIE;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	10	8	28	4	128846532	+	4	130881347	-	3.6384	1.0739	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-32-1970-01A	ENSG00000178982	ENSG00000079432	EIF3K	CIC	TTTATTTTATTTTTTTTTTGAGACGGAGCCTTGCTCTGTCACCCAGTCTG*GGGATGGTGGGATGGAGACAGTAGACTCAGCAAGTGGGAAATCTTAGGGT	18cancers,cancer	BOWTIE+BLAT	intronic/intronic	0	8	6	38	19	38625213	+	19	42271662	+	47.7261	12.3052	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-32-1970-01A	ENSG00000178982	ENSG00000079432	EIF3K	CIC	TCACCAACTTGCCGCACACAGACTTCACCCTGTGCAAGTGCATGATCGAC*CAGGTGGACAAAAATGAAGCCAATGAAGAAGGCATGCACTGGCCTTTCAG	18cancers,cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	8	6	33	19	38624188	+	19	42271771	+	47.7261	12.3052	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-32-1970-01A	ENSG00000178982	ENSG00000079432	EIF3K	CIC	CGCACACAGACTTCACCCTGTGCAAGTGCATGATCGACCAGGCACAT*GTGGACAAAAATGAAGCCAATGAAGAAGGCATGCACTGGCCTTTCAG	18cancers,cancer,exon-exon	BOWTIE;BOWTIE+STAR	CDS(truncated)/UTR	0	8	3	27	19	38624197	+	19	42271774	+	47.7261	12.3052	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-32-1970-01A	ENSG00000178982	ENSG00000079432	EIF3K	CIC	TGCTGTCTTTCAGGAATGGTAGAGGAAGCCTGACATAGGAATGATTTAAG*GTGGACAAAAATGAAGCCAATGAAGAAGGCATGCACTGGCCTTTCAGGTC	18cancers,cancer	BOWTIE+BLAT;BOWTIE+STAR	intronic/UTR	0	8	1	36	19	38625132	+	19	42271774	+	47.7261	12.3052	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-32-1970-01A	ENSG00000197128	ENSG00000104884	ZNF772	ERCC2	GTGCCCATGGAGACAGCATTTACACCAGCCTGGGGCCAGAAGCAAATTCC*GGGGCTGGGTAGCGAGGCCGGCTGGCTGCTGCTTCTGCCTCTGTCTCTCT	18cancers,cancer	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	UTR/intronic	0	6	7	37	19	57466745	-	19	45359378	-	4.3178	5.8012	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-32-1970-01A	ENSG00000197128	ENSG00000104884	ZNF772	ERCC2	CGGCACAGGTTCCCATGAACTCAGAAGTAATTGTGGACCCTATACAG*CTGCATGGACGCCTCGCTGGCCATCAAACCCGTATTTGAGCGTTTCC	18cancers,cancer,exon-exon	BOWTIE	out-of-frame	0	6	3	22	19	57476634	-	19	45357543	-	4.3178	5.8012	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-32-1970-01A	ENSG00000197128	ENSG00000104884	ZNF772	ERCC2	CTGATTTTAACATAATATCAAGAAGAAAGGCATTGAAGTGGGTAGGAAAG*GCTTCACCATCATCATCGAGCCCTTTGACGACAGAACCCCGACCATTGCC	18cancers,cancer	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	6	2	20	19	57466959	-	19	45357699	-	4.3178	5.8012	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-32-1970-01A	ENSG00000197128	ENSG00000104884	ZNF772	ERCC2	CGGCACAGGTTCCCATGAACTCAGAAGTAATTGTGGACCCTATACAG*GCTTCACCATCATCATCGAGCCCTTTGACGACAGAACCCCGACCATT	18cancers,cancer,exon-exon	BOWTIE	out-of-frame	0	6	2	19	19	57476634	-	19	45357699	-	4.3178	5.8012	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-32-1970-01A	ENSG00000153790	ENSG00000122642	C7ORF31	FKBP9	GCAGAGGTGTCCTCAGCAGGTTTCCCCGCTGCACACACACTCTTTCTTTC*ACGCACACGCACATCATGCTTTTCCAGCTCATCACACCCCGCCCCACTAT	NA	BOWTIE+STAR	intronic/UTR	0	4	1	14	7	25157409	-	7	33005897	+	2.4608	29.6041	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-32-1970-01A	ENSG00000141837	ENSG00000197780	CACNA1A	TAF13	AGATCATGCCATCACACTCCAGCTGGGGCGACAGAGCGAGACTCCGTCTC*AAAAAAAAAAAAGAAAGCAAGTTTCACATGAATAATGCTGTGTTGGAAGG	m3	BOWTIE+STAR	intronic/UTR	0	4	8	25	19	13622159	-	1	109063022	-	0.5282	31.9515	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-32-1970-01A	ENSG00000141837	ENSG00000197780	CACNA1A	TAF13	AGGCGGAGCTGCTGTACTCCAGCCTGGGCGACAGGGCGAGACTCCGTCTC*AAAAAAAAAAAAGAAAGCAAGTTTCACATGAATAATGCTGTGTTGGAAGG	m3	BOWTIE+STAR	intronic/UTR	0	4	3	29	19	13469489	-	1	109063022	-	0.5282	31.9515	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-32-1970-01A	ENSG00000141837	ENSG00000197780	CACNA1A	TAF13	TCCAGCCTGGGCAATAGAGCGAGACTCCATCTCAAAAAAAAAAAAGAAAA*CAAGTTTCACATGAATAATGCTGTGTTGGAAGGCTTTTTGATTTAAAATC	m3	BOWTIE+BOWTIE2	intronic/UTR	0	4	1	33	19	13569237	-	1	109063005	-	0.5282	31.9515	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-32-1970-01A	ENSG00000141837	ENSG00000197780	CACNA1A	TAF13	GCACTCCAGCCTGGGCAACAGAGAGAGACTCCGTCTCAAAAAAAAAAAAA*AAAGCAAGTTTCACATGAATAATGCTGTGTTGGAAGGCTTTTTGATTTAA	m3	BOWTIE+STAR	intronic/UTR	0	4	1	22	19	13489017	-	1	109063009	-	0.5282	31.9515	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-32-1970-01A	ENSG00000141837	ENSG00000197780	CACNA1A	TAF13	GCACTCCAGCCTGGGTGACAGAGTGAGACTCCGTCTCAAAAAAAAAAAAA*AAAGCAAGTTTCACATGAATAATGCTGTGTTGGAAGGCTTTTTGATTTAA	m3	BOWTIE+STAR	intronic/UTR	0	4	1	22	19	13563829	-	1	109063009	-	0.5282	31.9515	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-32-1970-01A	ENSG00000002746	ENSG00000254004	HECW1	ZNF260	TGAGTGATCTGTAATCCCAAAGTGCTGGGATTACAGGTGTGAGCCACCAC*GCCCGGCTAATTTTGTATTTTTAGTAGAGACGGAGTTGCACCATGTTGGC	18cancers	BOWTIE+STAR	intronic/UTR	0	4	1	23	7	43120943	+	19	36511511	-	2.1485	9.5769	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-32-1970-01A	ENSG00000002746	ENSG00000254004	HECW1	ZNF260	CCTTCACCTCAGCCTCTCAAAGTGCTGGGATTACAGGTGTGAGCCACCAC*GCCCGGCTAATTTTGTATTTTTAGTAGAGACGGAGTTGCACCATGTTGGC	18cancers	BOWTIE+STAR	intronic/UTR	0	4	1	23	7	43336459	+	19	36511511	-	2.1485	9.5769	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-32-1970-01A	ENSG00000002746	ENSG00000254004	HECW1	ZNF260	AGCTTCAGCAGCTGCGATTACAGGCGCCCGTCACCACGCCCAGCTAATTT*TTTTGTATTTTTAGTAGAGACGGAGTTGCACCATGTTGGCCAGGCTGGTC	18cancers	BOWTIE+BLAT	intronic/UTR	0	4	1	19	7	43305768	+	19	36511501	-	2.1485	9.5769	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-32-1970-01A	ENSG00000188185	ENSG00000011426	LINC00265	ANLN	TGCCTTTTTCCGCTGTAAATAATTAAGAAGACCAAGTAGCATCCAAG*AAAAGCAACATTCATTCTTCAGTCATGGCCAGTCCAGGAGGTCTTAG	lincrna,18cancers,cancer,exon-exon	BOWTIE;BOWTIE+STAR	exonic(no-known-CDS)/CDS(truncated)	0	4	6	29	7	39734044	+	7	36426015	+	2.253	7.098	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-32-1970-01A	ENSG00000254004	ENSG00000002746	ZNF260	HECW1	GCGCAGGCGCGGAATCTCCGACTTGCCATGGTCGTCTTTGTCTGCCG*ATTTTTAAAAGCATTGGTGCTGATGAGACCGTCCAAGGACAAGGAAG	18cancers,exon-exon	BOWTIE	UTR/CDS(truncated)	0	4	2	28	19	36528219	-	7	43396814	+	9.5769	2.1485	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-32-1970-01A	ENSG00000254004	ENSG00000002746	ZNF260	HECW1	AAAGAAATGTAAAGAAGGTTCTCTTTGTGTGAGTAAGCAAGAACCTG*ATTTTTAAAAGCATTGGTGCTGATGAGACCGTCCAAGGACAAGGAAG	18cancers,exon-exon	BOWTIE	UTR/CDS(truncated)	0	4	2	23	19	36525155	-	7	43396814	+	9.5769	2.1485	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-32-1970-01A	ENSG00000010361	ENSG00000167555	FUZ	ZNF528	CCTCCGAAACTTCTATACCCTGGTCACCTCCACGCACTTCCCACCAG*GTTCACAAATTTTAAGAAAGGGAGAATAAAGTGAAAAAAATCTCAGA	exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	3	3	20	19	49808414	-	19	52401685	+	7.8387	3.6842	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-32-1970-01A	ENSG00000105778	ENSG00000198131	AVL9	ZNF544	TACTGCACATCGTGGTGGTCGGATTTCACCACAAGAAGGGCTGCCAG*ACTGGAAAGCTACCCTTGAGGAGAATAGGTTGAATTCTGAAAAAGAT	exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	2	4	24	7	32495802	+	19	58260851	+	3.4684	6.7232	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-32-1970-01A	ENSG00000132434	ENSG00000146648	LANCL2	EGFR	GAAGACAGCTGATCCCCATGACTGCTCTGCTTATACTGGCTGGACAG*TGAGCCAAGGGAGTTTGTGGAGAACTCTGAGTGCATACAGTGCCACC	known,oncogene,18cancers,cancer,tumor,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	1	1	13	7	55391910	+	7	55163733	+	182.4564	544.7303	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0157-01A	ENSG00000163531	ENSG00000143842	NFASC	SOX13	GCGGACAGCTCGGACAGCGCCCAGGGCCGGAGCCCGAGCCCTTGGAG*GATGTCCATGAGGAGCCCCATCTCTGCCCAGCTGGCCCTGGATGGCG	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	UTR/UTR	0	24	20	29	1	204828782	+	1	204112915	+	7.3685	82.3982	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-06-0157-01A	ENSG00000163531	ENSG00000143842	NFASC	SOX13	GCGGACAGCTCGGACAGCGCCCAGGGCCGGAGCCCGAGCCCTTGGAG*GACTGTAGCTCTCCAGAGGGTAATGGGTCCCCAGAACCCAAGAGACC	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	24	6	27	1	204828782	+	1	204114321	+	7.3685	82.3982	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000076067	ENSG00000189067	RBMS2	LITAF	CCAGGCCCGGGATTTCGACTTTTGGCTACAATAGAAACAACAAGAAG*GTAAAATGTCGGTTCCAGGACCTTACCAGGCGGCCACTGGGCCTTCC	18cancers,tumor,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	22	18	29	12	56522089	+	16	11556735	-	3.6006	53.6696	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000078237	ENSG00000011105	TIGAR	TSPAN9	CGCGGCTCCGGGAACATGGCTCGCTTCGCTCTGACTGTTGTCCGGCA*AATTTAAGAAGTGCAACATGGCCAGGGGCTGCCTCTGCTGCTTGAAG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	22	25	29	12	4321303	+	12	3201177	+	1.8049	58.6649	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000078237	ENSG00000011105	TIGAR	TSPAN9	CGCGGCTCCGGGAACATGGCTCGCTTCGCTCTGACTGTTGTCCGGCA*CTCTGTGGCTGTGGGCTGCTGGGAGTGGGCATCTGGCTCTCCGTGTC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	22	16	29	12	4321303	+	12	3278421	+	1.8049	58.6649	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000078237	ENSG00000011105	TIGAR	TSPAN9	GGACGCGGCTCCGGGAACATGGCTCGCTTCGCTCTGACTGTTGTCCGGCA*CTTCCCTTCGTTGTCTGCAGCCAACCTGGTCATTGCCATAGGCACCATTG	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	in-frame	0	22	1	28	12	4321303	+	12	3278498	+	1.8049	58.6649	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000185818	ENSG00000003249	NAT8L	DBNDD1	GCACACGGACATGGCGGACATCGAGCAGTACTACATGAAGCCGCCCG*AGATCGTTAAGGAGGCTGAGGTGCCGCAGGCTGCGCTGGGCGTCCCA	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE;BOWTIE+BOWTIE2;BOWTIE+STAR	in-frame	0	14	14	27	4	2061162	+	16	90009430	-	19.2323	11.1204	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000178498	ENSG00000143850	DTX3	PLEKHA6	GGGAGACCGAATGTCATCACCTGGAACGACATCCACCACAAGACCAGCTG*GGGTCTCCCTGGGCAGGTGAGGAGCAGCACTACATTAGAGCCTGCTGTTG	18cancers,cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	8	1	16	12	57608719	+	1	204284315	-	340.0065	100.7286	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000178498	ENSG00000143850	DTX3	PLEKHA6	CAAGAACAAAGTGACTGTGTCCAAGCCCGTGTGGGACTTCCTGAGCAAAG*TCCCACCTCCCCTGCTTCCCCGGCTCCTCCAGCAAACCCCCTGTCGTCTG	18cancers,cancer	BOWTIE+STAR	out-of-frame	0	8	1	14	12	57606957	+	1	204223563	-	340.0065	100.7286	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000178498	ENSG00000143850	DTX3	PLEKHA6	ACAGATGACTGAAGGACATCGCCTTTGCCAAGGCCCCTGCTGTCTGCCTC*GAGGTAGAGGCAGAGAAGCAGGCAGCTCTCAACAAAGGTACTTTCTGTCC	18cancers,cancer	BOWTIE+STAR	UTR/CDS(truncated)	0	8	1	14	12	57609190	+	1	204241721	-	340.0065	100.7286	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000143850	ENSG00000178498	PLEKHA6	DTX3	CAGTGGTAAGAAGGAATGCCAGTGGGCTCACCAATGGACTCTCCTCCCAG*GCCCGGACCGTCATCCCAGCAACAGCCTCAGTCATGTGACCGGCAATGGC	18cancers,cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	8	15	37	1	204241375	-	12	57604795	+	100.7286	340.0065	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000143850	ENSG00000178498	PLEKHA6	DTX3	CAGTGGTAAGAAGGAATGCCAGTGGGCTCACCAATGGACTCTCCTCCCAG*CCTGCACCCCCTGCAATCCCCCACCTTTCGGGGTCTCCCCCTCCTTGTTG	18cancers,cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	8	1	17	1	204241375	-	12	57604740	+	100.7286	340.0065	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000143850	ENSG00000178498	PLEKHA6	DTX3	AGACGTGGGGGGCAGAGTTAACACAGCAGGTGTGGGCAGGGGCGGATTAG*GCAGAAGAGCAGGAGAGCACCTGCCCCATCTGTCTGGGGGAGATCCAGAA	18cancers,cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	8	1	17	1	204259940	-	12	57607332	+	100.7286	340.0065	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000143850	ENSG00000178498	PLEKHA6	DTX3	TTGTGGAGGGGGTGTGGACAAGAATTCCTTGGCTTGGAGGAGGAGGTGGA*AGCCCCACTTCTGCCCCCAGGAGCTCGGGGGCTCCCCCCTCCTCCTCCCC	18cancers,cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	8	1	16	1	204287315	-	12	57607244	+	100.7286	340.0065	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000143850	ENSG00000178498	PLEKHA6	DTX3	GCCCGCTCCCACCCACCCCAGGACACACCCACGAGCCCTGCCTGTGTGTC*AGCCCAATGCGACCAGACTCAGGGAAAACATCAGGCCCCTCCAGCTGAGC	18cancers,cancer	BOWTIE+STAR	intronic/UTR	0	8	1	16	1	204262946	-	12	57605604	+	100.7286	340.0065	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000143850	ENSG00000178498	PLEKHA6	DTX3	TCAGTCAGTGAGTTACTCAGGGATGGAGCTGGGCTTCCAAGTCACACAGG*TCCCCCACTGGCCAAGTGTTTCAATGCAGTGTGAGCCACTCCCTTCTGGC	18cancers,cancer	BOWTIE+STAR	intronic/UTR	0	8	1	15	1	204362856	-	12	57609312	+	100.7286	340.0065	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000143850	ENSG00000178498	PLEKHA6	DTX3	CCGCTCTGCAGAAGGGGGCCCCAGGGGCGGGGGAGGAGGACCCCAGCTGG*TTGGGTACCCAGACCCCACCTACCTGACCCGGGTGCAAGAGGAGCTGAGA	18cancers,cancer	BOWTIE+STAR	UTR/CDS(truncated)	0	8	1	15	1	204359771	-	12	57609079	+	100.7286	340.0065	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000143850	ENSG00000178498	PLEKHA6	DTX3	GGGTTTTGAGAGAGTAAACACTTGGTTGGGGGAATGTGGAGGAGCATGTG*GGGGAAGGGAGGGTCTCTTGATTCCTAACCGCCCCCACATACTGCTCCAC	18cancers,cancer	BOWTIE+STAR	intronic/UTR	0	8	1	15	1	204322718	-	12	57609495	+	100.7286	340.0065	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000143850	ENSG00000178498	PLEKHA6	DTX3	GGGTTTTGAGAGAGTAAACACTTGGTTGGGGGAATGTGGAGGAGCATGTG*GGGGAGGAGAAATTGGGCTGATGTGAGCTCCCCGTCACCCGCCATGGAGC	18cancers,cancer	BOWTIE+STAR	intronic/UTR	0	8	1	15	1	204322718	-	12	57609563	+	100.7286	340.0065	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000143850	ENSG00000178498	PLEKHA6	DTX3	GATCACATCAAATGTGAAAGCTCTTTAAAGTTCTCCATATGCTCCCGGTG*TCCCTTCCCCCATCCCCCACTGGCCAAGTGTTTCAATGCAGTGTGAGCCA	18cancers,cancer	BOWTIE+STAR	intronic/UTR	0	8	1	15	1	204353558	-	12	57609300	+	100.7286	340.0065	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000143850	ENSG00000178498	PLEKHA6	DTX3	GCCATTGTGGAGGTAAGAGATGAAGTGGATAAAGGTCTCTGAGGCAGGGA*GGCGAGACTTCTGACATCTATGTTCTCCAGCTTTCCCCACAGGGTCCTCC	18cancers,cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	8	1	14	1	204314717	-	12	57607017	+	100.7286	340.0065	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000143850	ENSG00000178498	PLEKHA6	DTX3	AGTGCACTAGAGGCAAACTGATTTCTGCTGATGACTCGGGAAGTGGCTGC*GGGGACGATGATGGAGGCATGAAGGGACAGCTGCTCCTTCTTGGATCAGT	18cancers,cancer	BOWTIE+STAR	intronic/UTR	0	8	1	14	1	204312749	-	12	57605478	+	100.7286	340.0065	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000143850	ENSG00000178498	PLEKHA6	DTX3	GGGGGCTTGGGCTGGGGTCTCTGTCCCCCTCCCCGGCCTCCCTCTGGGAT*CTCTCTGCCCCCTGCCCCCCACACCACACCTGTAGGGGACCTGTCTGACT	18cancers,cancer	BOWTIE+STAR	intronic/UTR	0	8	1	14	1	204361863	-	12	57609220	+	100.7286	340.0065	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000143850	ENSG00000178498	PLEKHA6	DTX3	CATGGAGATGTGAGGAGGTCTCAGACCCTGGCCCAGAGATGGGGCAGGGA*CCCCCCTGCCCCCACCTCTTCCTCCTCGCCTTCGGGAGGAGGCAGAAGAG	18cancers,cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	8	1	14	1	204282469	-	12	57607291	+	100.7286	340.0065	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000143850	ENSG00000178498	PLEKHA6	DTX3	CTTTTTCTTTCTGTGCTAGTTGTCAAGTTTTCCTGGGAGGGTGAAGGGTA*TCCCAGGTTTGGGTACCCAGACCCCACCTACCTGACCCGGGTGCAAGAGG	18cancers,cancer	BOWTIE+STAR	intronic/UTR	0	8	1	14	1	204294299	-	12	57609071	+	100.7286	340.0065	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000143850	ENSG00000178498	PLEKHA6	DTX3	ACTTCTTAGCTTCTCCCACATAGTGACTTTCAGTTTTTTCCCCACCCTAC*GCCCCTCCATTGCCCTTGGCTTTTTCTGGTATGTGCTGTGCTCCACGACC	18cancers,cancer	BOWTIE+STAR	intronic/UTR	0	8	1	14	1	204318083	-	12	57609423	+	100.7286	340.0065	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000143850	ENSG00000178498	PLEKHA6	DTX3	AGAGATCACCTTAAACTCTGACAGCCAGTGAGCCAGGCAGAACAGAGCCA*TGCAGTGTGAGCCACTCCCTTCTGGCAGAGGCCGACCTCCAAGGCTCTGT	18cancers,cancer	BOWTIE+STAR	intronic/UTR	0	8	1	14	1	204347329	-	12	57609336	+	100.7286	340.0065	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000143850	ENSG00000178498	PLEKHA6	DTX3	AGGAGCCAGAGGTCAGGGTCATTTGCTGGTTTTTCTCGGCTGTGTGTGTT*CCCCACATACTGCTCCACCGCTGAACTTCGGGTGCCGGGGAGGAGAAATT	18cancers,cancer	BOWTIE+STAR	intronic/UTR	0	8	1	14	1	204260995	-	12	57609527	+	100.7286	340.0065	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000143850	ENSG00000178498	PLEKHA6	DTX3	AATGCTTGTTGAATGAAAGATGCATTTGACATGGTCCTTGTCCTTTCCGT*TGTGTGTTCATCAGATACAGTTCTCCCTTAACCTTGTCCTTTCTCTCCTG	18cancers,cancer	BOWTIE+STAR	intronic/UTR	0	8	1	14	1	204321737	-	12	57609619	+	100.7286	340.0065	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000143850	ENSG00000178498	PLEKHA6	DTX3	TGACAAATGGAAGCCTTTTGACATCCCAAAAGGAAGGAGAGAAGAAGGAG*GCCTCTACTAGGACCCAGCAGAAGCCTCTTTCTCCTCTCTGCCCCCTGCC	18cancers,cancer	BOWTIE+STAR	intronic/UTR	0	8	1	14	1	204279487	-	12	57609186	+	100.7286	340.0065	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000143850	ENSG00000178498	PLEKHA6	DTX3	CTTCTCCACATGGGAGGCGGCAGCATTACTCAGGTGGATGGCATCAAGGT*GCTGAACACCCAAACCCAGGAGTTCGGTATCCTGGCACCACACGGGTGGC	18cancers,cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	8	1	14	1	204288339	-	12	57608520	+	100.7286	340.0065	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000143850	ENSG00000178498	PLEKHA6	DTX3	ACCCATCCCCTTGTTTCCCCCAAGGAGGACTTGGCCCCTCAGCCACCTAC*CCACCGCTGAACTTCGGGTGCCGGGGAGGAGAAATTGGGCTGATGTGAGC	18cancers,cancer	BOWTIE+STAR	CDS(truncated)/UTR	0	8	1	14	1	204244978	-	12	57609541	+	100.7286	340.0065	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Glioblastoma	TCGA-06-0157-01A	ENSG00000011105	ENSG00000118971	TSPAN9	CCND2	TAATTTTGTAGTTTTAGTAGAGACGGGGTTTCTCCATGTTGGTCAGGCTG*TTAGAAAGTGCTGATAAGTAGCATGATCAGTGTATGCGAAAAGGTTTTTA	cancer	BOWTIE+BLAT	intronic/UTR	0	4	1	22	12	3112390	+	12	4305103	+	58.6649	168.8951	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0157-01A	ENSG00000011105	ENSG00000118971	TSPAN9	CCND2	TAGTCATGTGCAGCCTTCACCTCCTGGGCTCAAGTGATCCTCCCTCCTCA*TCATGGAGGCCATCGGGCTCCCAGTTAGACCCTGGTATCCTCATCATGAT	cancer	BOWTIE+STAR	intronic/UTR	0	4	1	19	12	3138575	+	12	4302185	+	58.6649	168.8951	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0157-01A	ENSG00000011105	ENSG00000118971	TSPAN9	CCND2	TTTACCTGATTCCGCACCGCCCCTGCACCCGCCGTTTTTTTTTTTTTTTT*TTGTTGTTGTTAATTTTATTGCAAAGTTGTATTCAGCGTACTTGAATTTT	cancer	BOWTIE+STAR	intronic/UTR	0	4	1	17	12	3118272	+	12	4301368	+	58.6649	168.8951	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0157-01A	ENSG00000011105	ENSG00000118971	TSPAN9	CCND2	CCTAAAATGATGCTGCTTGAAGTTGGATGAGCAGGTGGTTTTTTTCTCCC*TTGTTGTTGTTCTTTCTCTTCTTTTTCTTACCTCCCACTAAAGGGGTTCC	cancer	BOWTIE+STAR	intronic/UTR	0	4	1	15	12	3133686	+	12	4303409	+	58.6649	168.8951	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0157-01A	ENSG00000011105	ENSG00000118971	TSPAN9	CCND2	AGAGAATCTTGCACGCACCTGCTCTTTCCCCCTGCCTTTTTTTCTTTTTC*TTTTTTTTTTGCTTTAAAACAAGTGTGATGCCATATCAAGTCCATGTTAT	cancer	BOWTIE+STAR	intronic/UTR	0	4	1	14	12	3102132	+	12	4305002	+	58.6649	168.8951	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0157-01A	ENSG00000011105	ENSG00000118971	TSPAN9	CCND2	GTTAGAGACATCTGGGGAGCTTTTCAATAATTCAGGCTCCTGGGCCCCCA*GGAAGTGGAGCAGCCAGCAAGTAAGCTAGCCAGAGTTTTCTCAAGAGCCA	cancer	BOWTIE+STAR	intronic/UTR	0	4	1	14	12	3149781	+	12	4302889	+	58.6649	168.8951	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0157-01A	ENSG00000131095	ENSG00000133056	GFAP	PIK3C2B	TCCCTCAGGACCGCAGCTCTTGCAGTGAATAAAGTTTTATGTTCCCTGCT*CTTAAAATTAAAAAAAAAAAAAAAAAGACTGGAAGACTGGTTATAGCTCA	NA	BOWTIE+STAR	UTR/intronic	0	2	1	19	17	44909684	-	1	204485067	-	3202.9814	121.9214	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0157-01A	ENSG00000134986	ENSG00000146648	NREP	EGFR	CTTCTTGCTCCCCCATTGGCCTGAGTTTCTTGTGCATTACTCCTCTCCCT*ATTCTAACTAAGAAGGATATTTGGCTACATGCTGGGAAGAGGGGTACTGA	oncogene,cancer,tumor	BOWTIE+STAR	UTR/intronic	0	2	1	15	5	111729515	-	7	55037877	+	2.6554	209.56	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0157-01A	ENSG00000134986	ENSG00000146648	NREP	EGFR	TCAGGCCTGGTTCGCTACAACAATGTCTTCCACAACTCAAACTCCCACCG*ATTGTGTGTGCGCGGATGTGCGTGTATGTGTGTGTATGTGTGCACGTGTG	oncogene,cancer,tumor	BOWTIE+STAR	UTR/intronic	0	2	1	15	5	111730622	-	7	55067799	+	2.6554	209.56	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0157-01A	ENSG00000143850	ENSG00000198625	PLEKHA6	MDM4	ATCTGCCAACACTGCCCACTCCCAGGGCATGGCCAGCTTGGGCCTGGGGG*GTGGAGGTTGCAGTGAGCTGAGATGGCACCACTGCAATCCAAGGTGGGTG	oncogene,cancer	BOWTIE+STAR	intronic/UTR	0	2	4	15	1	204230325	-	1	204556626	+	100.7286	228.316	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000143850	ENSG00000198625	PLEKHA6	MDM4	TCTCAACCTCCTAGGCTCAAGCGATCCTCCTACCTCAGCCTCCCAAGTGG*CTGGGACTACAGGCGTGCACCACCACACCTGGCTAATTTTTTTTATTTTT	oncogene,cancer	BOWTIE+BLAT	intronic/intronic	0	2	2	33	1	204356454	-	1	204546333	+	100.7286	228.316	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000143850	ENSG00000198625	PLEKHA6	MDM4	GGAGTGCAGTGGCACAATCTCGGCTCACTGCAACCTCTGCCTCCCGGGTT*CAGGAGAATCGCTTGAACCTGAGAGGGGGAGATTGCGGTGAGCTGAGATT	oncogene,cancer	BOWTIE+BLAT	intronic/UTR	0	2	2	33	1	204370974	-	1	204552178	+	100.7286	228.316	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0157-01A	ENSG00000143850	ENSG00000198625	PLEKHA6	MDM4	ATCTGCCAACACTGCCCACTCCCAGGGCATGGCCAGCTTGGGCCTGGGGG*GTGGAGGTTGCAGTGAGCCGAGACTGCACCACTGCGCTCCCACCTGGGTG	oncogene,cancer	BOWTIE+STAR	intronic/UTR	0	2	2	15	1	204230325	-	1	204555795	+	100.7286	228.316	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000143850	ENSG00000198625	PLEKHA6	MDM4	TAATCCCAGCACTTTGGGAGGCCAAGGTGGGCGGATCATGAGGTCAGGAG*TTTGAGACCAGCCTGACCGACATGGAGAAACCCCATTTTTACTAAAAATA	oncogene,cancer	BOWTIE+BLAT	intronic/UTR	0	2	1	35	1	204308914	-	1	204552067	+	100.7286	228.316	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000143850	ENSG00000198625	PLEKHA6	MDM4	GGTCTCGAACTCCTGACCTCAGGTGATCTGCCTGCCTTGGCCTCCCAAAG*AACTGGGACTACAGGCGTGCACCACCACACCTGGCTAATTTTTTTTATTT	oncogene,cancer	BOWTIE+BOWTIE2	intronic/intronic	0	2	1	35	1	204330949	-	1	204546331	+	100.7286	228.316	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000143850	ENSG00000198625	PLEKHA6	MDM4	TCTCAAACTCCTGGCCTCAAGTGATCTGCCCACCTTGGCCACTCCAGTAG*TAAGAAATTGAGGTCAGGCCAGGCGCGGTGGTTCACTCCTGTTATTCCAG	oncogene,cancer	BOWTIE+STAR	intronic/UTR	0	2	1	22	1	204329807	-	1	204556400	+	100.7286	228.316	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-06-0157-01A	ENSG00000143850	ENSG00000198625	PLEKHA6	MDM4	GGCATGCGCCGCCAACATGCATGGCTAATTTTTTTGTATTTTTAGTGGAG*ATGGGGGTTTCACTGTGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAT	oncogene,cancer	BOWTIE+BLAT	intronic/UTR	0	2	1	20	1	204331026	-	1	204552510	+	100.7286	228.316	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-06-0157-01A	ENSG00000143850	ENSG00000198625	PLEKHA6	MDM4	GGATACCTCAGTGTCCACACACCCACCATGCCCAGCCCTGGAGCCATCAC*ATAGCCACCATGCCCAGCTATTTTCTTTAAAGTCATAAATATGGGCATCT	oncogene,cancer	BOWTIE+STAR	UTR/intronic	0	2	1	16	1	204222560	-	1	204546496	+	100.7286	228.316	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-14-1034-02B	ENSG00000161960	ENSG00000173868	EIF4A1	PHOSPHO1	CCACCCAGGCCTTGGTCCTAGCACCCACTCGAGAATTGGCTCAGCAG*GTGTTGGATGTGCCAGCGCCTCTGGCCGTGGCCCGCTAACCAGCCTC	known,tcga,18cancers,chimerdb3seq,m124,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/CDS(no-known-start-or-end)	0	126	24	30	17	7575258	+	17	49225131	-	0.3984	27.0359	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-14-1034-02B	ENSG00000161960	ENSG00000173868	EIF4A1	PHOSPHO1	CCACCCAGGCCTTGGTCCTAGCACCCACTCGAGAATTGGCTCAGCAG*GACGGCAGGATGGCCGCGCAGGGCGCGCCGCGCTTCCTCCTGACCTT	known,tcga,18cancers,chimerdb3seq,m124,tcga-cancer,exon-exon	BOWTIE	in-frame	0	126	20	30	17	7575258	+	17	49225004	-	0.3984	27.0359	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-14-1034-02B	ENSG00000161960	ENSG00000173868	EIF4A1	PHOSPHO1	AAAGCTATTTCTTACCCAAACGTAACCATTGCTTCCTCCACCCATTTCCT*TGGGTCCTCCTCAGGTGTTGGATGTGCCAGCGCCTCTGGCCGTGGCCCGC	known,tcga,18cancers,chimerdb3seq,m124,tcga-cancer	BOWTIE+BOWTIE2	UTR/intronic	0	126	2	36	17	7575451	+	17	49225145	-	0.3984	27.0359	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-14-1034-02B	ENSG00000277957	ENSG00000173868	SENP3-EIF4A1	PHOSPHO1	AAGCCACCCAGGCCTTGGTCCTAGCACCCACTCGAGAATTGGCTCAGCAG*GACGGCAGGATGGCCGCGCAGGGCGCGCCGCGCTTCCTCCTGACCTTCGA	m120,exon-exon	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	122	7	21	17	7575258	+	17	49225004	-	0.0095	27.0359	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-14-1034-02B	ENSG00000277957	ENSG00000173868	SENP3-EIF4A1	PHOSPHO1	AAGCCACCCAGGCCTTGGTCCTAGCACCCACTCGAGAATTGGCTCAGCAG*GTGTTGGATGTGCCAGCGCCTCTGGCCGTGGCCCGCTAACCAGCCTCTCC	m120,exon-exon	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(no-known-start-or-end)	0	122	3	19	17	7575258	+	17	49225131	-	0.0095	27.0359	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-14-1034-02B	ENSG00000277957	ENSG00000173868	SENP3-EIF4A1	PHOSPHO1	TAAAAGCTATTTCTTACCCAAACGTAACCATTGCTTCCTCCACCCATTTC*CTTGGGTCCTCCTCAGGTGTTGGATGTGCCAGCGCCTCTGGCCGTGGCCC	m120	BOWTIE+BLAT;BOWTIE+STAR	intronic/intronic	0	122	1	20	17	7575449	+	17	49225147	-	0.0095	27.0359	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-14-1034-02B	ENSG00000277957	ENSG00000173868	SENP3-EIF4A1	PHOSPHO1	CCAGACCCCAAGCCCATAAATGGGAAGGGAGACATGGGAGTCCCTTCCCA*TTTGGGGGCTTGGGGAAGGGGGCTCAGAGCCGTCCCTATCTATTCAGTTA	m120	BOWTIE+STAR	intronic/UTR	0	122	1	14	17	7571543	+	17	49224110	-	0.0095	27.0359	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-14-1034-02B	ENSG00000105701	ENSG00000105143	FKBP8	SLC1A6	CCATCCCCATCCTGAGGGCAGCCCTGAAGCTGGAACCTTCCAACAAG*TGACCGGCTTCGCACAATGACCAACGTACTGGGGGACTCAATTGGAG	known,tcga,18cancers,chimerdb3seq,m43,tcga-cancer,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	57	33	30	19	18533270	-	19	14950390	-	109.6558	1.0179	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-14-1034-02B	ENSG00000105701	ENSG00000105143	FKBP8	SLC1A6	TGGAGCACCAGCCAGACAACATCAAGGCTCTCTTCCGCAAGGGCAAG*TGACCGGCTTCGCACAATGACCAACGTACTGGGGGACTCAATTGGAG	known,tcga,18cancers,chimerdb3seq,m43,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	57	3	28	19	18537601	-	19	14950390	-	109.6558	1.0179	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Glioblastoma	TCGA-14-1034-02B	ENSG00000140470	ENSG00000198121	ADAMTS17	LPAR1	CCAGAGCCCCAGGTCCGAAGGTGCAACTTGCACCCCTGCCAGTCACG*GGGCCTTTATCATCTGCTGGACTCCTGGATTGGTTTTGTTACTTCTA	18cancers,cancer,tcga-cancer,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	29	13	29	15	100048857	-	9	110875722	-	2.1937	17.6698	FALSE	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-14-1034-02B	ENSG00000198121	ENSG00000140470	LPAR1	ADAMTS17	TCGGGATACCATGATGAGTCTTCTGAAGACTGTGGTCATTGTGCTTG*GTGGGTGGCAGGCCCGTGGAGCCCCTGCTCGGCGACCTGTGAGAAAG	18cancers,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	29	1	13	9	110941421	-	15	99997589	-	17.6698	2.1937	FALSE	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Glioblastoma	TCGA-14-1034-02B	ENSG00000134668	ENSG00000227868	SPOCD1	TEX46	GGAGATTCAGCGGGACATGGACCAGACACTGACCCTGGAGGATCTGGTGG*CACCATAGGAGCAGTGGCAGCTTGGCTGATGAGCTATAAGCCAGCCTTGT	NA	BOWTIE+BOWTIE2	UTR/CDS(truncated)	0	5	1	28	1	31796589	-	1	23014015	-	18.378	18.0685	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-14-1034-02B	ENSG00000260170	ENSG00000133392	AC090527.2	MYH11	CTGAGTTGAACCCAGACAAGAACTGCATTCACACAGATGACGACGAGAAG*TTGTTAGCCGAGGAGAAAAACATCTCTTCCAAATACGCGGATGAGAGGGA	cancer,tumor,exon-exon	BOWTIE+BLAT;BOWTIE+STAR	CDS(no-known-start-or-end)/CDS(truncated)	0	3	2	21	15	45662125	+	16	15721634	-	0	0.1074	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-14-1034-02B	ENSG00000137767	ENSG00000133392	SQOR	MYH11	AGTTGAACCCAGACAAGAACTGCATTCACACAGATGACGACGAGAAG*TTGTTAGCCGAGGAGAAAAACATCTCTTCCAAATACGCGGATGAGAG	cancer,tumor,exon-exon	BOWTIE	in-frame	0	3	3	28	15	45662125	+	16	15721634	-	2.8168	0.1074	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Glioblastoma	TCGA-14-1034-02B	ENSG00000181722	ENSG00000119487	ZBTB20	MAPKAP1	AGAGGTTTCAGTCCACGTATTACCATAAATACCAGCAAACTTATGACTGG*GCTCATGGATTCTCCCTTATTCAGGTGGACAACACAAAGGTTACCATGAA	NA	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	16	3	115090839	-	9	125543161	-	0.263	17.2842	TRUE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7007-01A	ENSG00000151746	ENSG00000134532	BICD1	SOX5	ACAGCCTCAAACAGGAGCTGGAGCAGCTCAAAGAG*GTTCAAGGTCAGCTGCCGCCATTAATGATTCCCGT	tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	140	14	22	12	32107544	+	12	23665564	-	24.0854	6.7426	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7007-01A	ENSG00000151746	ENSG00000134532	BICD1	SOX5	ACAGCCTCAAACAGGAGCTGGAGCAGCTCAAAGAG*CAGGTTCAAGGTCAGCTGCCGCCATTAATGATTCC	tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	140	6	20	12	32107544	+	12	23665567	-	24.0854	6.7426	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7007-01A	ENSG00000139083	ENSG00000255750	ETV6	AC022509.1	GGAGGAAGACTCGATCCGCCTGCCTGCGCACCTGC*AAGAAAGAATCTTCAGGCCTCTGCTCTTGTGAGAG	antisense,oncogene,cancer,tumor,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	109	15	24	12	11752579	+	12	26231985	-	27.1661	4.6026	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7007-01A	ENSG00000139083	ENSG00000255750	ETV6	AC022509.1	GGAGGAAGACTCGATCCGCCTGCCTGCGCACCTGC*CTACTCCATGTGCTACTTTCTCTCGCAACTTTGAG	antisense,oncogene,cancer,tumor,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	109	2	23	12	11752579	+	12	26231119	-	27.1661	4.6026	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7007-01A	ENSG00000048392	ENSG00000247081	RRM2B	BAALC-AS1	AAAGGCCGGAAGCGGCCGGGCTGGATCAGGATGAG*GATCTTCTAAGGGTGTGAGGATACAGGCGTCAAAG	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	57	6	20	8	102238827	-	8	103246684	-	10.7038	2.2849	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7007-01A	ENSG00000048392	ENSG00000247081	RRM2B	BAALC-AS1	AAAGGCCGGAAGCGGCCGGGCTGGATCAGGATGAG*GAAACTGAGGCTAAAGAGTTTAGTATTCTGCCAAG	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	57	5	23	8	102238827	-	8	103268843	-	10.7038	2.2849	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7007-01A	ENSG00000048392	ENSG00000247081	RRM2B	BAALC-AS1	AAAGGCCGGAAGCGGCCGGGCTGGATCAGGATGAG*GCTGTCTCTACCAGGCCAGAATTTGGGGCAGGCAA	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	57	4	22	8	102238827	-	8	103267520	-	10.7038	2.2849	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7007-01A	ENSG00000048392	ENSG00000247081	RRM2B	BAALC-AS1	AAAGGCCGGAAGCGGCCGGGCTGGATCAGGATGAG*CTAGTGTGCATTTACTCCTGCCTCTCCATGCCTGA	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	57	3	20	8	102238827	-	8	103268472	-	10.7038	2.2849	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7007-01A	ENSG00000048392	ENSG00000247081	RRM2B	BAALC-AS1	AAAGGCCGGAAGCGGCCGGGCTGGATCAGGATGAG*AACAAAACAATCAGCAGGCGGGTCTGCGGCATTCT	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	57	3	20	8	102238827	-	8	103166296	-	10.7038	2.2849	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7007-01A	ENSG00000133687	ENSG00000118307	TMTC1	CASC1	CCTGGATGAACATGGGTGGCATCCAACACATCAAG*GAAAACCTCTGCATGTTATCTTCAATCAAACTAAA	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	46	10	23	12	29512043	-	12	25111939	-	15.2468	21.8072	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7007-01A	ENSG00000133687	ENSG00000118307	TMTC1	CASC1	CCTGGATGAACATGGGTGGCATCCAACACATCAAG*GTTCCTTTGGTAGAAGTGAAAGCTTATCGACAGAT	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	46	1	13	12	29512043	-	12	25110240	-	15.2468	21.8072	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7007-01A	ENSG00000060237	ENSG00000211455	WNK1	STK38L	AAACCACCGTGGAAGTCGCCTGGTGTGAACTGCAG*GCAGAAGAAATTAGAAGTGGCCATGGAAGAAGAAG	known,tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	31	7	22	12	754324	+	12	27302137	+	117.6023	89.1838	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7007-01A	ENSG00000060237	ENSG00000211455	WNK1	STK38L	AAACCACCGTGGAAGTCGCCTGGTGTGAACTGCAG*AAAAAGTTACGTCGATCACAACACGCTCGCAAAGA	known,tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	31	2	18	12	754324	+	12	27308339	+	117.6023	89.1838	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7007-01A	ENSG00000113732	ENSG00000113719	ATP6V0E1	ERGIC1	ATGTTGGTGACCTGTTCAGTTTGCTGCTATCTCTT*CCCTGGCCTCCCACGACTACATCCTGAAGATTGTG	oncogene,chimerdb3seq,tcga-cancer,oesophagus,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	7	2	19	5	172994822	+	5	172932436	+	102.0899	11.6708	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7007-01A	ENSG00000123104	ENSG00000082805	ITPR2	ERC1	AGCATCTTGCAACTGGAAACTATTTAGCTGCAGAG*CACATGCAGATGACAATCCAGGCTCTCCAGGATGA	cancer,exon-exon	BOWTIE	in-frame	0	3	1	13	12	26711173	-	12	1083164	+	48.2045	51.4162	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-TQ-A7RK-02A	ENSG00000068885	ENSG00000118849	IFT80	RARRES1	GACTGGGATGCTTAGATCAACTTTAGCTCAGCAAG*ATAATCATGGACATATTGATCCCTCTCTGAGACTC	cancer,m14,tcga-cancer,exon-exon	BOWTIE	in-frame	0	25	9	23	3	160375812	-	3	158704927	-	2.4657	2.1315	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-TQ-A7RK-02A	ENSG00000068885	ENSG00000118849	IFT80	RARRES1	ATCTTGTTGCAGGAAAACAAGTTCAGGGCTCCCACTGATTCTATGTTATG*ATTTTAGGTCCGAAAACAATGCCACAGAAAAAAATCTACCTGATTTCTTC	cancer,m14,tcga-cancer	BOWTIE+STAR	UTR/intronic	0	25	1	15	3	160373615	-	3	158705847	-	2.4657	2.1315	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-TQ-A7RK-02A	ENSG00000198721	ENSG00000137210	ECI2	TMEM14B	TGCACTTAAAGCTGCCAGCAAGGATGACTCAATCATCACTGTTTTAACAG*GAACGTATCTGTTCACAGAAAACTTGAGAAGAATCCTGTGGGGCTTTTAA	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	14	1	15	6	4127762	-	6	10833259	+	8.0331	6.7263	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-FG-6688-01A	ENSG00000163531	ENSG00000077157	NFASC	PPP1R12B	CGTCACAGAGGAGTCACCAGCACCCCCGAATGAAG*GTTGGAATCGGGAGGTAGTAATCCTACAACCAGTG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	53	11	22	1	204988806	+	1	202562778	+	15.9953	14.388	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6404-02B	ENSG00000183337	ENSG00000100393	BCOR	EP300	TTTTAATTATTGTGAAGGGTATCTAAAGACTGCATGACGTTTACCTATCA*ATATTTTTGTTATGGCTGGTTACCACCAGCCTTTCTTCCCCTTTGTGTGT	tcga,cell_lines,chimerdb3seq,cancer,m479,tcga-cancer	BOWTIE+BLAT	UTR/UTR	0	480	7	24	X	40072055	-	22	41179153	+	60.65	20.4352	FALSE	TRUE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6404-02B	ENSG00000100393	ENSG00000183337	EP300	BCOR	CCCAGCATGGTCAACCTTTGAACATGGCTCCACAACCAGGATTGGGCCAG*CGTGCAATGATGCGCTTCTCAGAGTTGGAGATGAAAGAAAGAGAAGGTGG	tcga,cell_lines,chimerdb3seq,cancer,m479,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	480	14	24	22	41177816	+	X	40071159	-	20.4352	60.65	TRUE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6404-02B	ENSG00000100393	ENSG00000183337	EP300	BCOR	CCCAGCATGGTCAACCTTTGAACATGGCTCCACAACCAGGATTGGGCCAG*ATGGAAGGATTACAAGAGGACAGTATTTTATGTCTACCCGCTGCTTACTG	tcga,cell_lines,chimerdb3seq,cancer,m479,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	480	13	23	22	41177816	+	X	40071690	-	20.4352	60.65	TRUE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6404-02B	ENSG00000100393	ENSG00000183337	EP300	BCOR	ATGTGGAGACACGCTGGCACTGTACTGTCTGTGAG*CGTGCAATGATGCGCTTCTCAGAGTTGGAGATGAA	tcga,cell_lines,chimerdb3seq,cancer,m479,tcga-cancer,exon-exon	BOWTIE	in-frame	0	480	7	23	22	41176528	+	X	40071159	-	20.4352	60.65	TRUE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6404-02B	ENSG00000100393	ENSG00000183337	EP300	BCOR	ATGTGGAGACACGCTGGCACTGTACTGTCTGTGAG*ATGGAAGGATTACAAGAGGACAGTATTTTATGTCT	tcga,cell_lines,chimerdb3seq,cancer,m479,tcga-cancer,exon-exon	BOWTIE	in-frame	0	480	5	22	22	41176528	+	X	40071690	-	20.4352	60.65	TRUE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6404-02B	ENSG00000100393	ENSG00000183337	EP300	BCOR	CATGCCACCCTACTTGCCCAGGACTCAAGCTGCTGGCCCTGTGTCCCAGG*CGTGCAATGATGCGCTTCTCAGAGTTGGAGATGAAAGAAAGAGAAGGTGG	tcga,cell_lines,chimerdb3seq,cancer,m479,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	480	1	22	22	41177406	+	X	40071159	-	20.4352	60.65	TRUE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6404-02B	ENSG00000205531	ENSG00000184956	NAP1L4	MUC6	TTAAAGTGAAATTTTCTGACCCTGGACAGCCTATG*GTGCCCACCAAGTGTGAGCCTGGCTGTGTCTGCGC	cancer,exon-exon	BOWTIE	in-frame	0	22	3	18	11	2964680	-	11	1026478	-	146.1092	20.4692	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6404-02B	ENSG00000136153	ENSG00000228021	LMO7	AL158835.1	GAAGAAGCATCTTCAGGTTTTCTTCCTGGTGACAG*GCTCTGGCATCCGGTGCAGTCTTGCTCGTCATCTC	cancer,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	3	1	13	13	75842916	+	10	125699066	+	0.7786	0.0956	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6404-02B	ENSG00000070047	ENSG00000161328	PHRF1	LRRC56	CTAAGAAACGCCAACATCGAGTGAAGAAGAGAAGAGGGAAGAAGGTAAAG*AGATGGGGTTTCACCGTGTTAACCAGGACGGTCTAGATCTCCTGACC	tcga,chimerdb3seq,tcga-cancer,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	3	16	24	11	601701	+	11	548645	+	57.8995	38.8988	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6404-02B	ENSG00000070047	ENSG00000161328	PHRF1	LRRC56	CAAGATCTAAGAAACGCCAACATCGAGTGAAGAAGAGAAGAGGGAAGAAG*GACGGTCTAGATCTCCTGACCTCGTGATCTGCCTGCCTCGGCCTCCCAAA	tcga,chimerdb3seq,tcga-cancer,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	3	1	22	11	601695	+	11	548671	+	57.8995	38.8988	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6404-02B	ENSG00000070047	ENSG00000161328	PHRF1	LRRC56	CTAAGAAACGCCAACATCGAGTGAAGAAGAGAAGAGGGAAGAAGGTAAAG*CGCGAAAGGACGGACCACCGGGAATGCACCTGAGGGCCCACAGAAGGAAG	tcga,chimerdb3seq,tcga-cancer,10K<gap<100K	BOWTIE+STAR	CDS(truncated)/intronic	0	3	1	19	11	601701	+	11	549048	+	57.8995	38.8988	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6404-02B	ENSG00000167244	ENSG00000021762	IGF2	OSBPL5	AGCACACAGCACACACACAAAGACACAGCACACACATGCACACACAGCAC*ACACACACACATGCACACACATGCGCGCACACATATGCACACACACACAC	oncogene,cancer	BOWTIE+BLAT	UTR/intronic	0	2	1	16	11	2131742	-	11	3112006	-	131.0281	25.4486	TRUE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-HT-7689-01A	ENSG00000112531	ENSG00000118507	QKI	AKAP7	GAATGGCACCTACAGAGATGCCAACATTAAATCAC*GTGAAAAGAACGGAGGGGAGCCCGATGACGCTGAA	cell_lines,18cancers,exon-exon	BOWTIE	in-frame	0	26	4	23	6	163562069	+	6	131281530	+	76.2855	5.7505	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-HT-7689-01A	ENSG00000103510	ENSG00000260953	KAT8	AC009093.4	ACATGAAATATGAGAAGAGCTACCGCTTCCACTTG*ATACTGAATTCCTTGAAACGTTGACCTCCAAGATG	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	16	6	23	16	31127353	+	16	29262683	-	6.3255	1.1095	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-HT-7689-01A	ENSG00000103510	ENSG00000260953	KAT8	AC009093.4	CCACCACAGCAGCCTTGGAGAAGGAGCATGAGGCG*ATACTGAATTCCTTGAAACGTTGACCTCCAAGATG	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	16	4	22	16	31127088	+	16	29262683	-	6.3255	1.1095	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-HT-7689-01A	ENSG00000167397	ENSG00000176476	VKORC1	SGF29	ACCGCCATCAGCTGTTCGCGCGTCTTCTCCTCCAG*GTGCCCCTGTAGACAATGGCCCTCGTGTCTGCCGA	m11,exon-exon	BOWTIE	CDS(truncated)/UTR	0	15	5	24	16	31094557	-	16	28581055	+	0.9756	7.16	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-HT-7689-01A	ENSG00000215241	ENSG00000226711	LINC02449	FAM66C	TCCTGAGACAACGGAATTCTGGCGATGGAGCACAG*ATATAATACGTAAGTTTGGAGGTGGATGCTTTCAG	lincrna,antisense,m3,10K<gap<100K,exon-exon	BOWTIE	exonic(no-known-CDS)/exonic(no-known-CDS)	0	4	2	24	12	8235999	+	12	8215806	+	0.4533	1.3306	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	lincRNA	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DH-A669-01A	ENSG00000109685	ENSG00000168993	NSD2	CPLX1	AGTTTTTGGTCTTCTGTCAAAAACACAGGGATGAG*GGGCCACCAAGGACATGGGGAAGATGCTGGGGGGT	oncogene,chimerdb3seq,cancer,tumor,m261,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	263	19	24	4	1918623	+	4	792608	-	5.6256	40.5067	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-DH-A669-01A	ENSG00000109685	ENSG00000168993	NSD2	CPLX1	CATCAGAGCTGGTTGGTGCCGAGCCAGTCAGCAGACTTTCCAAAGGGCTG*GGGCCACCAAGGACATGGGGAAGATGCTGGGGGGTGACGAGGAGAAGGAC	oncogene,chimerdb3seq,cancer,tumor,m261,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	263	2	20	4	1929527	+	4	792608	-	5.6256	40.5067	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-DH-A669-01A	ENSG00000148498	ENSG00000145220	PARD3	LYAR	AGGCGGTGACCCGCTACCGGAAGGCCATCGCCAAG*GAACCAGTCAATAAGGAACAGGATCAACGGCCACT	cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	169	20	24	10	34814876	-	4	4274769	-	2.1617	16.5533	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-DH-A669-01A	ENSG00000015171	ENSG00000154556	ZMYND11	SORBS2	GACGACGTAATCAAAGTGTGGAGCCCAAAAAGGAA*CCACAGCGTCCTGTGTTTACTCATGAAAATATTCA	cancer,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	117	8	23	10	247466	+	4	185593935	-	11.1096	2.745	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-DH-A669-01A	ENSG00000151726	ENSG00000270111	ACSL1	AL583859.2	CATGCGACCTCTCCATGCAGTCAGTGGAAGTGGCG*AAGCTAGAGTCATCCTAACAAGAGTGATAGTCTTT	lincrna,m41,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	43	2	15	4	184803320	-	10	10422774	-	3.6758	0.3643	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DH-A669-01A	ENSG00000150867	ENSG00000245067	PIP4K2A	IGFBP7-AS1	GGGAGAGGTTTGGAATTGATGATCAAGATTTCCAG*ATCAGTGTGGAAATGGATGTGGACGCGGTGCTGCT	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	39	10	24	10	22607927	-	4	57201133	+	10.8724	2.0415	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DH-A669-01A	ENSG00000150867	ENSG00000245067	PIP4K2A	IGFBP7-AS1	TCAAAAATAAAGGTGGACAATCACCTTTTTAACAA*ATCAGTGTGGAAATGGATGTGGACGCGGTGCTGCT	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	39	2	21	10	22609620	-	4	57201133	+	10.8724	2.0415	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DH-A669-01A	ENSG00000150867	ENSG00000245067	PIP4K2A	IGFBP7-AS1	TCTTCCGTAACCTGCGGGAGAGGTTTGGAATTGATGATCAAGATTTCCAG*GAGTCCAAAGCAAACCATTGATGATCAAGCACTGGATGACAGCAGTTTGG	antisense	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	39	2	21	10	22607927	-	4	57132921	+	10.8724	2.0415	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DH-A669-01A	ENSG00000150867	ENSG00000245067	PIP4K2A	IGFBP7-AS1	GGGAGAGGTTTGGAATTGATGATCAAGATTTCCAG*GGGACTGTTCTAAGAACTTATAAGAGTTAAGAAAA	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	39	1	13	10	22607927	-	4	57188170	+	10.8724	2.0415	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DH-A669-01A	ENSG00000154553	ENSG00000159733	PDLIM3	ZFYVE28	GCATAGACTTCAACCAGCCTTTGGTCATCACCAGG*AGGTCGGATCCGCAGCTGCTTGCCCGGTTCTACTA	tcga-cancer,exon-exon	BOWTIE	in-frame	0	18	2	22	4	185535342	-	4	2354073	-	1.1696	2.4417	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-DH-A669-01A	ENSG00000074211	ENSG00000159692	PPP2R2C	CTBP1	GCGGGCAGCTGCCCTGTGTGACAAGCATTCCAAGC*CTTTAGCCAGGGCCCTCTGAAGGATGCACCCAACC	tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	15	4	22	4	6347846	-	4	1213605	-	1.2949	5.5778	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-DH-A669-01A	ENSG00000125386	ENSG00000074211	FAM193A	PPP2R2C	CCGCACGCTCCATCAGCACCTTCCTTGGCACTCTG*TCTTTGAAGAGCCTGAGGACCCCAGTAACCGCTCA	tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	10	2	17	4	2631169	+	4	6333731	-	3.9291	1.2949	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-DH-A669-01A	ENSG00000159733	ENSG00000181982	ZFYVE28	CCDC149	TGAACAGGTTCCGAAAGTGGCTCTACAAACCCAAG*TACCTGGTGTGTAAGAGGAAGCTGGAGAGTAAGAA	cell_lines,tcga-cancer,exon-exon	BOWTIE	in-frame	0	8	3	23	4	2418285	-	4	24876697	-	2.4417	3.6672	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-DH-A669-01A	ENSG00000168993	ENSG00000120549	CPLX1	KIAA1217	TGGAAGCAGAGCAATCGCCATGGAGTTTGTGATGAAGCAGGCTCTAGGAG*CGTCCAACTAATGTTTTGGGGAAAATACTGGAAAACTGAAGTTAACTTGA	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	6	1	18	4	824492	-	10	24006989	+	40.5067	1.1181	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DH-A669-01A	ENSG00000035928	ENSG00000151474	RFC1	FRMD4A	AGTCTGATGAAGAAACTTTAAAAGCAAAGAAAGGAATAAAGGAAATCAAG*GTTGTCCTATCACCTTGGCACGAGGAAGGCTGCCTGCTCTACGTTGGGTA	NA	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	3	3	21	4	39351348	-	10	14265224	-	6.0476	2.1305	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DH-A669-01A	ENSG00000035928	ENSG00000151474	RFC1	FRMD4A	AGTCTGATGAAGAAACTTTAAAAGCAAAGAAAGGAATAAAGGAAATCAAG*GTCATGAGGAAATAAGAGTCGAAAGGAATCAGTAAAAAAGCACCTCCTAT	NA	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	3	1	19	4	39351348	-	10	14239024	-	6.0476	2.1305	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DH-A669-01A	ENSG00000035928	ENSG00000151474	RFC1	FRMD4A	AGTCTGATGAAGAAACTTTAAAAGCAAAGAAAGGAATAAAGGAAATCAAG*CCCAGGCTGGAGTGCAGTGGCACAATCTCAGCTCACCGCAACCTCCGCCT	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	3	1	19	4	39351348	-	10	14180011	-	6.0476	2.1305	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DH-A669-01A	ENSG00000154274	ENSG00000197712	C4ORF19	FAM114A1	CCGCCGCCGCCGCCGCCGCCGCCGTCTGGCCCCAG*GTTCAGTCATTTTTAGCATCACTTGATGGAGAGAA	exon-exon	BOWTIE	UTR/CDS(truncated)	0	2	2	15	4	37454040	+	4	38922770	+	0.1421	3.1853	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6407-02B	ENSG00000106278	ENSG00000105976	PTPRZ1	MET	CGCTTGCATTCAGCTCCTCTGTGTTTGCCGCCTGG*ATAAACCTCTCATAATGAAGGCCCCCGCTGTGCTT	known,oncogene,tcga,cell_lines,gliomas,chimerdb3pub,chimerdb3seq,cancer,tumor,m641,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/CDS(no-known-start-or-end)	0	643	22	24	7	121873557	+	7	116699071	+	404.5102	226.1286	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6407-02B	ENSG00000106278	ENSG00000105976	PTPRZ1	MET	CGCTTGCATTCAGCTCCTCTGTGTTTGCCGCCTGG*GGTGGTGATGAAGAGTAAATCAAAGAGTTTAGCAG	known,oncogene,tcga,cell_lines,gliomas,chimerdb3pub,chimerdb3seq,cancer,tumor,m641,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	643	15	24	7	121873557	+	7	116695750	+	404.5102	226.1286	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6407-02B	ENSG00000106278	ENSG00000105976	PTPRZ1	MET	CGCTTGCATTCAGCTCCTCTGTGTTTGCCGCCTGG*ACACTTCTGAGAAATTCATCAGGCTGTGAAGCGCG	known,oncogene,tcga,cell_lines,gliomas,chimerdb3pub,chimerdb3seq,cancer,tumor,m641,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	643	15	23	7	121873557	+	7	116731668	+	404.5102	226.1286	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6407-02B	ENSG00000106278	ENSG00000105976	PTPRZ1	MET	CCTAAAGCGTTTCCTCGCTTGCATTCAGCTCCTCTGTGTTTGCCGCCTGG*CAAGGGAAGCTTTTGGAAGCCACCCGGTAGAGCTGGAAGAGAATTTCGAA	known,oncogene,tcga,cell_lines,gliomas,chimerdb3pub,chimerdb3seq,cancer,tumor,m641,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	643	2	21	7	121873557	+	7	116724693	+	404.5102	226.1286	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6407-02B	ENSG00000106278	ENSG00000105976	PTPRZ1	MET	CAAAGAAGACTGGAAAATTTAGCATTTATTCTGGATGGCCAGGTGCTCAG*GGTGGTGATGAAGAGTAAATCAAAGAGTTTAGCAGAATGCTTCCCATATG	known,oncogene,tcga,cell_lines,gliomas,chimerdb3pub,chimerdb3seq,cancer,tumor,m641,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	intronic/UTR	0	643	1	23	7	121893626	+	7	116695750	+	404.5102	226.1286	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6407-02B	ENSG00000163029	ENSG00000223850	SMC6	MYCNUT	TTCTAATGTCAACTTTGTTGTTGGCAACAATGGAA*GATGGATCATGAAGAGTGGAATTGCTTTTCCTCTT	lincrna,m83,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	84	12	24	2	17741612	-	2	15935774	+	39.5695	1.855	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6407-02B	ENSG00000007392	ENSG00000103126	LUC7L	AXIN1	CAAGTAAAGAAAGAGACCTGTTTTTTGAATTAGAT*GTATGGATCCTGGCGGGAGCCAGTCAACCCCTATT	chimerdb3seq,cancer,tumor,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	50	14	23	16	220649	-	16	314683	-	17.8536	14.0263	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6407-02B	ENSG00000007392	ENSG00000103126	LUC7L	AXIN1	TGGACTGCTGCCCCCATGACATCCTGGCTGGGACG*GTATGGATCCTGGCGGGAGCCAGTCAACCCCTATT	chimerdb3seq,cancer,tumor,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	50	2	22	16	227242	-	16	314683	-	17.8536	14.0263	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6407-02B	ENSG00000007392	ENSG00000103126	LUC7L	AXIN1	CAGATTATGAGATTGCAAGTAAAGAAAGAGACCTGTTTTTTGAATTAGAT*CCGCCTTCTCCCGCTTCTCTCCCCTTTGCTGCCTGACCTTGGTGCTTGTG	chimerdb3seq,cancer,tumor,tcga-cancer,10K<gap<100K	BOWTIE+STAR	CDS(complete)/intronic	0	50	1	14	16	220649	-	16	318391	-	17.8536	14.0263	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6407-02B	ENSG00000223482	ENSG00000229227	NUTM2A-AS1	AL356056.1	GCCTGCCTCAGCCTCCAAAGTAGCTGAGACTACAG*TTACAAGCTATTGAGGCACTCCAGAGTGACGGCAT	lincrna,antisense,m4,exon-exon	BOWTIE	exonic(no-known-CDS)/exonic(no-known-CDS)	0	17	2	22	10	87246115	-	10	46611909	+	1.1569	0.0164	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6407-02B	ENSG00000223482	ENSG00000229227	NUTM2A-AS1	AL356056.1	CGCCTATAATCCCAGCACTTTGGGAGGCCAAGGCCAGTGGATCACCTGAG*TTACAAGCTATTGAGGCACTCCAGAGTGACGGCATGTGATCCCCCTGACA	lincrna,antisense,m4	BOWTIE+BLAT;BOWTIE+STAR	intronic/exonic(no-known-CDS)	0	17	1	22	10	87208422	-	10	46611909	+	1.1569	0.0164	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6407-02B	ENSG00000163029	ENSG00000237326	SMC6	AC113608.2	CCGATAATAGTTTCTGAGTTTCGGAATGAGATATATGATGTAAGACACAG*GTCTCATCCCTAGAGGCTGGGGTCCTTAGCAACAGCCAATGGAAGTAGTG	lincrna	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	11	1	21	2	17714861	-	2	15806442	-	39.5695	2.659	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-FG-7636-01A	ENSG00000145982	ENSG00000111846	FARS2	GCNT2	AAGGTTGATCTCATAGACAAGTTTGTACATCCAAA*GTGTTCCTGGCTCTATGCCAAATGCATCCTGGACT	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	6	1	14	6	5613320	+	6	10621351	+	3.5303	1.0341	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-FG-7643-01A	ENSG00000183137	ENSG00000135537	CEP57L1	AFG1L	AGCGGTGGCAGGGGCTGACTGAGAGCGTCTGCTTG*CACAAGTGAAGCTGATGTGGAGGCTGTCATGGATA	exon-exon	BOWTIE	UTR/CDS(truncated)	0	7	3	21	6	109095575	+	6	108476865	+	0.7567	1.5307	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-FG-7643-01A	ENSG00000143409	ENSG00000198933	MINDY1	TBKBP1	CTTCTCAATCTTGGAACAGCACCCCCTTCTTTAAG*GAGGCCCCGTGTGGGCCGCGGCCCGGCCCTCACCA	exon-exon	BOWTIE	UTR/UTR	0	3	2	23	1	151006312	-	17	47696079	+	11.0415	7.5315	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-5870-01A	ENSG00000215241	ENSG00000226711	LINC02449	FAM66C	TCCTGAGACAACGGAATTCTGGCGATGGAGCACAG*ATATAATACGTAAGTTTGGAGGTGGATGCTTTCAG	lincrna,antisense,m2,10K<gap<100K,exon-exon	BOWTIE	exonic(no-known-CDS)/exonic(no-known-CDS)	0	9	2	21	12	8235999	+	12	8215806	+	1.2612	3.7812	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	lincRNA	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6407-02A	ENSG00000196417	ENSG00000130433	ZNF765	CACNG6	GATGCTGGAGAATTATAGGAACCTGGTCTCCCTGG*AAGCAAACTGCACCTATTTTAAATTCTTCACCACG	18cancers,m28,exon-exon	BOWTIE	in-frame	0	272	20	24	19	53402191	+	19	53998239	+	0.383	27.7741	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6407-02A	ENSG00000196417	ENSG00000130433	ZNF765	CACNG6	GATGCTGGAGAATTATAGGAACCTGGTCTCCCTGG*GCCTGCTGCTCTTGGTGAGCCTGGAGGTGTTCCGG	18cancers,m28,exon-exon	BOWTIE	in-frame	0	272	12	24	19	53402191	+	19	54011951	+	0.383	27.7741	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6407-02A	ENSG00000196417	ENSG00000130433	ZNF765	CACNG6	GGAAAGCAAAGGAGTCAGGGATGGCTCTTCCTCAG*GCCTGCTGCTCTTGGTGAGCCTGGAGGTGTTCCGG	18cancers,m28,exon-exon	BOWTIE	out-of-frame	0	272	3	22	19	53398030	+	19	54011951	+	0.383	27.7741	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6407-02A	ENSG00000196417	ENSG00000130433	ZNF765	CACNG6	GGAAAGCAAAGGAGTCAGGGATGGCTCTTCCTCAG*AAGCAAACTGCACCTATTTTAAATTCTTCACCACG	18cancers,m28,exon-exon	BOWTIE	out-of-frame	0	272	3	19	19	53398030	+	19	53998239	+	0.383	27.7741	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6407-02A	ENSG00000196417	ENSG00000130433	ZNF765	CACNG6	TCTATACAGGGACGTGATGCTGGAGAATTATAGGAACCTGGTCTCCCTGG*CTTCCCAAATGCTGCCTGCTATATAGTAGGTGTTTAGTAAGTATTTGTTG	18cancers,m28	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	272	1	20	19	53402191	+	19	54011785	+	0.383	27.7741	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6407-02A	ENSG00000196417	ENSG00000130433	ZNF765	CACNG6	CCTGGAAGAGGAAGAGGAAAGCAAAGGAGTCAGGGATGGCTCTTCCTCAG*AGATAGGGTTTCGCTGTGTTGCCCAGGCTGGTCTCCAACTCCTGAGCTCA	18cancers,m28	BOWTIE+STAR	CDS(truncated)/intronic	0	272	1	15	19	53398030	+	19	54002303	+	0.383	27.7741	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-6407-02A	ENSG00000111676	ENSG00000215039	ATN1	CD27-AS1	CCTGCACCTGCACCAGCAAGATGCTATCCATGCAG*GTAGACCCAGTGTAATCACAAGCATCCTTGTAAGT	18cancers,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	39	6	20	12	6939177	+	12	6439676	-	65.7563	21.5461	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-6407-02A	ENSG00000111676	ENSG00000215039	ATN1	CD27-AS1	GGGAAGCCCGTGAACGAGACCTCCGTGACCGCCTCAAGCCTGGCTTTGAG*GTAGACCCAGTGTAATCACAAGCATCCTTGTAAGTGGCAAAGAGGCAGAG	18cancers	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	39	3	22	12	6938816	+	12	6439676	-	65.7563	21.5461	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-6407-02A	ENSG00000078246	ENSG00000111678	TULP3	C12ORF57	TGATGAAGATGCGACAGGCTAAGCTGGATTATCAG*GTGTCCTTAAGTTTGCTCGCTTGGTCAAGTCCTAC	18cancers,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	36	11	24	12	2909580	+	12	6945771	+	7.9545	30.4068	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-TQ-A7RV-01A	ENSG00000223482	ENSG00000229227	NUTM2A-AS1	AL356056.1	GCCTGCCTCAGCCTCCAAAGTAGCTGAGACTACAG*TTACAAGCTATTGAGGCACTCCAGAGTGACGGCAT	lincrna,antisense,m3,exon-exon	BOWTIE	exonic(no-known-CDS)/exonic(no-known-CDS)	0	19	2	22	10	87246115	-	10	46611909	+	1.8042	0.034	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	antisense_RNA	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-TQ-A7RV-01A	ENSG00000078403	ENSG00000095787	MLLT10	WAC	ACTCTCAGGATAAACATCATGAGAAAGAGAAAAAA*GCACTTAAGTATTCATCGAAGAGTCACCCCAGTAG	cancer,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	10	4	20	10	21617207	+	10	28535562	+	2.7237	19.6034	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-TQ-A7RV-01A	ENSG00000078403	ENSG00000095787	MLLT10	WAC	ACTGTGGCTACTGTAAATACCATTTTAGTAAGCTG*GCACTTAAGTATTCATCGAAGAGTCACCCCAGTAG	cancer,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	10	2	24	10	21614924	+	10	28535562	+	2.7237	19.6034	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-DU-5870-02A	ENSG00000103978	ENSG00000243147	TMEM87A	MRPL33	ATGGAACAAACCTTACCTTTATTGGAGACAAAACC*GCTGTGGTTATGGTTTTTGGAAGACCACAGAGGTG	ribosomal,exon-exon	BOWTIE	out-of-frame	0	16	4	19	15	42260958	-	2	27782572	+	7.5378	9.8151	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-5870-02A	ENSG00000103978	ENSG00000243147	TMEM87A	MRPL33	TAAAGGCTAAGGAGAATGGAACAAACCTTACCTTTATTGGAGACAAAACC*ATGTCTGCAAACTATGGCCTGCAGGATGTTCTTGTAAGGCTTGGGAGGTA	ribosomal	BOWTIE+STAR	CDS(truncated)/intronic	0	16	1	19	15	42260958	-	2	27888709	+	7.5378	9.8151	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-5870-02A	ENSG00000215241	ENSG00000226711	LINC02449	FAM66C	TCCTGAGACAACGGAATTCTGGCGATGGAGCACAG*ATATAATACGTAAGTTTGGAGGTGGATGCTTTCAG	lincrna,antisense,m4,10K<gap<100K,exon-exon	BOWTIE	exonic(no-known-CDS)/exonic(no-known-CDS)	0	14	4	23	12	8235999	+	12	8215806	+	1.4368	3.18	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-5870-02A	ENSG00000215241	ENSG00000226711	LINC02449	FAM66C	ATTCCAGCAGGATCAATGAAGAGAATTCACCAGAGGAACTAGTTCCAAAG*ATATAATACGTAAGTTTGGAGGTGGATGCTTTCAGCCATTAAGTTCAAAA	lincrna,antisense,m4,10K<gap<100K	BOWTIE+STAR	intronic/exonic(no-known-CDS)	0	14	2	17	12	8238252	+	12	8215806	+	1.4368	3.18	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-EZ-7264-01A	ENSG00000215241	ENSG00000226711	LINC02449	FAM66C	TCCTGAGACAACGGAATTCTGGCGATGGAGCACAG*ATATAATACGTAAGTTTGGAGGTGGATGCTTTCAG	lincrna,antisense,m2,10K<gap<100K,exon-exon	BOWTIE	exonic(no-known-CDS)/exonic(no-known-CDS)	0	4	1	13	12	8235999	+	12	8215806	+	1.1169	5.8519	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	lincRNA	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-FG-5963-01A	ENSG00000135164	ENSG00000153993	DMTF1	SEMA3D	ATGAGGTTACTGAGGGGACTGTGACACAGATACAG*ACAGAATGTGCAAATTTCATCAGAGTACTTCAGCC	tcga,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	13	5	23	7	87171089	+	7	85073081	-	7.168	3.232	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-FG-5963-01A	ENSG00000166025	ENSG00000168071	AMOTL1	CCDC88B	TGGAGAGAGAGCTGGATGCACTGAGAACCCAGCAG*AATGCGATGCTGGTGGCAGAGAAGGCAGCTTTGCA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	12	4	20	11	94854082	+	11	64351476	+	3.8737	4.9005	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-FG-5963-01A	ENSG00000166025	ENSG00000168071	AMOTL1	CCDC88B	TGGAGAGAGAGCTGGATGCACTGAGAACCCAGCAG*GCCGAGAAGTCTGTGCTGGAGATTCAGGGCCAGGA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	12	2	23	11	94854082	+	11	64352130	+	3.8737	4.9005	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-FG-5963-01A	ENSG00000114279	ENSG00000078081	FGF12	LAMP3	CATGGAGCCTCTGGAAAACACATTATCATAAGAAAATGATAATGAAAAAG*GTAGGTTTCTCTGGCACCGATTCGGGGCCTGCCCGGACTTCGCCGCACGC	tcga,chimerdb3seq,cancer,tcga-cancer	BOWTIE+STAR	intronic/UTR	0	7	1	22	3	192669731	-	3	183162730	-	3.1672	7.6703	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-FG-5963-01A	ENSG00000149187	ENSG00000129151	CELF1	BBOX1	AGAAAAATATTATGAAGAGCTCAAATATAAAACCTGCAACCTACAAAAAG*GTTCAGCTTCTTCACTGCATAAAGCAAACAGTCACAGGGGGTGATTCAGA	tcga,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	6	1	17	11	47564842	-	11	27119649	+	8.787	8.7966	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-FG-5963-01A	ENSG00000149187	ENSG00000129151	CELF1	BBOX1	CCTGTGGCCGGTGACCTCCCTCCTCCGAGGGAGGGGGGTTGTGACCCCAG*GCATTCCAGATTTTGTCCTCTACCTTTGTGGACTTTACAGACATTGGAGT	tcga,chimerdb3seq,tcga-cancer	BOWTIE+STAR	UTR/CDS(truncated)	0	6	1	16	11	47565274	-	11	27119751	+	8.787	8.7966	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-FG-5963-01A	ENSG00000099381	ENSG00000236197	SETD1A	AC002429.2	TCGTCCCTCCACTCCTGCTGAGGAAGATGAAGACG*GTCCCGGTTTATGACTGCAAAACAATGGTTTAAAC	exon-exon	BOWTIE	CDS(truncated)/UTR	0	5	6	23	16	30967588	+	7	95108941	-	9.5405	0.4922	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7018-01A	ENSG00000139364	ENSG00000253821	TMEM132B	AC090796.1	AGACAACCTTCGTGGGCATCGTCCCTCTTGCCATG*AGAAAGACACTGAAGGAATTAAATCAGCTTGTCCA	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	13	4	20	12	125519625	+	8	57591480	+	19.7705	2.1889	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-CS-4941-01A	ENSG00000111605	ENSG00000127329	CPSF6	PTPRB	ACATTTACGCGGATGTCGGCGAAGAGTTCAACCAG*TGCCTGCCCAAGTGACTGACTTGCATGTGGCCAAC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	1553	23	24	12	69239706	+	12	70581302	-	7.8093	451.4241	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-CS-4941-01A	ENSG00000111605	ENSG00000127329	CPSF6	PTPRB	ACATTTACGCGGATGTCGGCGAAGAGTTCAACCAG*TTCCAGAGCCTGTTAAGGATCTAACATTGCGCAAC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	1553	2	16	12	69239706	+	12	70571289	-	7.8093	451.4241	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-CS-4941-01A	ENSG00000111605	ENSG00000127329	CPSF6	PTPRB	ACATTTACGCGGATGTCGGCGAAGAGTTCAACCAG*TGCCTGACAAAGTCCAGGGAGTCAGTGTTAGCAAC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	1553	1	13	12	69239706	+	12	70572087	-	7.8093	451.4241	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-CS-4941-01A	ENSG00000154978	ENSG00000135679	VOPP1	MDM2	CGCGATCTTGGCTCACTGCAATCTCCGCCTCCTGGGTTCAAGCTATTCTC*CTGCCTCAGCCTCCCAATTAGCTTGGCCTACAGTCATCTGCCACCACACC	known,oncogene,cancer,tumor	BOWTIE+BLAT	intronic/UTR	0	4	1	23	7	55570850	-	12	68840255	+	308.8174	144.4766	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-CS-4941-01A	ENSG00000135643	ENSG00000257815	KCNMB4	LINC01481	GATGAGATTGGTTCCCAGCCATTTACTTGCTATTTTAATCAACATCAAAG*ATGGAGTTGCGTTCTGTCGCCCAGGCTGGAGTGCAGGGGCGCGATCTCGG	antisense	BOWTIE+STAR	CDS(truncated)/intronic	0	3	1	17	12	70400336	+	12	69998095	-	117.7165	14.231	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-CS-4941-01A	ENSG00000258168	ENSG00000166225	AC025569.1	FRS2	TTTATATTGCTGGACATCTGGTAAATGGTTTAATATTATTTTCACATGTC*ATTTTGGAGGTTGGGTACTTTATTCTTTCTTTCCGTCATCCTTTTCATTG	antisense	BOWTIE+BLAT	intronic/UTR	0	2	1	18	12	70518037	+	12	69577080	+	6.7446	548.3924	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-CS-4941-01A	ENSG00000166226	ENSG00000263001	CCT2	GTF2I	TTTGGTTCCCGGGTAAGAGTTGACTCTACAGCAAAGGTTGCAGAAATAGA*CGGGGAGTGAGGAGGGGTCAGGGGGCTAAGGATGCAACCTCTGACGTTCT	NA	BOWTIE+BLAT	CDS(truncated)/UTR	0	2	1	23	12	69593028	+	7	74760397	+	1523.6578	3.6944	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-CS-4941-01A	ENSG00000135643	ENSG00000166225	KCNMB4	FRS2	GCAACCTCCCTTCATGTATCCTTGTTCACAGTGAGTTCCTTTGCCCACAC*CTAATGGATATCCCCGATATCCCTCATTTGGAGATGCTTCATCCCATCCG	NA	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	20	12	70402988	+	12	69572145	+	117.7165	548.3924	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-CS-4941-01A	ENSG00000005483	ENSG00000154978	KMT2E	VOPP1	GAGAAATTCAAATATTAAGTGGAATGTAAAATTTGATATTTTTATGGAAA*TGCATGTAGAGCGTCCTGCCCTTTGAAATCAGACTGGGTGTGTGTCTTCC	NA	BOWTIE+STAR	intronic/UTR	0	2	1	16	7	105064625	+	7	55472049	-	13.1067	308.8174	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-CS-4941-01A	ENSG00000257815	ENSG00000127328	LINC01481	RAB3IP	AGCTAACTTTTAATAATTTTTTTGTAGAGACAAGGTCTCCCTATATTGCC*CAAGTCCAACTTGGGCAACATAGGGAGACCTTGTCTCTAAAAAAAAAACT	antisense	BOWTIE+BLAT	intronic/UTR	0	2	1	24	12	70230992	-	12	69817742	+	14.231	195.4048	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-CS-4941-01A	ENSG00000127329	ENSG00000135643	PTPRB	KCNMB4	ACAGGGTCTTTCTATGTTGCCCAGGCTGAAGTGCAGTAGCTATTCACAGG*CCAATGTTTTCTTAATCTTAGAATGTGAATAACTGAAAATCATAGTCTGT	NA	BOWTIE+BLAT	intronic/UTR	0	2	1	20	12	70599928	-	12	70432308	+	451.4241	117.7165	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7292-01A	ENSG00000163531	ENSG00000058668	NFASC	ATP2B4	CGTCACAGAGGAGTCACCAGCACCCCCGAATGAAG*ATCAAAGTGGTCAAAGCGTTCCATAGTTCCCTCCA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	21	4	22	1	204988806	+	1	203739546	+	24.4324	512.6077	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7292-01A	ENSG00000163531	ENSG00000058668	NFASC	ATP2B4	CGTCACAGAGGAGTCACCAGCACCCCCGAATGAAG*ATCGACGTAATTAACACATTCCAGACGGGAGCCTC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	21	2	24	1	204988806	+	1	203733223	+	24.4324	512.6077	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-TQ-A7RV-02A	ENSG00000078403	ENSG00000095787	MLLT10	WAC	ACTCTCAGGATAAACATCATGAGAAAGAGAAAAAA*GCACTTAAGTATTCATCGAAGAGTCACCCCAGTAG	cancer,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	11	2	21	10	21617207	+	10	28535562	+	1.8938	16.6251	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-TQ-A7RV-02A	ENSG00000164944	ENSG00000147642	VIRMA	SYBU	GCCACAACCAAGTTTGAAAAGGAATCCAAAACATG*ATGACACAGGCTGTCCTAGCAGCCAGTCAGTGTCT	tcga-cancer,exon-exon	BOWTIE	in-frame	0	6	2	19	8	94534839	-	8	109619039	-	5.0109	23.1217	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-TQ-A7RV-02A	ENSG00000164944	ENSG00000147642	VIRMA	SYBU	AGAATACTTCCATCATCTTTAGACCTAACTCAAAG*ATGACACAGGCTGTCCTAGCAGCCAGTCAGTGTCT	tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	6	1	13	8	94537103	-	8	109619039	-	5.0109	23.1217	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-CS-6668-01A	ENSG00000197102	ENSG00000078687	DYNC1H1	TNRC6C	CAGCTCTATCAGATCACCCAGATCAATCATGGCCTGATGATGGTGGGGCC*CACGGGGAAGTGGGAAGGGGGTCTGCAGGGACTGTGAGGTTTTGGTTTAC	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	14	14	102011930	+	17	78102267	+	19.0545	15.7563	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-5854-01A	ENSG00000185345	ENSG00000125695	PRKN	AC046185.1	TCACCTGCGAAGGGGGCAATGGCCTGGGCTGTGGG*ATGCTGCTAGAGAAACTGAACGGCACAGTGCCCTG	exon-exon	BOWTIE	CDS(truncated)/UTR	0	9	2	22	6	161548854	-	17	63704582	-	0.7097	0	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-5854-01A	ENSG00000266173	ENSG00000185345	STRADA	PRKN	CAGCCACCCAGCCTGGCCTCCCCTTGGGCATCTTGCTCCCGTGTGGCCTG*TTTGGGAGGCCGAGACGGGCGGATCACGAGGTCAGGAGATGGAGAGCATC	tcga,cell_lines,chimerdb3seq,tcga-cancer	BOWTIE+STAR	UTR/intronic	0	9	1	19	17	63705031	-	6	161440215	-	0.6346	0.7097	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DH-A669-02A	ENSG00000109685	ENSG00000168993	NSD2	CPLX1	AGTTTTTGGTCTTCTGTCAAAAACACAGGGATGAG*GGGCCACCAAGGACATGGGGAAGATGCTGGGGGGT	oncogene,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	136	15	24	4	1918623	+	4	792608	-	3.155	51.0185	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-DH-A669-02A	ENSG00000148498	ENSG00000145220	PARD3	LYAR	AGGCGGTGACCCGCTACCGGAAGGCCATCGCCAAG*GAACCAGTCAATAAGGAACAGGATCAACGGCCACT	cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	72	15	24	10	34814876	-	4	4274769	-	2.6867	18.3804	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-DH-A669-02A	ENSG00000151726	ENSG00000270111	ACSL1	AL583859.2	CATGCGACCTCTCCATGCAGTCAGTGGAAGTGGCG*AAGCTAGAGTCATCCTAACAAGAGTGATAGTCTTT	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	42	8	22	4	184803320	-	10	10422774	-	1.7441	0.8343	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DH-A669-02A	ENSG00000150867	ENSG00000245067	PIP4K2A	IGFBP7-AS1	TCTTCCGTAACCTGCGGGAGAGGTTTGGAATTGATGATCAAGATTTCCAG*GGTTGAAGATGACTCACTACCACCATGTCCAACCTCCAATTTGAAGGAAA	antisense	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	15	1	22	10	22607927	-	4	57179144	+	6.7629	1.9985	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DH-A669-02A	ENSG00000015171	ENSG00000154556	ZMYND11	SORBS2	GACGACGTAATCAAAGTGTGGAGCCCAAAAAGGAA*CCACAGCGTCCTGTGTTTACTCATGAAAATATTCA	cancer,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	10	3	18	10	247466	+	4	185593935	-	6.433	1.6814	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-DH-A669-02A	ENSG00000168993	ENSG00000120549	CPLX1	KIAA1217	TGGAAGCAGAGCAATCGCCATGGAGTTTGTGATGAAGCAGGCTCTAGGAG*GTCAAGCTTTGGAGAAATGGGACAGAAAGTCAAGGAGAGTTTTAACTTTA	NA	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	18	4	824492	-	10	23994500	+	51.0185	0.788	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-FG-A4MT-01A	ENSG00000215241	ENSG00000226711	LINC02449	FAM66C	TCCTGAGACAACGGAATTCTGGCGATGGAGCACAG*ATATAATACGTAAGTTTGGAGGTGGATGCTTTCAG	lincrna,antisense,10K<gap<100K,exon-exon	BOWTIE	exonic(no-known-CDS)/exonic(no-known-CDS)	0	2	3	24	12	8235999	+	12	8215806	+	0.9309	1.8828	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	lincRNA	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-HT-7602-01A	ENSG00000187164	ENSG00000197971	SHTN1	MBP	ACATTCACCTATTTTATGGACTAGTTTTCAAGGATTATTTTGGGATGTGG*ATGCGGGCTGGGCAGCTGTTAGAGTCCAACGTGGGGCAGCACAGAGAGGG	NA	BOWTIE+STAR	intronic/UTR	0	2	1	14	10	116980946	-	18	76979861	-	27.9484	715.1436	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7008-01A	ENSG00000055609	ENSG00000066427	KMT2C	ATXN3	GGCCGGCCTCGCAAAGATGGCGCTTCCCCTTTCCAGAGAGCCAGAAAGAA*ACTCAGCCCACCTGCACCCAGGTGAAATAAACAGCTTTATTGCTCACACA	cancer,m3	BOWTIE+BLAT	CDS(truncated)/UTR	0	5	3	22	7	152435626	-	14	92041844	-	14.3837	1.6987	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-FG-5965-01B	ENSG00000262583	ENSG00000166822	AC009163.5	TMEM170A	CAGGGATTTTCCTGGACGGGATTGTGAAGTAGCGG*AGATGTGGTATGGTGTATTCCTGTGGGCACTGGTG	pseudogene,10K<gap<100K,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	3	2	23	16	75516203	-	16	75451839	-	1.0419	11.9346	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	transcribed_unprocessed_pseudogene	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-TQ-A7RK-02B	ENSG00000068885	ENSG00000118849	IFT80	RARRES1	GACTGGGATGCTTAGATCAACTTTAGCTCAGCAAG*ATAATCATGGACATATTGATCCCTCTCTGAGACTC	cancer,m16,tcga-cancer,exon-exon	BOWTIE	in-frame	0	24	6	23	3	160375812	-	3	158704927	-	2.598	2.4072	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-TQ-A7RK-02B	ENSG00000124786	ENSG00000182793	SLC35B3	GSTA5	ATAGAACTTCAGCTTATTCAGGACAAAAGGAGGAG*GATTGATATGTACACAGAAGGTATAGTAGATTTGA	m4,tcga-cancer,exon-exon	BOWTIE	in-frame	0	6	4	23	6	8427937	-	6	52834282	-	3.6789	0.9029	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-FG-8182-01A	ENSG00000198740	ENSG00000197971	ZNF652	MBP	GCGGAGCGCTCACAATGTGGCAGGAGACAGAAAAG*GACTGTCCCTGAGCAGATTTAGCTGGGGGGCCGAA	exon-exon	BOWTIE	UTR/CDS(truncated)	0	2	1	14	17	49362413	-	18	76988520	-	6.138	231.6203	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-7304-01A	ENSG00000140262	ENSG00000110195	TCF12	FOLR1	CCTTGACTGGAATTTGATGTGCAGGGCTGTGCCAG*GGACAGACATGGCTCAGCGGATGACAACACAGCTG	cancer,exon-exon	BOWTIE	UTR/UTR	0	6	2	21	15	57134500	+	11	72192166	+	60.5562	19.4565	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-7304-01A	ENSG00000140262	ENSG00000110195	TCF12	FOLR1	CAGTTCAAGTGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGACTGCAA*GAACTGAACCCAAAGGATCACCTGGTATTCCCTGAGAGTACAGATTTCTC	cancer	BOWTIE+STAR	intronic/UTR	0	6	1	23	15	57119235	+	11	72190576	+	60.5562	19.4565	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-7304-01A	ENSG00000140262	ENSG00000110195	TCF12	FOLR1	CAGTTCAAGTGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGACTGCAA*GGACAGACATGGCTCAGCGGATGACAACACAGCTGCTGCTCCTTCTAGTG	cancer	BOWTIE+STAR	intronic/UTR	0	6	1	20	15	57119235	+	11	72192166	+	60.5562	19.4565	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-IK-7675-01A	ENSG00000066084	ENSG00000176225	DIP2B	RTTN	AAGATAGTTTCCAGTGGATGAGCCGCGTGCTGCAG*GTACCATCTACCTGTTCATGTAATTGGACACCATG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	16	4	20	12	50708562	+	18	70128546	-	31.0476	2.2951	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-IK-7675-01A	ENSG00000224533	ENSG00000155962	TMLHE-AS1	CLIC2	ATTGCTGATGGGAATCCTGCCCTAAGCAAACGGTG*GCTGGAAGTGATGGAGAGAGTATTGGAAACTGTCC	antisense,m3,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	7	2	23	X	155474601	+	X	155299145	-	0.0088	11.0725	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-IK-7675-01A	ENSG00000224533	ENSG00000155962	TMLHE-AS1	CLIC2	TAATTAATGAGTCAAGGTCTCAGGAGAGACAGAAG*GCTGGAAGTGATGGAGAGAGTATTGGAAACTGTCC	antisense,m3,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	7	1	13	X	155489389	+	X	155299145	-	0.0088	11.0725	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6401-01A	ENSG00000057608	ENSG00000106066	GDI2	CPVL	GAGGAGAGAGTGCATCTATAACACCATTGGAAGAT*ACCCTGAGAGATGGTTGGTGCCATGTGGAAGGTGA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	33	12	23	10	5800598	-	7	29121071	-	26.2177	8.1438	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-DU-6401-01A	ENSG00000234722	ENSG00000234338	LINC01287	AC073349.2	GGGAACCCCTCTCACCCTTGCCGAGCCCAGGGTAATGCTTCAGGTAGCGG*TACAGTTTCTCCGCCAGCGGATACAAGAAATCACCAGGGTCACTTTCAAC	pseudogene,lincrna	BOWTIE+STAR	exonic(no-known-CDS)/exonic(no-known-CDS)	0	2	2	19	7	153412091	-	7	64835419	-	0.0967	28.9978	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	processed_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-6401-01A	ENSG00000008441	ENSG00000129353	NFIX	SLC44A2	GCCCAGCTATGTACTCCCCGTACTGCCTCACCCAG*TGGAGGACCTGGAGAGGAATGACGGCTCGGCCGAG	cancer,exon-exon	BOWTIE	out-of-frame	0	2	1	13	19	12995864	+	19	10643279	+	149.1754	100.4396	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-HT-8104-01A	ENSG00000133789	ENSG00000166478	SWAP70	ZNF143	AAAGCAAGCAGCAGGAGCTGGAGGCCGTGCGGAAG*ATTGTTTTACAAGGACATGCTACAAGAGTAACTGC	oncogene,tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	33	6	23	11	9732710	+	11	9494646	+	10.5655	5.4175	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-HT-8104-01A	ENSG00000143850	ENSG00000087250	PLEKHA6	MT3	CAGCCCTCTCCTCTCTCCCTCGTGGGACTGGGAAAGCCAGAAAAAGGCAG*GCTGCTGCTCCTGCTGCCCTGCGGAGTGTGAGAAGTGTGCCAAGGACTGT	NA	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	17	2	21	1	204350880	-	16	56590840	+	3.2705	499.3267	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-HT-8104-01A	ENSG00000143850	ENSG00000087250	PLEKHA6	MT3	AGCTTTCCAGCGCGGGGATCACACCTCAGAAGCCG*GCTGCTGCTCCTGCTGCCCTGCGGAGTGTGAGAAG	exon-exon	BOWTIE	UTR/CDS(truncated)	0	17	2	18	1	204359694	-	16	56590840	+	3.2705	499.3267	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-HT-8104-01A	ENSG00000143850	ENSG00000087250	PLEKHA6	MT3	GATTCCACCCAGGAAGGAGCTGTGTATTTCATCAA*GCTGCTGCTCCTGCTGCCCTGCGGAGTGTGAGAAG	exon-exon	BOWTIE	CDS(no-known-start-or-end)/CDS(truncated)	0	17	1	14	1	204367799	-	16	56590840	+	3.2705	499.3267	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-HT-8104-01A	ENSG00000146648	ENSG00000197971	EGFR	MBP	GCTGTCCCATCAAGGAAGACAGCTTCTTGCAGCGATACAGCTCAGACCCC*AGAGATAGTCGCTCTGGATCACCCATGGCTAGACGCTGAAAACCCACCTG	oncogene,cancer,tumor	BOWTIE+BLAT	in-frame	0	13	1	22	7	55202573	+	18	76980465	-	1091.9211	102.9654	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-HT-8104-01A	ENSG00000102900	ENSG00000087258	NUP93	GNAO1	AGCCTCTTGAGCCTGTGAAGGACACTGACATTCAG*GATCATCCATGAAGATGGCTTCTCCGGAGAAGACG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	11	6	23	16	56758655	+	16	56275931	+	6.8328	17.9388	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-HT-8104-01A	ENSG00000145362	ENSG00000073331	ANK2	ALPK1	AATTGGTATTTCAAATGACCACCATGTTGCAAAAG*AGCCTGCTGAAGGAGTTTGACCACCATTTGCTGTC	known,tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	8	7	24	4	112904514	+	4	112429149	+	22.2836	2.5669	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-HT-8104-01A	ENSG00000145362	ENSG00000073331	ANK2	ALPK1	CCATGATCAGAATTCCTGCGGCTGATACAAACTGTAGGACTACATTGGAG*AGCCTGCTGAAGGAGTTTGACCACCATTTGCTGTCCGCTGCAGAAGCCTG	known,tcga,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	8	1	18	4	112917471	+	4	112429149	+	22.2836	2.5669	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-HT-8104-01A	ENSG00000146648	ENSG00000280890	EGFR	AC073324.2	GCCTTCATGGCCCCAGCAGGCCGGATCGGTACTGTATCAAGTCATGGCAG*GCACAGTAGGGTAAAGCAAAAGACAACCACACCCCAATCTCCAGGAAAAC	lincrna,oncogene,cancer,tumor	BOWTIE+STAR	UTR/intronic	0	8	1	18	7	55206197	+	7	55251805	-	1091.9211	12.3134	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-HT-8104-01A	ENSG00000146535	ENSG00000146648	GNA12	EGFR	CCAGAGCGCTGGGATTATAGGCATGAGCCACCGCGCCCAGCAGAGACCCA*AGCGATACAGCTCAGACCCCACAGGCGCCTTGACTGAGGACAGCATAGAC	oncogene,cancer,tumor	BOWTIE+BLAT	intronic/CDS(truncated)	0	3	1	20	7	2758855	-	7	55202554	+	60.8627	1091.9211	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-HT-8104-01A	ENSG00000146535	ENSG00000146648	GNA12	EGFR	CCCAGAGCGCTGGGATTATAGGCATGAGCCACCGCGCCCAGCAGAGACCC*AGCATAGACGACACCTTCCTCCCAGTGCCTGGTGAGTGGCTTGTCTGGAA	oncogene,cancer,tumor	BOWTIE+BLAT	intronic/CDS(truncated)	0	3	1	19	7	2758856	-	7	55202595	+	60.8627	1091.9211	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-HT-8104-01A	ENSG00000146535	ENSG00000146648	GNA12	EGFR	TCCCAGAGCGCTGGGATTATAGGCATGAGCCACCGCGCCCAGCAGAGACC*CAGTCCGTTCCCAAAAGGCCCGCTGGCTCTGTGCAGAATCCTGTCTATCA	oncogene,cancer,tumor	BOWTIE+BLAT	intronic/CDS(truncated)	0	3	1	18	7	2758857	-	7	55205267	+	60.8627	1091.9211	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-HT-8104-01A	ENSG00000130402	ENSG00000146648	ACTN4	EGFR	CAGGAAGGCTTGTAGGTGGGGCGAGCCAGGGTGAGAGTGTAGCCCTGTTC*ATGTAAGAAAAGCAATAACATAGCACTTTGTTGGTTTATATATATAATGT	oncogene,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	2	1	15	19	38684629	+	7	55210170	+	70.7088	1091.9211	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-5872-01A	ENSG00000100320	ENSG00000111716	RBFOX2	LDHB	ATTTACTTTTGGCGGGGGGAGGGAGAGAGAGAGAGAGAGAGAGTGTGTGT*GTGGCTGTGTGGAGTGGTGTGAATGTGGCAGGTGTTTCTCTCCAGGAATT	oncogene	BOWTIE+BLAT	intronic/UTR	0	2	1	22	22	35801441	-	12	21638471	-	8.423	8.5512	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7294-01A	ENSG00000187122	ENSG00000113140	SLIT1	SPARC	CGGATGGTTAATCTGCTCACAGACACACGCAACTGGCAGCTGGTGGGTGC*CAAGAAGGGCCACAAGCTCCACCTGGACTACATCGGGCCTTGCAAATGTG	oncogene	BOWTIE+STAR	intronic/CDS(truncated)	0	3	1	16	10	97140966	-	5	151669710	-	45.885	1493.7081	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-CS-5395-01A	ENSG00000143799	ENSG00000197971	PARP1	MBP	TGATTGAGAAACTCGGGGGGAAGTTGACGGGGACGGCCAACAAGGCTTCC*CTGCCCCAGAAGTCACACGGCCGGACCCAAGATGAAAACCCCGTAGTCCA	NA	BOWTIE+BLAT	in-frame	0	4	1	17	1	226381087	-	18	76990021	-	178.2415	66.6868	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-CS-6669-01A	ENSG00000133083	ENSG00000124507	DCLK1	PACSIN1	AGCTGGACTCGGGAGTGGTGAAACGCCTGTACACGTTGGATGGGAAACAG*ACGGAGTCTCACTCTGTCACCCAGGCTAAAGTGCAGTGGCACTATCTTGG	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	14	13	36111869	-	6	34495474	+	43.5175	183.5386	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6404-02A	ENSG00000183337	ENSG00000100393	BCOR	EP300	TTTTAATTATTGTGAAGGGTATCTAAAGACTGCATGACGTTTACCTATCA*ATATTTTTGTTATGGCTGGTTACCACCAGCCTTTCTTCCCCTTTGTGTGT	tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer	BOWTIE+BLAT	UTR/UTR	0	308	6	22	X	40072055	-	22	41179153	+	24.9805	9.9492	FALSE	TRUE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6404-02A	ENSG00000100393	ENSG00000183337	EP300	BCOR	CCCAGCATGGTCAACCTTTGAACATGGCTCCACAACCAGGATTGGGCCAG*CGTGCAATGATGCGCTTCTCAGAGTTGGAGATGAAAGAAAGAGAAGGTGG	tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	308	14	24	22	41177816	+	X	40071159	-	9.9492	24.9805	TRUE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6404-02A	ENSG00000100393	ENSG00000183337	EP300	BCOR	CCCAGCATGGTCAACCTTTGAACATGGCTCCACAACCAGGATTGGGCCAG*ATGGAAGGATTACAAGAGGACAGTATTTTATGTCTACCCGCTGCTTACTG	tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	308	12	24	22	41177816	+	X	40071690	-	9.9492	24.9805	TRUE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6404-02A	ENSG00000100393	ENSG00000183337	EP300	BCOR	ATGTGGAGACACGCTGGCACTGTACTGTCTGTGAG*ATGGAAGGATTACAAGAGGACAGTATTTTATGTCT	tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	308	2	23	22	41176528	+	X	40071690	-	9.9492	24.9805	TRUE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6404-02A	ENSG00000100393	ENSG00000183337	EP300	BCOR	AGTAGCCGTTTGTGGTTTAAAGCAAACATGCAAGATGAACCTGAGGGATG*ATACCTGGTAGAGATGTGTAGCAGCCGCATGTCTGTGGGATTCATGCAAA	tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer	BOWTIE+BLAT	UTR/UTR	0	308	1	20	22	41179136	+	X	40071985	-	9.9492	24.9805	TRUE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6404-02A	ENSG00000133028	ENSG00000004848	SCO1	ARX	GCCCTGGCCCCAAGGACGAAGATGAAGACTACATA*GCTCTTTTCCACAATGGCCCCCCTGACCAGCGCGT	tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	25	9	22	17	10686727	-	X	25004910	-	2.5358	8.1732	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6405-01A	ENSG00000101752	ENSG00000260372	MIB1	AQP4-AS1	GCTCTGCATCATGCTGCACTAAGGGGAAATCCCAG*GAACCTGTGGATTGGATGATTCTGCGTTGTGGCAG	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	9	3	24	18	21819646	+	18	26764216	+	4.7636	2.1611	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-6404-01A	ENSG00000183337	ENSG00000100393	BCOR	EP300	TTTTAATTATTGTGAAGGGTATCTAAAGACTGCATGACGTTTACCTATCA*ATATTTTTGTTATGGCTGGTTACCACCAGCCTTTCTTCCCCTTTGTGTGT	tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer	BOWTIE+BLAT	UTR/UTR	0	320	9	23	X	40072055	-	22	41179153	+	21.3349	12.7203	FALSE	TRUE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6404-01A	ENSG00000100393	ENSG00000183337	EP300	BCOR	CCCAGCATGGTCAACCTTTGAACATGGCTCCACAACCAGGATTGGGCCAG*CGTGCAATGATGCGCTTCTCAGAGTTGGAGATGAAAGAAAGAGAAGGTGG	tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	320	13	22	22	41177816	+	X	40071159	-	12.7203	21.3349	TRUE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6404-01A	ENSG00000100393	ENSG00000183337	EP300	BCOR	CCCAGCATGGTCAACCTTTGAACATGGCTCCACAACCAGGATTGGGCCAG*ATGGAAGGATTACAAGAGGACAGTATTTTATGTCTACCCGCTGCTTACTG	tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	320	10	23	22	41177816	+	X	40071690	-	12.7203	21.3349	TRUE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6404-01A	ENSG00000100393	ENSG00000183337	EP300	BCOR	ATGTGGAGACACGCTGGCACTGTACTGTCTGTGAG*ATGGAAGGATTACAAGAGGACAGTATTTTATGTCT	tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	320	2	20	22	41176528	+	X	40071690	-	12.7203	21.3349	TRUE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-DU-6404-01A	ENSG00000100393	ENSG00000183337	EP300	BCOR	AGAAACTATATGCCACCATGGAGAAGCATAAAGAG*CGTGCAATGATGCGCTTCTCAGAGTTGGAGATGAA	tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	320	2	18	22	41173784	+	X	40071159	-	12.7203	21.3349	TRUE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-DU-6404-01A	ENSG00000075303	ENSG00000105784	SLC25A40	RUNDC3B	ATTAAATCTCTATGGAGTGGCCTTCCTCCTACCCT*GAAAAGTTATCAAAGTCTTGACCAGTTATCAGCAG	exon-exon	BOWTIE	in-frame	0	2	2	19	7	87849881	-	7	87816141	+	2.9204	1.1631	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-FG-5965-02A	ENSG00000164808	ENSG00000126267	SPIDR	COX6B1	TGAAAACACCTGGCCGCGACCAGCCCTGTGAAGAG*GTCACAGACTGGGATGAGCAACGGGCTGAAGGCAC	cell_lines,tcga-cancer,exon-exon	BOWTIE	in-frame	0	48	7	23	8	47700490	+	19	35658594	+	6.2241	66.4127	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-HW-7495-01A	ENSG00000173517	ENSG00000169783	PEAK1	LINGO1	ATGCAAAAGATCCACTTAATAACTATGCAGTCAAG*GGATCTTATGACCATGACCTGGCTACCTTGAGTCT	cell_lines,100K<gap<200K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	6	2	24	15	77133005	-	15	77690901	-	5.1499	30.2776	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-7010-01A	ENSG00000105497	ENSG00000111012	ZNF175	CYP27B1	GGAGGAGGCTGAAGTCTCACATCAGAGGTGTCAAG*GTGTCCAACACGCTCTCTTGGGCTCTGTATGAGCT	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	348	17	24	19	51581882	+	12	57764550	-	7.1436	24.9062	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-7010-01A	ENSG00000105497	ENSG00000111012	ZNF175	CYP27B1	TTAAAAATATACCTGAATAGTTTTCATCACTCATGCTCTGCTCCATTGTT*TGACAGAGTTGCTATTGGCGGGAGTGGACACGGTGAGGTTCTCCCTCCGT	tcga,chimerdb3seq,tcga-cancer	BOWTIE+BLAT	intronic/CDS(truncated)	0	348	1	22	19	51583815	+	12	57764785	-	7.1436	24.9062	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7010-01A	ENSG00000159267	ENSG00000182362	HLCS	YBEY	CCTTAACTCCTCTTTACTTGCTGTCAGCTGCGGAG*CATCTGAAAGCAGGTGAATTTCCCCAGCCTGATTT	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	18	2	19	21	36930251	-	21	46291334	+	2.7614	4.4447	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7010-01A	ENSG00000155980	ENSG00000167685	KIF5A	ZNF444	CTGCAGGCCACACCCAGCTCCACCTCAGATATGTA*GGGCCAGCAGCCTCCCCCGATGGGTCGTCAGCAAC	exon-exon	BOWTIE	out-of-frame	0	10	2	17	12	57581568	+	19	56158494	+	29.071	4.1928	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-7010-01A	ENSG00000135439	ENSG00000007255	AGAP2	TRAPPC6A	CGGGCGCGCTTCAGCGCCGGACAACGACCTACCTCATCTCGCTGACCCTG*CTACTGGGGAGGCTGAGGCAGGAGATTCACTTGAACCCGGGAGGCAGAGG	oncogene,cancer,tumor	BOWTIE+STAR	CDS(truncated)/intronic	0	8	2	22	12	57738184	-	19	45167613	-	5.3961	74.5069	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-7010-01A	ENSG00000135439	ENSG00000007255	AGAP2	TRAPPC6A	GTGAGGGGAGCGCCCGGACACAGCGCGCATCCGGACCAAGCCGAGCCCAG*CCTGGGCAACAAGAGCGAAACTCCGACCTCCCAAAGTGCTGGAATTACAG	oncogene,cancer,tumor	BOWTIE+BLAT	intronic/intronic	0	8	1	22	12	57738912	-	19	45167528	-	5.3961	74.5069	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7006-01A	ENSG00000257621	ENSG00000100578	PSMA3-AS1	KIAA0586	CTCCATCGCATTTTATGTTTCTGGCGAGAAGGGAACGGAGTTTTCATCAG*GTGGGAAAGCAGTGCCACTCTCCGCTTCACAGATGCCCCCTGCCAAGATG	antisense,chimerdb3seq	BOWTIE+BLAT;BOWTIE+STAR	exonic(no-known-CDS)/CDS(truncated)	0	227	1	21	14	58298044	-	14	58547781	+	2.6225	3.3973	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7006-01A	ENSG00000100575	ENSG00000119616	TIMM9	FCF1	TCCAGAACAGAAAGGAAACTCATGCATCAGAAAAG*GTATCCCATGTATAACCGATTGTGTAATGGCTGAA	tcga,chimerdb3seq,m115,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	157	17	23	14	58424008	-	14	74723272	+	6.4843	12.555	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7006-01A	ENSG00000100575	ENSG00000119616	TIMM9	FCF1	TTGTACTGATGTCGGATGCGAGAGCCTGTGCTTAA*GTATCCCATGTATAACCGATTGTGTAATGGCTGAA	tcga,chimerdb3seq,m115,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	157	3	23	14	58427054	-	14	74723272	+	6.4843	12.555	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7006-01A	ENSG00000103429	ENSG00000169682	BFAR	SPNS1	GCGTGAAGCCCCCCCAGAATCTCTGGGAATATAAG*ATTTTCATCTTCATTGGAGAGACCCTCCTGTCCAT	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	57	11	22	16	14655210	+	16	28982857	+	12.7268	0.103	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7006-01A	ENSG00000103429	ENSG00000169682	BFAR	SPNS1	AGGGAAAGGTTTTTATCTGAACGAGTAAATGGAAG*TCTCATCTTTGGACTCATCACCTGCCTGACCGGAG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	57	5	24	16	14649973	+	16	28982356	+	12.7268	0.103	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7006-01A	ENSG00000103429	ENSG00000169682	BFAR	SPNS1	GCGTGAAGCCCCCCCAGAATCTCTGGGAATATAAG*TCTCATCTTTGGACTCATCACCTGCCTGACCGGAG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	57	3	21	16	14655210	+	16	28982356	+	12.7268	0.103	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7006-01A	ENSG00000071242	ENSG00000152034	RPS6KA2	MCHR2	ATGTGGAGCCCACCACAGAAGACACTGCAGAAGAA*CTTTAATCCCTGGAAAGTCCACGAACAATGAATCC	known,ribosomal,tcga,chimerdb3seq,tumor,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	12	6	23	6	166858200	-	6	99956174	-	8.7858	2.3357	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7006-01A	ENSG00000071242	ENSG00000152034	RPS6KA2	MCHR2	CTGCCTGCAAGACAAAGGTAGCTGGATCCGTAGAG*CTTTAATCCCTGGAAAGTCCACGAACAATGAATCC	known,ribosomal,tcga,chimerdb3seq,tumor,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	12	2	21	6	166770863	-	6	99956174	-	8.7858	2.3357	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7006-01A	ENSG00000182732	ENSG00000151322	RGS6	NPAS3	TTCCTGGAGTCCGAATTCAGTTCAGAAAACCTCAG*GTGGAGCTGACAGGCAGCAGTGTCTTTGACTATGT	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	11	3	24	14	72510279	+	14	33676211	+	2.4671	6.1121	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7006-01A	ENSG00000182732	ENSG00000151322	RGS6	NPAS3	GACCAGTTTCTACGATTCCTGGAGTCCGAATTCAGTTCAGAAAACCTCAG*CAGGAAAACTTTACAAGGTCACAACAGAGCATATTGTTTGTGGTGTCAGA	tcga,chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	11	1	21	14	72510279	+	14	33642722	+	2.4671	6.1121	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7006-01A	ENSG00000120063	ENSG00000113580	GNA13	NR3C1	AGAATGCCTATGACCGGCGTCGAGAATTTCAACTG*TTCCTAAGGACGGTCTGAAGAGCCAAGAGCTATTT	oncogene,tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	9	7	23	17	65053502	-	5	143282725	-	17.794	11.763	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7006-01A	ENSG00000113594	ENSG00000135241	LIFR	PNPLA8	CAGGGGATGGCAAGATAGCGGCGCGGGAGCGTACC*ATTGTCTTCTCCTCCAAGGTCTACATGATTACCTG	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	UTR/UTR	0	2	2	17	5	38556334	-	7	108521521	-	7.7627	19.3451	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-DU-6402-01A	ENSG00000159842	ENSG00000104774	ABR	MAN2B1	GCCAGGTCACCATGGGCCACCTCTTCCAGAAGCTG*ACATGCCCCACAGTGCAGCCGAACATGCTGAACGT	tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	38	9	23	17	1091665	-	19	12665805	-	16.9157	16.2406	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-DU-6402-01A	ENSG00000196419	ENSG00000131508	XRCC6	UBE2D2	CGCGCCAAGGAGACCAGGAAGCGAGCACTCAGCAG*TGTTCCATTGGCAAGCTACAATAATGGGGCCAAAT	cancer,m9,exon-exon	BOWTIE	out-of-frame	0	10	5	22	22	41637791	+	5	139614586	+	101.3301	25.0302	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-6402-01A	ENSG00000196419	ENSG00000131508	XRCC6	UBE2D2	GGCCAGGACCAAAGCCGGTGATCTCCGAGATACAG*TGTTCCATTGGCAAGCTACAATAATGGGGCCAAAT	cancer,m9,exon-exon	BOWTIE	in-frame	0	10	1	13	22	41636770	+	5	139614586	+	101.3301	25.0302	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-CS-6186-01A	ENSG00000068078	ENSG00000196361	FGFR3	ELAVL3	ACCTGGACCGTGTCCTTACCGTGACGTCCACCGAC*CAGATACTGGGGGCCATGGAGTCTCAGGTGGGGGG	known,oncogene,tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	294	15	24	4	1806934	+	19	11466827	-	332.5462	162.1026	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-CS-6186-01A	ENSG00000068078	ENSG00000196361	FGFR3	ELAVL3	ACCCAGCAGTGGGGGCTCGCGGACGTGAAGGGCCACTGGTCCCCAACAAT*ATACTGGGGGCCATGGAGTCTCAGGTGGGGGGGGGCCCGGCCGGCCC	known,oncogene,tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer	BOWTIE+STAR	out-of-frame	0	294	12	24	4	1807284	+	19	11466824	-	332.5462	162.1026	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-CS-6186-01A	ENSG00000068078	ENSG00000196361	FGFR3	ELAVL3	CCCCGGCATGAGACTCAGTGCAGATGGAGAGACAGCTACACAGAGCTTTG*ATACTGGGGGCCATGGAGTCTCAGGTGGGGGGGGGCCCGGCCGGCCC	known,oncogene,tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer	BOWTIE+STAR	UTR/CDS(truncated)	0	294	9	23	4	1807380	+	19	11466824	-	332.5462	162.1026	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-CS-6186-01A	ENSG00000068078	ENSG00000267477	FGFR3	AC008481.3	AGCAGCTGGTGGAGGACCTGGACCGTGTCCTTACCGTGACGTCCACCGAC*ATACTGGGGGCCATGGAGTCTCAGGTGGGGGGGGGCCCGGCCGGCCCGGC	oncogene,cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/CDS(no-known-start-or-end)	0	282	15	24	4	1806934	+	19	11466824	-	332.5462	0	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-CS-6186-01A	ENSG00000068078	ENSG00000267477	FGFR3	AC008481.3	ACCCAGCAGTGGGGGCTCGCGGACGTGAAGGGCCACTGGTCCCCAACAAT*CAGATACTGGGGGCCATGGAGTCTCAGGTGGGGGGGGGCCCGGCCGGCCC	oncogene,cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/CDS(no-known-start-or-end)	0	282	12	24	4	1807284	+	19	11466827	-	332.5462	0	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-CS-6186-01A	ENSG00000068078	ENSG00000267477	FGFR3	AC008481.3	CCCCGGCATGAGACTCAGTGCAGATGGAGAGACAGCTACACAGAGCTTTG*CAGATACTGGGGGCCATGGAGTCTCAGGTGGGGGGGGGCCCGGCCGGCCC	oncogene,cancer	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(no-known-start-or-end)	0	282	8	23	4	1807380	+	19	11466827	-	332.5462	0	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-CS-6186-01A	ENSG00000068078	ENSG00000267477	FGFR3	AC008481.3	CCCCTCCAAGCCTAAAAGGTTGTTAATAGTTGGAGGTGATTCCAGTGAAG*AGATCTCACTGTGTTGCCCAGGCTGGGCTTGAACTCCTGAGCTCAACCAG	oncogene,cancer	BOWTIE+BLAT	UTR/intronic	0	282	1	20	4	1808332	+	19	11472528	-	332.5462	0	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DB-5278-01A	ENSG00000131095	ENSG00000008441	GFAP	NFIX	GTTGCTCCGCCTCTGCTGGCACATTTCCCCAGACCTGAGCTCCCCACCAC*CCCCTCTTCTCTGCCCTCCACCCCCGTCTCTGCACTGAGATACATAAGAA	cancer	BOWTIE+BLAT	UTR/UTR	0	5	1	23	17	44907236	-	19	13098532	+	1136.1813	78.4674	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DB-5278-01A	ENSG00000069667	ENSG00000158258	RORA	CLSTN2	GGTGCGCAGACAGAGCTATTCCAGCACCAGCAGAG*TCAATAAGCACAAGCCATGGATCGAGACTTCATAT	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	3	3	23	15	61229053	-	3	140175951	+	0.8997	6.3249	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-TM-A7CF-02A	ENSG00000178951	ENSG00000186529	ZBTB7A	CYP4F3	TCCTGGGGGCCACAGCCTCTGCATGGGCCCAGAGCCGGGACCCCCCCAGC*CCTGGGGGAGGGGGACATAGCGAGACTCGGTCTCAAAAACAAAACAAAAC	oncogene,m34	BOWTIE+BLAT	UTR/UTR	0	36	4	24	19	4044977	-	19	15661234	+	16.1204	1.46	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-TM-A7CF-02A	ENSG00000074842	ENSG00000177558	MYDGF	FAM187B	GAAAACTGAGGAATTTGAAGTGACCAAAACAGCAG*GCCCGTCAACTGGCGTGCCAACGACACCCCCCTGA	tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	20	4	23	19	4659931	-	19	35225212	-	41.3918	0.7379	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-TM-A7CF-02A	ENSG00000105325	ENSG00000104946	FZR1	TBC1D17	GCAATCTGGCCTGGTCCAAGCACGCCAACGAGCTG*ATTCCCAGGACTCCGGCTCTCTCTGCTTCTGTTTC	oncogene,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	13	6	23	19	3532650	+	19	49887476	+	18.4396	29.0442	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-TM-A7CF-02A	ENSG00000064932	ENSG00000104938	SBNO2	CLEC4M	CCAGCTTGCCACCAAAGACCTGCGACTTTGCTCAG*TGTCCAAGGTCCCCAGCTCCCTAAGTCAGGAACAA	m9,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	12	4	20	19	1147309	-	19	7765638	+	4.771	1.0769	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-TM-A7CF-02A	ENSG00000126461	ENSG00000010030	SCAF1	ETV7	GCAAGAGCAGCCAGAAGGATCGGCGCCGCTCGGGGGCCGCCTCCTCCTCC*GGCCCTTGTCTCCTCTATCCACTTCCATCCTGTTGCCTCCCACCCGCTAC	cancer	BOWTIE+BLAT	CDS(truncated)/intronic	0	10	3	24	19	49652669	+	6	36375601	-	32.1726	4.9815	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-TM-A7CF-02A	ENSG00000126461	ENSG00000010030	SCAF1	ETV7	GCCCCGTCTCAGGGCCTGGAGGACGGGCAAAACGG*GTGACGTCCTGTATGAGCTGCTCCAGTACATCAAG	cancer,exon-exon	BOWTIE	in-frame	0	10	3	23	19	49646830	+	6	36373578	-	32.1726	4.9815	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-TM-A7CF-02A	ENSG00000126461	ENSG00000010030	SCAF1	ETV7	GACCCTGGCGGGCATCTACGATGACAACAGCCTGAGCCAGGACTTCCCAG*GTGACGTCCTGTATGAGCTGCTCCAGTACATCAAGACCCAGCGGCGAGCC	cancer	BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	10	1	19	19	49651335	+	6	36373578	-	32.1726	4.9815	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-TM-A7CF-02A	ENSG00000112715	ENSG00000112079	VEGFA	STK38	GTGTGCCCACTGAGGAGTCCAACATCACCATGCAG*GCCTTCTCCACAGTAGGCACTCCTGACTACATTGC	known,tcga,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	9	5	22	6	43777665	+	6	36499990	-	2.3935	11.9886	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-TM-A7CF-02A	ENSG00000124713	ENSG00000125650	GNMT	PSPN	TGGGCGACTTCAAGCCTTACAAGCCAGGCCAAACCTACATTCCCTGCTAC*CCAGAAGCTGCAGTGCTGGGGGAGCTCGGCTGACTTATTTATTGGAGACC	NA	BOWTIE+BLAT	CDS(truncated)/UTR	0	5	1	18	6	42963676	+	19	6375275	-	1.8813	1.8143	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-TM-A7CF-02A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	GCCTGCCTCAGCCTCCAAAGTAGCTGAGACTACAG*CAGTTTAAGTATAGTGTGCCTGGGTTGGGTGCGGT	antisense,m2,exon-exon	BOWTIE	exonic(no-known-CDS)/UTR	0	5	5	22	10	87246115	-	10	46593287	+	1.2442	0.1101	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-TM-A7CF-02A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	GGAGCTTCTCAGAAGACAGAGGGTTTTCTTTTGAG*CAGTTTAAGTATAGTGTGCCTGGGTTGGGTGCGGT	antisense,m2,exon-exon	BOWTIE	exonic(no-known-CDS)/UTR	0	5	4	24	10	87288442	-	10	46593287	+	1.2442	0.1101	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-TM-A7CF-02A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	GCCTGCCTCAGCCTCCAAAGTAGCTGAGACTACAG*GTGTGTTTGTCAAAGTGTCTCTGATGAACCACAAC	antisense,m2,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	5	2	23	10	87246115	-	10	46585598	+	1.2442	0.1101	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-TM-A7CF-02A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	GGAGCTTCTCAGAAGACAGAGGGTTTTCTTTTGAG*GTGTGTTTGTCAAAGTGTCTCTGATGAACCACAAC	antisense,m2,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	5	2	16	10	87288442	-	10	46585598	+	1.2442	0.1101	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-TM-A7CF-02A	ENSG00000137413	ENSG00000080573	TAF8	COL5A3	CGGCCGGTGAAGAAGCCCAAGATCCGCAGGAAGAA*ATCCTGTGGATGTCCTGAAGGCCCTGGGTGTGCAG	tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	4	4	22	6	42077239	+	19	10006231	-	3.6677	6.3174	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-TM-A7CF-02A	ENSG00000130287	ENSG00000142546	NCAN	NOSIP	CCTCCCCAGCTATGGGGGCAGCTTTTGTGAGAAAG*GATGACGCGGCATGGCAAGAACTGCACCGCAGGGG	tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	3	4	23	19	19235096	+	19	49560692	-	82.4129	12.5175	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-TM-A7CF-02A	ENSG00000013297	ENSG00000197971	CLDN11	MBP	GGGAAATGTGGGTAAGGTTTTTCATGCTCTGTGACCATGTAGGCTGTCAC*CTGTGATTGATAGGCCTTCCAAAGAGTCCCACGCTGGCATCACCCTCCCC	NA	BOWTIE+STAR	intronic/UTR	0	2	1	16	3	170630328	+	18	76979197	-	106.7194	784.228	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-TM-A7CF-02A	ENSG00000013297	ENSG00000197971	CLDN11	MBP	AAATAAATGAGCAGACCTGTGGGGCGAGGGGAAAG*GGGAGAGGACTGTCCCTGAGCAGATTTAGCTGGGG	exon-exon	BOWTIE	UTR/CDS(truncated)	0	2	1	14	3	170467396	+	18	76988527	-	106.7194	784.228	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-TM-A7CF-02A	ENSG00000141985	ENSG00000183207	SH3GL1	RUVBL2	GGCTCCCGCCTAGCGGGCCGCAGTTCCACACCTGG*GTGACACAGGGGAGATCAAGTCAGAAGTCCGTGAG	cancer,tumor,exon-exon	BOWTIE	UTR/CDS(truncated)	0	2	7	23	19	4390052	-	19	49010999	+	35.6084	18.623	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-TQ-A7RK-01A	ENSG00000068885	ENSG00000118849	IFT80	RARRES1	GACTGGGATGCTTAGATCAACTTTAGCTCAGCAAG*ATAATCATGGACATATTGATCCCTCTCTGAGACTC	cancer,m12,tcga-cancer,exon-exon	BOWTIE	in-frame	0	24	11	23	3	160375812	-	3	158704927	-	2.1995	3.9067	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-HT-7475-01A	ENSG00000133243	ENSG00000220008	BTBD2	LINGO3	CACTTCCTGGTGGGCAAGGGGCTCAGCTCGCAGCGCATCCCCGCGCACAG*GTGCGCAGGAGGATGGTGGCGCGGCCCTAGGCCCACGCTCCGCACCATGA	tcga,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	12	2	23	19	2015297	-	19	2291822	-	27.8817	3.6073	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-HT-A5R7-01A	ENSG00000109265	ENSG00000184178	KIAA1211	SCFD2	TCCAACAAGAAAAAGACCTGTGGCTATTAAGATAG*GCATCTTATAAGCCATTGTTGAAGCAAGTTGTGGA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	175	13	24	4	56179430	+	4	52907591	-	5.2564	19.139	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-HT-A5R7-01A	ENSG00000109265	ENSG00000184178	KIAA1211	SCFD2	TCCAACAAGAAAAAGACCTGTGGCTATTAAGATAG*GTGAGCCGGCCTCATCCTAGTGACTACCCCCTCCT	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	175	5	22	4	56179430	+	4	52885866	-	5.2564	19.139	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-HT-A5R7-01A	ENSG00000109265	ENSG00000184178	KIAA1211	SCFD2	TAAACTTACAAAGAATGTCCATAATGAGGCTGTGAGTGCTGATGTTTCAG*GCATCTTATAAGCCATTGTTGAAGCAAGTTGTGGAGGAAATATTTCATCC	tcga,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	175	2	24	4	56196427	+	4	52907591	-	5.2564	19.139	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-HT-A5R7-01A	ENSG00000131095	ENSG00000196535	GFAP	MYO18A	TGGAGAGGCAGATGCGCGAGCAGGAGGAGCGGCAC*CTGGAGGAGCAGCTGAGCCGCCTTCAGCGTGAGAA	exon-exon	BOWTIE	in-frame	0	2	1	13	17	44911412	-	17	29090926	-	2312.6933	7.8955	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-HT-A5R7-01A	ENSG00000109265	ENSG00000134853	KIAA1211	PDGFRA	GCTCTGCCAGCCGGAGCGCCAGGCGGGGACCTCAG*ATGTAATAATGAAACTTCCTGGACTATTTTGGCCA	oncogene,cancer,tumor,exon-exon	BOWTIE	UTR/CDS(truncated)	0	2	4	24	4	56049299	+	4	54273537	+	5.2564	37.7633	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-7301-01A	ENSG00000117528	ENSG00000137962	ABCD3	ARHGAP29	GTTTGGATGATTCAAAATGGGACACTAATTGAAAG*GTGACGTTATATTCCTATTCGAAGACCAAGAGCTC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	7	2	22	1	94468007	+	1	94150515	-	25.2909	0.9125	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7301-01A	ENSG00000108100	ENSG00000079308	CCNY	TNS1	AGAATTAGCATGTGTGTTTATATAAATTGTGAAATCATCTTCTCCCACTT*TTTTTTTTTCAGCTTTAGGACCTGGGGAGATCCTGTGAGTCAAGGCAGAC	NA	BOWTIE+STAR	intronic/UTR	0	2	2	14	10	35451223	+	2	217800757	-	20.6991	10.1164	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7013-01A	ENSG00000135506	ENSG00000155980	OS9	KIF5A	TGAGCCCAATGAGAGATGCTCCCTGCTTGCTGAAG*GGTTGTACTGAACGCTTTGTGTCCAGCCCGGAGGA	known,tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	61	11	24	12	57694926	+	12	57567126	+	521.1991	116.9605	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-DU-7013-01A	ENSG00000135407	ENSG00000166987	AVIL	MBD6	ACTTCTATGAGGGGGACTGCTACGTCATCCTCTCG*GTGACCTGTCTTCACTGACCAGCAGCCCTGGAGCC	exon-exon	BOWTIE	out-of-frame	0	17	10	24	12	57814152	-	12	57527848	+	11.491	99.4865	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-DU-7013-01A	ENSG00000135407	ENSG00000175203	AVIL	DCTN2	ACTTCTATGAGGGGGACTGCTACGTCATCCTCTCG*GAGCTGGAGGAGCTGACAAGCACAAGTGTGGAACA	cell_lines,exon-exon	BOWTIE	in-frame	0	8	7	24	12	57814152	-	12	57538524	-	11.491	161.5213	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7013-01A	ENSG00000106278	ENSG00000155980	PTPRZ1	KIF5A	CTCTCTCACACACACACACACACACACAAACACACATACGCACGCACGAT*CCCACCTCTTCCTCCACCCTGAAATAATTTTGGATGGATAGGTGTTTTTG	NA	BOWTIE+BLAT;BOWTIE+STAR	UTR/intronic	0	5	1	21	7	121873372	+	12	57583582	+	894.0692	116.9605	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7013-01A	ENSG00000120885	ENSG00000166025	CLU	AMOTL1	ACAAACGAAGAGCGCAAGACACTGCTCAGCAACCTAGAAGAAGCCAAGAA*GAAGACAAGAGGTGTAAGCTGGAGAGGGAAGGGAAGAAATCAGTGGCTTT	cancer	BOWTIE+BLAT	CDS(truncated)/UTR	0	2	1	22	8	27608948	-	11	94872541	+	1858.4987	5.5272	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7013-01A	ENSG00000120885	ENSG00000092820	CLU	EZR	CAGCAACCTAGAAGAAGCCAAGAAGAAGAAAGAGG*ACGCTGAGCAGCGAGCTGTCCCAGGCCCGAGATGA	cancer,exon-exon	BOWTIE	CDS(no-known-start-or-end)/CDS(truncated)	0	2	1	13	8	27608937	-	6	158767078	-	1858.4987	97.4048	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-7013-01A	ENSG00000175215	ENSG00000135454	CTDSP2	B4GALNT1	GCGGAGGGAAGACGCCCTGGTGCTCACCAAGCAAG*GATGTGGCTGGGCCGCCGGGCCCTGTGCGCTCTGG	chimerdb3seq,100K<gap<200K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	2	2	23	12	57846372	-	12	57632133	-	256.5487	95.6653	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-FG-6692-01A	ENSG00000127483	ENSG00000162542	HP1BP3	TMCO4	AAGCAAGCTTGCTGAAGGGGAGGAAGAAAAGCCAG*GGGCGACGACCTGTCACCTTGATTGGCTTCAGCCT	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	25	4	21	1	20779812	-	1	19737456	-	16.9917	8.4619	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-E1-5318-01A	ENSG00000138468	ENSG00000066422	SENP7	ZBTB11	TTCCTGATTCAATCTTGTAGGTTGTATGTCTCTAGGAATTTTTCAGTTTC*CTGGAACGGGTGTGTGAAAAATGTGGAAGAAAATTCACTCAGCTAAGAGA	100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	17	4	20	3	101391491	-	3	101652574	-	5.7833	6.5646	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-E1-5318-01A	ENSG00000138092	ENSG00000173960	CENPO	UBXN2A	GAACCCTTTACGTCCAGATGGCGAGTCCAAAGGAG*TAAGGCGAAAGAGAATGAAAGACGTAGATAACCTC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	4	2	15	2	24793965	+	2	23958301	+	2.0993	4.127	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-E1-5303-01A	ENSG00000123066	ENSG00000196091	MED13L	MYBPC1	TGCCATGTCTATTTTCAGTTCTGCTACTAAAACAG*CTGAGGACTGGATAGTTGCAAACAAAGATCTGATT	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	31	7	24	12	116006306	-	12	101667732	+	3.3882	15.539	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-E1-5303-01A	ENSG00000089159	ENSG00000196091	PXN	MYBPC1	AGCCGGCGCCCGTGGTCCGGCCATGGACGACCTCG*AGCCTCCAATTATGGTGACCAAACAGCTGGAAGAT	tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	12	3	18	12	120265617	-	12	101648045	+	3.1155	15.539	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-DU-6397-02A	ENSG00000140945	ENSG00000103154	CDH13	NECAB2	TTGTCGGGGGGAAAGACATCCAGGGCTCCTTGCAG*CACCTGCAGCTGGTCCGGCAGGAGATGGCCGTGTG	cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	9	6	23	16	83032218	+	16	83998205	+	2.6885	4.9819	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-6397-02A	ENSG00000182670	ENSG00000215386	TTC3	MIR99AHG	TGCCCGCGTCCGAGGCTCGCGGGCGGCGGGCCCGG*GGAAAAACTTAAAATGGATATGAAAAGTGAAGAAA	lincrna,oncogene,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	9	2	20	21	37073364	+	21	16537379	+	32.6638	0.6436	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-6397-02A	ENSG00000182670	ENSG00000215386	TTC3	MIR99AHG	TGCCCGCGTCCGAGGCTCGCGGGCGGCGGGCCCGG*ATGACAAGAGCACCTCAAAGGCAGCAGCCTCAAGG	lincrna,oncogene,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	9	2	16	21	37073364	+	21	16606994	+	32.6638	0.6436	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-DU-6397-02A	ENSG00000275052	ENSG00000115607	PPP4R3B	IL18RAP	CCACAAACTTGCCTACGTCAGTAACAGCCACCAAG*AATGGAAAACTCCTCTCTGTGGAAAGGAGCAACCG	tcga-cancer,exon-exon	BOWTIE	in-frame	0	8	2	17	2	55558775	-	2	102437212	+	15.498	0.951	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-HT-A61B-01A	ENSG00000186111	ENSG00000105289	PIP5K1C	TJP3	CCCCTGCGCCCGGAAGAGCTCAGCACAGTGCAGATCCTGGTGAACATCAG*GTGGCTGACATGGAGGAGCTGACCATCTGGGAACAGCACACGGCCACACT	cell_lines,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	20	19	3696277	-	19	3728424	+	14.1882	2.6393	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-TM-A7CF-01A	ENSG00000178951	ENSG00000186529	ZBTB7A	CYP4F3	TCCTGGGGGCCACAGCCTCTGCATGGGCCCAGAGCCGGGACCCCCCCAGC*CCTGGGGGAGGGGGACATAGCGAGACTCGGTCTCAAAAACAAAACAAAAC	oncogene,m39	BOWTIE+BLAT	UTR/UTR	0	43	6	23	19	4044977	-	19	15661234	+	18.5374	1.1214	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-TM-A7CF-01A	ENSG00000112715	ENSG00000112079	VEGFA	STK38	GTGTGCCCACTGAGGAGTCCAACATCACCATGCAG*GCCTTCTCCACAGTAGGCACTCCTGACTACATTGC	known,tcga,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	23	5	23	6	43777665	+	6	36499990	-	1.9996	9.8408	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-TM-A7CF-01A	ENSG00000126461	ENSG00000010030	SCAF1	ETV7	GCCCCGTCTCAGGGCCTGGAGGACGGGCAAAACGG*GTGACGTCCTGTATGAGCTGCTCCAGTACATCAAG	cancer,exon-exon	BOWTIE	in-frame	0	13	3	22	19	49646830	+	6	36373578	-	31.1998	3.8196	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-TM-A7CF-01A	ENSG00000126461	ENSG00000010030	SCAF1	ETV7	GCAAGAGCAGCCAGAAGGATCGGCGCCGCTCGGGGGCCGCCTCCTCCTCC*GGCCCTTGTCTCCTCTATCCACTTCCATCCTGTTGCCTCCCACCCGCTAC	cancer	BOWTIE+BLAT	CDS(truncated)/intronic	0	13	2	20	19	49652669	+	6	36375601	-	31.1998	3.8196	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-TM-A7CF-01A	ENSG00000105325	ENSG00000104946	FZR1	TBC1D17	GCAATCTGGCCTGGTCCAAGCACGCCAACGAGCTG*ATTCCCAGGACTCCGGCTCTCTCTGCTTCTGTTTC	oncogene,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	12	6	23	19	3532650	+	19	49887476	+	13.3109	19.4545	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-TM-A7CF-01A	ENSG00000105325	ENSG00000104946	FZR1	TBC1D17	CGGGCTCCCAAGTGTGCAATCTGGCCTGGTCCAAGCACGCCAACGAGCTG*GACCCCCGGGGGAGGGAGCTGAGATACTCTGTCCTCACCTTACTGATGAG	oncogene,cancer,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	12	1	23	19	3532650	+	19	49886370	+	13.3109	19.4545	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-TM-A7CF-01A	ENSG00000104886	ENSG00000236366	PLEKHJ1	AL359313.1	CGAGCTGGGCATGAGGGGCCCCAAGAAGGGCAGCG*TCCCAATATCATCACCAGATGAGAATATGTATGGA	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	10	3	24	19	2236155	-	6	142528383	-	10.0747	2.1896	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-TM-A7CF-01A	ENSG00000204310	ENSG00000112406	AGPAT1	HECA	GGGGGCCAGCCCCCCAGGCCCCCTACCCCTCTGAG*AAGCCCCATGTGCCACTCCCCTGATCTGCAGCTTC	tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	9	3	24	6	32175814	-	6	139166284	+	17.745	5.4748	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-TM-A7CF-01A	ENSG00000085872	ENSG00000112077	CHERP	RHAG	CTACAAGTGCAAGCTGGCGCTGGAGCAGCAGCAGC*TGTTCCAAGATGTACATGTTATGATATTTGTTGGG	tcga-cancer,exon-exon	BOWTIE	in-frame	0	7	3	21	19	16541870	-	6	49619362	-	9.0766	1.3833	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-TM-A7CF-01A	ENSG00000137269	ENSG00000141985	LRRC1	SH3GL1	CATGCAGCTGGTGGAACTAGATGTGTCTCGAAATG*CTGGTCAGTGAGAAGGTCGGAGGGGCCGAGGGGAC	cancer,tumor,m5,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	7	4	23	6	53842227	+	19	4366994	-	4.4087	31.4128	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-TM-A7CF-01A	ENSG00000064932	ENSG00000104938	SBNO2	CLEC4M	CCAGCTTGCCACCAAAGACCTGCGACTTTGCTCAG*TGTCCAAGGTCCCCAGCTCCCTAAGTCAGGAACAA	m3,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	7	4	23	19	1147309	-	19	7765638	+	3.0652	0.8194	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-TM-A7CF-01A	ENSG00000141985	ENSG00000183207	SH3GL1	RUVBL2	GGCTCCCGCCTAGCGGGCCGCAGTTCCACACCTGG*GTGACACAGGGGAGATCAAGTCAGAAGTCCGTGAG	cancer,tumor,exon-exon	BOWTIE	UTR/CDS(truncated)	0	6	3	22	19	4390052	-	19	49010999	+	31.4128	16.037	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-TM-A7CF-01A	ENSG00000204574	ENSG00000129946	ABCF1	SHC2	CGCTACTCCTGCTGCTGACTGGCAAGCTGACACCG*TACATGGGCTGCATCGAGGTTCTCCGCTCTATGCG	tcga-cancer,exon-exon	BOWTIE	in-frame	0	5	3	15	6	30586711	+	19	440932	-	19.4123	25.3575	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-TM-A7CF-01A	ENSG00000074842	ENSG00000177558	MYDGF	FAM187B	GAAAACTGAGGAATTTGAAGTGACCAAAACAGCAG*GCCCGTCAACTGGCGTGCCAACGACACCCCCCTGA	tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	5	4	23	19	4659931	-	19	35225212	-	29.7509	0.718	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-TM-A7CF-01A	ENSG00000161082	ENSG00000080511	CELF5	RDH8	GGGGGACACGGATGCCCAGGACCCCAGGCTAATCG*TCGTGGCCACCATGAGGGACCTGGGGAAGAAGGAG	tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	4	3	19	19	3225618	+	19	10017057	+	19.1567	2.9267	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-TM-A7CF-01A	ENSG00000161082	ENSG00000080511	CELF5	RDH8	GGTGCTCAAAGACCCCTACACGGGGATGCACAAAG*TCGTGGCCACCATGAGGGACCTGGGGAAGAAGGAG	tcga-cancer,exon-exon	BOWTIE	in-frame	0	4	1	13	19	3224998	+	19	10017057	+	19.1567	2.9267	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-TM-A7CF-01A	ENSG00000130309	ENSG00000240053	COLGALT1	LY6G5B	CATCATCGTCTTTGCCTTCTCCTGCAAGCAGGCAG*TTCCTGTTCCCGACATCCGGACGTGCCACTTCTGC	exon-exon	BOWTIE	in-frame	0	4	3	23	19	17568713	+	6	31671156	+	6.5749	0.8414	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-TM-A7CF-01A	ENSG00000137413	ENSG00000080573	TAF8	COL5A3	CGGCCGGTGAAGAAGCCCAAGATCCGCAGGAAGAA*ATCCTGTGGATGTCCTGAAGGCCCTGGGTGTGCAG	tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	4	3	18	6	42077239	+	19	10006231	-	3.2506	8.1394	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lower grade glioma	TCGA-TM-A7CF-01A	ENSG00000135334	ENSG00000044090	AKIRIN2	CUL7	CCCCTTCGGCGACGTCTCCTCCCGCCTCACCACAG*GTGCCAGGATGGTGGGAGAACTCCGCTACAGGGAA	oncogene,tcga-cancer,exon-exon	BOWTIE	in-frame	0	3	2	22	6	87701450	-	6	43052796	-	20.0852	5.949	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-TM-A7CF-01A	ENSG00000123908	ENSG00000197653	AGO2	DNAH10	GGAGGCGTGAACAACATCCTGCTGCCCCAGGGCAG*GAATTGTACCTGCGCTTTTTTCTGAAGAGGAGAAA	tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	2	2	19	8	140547468	-	12	123893233	+	4.2871	0.4538	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Lower grade glioma	TCGA-TM-A7CF-01A	ENSG00000204463	ENSG00000132016	BAG6	C19ORF57	CTGCCTTTCTCCAAGGCATGACTGACTTCTTGCAG*GAGAGGGACTCTGTCCTCCAAAACCCCTAAAGAAC	exon-exon	BOWTIE	out-of-frame	0	2	1	13	6	31642829	-	19	13895546	-	32.0095	2.6627	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-TM-A7CF-01A	ENSG00000132692	ENSG00000205336	BCAN	ADGRG1	GCATCAATACTTTCCTCCTGCCACAGACTCGGCCCAGCCTTCTGCCATCC*CTGTGCCCCTGCCTGGGACAGAAATGTGGCTCCAGTTGCTCTGTCTCTCG	NA	BOWTIE+BLAT	CDS(truncated)/UTR	0	2	1	18	1	156651479	+	16	57663954	+	1185.4554	74.2568	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-TM-A7CF-01A	ENSG00000184640	ENSG00000115306	SEPT9	SPTBN1	TGGTCTCAAACTCCTGTCCTCAAGTGATCCATCCATCTCGGCCTCCCAAG*AGATCCATCAGTTCAACAGGGATGTGGAGGACGAGATCGTGAGTCGACCC	oncogene,cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	16	17	77385481	+	2	54645416	+	17.2455	53.5519	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lower grade glioma	TCGA-TM-A7CF-01A	ENSG00000184640	ENSG00000115306	SEPT9	SPTBN1	GGTGGCTGAGGCTGCGGTGAGGTCTCCATGGCTCCCTCGTCCTGCACATC*CTCCAGACTGTGCAGCTGTTAATAAAGAAAAATCAGGTAAGCCTTTCTGC	oncogene,cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	15	17	77434431	+	2	54645982	+	17.2455	53.5519	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lower grade glioma	TCGA-TM-A7CF-01A	ENSG00000174652	ENSG00000127616	ZNF266	SMARCA4	AATAAGAGCTGGGCAAAGCATTCTGTGAATTGGCTGACTCCACTTCTATG*GGATCCCCAGCAGCAAGACGGGCCTTTGTCCCCCAGCTCCGGAGTGGGAA	cancer	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	2	1	19	19	9434110	-	19	11019591	+	2.6734	13.3192	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-44-5645-01A	ENSG00000136237	ENSG00000153774	RAPGEF5	CFDP1	CTTGCACCTGGAAGAAGTCCAGGACAAAGAAACAG*GTTAAAAAGATCAAGTGGCATGAGCAGCCTTTTGG	tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	10	2	22	7	22193367	-	16	75305182	-	31.8649	21.2451	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-44-6147-01A	ENSG00000183172	ENSG00000235568	SMDT1	NFAM1	CCCGCAGCGGCGCCATTTTGCCCAAACCGGTGAAA*GCTCTGCAGCGCCGCGAGACCGAGGTCTATGCCTG	tcga-cancer,exon-exon	BOWTIE	in-frame	0	4	2	24	22	42079954	+	22	42387078	-	19.4232	4.5121	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-44-6147-01A	ENSG00000162896	ENSG00000113712	PIGR	CSNK1A1	CATGCCTCAGCCTCTCAAGTAGCTGGGACTACAGATGTGGGCCACCATGT*CTGTAGTCCCAGCTACTTGAGAGGCTGAGGCAGGAGAATGGCGTGAACCC	cancer	BOWTIE+BLAT	UTR/intronic	0	2	4	21	1	206929102	-	5	149500111	-	924.2037	14.9296	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-05-4417-01A	ENSG00000075568	ENSG00000144962	TMEM131	SPATA16	AAGTACTGCGTTTTGATGATGGAGGGCTACTACAG*CTTTGCAGCAAAGGAGCAGTTCTGGGAGAACCATT	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	15	4	24	2	97927426	-	3	173049094	-	5.9973	4.8699	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-44-3918-01A	ENSG00000206418	ENSG00000154845	RAB12	PPP4R1	GACGACACCTTCTGCGAGGCCTGCAAGTCCACCGTGG*GTTCGCCAAGCAGCTTTTCAGTCTCTGGGACCTTTCA	tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	8	3	25	18	8609953	+	18	9577191	-	34.5183	24.7199	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-44-3918-01A	ENSG00000196642	ENSG00000126005	RABL6	MMP24-AS1	GAGATCCAGGTCACCAGCATCCACTGGAGCTACAAGA*AGACAGGATCTCACTCTGTCACCCAGGCTGGAGTGCA	exon-exon	BOWTIE	CDS(truncated)/UTR	0	6	2	24	9	136823659	+	20	35216871	-	9.144	5.4332	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-44-3918-01A	ENSG00000049246	ENSG00000141404	PER3	GNAL	CTCACTGTGGTTGAAAAGATTCACTCTGGTTATGAAG*CTTCCTGGAAAGAATCGACAGCGTCAGCTTGGTTGAC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	4	2	24	1	7798673	+	18	11862395	+	1.3911	0.3548	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-44-3918-01A	ENSG00000105810	ENSG00000180104	CDK6	EXOC3	GGTTGGGAGTAGTACTTGGCTGAGGCAGGAGAATCGCTTGAACCTGGGAG*GCAGAGCATCAACACCATTGAGAGCCTCAAGGACGTCAAAGACGCCGTGG	oncogene,cancer	BOWTIE+BLAT	intronic/CDS(truncated)	0	2	1	17	7	92777321	-	5	447649	+	1.2187	7.7515	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-44-3918-01A	ENSG00000196792	ENSG00000184304	STRN3	PRKD1	GCGGGCGCACTGGGAGGTGGAACGGGCCGAACTGCAG*TTCCCTGAATGTGGTTTCTACGGAATGTATGATAAGA	cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	2	6	24	14	31025904	-	14	29725674	-	10.1901	4.1447	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-49-4501-01A	ENSG00000156076	ENSG00000247131	WIF1	AC025263.1	CCCTCCAGGACTAGAGGGAGAGCAGTGTGAAATCA*ATACAGGAAAAGACCTTAACTGAGGGATGGTTTCC	antisense,cancer,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	19	4	24	12	65062481	-	12	69715587	-	7.5781	0.5684	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-49-4501-01A	ENSG00000139116	ENSG00000103227	KIF21A	LMF1	GCCCCGGACGAGAGCTCCGTGCGGGTGGCTGTCAG*GTACTCTTTCGGATGGGAGTCCCAGCTTCTGGAGA	tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	13	8	24	12	39442927	-	16	934254	-	6.398	3.8032	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-50-5935-01A	ENSG00000006831	ENSG00000111728	ADIPOR2	ST8SIA1	TCCGAGACACGCGGTGAGGCGGCGACGGGCTCCGG*GTGAGACGGGAAAGTGGGCTGGAGTTGAGCAGAGT	exon-exon	BOWTIE	UTR/UTR	0	25	13	23	12	1691213	+	12	22070625	-	6.8111	1.4742	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-50-5935-01A	ENSG00000006831	ENSG00000111728	ADIPOR2	ST8SIA1	CTCAGCGGTGGCTCCCAAGAAGTCCGAGACACGCG*GTGAGACGGGAAAGTGGGCTGGAGTTGAGCAGAGT	exon-exon	BOWTIE	UTR/UTR	0	25	9	24	12	1691191	+	12	22070625	-	6.8111	1.4742	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-50-5935-01A	ENSG00000006831	ENSG00000111728	ADIPOR2	ST8SIA1	GTGGCTCCCAAGAAGTCCGAGACACGCGGTGAGGCGGCGACGGGCTCCGG*ACAAACTCTCACTTTGTTACCCAGGCTGGAGTAACAAAGTGATCTTTGGC	NA	BOWTIE+STAR	UTR/intronic	0	25	1	14	12	1691213	+	12	22073330	-	6.8111	1.4742	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-05-4424-01A	ENSG00000153066	ENSG00000227630	TXNDC11	LINC01132	CTTCTTCACCTCAGCATTACATTCATTAAAGAAAG*CTTGTTTCCCATTGCAACAAGGCCTCCCACTGCAA	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	21	4	24	16	11721577	-	1	234728348	+	19.2269	3.3162	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-05-4424-01A	ENSG00000153066	ENSG00000227630	TXNDC11	LINC01132	CTTCTTCACCTCAGCATTACATTCATTAAAGAAAG*GCTTGTCAGGCAGACTGAAGAGGAGGATCCTAGGA	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	21	3	18	16	11721577	-	1	234726879	+	19.2269	3.3162	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-05-4424-01A	ENSG00000145555	ENSG00000184005	MYO10	ST6GALNAC3	ACTGCGCTGGAACAATGGATAACTTCTTCACCGAG*AGAAAGTCTGTGATTGCTGTGAGCTTCATAGCAGC	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	9	2	21	5	16935788	-	1	76313805	+	12.7953	2.3133	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-05-4424-01A	ENSG00000163960	ENSG00000213123	UBXN7	TCTEX1D2	GAAGGGGTTAATTCAACAGTTCACCACCATTACCG*AAATGGGATTTGACCGATACAAAATGGTGGTGCAA	cell_lines,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	9	2	22	3	196432327	-	3	196307012	-	7.2128	0.2773	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-05-4424-01A	ENSG00000170242	ENSG00000187398	USP47	LUZP2	CAAAGCTGAACCTTATGCTGCAGATGAAGGTTCTGGGGAAGGACATAAAT*ATAACTTTTTGGAGTCTCCATAGATCATACAAAGAGAGAACAGAGAAACA	m6	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	7	1	23	11	11943112	+	11	24891754	+	7.2608	0.3093	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-44-6147-01A	ENSG00000085231	ENSG00000049192	AK6	ADAMTS6	GAAATACATTAATGTGGGTGATTTAGCTCGAGAAG*GCTTGGCCTCTGTGGCTGGAATGTGTGAGCCTGAA	exon-exon	BOWTIE	in-frame	0	2	2	23	5	69366503	-	5	65329483	-	4.3224	0.6736	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-38-6178-01A	ENSG00000156471	ENSG00000169398	PTDSS1	PTK2	TGCAAGCGCGTAGGAACACAATGCTGGGTGTTTGG*AAAAGATGTTGGTTTAAAGCGATTTTTTCCTAAGA	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	3	2	24	8	96309622	+	8	140830526	-	21.1487	24.3474	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-38-6178-01A	ENSG00000226887	ENSG00000185774	ERVMER34-1	KCNIP4	ATTCGTTGTCTACGTCTGCGGAGGTGCGGCAGCCTCAGTTTTAAGCGCAG*GTGTCAAGGGAGAGAGCAGGTGGAGTAATTGAATCATGGAGGCAGTTCCC	NA	BOWTIE+STAR	UTR/intronic	0	2	1	20	4	52750930	-	4	20763097	-	0.678	0.0693	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-75-5147-01A	ENSG00000039560	ENSG00000005981	RAI14	ASB4	TGAAGAGCTTGAAAGCGAAGTTCAGGAAGAGTGAC*GGGCGAATGTGAACATGAAGACCAACAACCAAGAT	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	96	16	23	5	34686955	+	7	95527813	+	31.465	14.109	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-75-5147-01A	ENSG00000039560	ENSG00000005981	RAI14	ASB4	TGTTTAAGCCACCCAGTCTGCAGTATTCTGTTACAGCAGCCTGAACTGAG*GGGCGAATGTGAACATGAAGACCAACAACCAAGATGAGGAGACGCCCTTG	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	96	1	23	5	34711836	+	7	95527813	+	31.465	14.109	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-75-5147-01A	ENSG00000039560	ENSG00000005981	RAI14	ASB4	ATCCTGCAGGCTGCAGCCTCATCCCCCTCACAATGTATTTTTTGTAATAG*GGGCGAATGTGAACATGAAGACCAACAACCAAGATGAGGAGACGCCCTTG	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	96	1	15	5	34716968	+	7	95527813	+	31.465	14.109	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-75-5147-01A	ENSG00000133789	ENSG00000166478	SWAP70	ZNF143	ACCACAGCGGCAAGGTCTCCAAGTCCCAGCTCAAG*GAGAAAGGCCCTTTAAGTGTCCCTTCGAAGGCTGC	oncogene,tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	14	2	17	11	9664278	+	11	9501091	+	26.7496	10.5057	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-75-5147-01A	ENSG00000117298	ENSG00000001461	ECE1	NIPAL3	GCTGCGCGAAGCCGGGGCGGAGCACGCGAGCTATG*GAAAACCTGATTGGCGCCCTCTTGGCGATCTTCGG	18cancers,exon-exon	BOWTIE	in-frame	0	10	6	23	1	21345376	-	1	24440172	+	20.9562	5.7504	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-75-5147-01A	ENSG00000113448	ENSG00000250584	PDE4D	LINC01511	GAAATACCTGTGATTTGCTTTCTCGGAGCAAAAGT*ACTTTATCTTCTATTCCGTTGGTCTGCCTATCTAG	lincrna,tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	10	10	24	5	60185557	-	5	1364691	-	1.2134	1.2652	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-75-5147-01A	ENSG00000113448	ENSG00000250584	PDE4D	LINC01511	ACACCACGATGAAAAGAAATACCTGTGATTTGCTTTCTCGGAGCAAAAGT*ATGCATTTTGTGGGTGTGTCTCAGTTATTTATTAAACCTTCTGCTCTTTG	lincrna,tcga,18cancers,chimerdb3seq,cancer,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	10	1	22	5	60185557	-	5	1368487	-	1.2134	1.2652	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-75-5147-01A	ENSG00000205885	ENSG00000111678	C1RL-AS1	C12ORF57	AACAAGCTCAGGGCTCCCACTGATTCTACATTACG*TGGTCCTCGCGGAGGTGATCCAGGCGTTCTCCGCC	antisense,100K<gap<200K,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	3	2	24	12	7112064	+	12	6944476	+	0.6426	15.5745	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-05-4396-01A	ENSG00000145555	ENSG00000039139	MYO10	DNAH5	AAGGCATCGTCGTCTTCCGGACAGACTATGGTCAG*CAAAGACTGAAGGGAGAGAAGGAAGCCAAGCGGGC	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	5	2	16	5	16877609	-	5	13931244	-	15.596	5.4203	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-05-4397-01A	ENSG00000145715	ENSG00000158987	RASA1	RAPGEF6	GTGGCCATACCGTTGACCGCTCCTCCAACTAACCA*GTCACTGAGTCAAGGAAGCACAAATTCAAACATGC	cell_lines,18cancers,cancer,tumor,exon-exon	BOWTIE	in-frame	0	6	3	18	5	87268990	+	5	131446703	-	3.2469	0.8993	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-05-4382-01A	ENSG00000164933	ENSG00000236939	SLC25A32	BAALC-AS2	GCATCCGCTCGACCTCGTGAAGATCCGCTTCGCCG*GGGTGAACTTACGTGCTCGCTGACAATGTCCTTAA	antisense,chimerdb3seq,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	9	3	20	8	103414784	-	8	103133369	-	0.0862	1.57	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-05-4382-01A	ENSG00000278318	ENSG00000104881	ZNF229	PPP1R13L	GGCAGCTGTACCAAGATGTGATGCAGGAGAATTTCAGGAACCTACTCTCA*GCGCCCGCTCCGGCCGGCACCATGGACAGCGAGGCATTCCAGAGCGCGCG	oncogene,cancer	BOWTIE+STAR	CDS(truncated)/UTR	0	6	1	16	19	44432244	-	19	45398339	-	1.9525	11.9417	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-49-6743-01A	ENSG00000197410	ENSG00000171557	DCHS2	FGG	CAGAGCATGCCCCGGTTGGACACTGCTTTCTGCAG*GGTAGTTATTGTCCAACTACCTGTGGCATTGCAGA	tcga,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	221	18	24	4	154489304	-	4	154612201	-	9.3167	1236.3689	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-49-6743-01A	ENSG00000197410	ENSG00000171557	DCHS2	FGG	CAGAGCATGCCCCGGTTGGACACTGCTTTCTGCAG*ATATGATAGACGCTGCTACTTTGAAGTCCAGGAAA	tcga,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	221	4	17	4	154489304	-	4	154611898	-	9.3167	1236.3689	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-49-6743-01A	ENSG00000142039	ENSG00000140307	CCDC97	GTF2A2	GGCGACGGCGACGGCGGCGAAGGAACCCGATAAGG*GACATCAATGCAAGCTTGAATAAGAAAAACAAATT	tcga,chimerdb3seq,m116,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	138	16	24	19	41310356	+	15	59652326	-	13.871	15.8454	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-49-6743-01A	ENSG00000142039	ENSG00000140307	CCDC97	GTF2A2	TGTGGAAGCCAGATGGAGATGATTGGTATATGGAG*GACATCAATGCAAGCTTGAATAAGAAAAACAAATT	tcga,chimerdb3seq,m116,tcga-cancer,exon-exon	BOWTIE	UTR/UTR	0	138	3	16	19	41311015	+	15	59652326	-	13.871	15.8454	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-49-6743-01A	ENSG00000013364	ENSG00000162924	MVP	REL	CTGCGGCTCAGGGCCCGCAAGGAGTGCTGGGACCGGGACGGCAAGGAGAG*TGGTGCAGTCATGGCTCACTGCATGGCAAATGCTGGCTCAAAGGATATGG	oncogene,tcga,cell_lines,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+BLAT	CDS(truncated)/intronic	0	87	1	23	16	29834058	+	2	60917587	+	42.0596	3.6917	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-49-6743-01A	ENSG00000162924	ENSG00000013364	REL	MVP	TCCTCCTGTTGTCTCGAACCCAATTTATGACAACC*GGGAAGAATGGCTGGTCACCACAGTAGGGGCGTAC	oncogene,tcga,cell_lines,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	87	15	23	2	60917017	+	16	29835704	+	3.6917	42.0596	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-49-6743-01A	ENSG00000162924	ENSG00000013364	REL	MVP	TTTGACGACTGCTCTTCCTCCTGTTGTCTCGAACCCAATTTATGACAACC*TGGCCATGACTTACCTGATTCTGGATCAACAAAGAAGATGTTCAAATACA	oncogene,tcga,cell_lines,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	87	1	22	2	60917017	+	16	29834326	+	3.6917	42.0596	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-49-6743-01A	ENSG00000110906	ENSG00000170605	KCTD10	OR9K2	CAGCGGGCGCATGGAAGTGCTCACCGACAGTGAAG*AATTAAAACAATAAACAGAGGAAAACATTGGAACT	exon-exon	BOWTIE	CDS(truncated)/UTR	0	12	2	21	12	109469515	-	12	55126828	+	8.4692	0.1312	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-49-6743-01A	ENSG00000111300	ENSG00000258830	NAA25	AC137834.1	CCTCCCGGATTGATATTCTTCGTTTGCTCCTTCAACAGCTGGAGGCAACC*CTCCTATTATGTAGACTTCCATTCTGAGTCAGAAAAGTCCATCTTCCAAA	NA	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	4	6	22	12	112043664	-	12	57291115	-	4.6647	0	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-49-6743-01A	ENSG00000111300	ENSG00000258830	NAA25	AC137834.1	CCTCCCGGATTGATATTCTTCGTTTGCTCCTTCAACAGCTGGAGGCAACC*CTTTGTCCATTGAGATGTAGCTGTTGTCTCTCACTTCAGGTCTGGTTCTG	NA	BOWTIE+BLAT	CDS(truncated)/intronic	0	4	3	23	12	112043664	-	12	57285660	-	4.6647	0	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-49-6743-01A	ENSG00000111300	ENSG00000258830	NAA25	AC137834.1	CCTCCCGGATTGATATTCTTCGTTTGCTCCTTCAACAGCTGGAGGCAACC*CTCTAGTGTCAAAATTAGTTTTCTTGGGATATTGTATGGTCTTGAGACCA	NA	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	4	1	24	12	112043664	-	12	57294573	-	4.6647	0	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-49-6743-01A	ENSG00000111725	ENSG00000249345	PRKAB1	LINC02405	TACTTATCTGGGTCCTTCAACAACTGGAGTAAACTTCCCCTCACCAGAAG*GTTATTGGCAAACAAATGGTGTTTGGTGGCATGAGTAAGTTCCTTAGTGG	lincrna,cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	2	9	24	12	119672464	+	12	127019403	-	16.3532	0.4705	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-49-6743-01A	ENSG00000111725	ENSG00000249345	PRKAB1	LINC02405	TACTTATCTGGGTCCTTCAACAACTGGAGTAAACTTCCCCTCACCAGAAG*AAGTGTAACCCACCATTCACCTTCCACCCCACTGAGAGTTCTGAAGTCAT	lincrna,cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	2	3	22	12	119672464	+	12	127012449	-	16.3532	0.4705	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-73-4662-01A	ENSG00000143702	ENSG00000054282	CEP170	SDCCAG8	CCTCCCCCGTCCGGTCCCTCTCTCCACGGTAAGGG*GAGAAGCTAAAACTTACTTATGAGGAAAAGTGTGA	tcga,cell_lines,chimerdb3seq,cancer,m32,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	33	12	23	1	243255040	-	1	243304713	+	3.8481	9.6079	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-73-4662-01A	ENSG00000143702	ENSG00000054282	CEP170	SDCCAG8	CGCCCCGCCTCCCCCGTCCGGTCCCTCTCTCCACG*GAGAAGCTAAAACTTACTTATGAGGAAAAGTGTGA	tcga,cell_lines,chimerdb3seq,cancer,m32,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	33	2	24	1	243255047	-	1	243304713	+	3.8481	9.6079	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-73-4662-01A	ENSG00000143702	ENSG00000054282	CEP170	SDCCAG8	TGTTTTCCCTACTACCTAATGGTAGCTACTTAACG*GAGAAGCTAAAACTTACTTATGAGGAAAAGTGTGA	tcga,cell_lines,chimerdb3seq,cancer,m32,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	33	2	24	1	243253102	-	1	243304713	+	3.8481	9.6079	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-73-4662-01A	ENSG00000143702	ENSG00000054282	CEP170	SDCCAG8	GCTTCATTGTCCTAGGATTCAGATGTAGGGTTTTG*GAGAAGCTAAAACTTACTTATGAGGAAAAGTGTGA	tcga,cell_lines,chimerdb3seq,cancer,m32,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	33	2	22	1	243254351	-	1	243304713	+	3.8481	9.6079	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-38-4629-01A	ENSG00000198331	ENSG00000271334	HYLS1	LINC02104	CAGCATATATATGTCCCAAACAATTATCTAGTACCAACAGAGAAGAAAAG*GTCTTTGAGGAATCGCCACACTGCCTTCCACATGGAAAGGACACAAATGG	lincrna	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	13	4	24	11	125900183	+	5	39521519	+	5.875	1.4604	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4629-01A	ENSG00000127993	ENSG00000154415	RBM48	PPP1R3A	AAAACTACAAATGCGGAAGGCATATGTAGTAAAAACTACTGAAAATAAAG*GGTTAATGCTGGAATCACACACAAGTCAAGGGAGAATCCAGTTGACCACT	NA	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	12	3	19	7	92532549	+	7	113924687	-	3.4492	0.2816	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-38-4629-01A	ENSG00000127993	ENSG00000154415	RBM48	PPP1R3A	GAAGGCATATGTAGTAAAAACTACTGAAAATAAAG*AAAGAACAAGAGCCGGAGCCTGTAAAACCATGGAA	exon-exon	BOWTIE	in-frame	0	12	3	18	7	92532549	+	7	113918297	-	3.4492	0.2816	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-38-4629-01A	ENSG00000127993	ENSG00000154415	RBM48	PPP1R3A	AAAACTACAAATGCGGAAGGCATATGTAGTAAAAACTACTGAAAATAAAG*CAACATGAAAATGGACTAATACAAGAACCAAGAGCAAACTAACTCCAAAG	NA	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	12	1	23	7	92532549	+	7	113931272	-	3.4492	0.2816	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-38-4629-01A	ENSG00000127993	ENSG00000154415	RBM48	PPP1R3A	AAAACTACAAATGCGGAAGGCATATGTAGTAAAAACTACTGAAAATAAAG*GCTCATAGGTGGAATGGACTTGCCTTGTCCCAGATGAGACTTTGGACTGT	NA	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	12	1	19	7	92532549	+	7	113931778	-	3.4492	0.2816	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-38-4629-01A	ENSG00000075213	ENSG00000135272	SEMA3A	MDFIC	GAACAATGTGCCAAGGCTGAAATTATCCTACAAAG*ATTGTTGTGTCCACTGTATCCTGGCTTGCTTGTTC	cell_lines,exon-exon	BOWTIE	in-frame	0	7	4	23	7	84194475	-	7	115015688	+	19.7398	87.0844	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-91-6831-01A	ENSG00000125844	ENSG00000089123	RRBP1	TASP1	CAGCTGCCTTCGAGAAGCAGGTCCTGCAGCTGCAG*TGGAATTTCTGTGGAGCCACACGACGGAGAGCATG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	62	11	23	20	17633460	-	20	13417521	-	55.9835	9.8563	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-91-6831-01A	ENSG00000130699	ENSG00000182463	TAF4	TSHZ2	AAGTGGACTGTCCGGGGCCGGGCTCAGGAGCAGAG*GACGAATGCCTTAGTTTCCACTTTCCAGCCTGGAT	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	38	10	22	20	61997550	-	20	53487144	+	11.3762	7.0213	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-91-6831-01A	ENSG00000130699	ENSG00000182463	TAF4	TSHZ2	CCAGGAAAAAGAGGAAAGTGGACTGTCCGGGGCCGGGCTCAGGAGCAGAG*CATATTCTGGAAACTCTCAAGAAACAAAAGTTGCTGCCAGACAATGCTCT	tcga,chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	38	4	24	20	61997550	-	20	53444251	+	11.3762	7.0213	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-91-6831-01A	ENSG00000130699	ENSG00000182463	TAF4	TSHZ2	CCAGGAAAAAGAGGAAAGTGGACTGTCCGGGGCCGGGCTCAGGAGCAGAG*CTTCACTGGGAAATGGCTGTGTGAATGCAGGGGACAATTTAACCTCCCGA	tcga,chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	38	1	22	20	61997550	-	20	53465112	+	11.3762	7.0213	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-91-6831-01A	ENSG00000099810	ENSG00000234840	MTAP	LINC01239	GGCGATATTGTCATTATTGATCAGTTCATTGACAG*ACTATGGAAATGATGTTAGACAAAAAGCAAATTTG	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	16	4	22	9	21818202	+	9	22820738	+	0.4729	5.1119	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-91-6831-01A	ENSG00000133318	ENSG00000168004	RTN3	HRASLS5	CCTGGGGACGAAGAGCTGCAGCTCCTCCTGTGCGG*GTGAGGAGTTTGAGGTGGGCAGCATTACTTCCATC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	4	3	21	11	63681778	+	11	63466372	-	41.4993	3.599	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-75-5125-01A	ENSG00000099783	ENSG00000125648	HNRNPM	SLC25A23	GTGCCGAGCGGCAACGGGGCTCCGGGCCCTAAGGG*GATTTCATCATGTTGCCCAGGCTCATCTCGAACTC	tcga,chimerdb3seq,cancer,m127,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/CDS(no-known-start-or-end)	0	131	14	22	19	8445111	+	19	6438534	-	34.1465	11.6449	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-75-5125-01A	ENSG00000099783	ENSG00000125648	HNRNPM	SLC25A23	AGCGGCGCGCCCGGCGTGCCGAGCGGCAACGGGGCTCCGGGCCCTAAGGG*GAAGCCGGTGGTCATGCCATGAGCAGCCTTATGGAGAGGACCATGTGGTA	tcga,chimerdb3seq,cancer,m127,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	131	8	23	19	8445111	+	19	6436468	-	34.1465	11.6449	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-75-5125-01A	ENSG00000099783	ENSG00000125648	HNRNPM	SLC25A23	GTGCCGAGCGGCAACGGGGCTCCGGGCCCTAAGGG*CCGGTGGTCATGCCATGAGCAGCCTTATGGAGAGG	tcga,chimerdb3seq,cancer,m127,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	131	7	24	19	8445111	+	19	6436464	-	34.1465	11.6449	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-75-5125-01A	ENSG00000099783	ENSG00000125648	HNRNPM	SLC25A23	GTGCCGAGCGGCAACGGGGCTCCGGGCCCTAAGGG*GCTGGAGTACAGTGGCTCGATTTCAGATCACTGCA	tcga,chimerdb3seq,cancer,m127,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	131	3	22	19	8445111	+	19	6438821	-	34.1465	11.6449	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-75-5125-01A	ENSG00000099783	ENSG00000125648	HNRNPM	SLC25A23	AGCGGCGCGCCCGGCGTGCCGAGCGGCAACGGGGCTCCGGGCCCTAAGGG*GAGTCTTGCTCTTGTTTCCCAGGCTGGAGTACAGTGGCTCGATTTCAGAT	tcga,chimerdb3seq,cancer,m127,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	131	1	21	19	8445111	+	19	6438843	-	34.1465	11.6449	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-44-2656-01A	ENSG00000128563	ENSG00000228486	PRKRIP1	LINC01125	AAAGAAGATGAAACTTGAACAGAAGAAACAAGAAG*GAACCAGCATTGCTTGGAATTCTCCTAAACCAGAA	exon-exon	BOWTIE	in-frame	0	5	2	18	7	102407498	+	2	97690256	+	6.8656	1.4306	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-05-5429-01A	ENSG00000065361	ENSG00000262117	ERBB3	BCAR4	GCCTACCAGTTGGAACACTTAATCGGCCACGTGGG*CAAAAAATCACCATGTACCAACCTATCCAAACTTA	lincrna,oncogene,18cancers,chimerdb3seq,cancer,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	133	10	24	12	56100029	+	16	11820297	-	38.8202	29.743	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-05-5429-01A	ENSG00000065361	ENSG00000262117	ERBB3	BCAR4	GCCTACCAGTTGGAACACTTAATCGGCCACGTGGG*GGTCTTGTCCTGTCACTCTGGCTGGAATACAATGG	lincrna,oncogene,18cancers,chimerdb3seq,cancer,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	133	9	24	12	56100029	+	16	11821755	-	38.8202	29.743	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-05-5429-01A	ENSG00000065361	ENSG00000262117	ERBB3	BCAR4	TGGCCCGAGACCCACCACGGTATCTGGTCATAAAG*GGTCTTGTCCTGTCACTCTGGCTGGAATACAATGG	lincrna,oncogene,18cancers,chimerdb3seq,cancer,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	133	4	23	12	56099745	+	16	11821755	-	38.8202	29.743	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-05-5429-01A	ENSG00000065361	ENSG00000262117	ERBB3	BCAR4	TGGCCCGAGACCCACCACGGTATCTGGTCATAAAG*CAAAAAATCACCATGTACCAACCTATCCAAACTTA	lincrna,oncogene,18cancers,chimerdb3seq,cancer,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	133	4	22	12	56099745	+	16	11820297	-	38.8202	29.743	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-05-5429-01A	ENSG00000184640	ENSG00000005381	SEPT9	MPO	CCGGCTCCGGAGGCTTGGTGACTCCAGTGGCCCAG*GGGACACCCGTTCCAGTGAGATGCCCGAGCTCACC	oncogene,tcga,cell_lines,cancer,exon-exon	BOWTIE	in-frame	0	6	2	14	17	77307197	+	17	58275702	-	24.1076	1.7677	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-05-5429-01A	ENSG00000120899	ENSG00000253875	PTK2B	AC013643.2	ACACCCCACCTCTCCACCGGCACAATGTCTTCAAACGCCACAGCATGCGG*ATCATTCATTCAGGACATGCTGCATCTGGGGTTGGCATCATTTCCCTTTT	antisense,oncogene	BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	3	1	15	8	27445919	+	8	27733356	+	4.1656	0.0667	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-75-5122-01A	ENSG00000111596	ENSG00000127328	CNOT2	RAB3IP	CCATCTTGGATCCGCGGGACAAGAAAATTCATGCG*AAAATGTGCTCTCACTGGCCAGAGTAAGTCCTGTA	tcga,18cancers,chimerdb3pub,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	5	9	22	12	70243480	+	12	69812778	+	32.0749	12.7047	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-75-5122-01A	ENSG00000111596	ENSG00000127328	CNOT2	RAB3IP	CCATCTTGGATCCGCGGGACAAGAAAATTCATGCG*ATCACTTCTGTATGTAACTTTTTTACATACATTCG	tcga,18cancers,chimerdb3pub,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE;BOWTIE+BLAT	UTR/CDS(truncated)	0	5	7	23	12	70243480	+	12	69812964	+	32.0749	12.7047	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-75-5122-01A	ENSG00000166148	ENSG00000203585	AVPR1A	LINC02408	TTATTCTAACAATCGAAGCCCAACAAACAGTACGG*CACTGTTTTCAGCAGACAGAGTCCTAAGTGGATGC	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	2	1	14	12	63147421	-	12	67565514	+	0.4951	1.6666	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-44-2656-01A	ENSG00000101210	ENSG00000130584	EEF1A2	ZBTB46	GCGCCTGCCGCTGCAGGACGTGTACAAGATTGGCG*ATGCGGACCTGTCCGTCACCGAAGCCAGCAGCTCC	oncogene,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	13	3	21	20	63493137	-	20	63775962	-	5.3713	1.5469	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-44-2656-01A	ENSG00000101210	ENSG00000130584	EEF1A2	ZBTB46	AACGTCGGCTTCAATGTGAAGAACGTGTCGGTGAAGGACATCCGGCGGGG*CACCTTTTGTTGTTTTTGTTGTTGTTGTTAAATAGAAGCTTTACTGAGAG	oncogene,cancer,tcga-cancer	BOWTIE+BLAT	CDS(truncated)/intronic	0	13	1	24	20	63490540	-	20	63778239	-	5.3713	1.5469	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-44-2656-01A	ENSG00000128563	ENSG00000228486	PRKRIP1	LINC01125	AAAGAAGATGAAACTTGAACAGAAGAAACAAGAAG*GAACCAGCATTGCTTGGAATTCTCCTAAACCAGAA	exon-exon	BOWTIE	in-frame	0	11	3	22	7	102407498	+	2	97690256	+	7.73	0.9177	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-44-2656-01A	ENSG00000127080	ENSG00000127083	IPPK	OMD	AGGTCTGTCGATACTGCATGCACCAGCACCTCAAG*AGATGAATCTTACAGTGATGTGTCCTTCTATTGAC	cancer,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	4	1	13	9	92648059	-	9	92415477	-	1.4042	2.4092	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4628-01A	ENSG00000100426	ENSG00000175600	ZBED4	SUGCT	AGCCGGCCGGGAGCCGCCCCAGAGGCCGGGCCGAG*GGTATGGTCAGACAGGTCCAATTTCTCAGCGAGCT	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	16	6	23	22	49853989	+	7	40237635	+	1.326	14.8934	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4628-01A	ENSG00000100426	ENSG00000175600	ZBED4	SUGCT	AGCCGGCCGGGAGCCGCCCCAGAGGCCGGGCCGAG*GTGGCGTGTTTGTCTCACATAGCTGCAAATTATCT	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	16	3	24	22	49853989	+	7	40316760	+	1.326	14.8934	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4628-01A	ENSG00000100426	ENSG00000175600	ZBED4	SUGCT	CATGTCTCAGCCCAGACGGGTCCTTGCGACGCGCCCCGAGGCAGGTTATT*GGTATGGTCAGACAGGTCCAATTTCTCAGCGAGCTGGTTATGATGCTGTT	tcga,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	16	1	19	22	49854490	+	7	40237635	+	1.326	14.8934	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4628-01A	ENSG00000100426	ENSG00000175600	ZBED4	SUGCT	AACCTCTGCTCTTTAAGGTTACCTCCTCCCCAACCCCCTCCACACACACA*GGTATGGTCAGACAGGTCCAATTTCTCAGCGAGCTGGTTATGATGCTGTT	tcga,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	16	1	14	22	49855455	+	7	40237635	+	1.326	14.8934	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4628-01A	ENSG00000155974	ENSG00000241749	GRIP1	RPSAP52	TGGAGCGTTGGCTGTGAGGAGACAGAGCATCCCAG*ATTCCTGTCATGACTTAAAGAGAAACTTTCACAAT	pseudogene,ribosomal,m8,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	9	6	22	12	66596847	-	12	65759031	-	1.6885	4.3101	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	transcribed_processed_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4628-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	GCCTGCCTCAGCCTCCAAAGTAGCTGAGACTACAG*CAGTTTAAGTATAGTGTGCCTGGGTTGGGTGCGGT	antisense,m2,exon-exon	BOWTIE	exonic(no-known-CDS)/UTR	0	5	3	22	10	87246115	-	10	46593287	+	0.5921	0.2652	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-50-5066-01A	ENSG00000245958	ENSG00000146733	AC093752.1	PSPH	AGCCCCGGCCGCCCACTCGCCTCACCTGAGCCTGG*GAGGAAAATTCTTCCAGCGATGGTCTCCCACTCAG	pseudogene,exon-exon	BOWTIE	exonic(no-known-CDS)/UTR	0	19	2	16	4	119455133	+	7	56021231	-	1.1095	21.0018	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	transcribed_unprocessed_pseudogene	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-50-5066-01A	ENSG00000273559	ENSG00000167080	CWC25	B4GALNT2	ATGCAGCGCTATGCGGAGGATGTTGGGGCCGTCAA*CTCGAGATTTCTGTGGCTCCTCAAGATATTGGTCA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	8	4	21	17	38820901	-	17	49141247	+	4.1935	2.5236	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-50-5066-01A	ENSG00000166526	ENSG00000105784	ZNF3	RUNDC3B	GATGCTGGAGAATTACGGGAATGTGTTCTCACTGG*AGATTTCCCAAAGTTGCAGATGGCTGGCTCATCTC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	7	2	22	7	100075135	-	7	87693908	+	10.3414	3.4797	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-05-4433-01A	ENSG00000110042	ENSG00000137497	DTX4	NUMA1	GCTTTGAGGTGGGAGGGGCCATGGAGACTGCAGGACAGGAAGTGAGGAGA*ATGACCATGCTGCTCTTATACCACTCTACCATGAGCTCCAAAAGTCCCAG	cancer	BOWTIE+STAR	UTR/CDS(truncated)	0	2	1	19	11	59204969	+	11	72022419	-	25.6895	21.9485	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-55-7281-01A	ENSG00000130723	ENSG00000049323	PRRC2B	LTBP1	GCATTTGGTTTGGTTTTCTTAACTGTTGGCTTCTCCCCACAGCGTTTTTT*TTTTTTTTTTTAAACAATAAACATTATTTTTCGATAATTTTTAGATTCAC	NA	BOWTIE+STAR	UTR/intronic	0	2	1	15	9	131498977	+	2	33068259	+	6.6382	8.9892	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-38-4631-01A	ENSG00000105865	ENSG00000243193	DUS4L	AC006387.1	GTAAAAGTCTGTGCCCCAATGGTTCGATATTCAAA*ATTACCACTCAGCAACCTGCTAAAACTCAGCACGT	exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	27	9	20	7	107567186	+	7	107082088	-	4.1766	0.7237	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-38-4631-01A	ENSG00000105865	ENSG00000243193	DUS4L	AC006387.1	GTAAAAGTCTGTGCCCCAATGGTTCGATATTCAAA*ATCACACAGTCACTCTTCATCACAGCTGGAGAATC	exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	27	6	23	7	107567186	+	7	107068868	-	4.1766	0.7237	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-38-4631-01A	ENSG00000105865	ENSG00000243193	DUS4L	AC006387.1	CATTCTGGACAGCTGGTAAAAGTCTGTGCCCCAATGGTTCGATATTCAAA*TCTCCCCCTCTGTCGCTCAGGCTGGAGTACGGTGGCGCAATCTCAGCTCA	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	27	1	14	7	107567186	+	7	107074790	-	4.1766	0.7237	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-38-4631-01A	ENSG00000128585	ENSG00000184903	MKLN1	IMMP2L	AATATCAGATGGCACCAAGAAAGACTCTGGGATGG*GTTTCCCTAGGACTTCTGCATGCCCATGCCACACA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	24	4	21	7	131445903	+	7	110663721	-	5.7089	2.2561	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-38-4631-01A	ENSG00000128585	ENSG00000184903	MKLN1	IMMP2L	TGATCATGTAGACATAATATCAGATGGCACCAAGAAAGACTCTGGGATGG*GTTAAAAACACAATAAGCTGCCACGTACAACAATAGAGCCTGAGGCTTGA	tcga,chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	24	1	21	7	131445903	+	7	110842573	-	5.7089	2.2561	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-38-4631-01A	ENSG00000128585	ENSG00000184903	MKLN1	IMMP2L	TGATCATGTAGACATAATATCAGATGGCACCAAGAAAGACTCTGGGATGG*GGCTCTCAGGATGTTTGGGGAAAGCAGGTTGATGAGCCAGAGACCTTCTT	tcga,chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	24	1	19	7	131445903	+	7	110835493	-	5.7089	2.2561	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-38-4631-01A	ENSG00000112561	ENSG00000198898	TFEB	CAPZA2	GCGCGGGCGGCGGACAGATTGACCTTCAGAGCGAG*GTGCGTATAGCAGCAAAATTCATCATTCATGCCCC	cancer,m12,exon-exon	BOWTIE	UTR/CDS(truncated)	0	14	5	23	6	41735350	-	7	116888127	+	2.462	928.4837	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-38-4631-01A	ENSG00000112561	ENSG00000198898	TFEB	CAPZA2	TTTCTGTCCAGCAACATGACAGCAAGCTCAGGCTG*GTGCGTATAGCAGCAAAATTCATCATTCATGCCCC	cancer,m12,exon-exon	BOWTIE	out-of-frame	0	14	2	14	6	41736146	-	7	116888127	+	2.462	928.4837	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-38-4631-01A	ENSG00000112561	ENSG00000198898	TFEB	CAPZA2	GGCTGGGGCCGGCGATGCCTGAGAGGGGGTCGGAG*GTGCGTATAGCAGCAAAATTCATCATTCATGCCCC	cancer,m12,exon-exon	BOWTIE	UTR/CDS(truncated)	0	14	1	13	6	41734900	-	7	116888127	+	2.462	928.4837	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-38-4631-01A	ENSG00000164597	ENSG00000105879	COG5	CBLL1	CTAAGCGCCTACTAGAGCAGGGTTTGGAGACTCAG*CTGTAGTGATCCTGTGCAGCGAATTGAGCAGTGTA	oncogene,tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	10	2	18	7	107412502	-	7	107758143	+	17.4702	19.5958	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-38-4631-01A	ENSG00000082701	ENSG00000144810	GSK3B	COL8A1	GAGCCAAACAGACGCTCCCTGTGATTTATGTCAAG*GTGATGGCTGTGCTGCCTGGCCCTCTGCAGCTGCT	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	4	2	18	3	119923373	-	3	99790680	+	4.4034	6.6015	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-38-4631-01A	ENSG00000004864	ENSG00000099917	SLC25A13	MED15	GTGGGTCCCGCAGTCGCCCGCAACCGGGGCGAATCATGGCGGCCGCCAAG*GCTGGAGTGCAGTGGCATGGTGGCATGATCTTGGCTCACTGCAACTGCTG	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	3	2	15	7	96321942	-	22	20499241	+	29.8842	28.0045	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-38-4631-01A	ENSG00000228022	ENSG00000184903	HCG20	IMMP2L	GCTGTCTGGGCTCTGAGCCATCTTCGGCCTCCTGG*GTCTCCTAAAAACCCAGAACAGAAGATCATTAAGA	lincrna,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	2	1	13	6	30782126	+	7	110963565	-	0.1639	2.2561	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-91-6829-01A	ENSG00000120278	ENSG00000163933	PLEKHG1	RFT1	CACATTTATACCCAGTATTGCACTAACTATCCAAG*GTACAATTTTGTGATGCTGGCCCTGTCCTCCTCAT	exon-exon	BOWTIE	in-frame	0	5	3	19	6	150795902	+	3	53092618	-	4.9208	3.5011	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-75-6206-01A	ENSG00000180776	ENSG00000163631	ZDHHC20	ALB	TGCAAATGAGTCTATGCCCGTTTAAAAGAAAAGATGGACACTATTTTAAA*GGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATC	m7	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	8	5	22	13	21372823	-	4	73406629	+	18.3331	4.8512	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-75-6206-01A	ENSG00000180776	ENSG00000163631	ZDHHC20	ALB	TAAAGAAGCAAGGAATTGTACTTGTATTAAAAGATGAAGAAAGCTATTAG*GGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATC	m7	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	8	2	18	13	21372890	-	4	73406629	+	18.3331	4.8512	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-75-6206-01A	ENSG00000180776	ENSG00000163631	ZDHHC20	ALB	GCTTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCACGCCCCGCCCCG*GGTGTTGATTGCCTTTGCTCAGTATCTTCAGCAGTGTCCATTTGAAGATC	m7	BOWTIE+STAR	UTR/CDS(truncated)	0	8	1	15	13	21374849	-	4	73406629	+	18.3331	4.8512	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-05-4390-01A	ENSG00000138814	ENSG00000138670	PPP3CA	RASGEF1B	GGGACTATGTTGACAGAGGGTACTTCAGTATTGAA*GAACAGCAATGGAAACCTTCCATGTACAGCAGCAT	exon-exon	BOWTIE	in-frame	0	18	2	21	4	101108954	-	4	81602922	-	7.8024	1.9846	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-05-4390-01A	ENSG00000138814	ENSG00000138670	PPP3CA	RASGEF1B	GGGACTATGTTGACAGAGGGTACTTCAGTATTGAA*AGGCTGTGTTCCCTGCCACGTGGGGTGAGCCAATG	exon-exon	BOWTIE	in-frame	0	18	1	14	4	101108954	-	4	81635897	-	7.8024	1.9846	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-67-6215-01A	ENSG00000176715	ENSG00000078814	ACSF3	MYH7B	TCACTGTCCCACAGGGAGCTCAAAGAGTGGGCCAG*GAGAACCTCAACAAGCTGATGACCAACCTGCGGGC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	6	2	23	16	89146049	+	20	34990738	+	1.4311	0.9832	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-67-6215-01A	ENSG00000176715	ENSG00000078814	ACSF3	MYH7B	CTCAAAAGAAAAAAAAATCTACACATCCCTCACCACACTGTACATAGGAC*TGCGGCATCCAATTCTGGTTCTCTGCCCCCTTTGTGCCTTTCCCTCACTC	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT	UTR/intronic	0	6	2	23	16	89152654	+	20	34990674	+	1.4311	0.9832	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-44-4112-01B	ENSG00000178974	ENSG00000131981	FBXO34	LGALS3	CCCCGGGCCAGGCCGCGGCCGGGGCAGGAGCGCAG*ATTGTGCCTTATAACCTGCCTTTGCCTGGGGGAGT	tcga,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	4	4	24	14	55271537	+	14	55140275	+	30.4784	49.8344	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-44-4112-01B	ENSG00000178974	ENSG00000131981	FBXO34	LGALS3	GTCGCGCCCTCCCGGGCTCGGCCACTCTGCCCTTCCCTGCCCCAGCGCAG*ATTGTGCCTTATAACCTGCCTTTGCCTGGGGGAGTGGTGCCTCGCATGCT	tcga,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K	BOWTIE+STAR	intronic/CDS(truncated)	0	4	1	16	14	55271984	+	14	55140275	+	30.4784	49.8344	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-78-7143-01A	ENSG00000166704	ENSG00000104381	ZNF606	GDAP1	AGAAGAGCCGTGGTCAGTGGAGCAGGCATGTCCTCAACGCACTTGTCCAG*AGATGGGATCTCTGTCACCTTGGTTGGAGTGCAGTGGCATGATCATAGTT	18cancers	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	8	5	23	19	57988207	-	8	74438624	+	3.0659	0.6458	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-78-7143-01A	ENSG00000166704	ENSG00000104381	ZNF606	GDAP1	AGAAGAGCCGTGGTCAGTGGAGCAGGCATGTCCTCAACGCACTTGTCCAG*GTTCTTGACTGAGCTGCTCCTGTGCTTCCATGAATGGCTGCATCTCATCT	18cancers	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	8	4	24	19	57988207	-	8	74432601	+	3.0659	0.6458	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-78-7143-01A	ENSG00000166704	ENSG00000104381	ZNF606	GDAP1	AGTGGAGCAGGCATGTCCTCAACGCACTTGTCCAG*CTTCTCATATGCAGCATACTGGTGGAAGAACAGCT	18cancers,exon-exon	BOWTIE	CDS(truncated)/UTR	0	8	4	21	19	57988207	-	8	74488678	+	3.0659	0.6458	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-78-7143-01A	ENSG00000127328	ENSG00000149948	RAB3IP	HMGA2	AACGATTAAAAGAAGAACTCGCAAAAGCTCAGAGG*GAGGAAACTGAAGAGACATCCTCACAAGAGTCTGC	oncogene,cell_lines,cancer,tumor,exon-exon	BOWTIE	in-frame	0	7	2	15	12	69756663	+	12	65963245	+	9.1941	1.9305	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-78-7143-01A	ENSG00000166225	ENSG00000131069	FRS2	ACSS2	TTCGCGCCCGCCGACCCGCGCCCTGCTCCCTCTCAGCACCTGGGCGGACG*GTGTGGTGGTGCACGCCTGTAATCCCAGCTACTCAGGAGTCTGAGGCAGA	tcga,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	UTR/UTR	0	6	1	20	12	69470530	+	20	34908720	+	23.8118	18.3405	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-78-7143-01A	ENSG00000166225	ENSG00000131069	FRS2	ACSS2	CCGCGCCCTGCTCCCTCTCAGCACCTGGGCGGACG*GTGTTCAAGCAGCCCTGGCCAGGGATCATGCGCAC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	6	1	13	12	69470530	+	20	34923323	+	23.8118	18.3405	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-91-6836-01A	ENSG00000131591	ENSG00000078808	C1ORF159	SDF4	CGCCAGCTGCCCAGGCGCAAGTCTGTGTGGTCCAG*ACTGTGAGCTGCTTGTCCCCATCCTGCGGCCGTCC	tcga,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	17	3	20	1	1090353	-	1	1228946	-	3.7019	34.3793	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-91-6836-01A	ENSG00000176444	ENSG00000116539	CLK2	ASH1L	CCACATGGCCTTCCAGCTGTGCCAGGCTGTCAAGT*GTGACTGTGTGTATCTGATGAGGGATAGTCGGCGC	tcga,cell_lines,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	15	8	24	1	155266729	-	1	155343742	-	40.1069	32.1851	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-91-6836-01A	ENSG00000032219	ENSG00000100578	ARID4A	KIAA0586	AGATTAAGACTGTGAAAAGGCTGGTGAAAGTTAAG*TTTCACCAGGTGATATGGATCGGACACAAATTGAG	cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	11	3	23	14	58301690	+	14	58540071	+	2.3099	0.9107	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-91-6836-01A	ENSG00000039068	ENSG00000260914	CDH1	AC026464.4	GCTCAAGCCATCTGCCCGCCTCAGCCTCCCAAAGTGCTGGGATTACGGAT*AAAGCCATTGATCTGGTGACGAAAGCCACAGAGGAGGACAAAGCCAAGAA	oncogene,cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	6	2	24	16	68758093	+	16	69316008	+	100.599	0	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-44-6777-01A	ENSG00000179818	ENSG00000115998	PCBP1-AS1	C2ORF42	CAATGTCGGGGATGGACCTCCAGATTTCCTTACTG*ATGCCCTTGGAAATCACCCGTAGCTTTATCCAGAA	10K<gap<100K,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	4	2	17	2	70085547	-	2	70160787	-	0.4234	2.6487	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	processed_transcript	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-49-4505-01A	ENSG00000164463	ENSG00000184347	CREBRF	SLIT3	CGGACCCAGTCCCTGAGCCGCCCCTACACCCACAG*GCAACTGGACAACAACCACATCAGCTGCATTGAAG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	5	1	13	5	173056479	+	5	168844655	-	1.6506	0.9862	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-49-4505-01A	ENSG00000134516	ENSG00000204754	DOCK2	LINC01951	CGGCGATGTGGTGCGAATACAGGAGACGTGTGGAG*GTGAGGAAGCTGAACTGACTTTGGTGACATATATT	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	4	2	22	5	169654486	+	5	174976532	-	1.8991	0	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-44-2666-01A	ENSG00000179915	ENSG00000119537	NRXN1	KDSR	AATGAATGTTAAGACTGACAGTGAAAAAAATGAGTTTTTGTTTTTTAAAA*GATCACATTGATTCAACACCTTCTATTGGACCCAGAAGTGCGTAAATATT	cancer,tumor	BOWTIE+STAR	intronic/UTR	0	2	1	14	2	50987101	-	18	63329012	-	0.0032	12.6017	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-44-2666-01A	ENSG00000179915	ENSG00000119537	NRXN1	KDSR	AAGGGGTTACGTCATTCATAGTGCAAGTTTTGTTTGTTTGTTTTTTAAAT*GATCACATTGATTCAACACCTTCTATTGGACCCAGAAGTGCGTAAATATT	cancer,tumor	BOWTIE+STAR	intronic/UTR	0	2	1	14	2	50116758	-	18	63329012	-	0.0032	12.6017	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-64-5779-01A	ENSG00000146670	ENSG00000174080	CDCA5	CTSF	TCCCAGCTGTCCAATCACCTCGCAGGAGCCCTAGG*AAGCCCGGTGGCGCCTGTCCGTCTTTGTCAATAAC	exon-exon	BOWTIE	out-of-frame	0	2	2	16	11	65083364	-	11	66566404	-	7.8017	30.9012	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-91-6840-01A	ENSG00000069122	ENSG00000112818	ADGRF5	MEP1A	CTGGAGCCCATCTATGAAGCTGAATCTGGTTCCTG*CGATAAATGACACTGTCATCTGGGACAGGCCGTCC	tcga,18cancers,chimerdb3seq,m96,tcga-cancer,exon-exon	BOWTIE	in-frame	0	218	20	24	6	46865042	-	6	46834578	+	66.2965	35.7031	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-91-6840-01A	ENSG00000137413	ENSG00000124812	TAF8	CRISP1	CAGACACAGAGAACCTTGCTCTTCATATCAGCATG*AAGAAATCAGCTAGAGACCAATTTAATAAGCTCGT	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	49	13	23	6	42068607	+	6	49852129	-	15.6276	15.2748	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-91-6840-01A	ENSG00000137413	ENSG00000124812	TAF8	CRISP1	GAGTCTTTTCAAAGATGACGTCAGCACATTTCCAT*GGATGGAAATTAAACACCTCTTGTTTTTGGTTGCT	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	49	2	15	6	42066459	+	6	49857402	-	15.6276	15.2748	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-91-6840-01A	ENSG00000137413	ENSG00000124812	TAF8	CRISP1	GGGTTCAAGCGATTCTCCAGCCTCAGCCTCCTGAGTAGCTGGAATTACAG*GCATTTACCTTGTACTGACTACCTCATTGAACAAATCTCCCCTGTGGACT	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	49	1	23	6	42071468	+	6	49866560	-	15.6276	15.2748	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-91-6840-01A	ENSG00000137413	ENSG00000124812	TAF8	CRISP1	GACAGGCGAGACTCAGAGTCTTTTCAAAGATGACGTCAGCACATTTCCAT*GCTCTCTTGACCTTGACTTCGAGTCAGTTTTGGCCAAAGTCCAAGGTATG	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	49	1	19	6	42066459	+	6	49870599	-	15.6276	15.2748	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-91-6840-01A	ENSG00000196850	ENSG00000111229	PPTC7	ARPC3	CTTCGTGGCCCGGCACCGTTCCGCGGACGTGCTCG*CAAAAGATACAGATATTGTGGATGAAGCCATCTAT	18cancers,chimerdb3seq,cancer,m5,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	14	8	23	12	110582809	-	12	110440388	-	6.8758	47.4101	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-91-6840-01A	ENSG00000165185	ENSG00000119333	KIAA1958	WDR34	CGCGTTCCTATGGACAGACGCACAGACACCTGCAG*AAAAGTTGCCAGACGGCCAGCATTGCCACTGCCAG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	8	3	22	9	112487118	+	9	128640939	-	2.4442	44.065	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-91-6840-01A	ENSG00000070413	ENSG00000115504	DGCR2	EHBP1	CCCGAGCGGAGCTTTGGTTGGAAGGACCAGCGCAA*AGTGGCACAGAAGATCTCCGGACTGAACGATTACA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	6	1	13	22	19064848	-	2	62993530	+	17.7794	5.0357	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-44-6778-11A	ENSG00000183826	ENSG00000213853	BTBD9	EMP2	TCTCTACAAAAAAATTTGCTAGGCATGGTGGTGCATGCCTGTAGTCCCAG*GGGTACAGTGGCTCATGCTTGTAATCCCAGCACTTTGGGAGGCTGAGGCG	NA	BOWTIE+BLAT	intronic/UTR	0	3	1	22	6	38349039	-	16	10531625	-	4.6682	107.3173	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-49-6745-01A	ENSG00000139620	ENSG00000255968	KANSL2	AC024145.1	GATAGCATAGACAGTGATCAAGAAGATCCCCTAAA*GTCTTCAGCATTGCTTACAAACTGGCACGTAAACA	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	4	4	24	12	48679036	-	12	26419408	+	21.3497	0.8525	TRUE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-49-6745-01A	ENSG00000139620	ENSG00000255968	KANSL2	AC024145.1	CCTGACAGTGAAGCTGATAGCATAGACAGTGATCAAGAAGATCCCCTAAA*GGACGTCTTTACCAAGAATCACCCAACTGTGGTCCTATTTCTCCTCTATC	antisense	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	4	3	22	12	48679036	-	12	26366421	+	21.3497	0.8525	TRUE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-49-6745-01A	ENSG00000139620	ENSG00000255968	KANSL2	AC024145.1	CCTGACAGTGAAGCTGATAGCATAGACAGTGATCAAGAAGATCCCCTAAA*GCTGAAAGAGGACAGAGCTCCAGGTGAGGTGACCCAAGGGAAGAAAGAAT	antisense	BOWTIE+STAR	CDS(truncated)/intronic	0	4	1	15	12	48679036	-	12	26396038	+	21.3497	0.8525	TRUE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-49-6745-01A	ENSG00000139620	ENSG00000255968	KANSL2	AC024145.1	GGGGTCTCAGACTCCAGAAAGTAGTCGCAGTGAAGCCAGCCGAATACTAG*TGAAAGCTTCCTGAGGCCTCACCAGAAGCTGAGCAGATGCCAGTTCCATG	antisense	BOWTIE+STAR	CDS(truncated)/intronic	0	4	1	15	12	48679655	-	12	26383200	+	21.3497	0.8525	TRUE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-49-6745-01A	ENSG00000134287	ENSG00000175215	ARF3	CTDSP2	TGAAGTCGGCTTGGGGAGCCAGAGGGAGCGGAGCGGAACCTGCGGGGCAG*TCGGATCTGCTCCAGTGTCTCCAGTACCAGTTCTACCAGGTACGTGACTC	NA	BOWTIE+BLAT	UTR/CDS(truncated)	0	2	3	22	12	48957349	-	12	57827590	-	276.4151	121.8906	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-05-4415-01A	ENSG00000106070	ENSG00000002822	GRB10	MAD1L1	CCAGCAGACAGTGCTACAGAGCCAACTCCTGACAG*GACTCCAGAAGACCTTTCCAGATTCGTGGTTGAGC	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	21	6	23	7	50755887	-	7	2149238	-	5.1979	0.1196	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-05-4415-01A	ENSG00000123106	ENSG00000101188	CCDC91	NTSR1	AGGCACACAAGTGTGAGGAGTTGCTAAATGCTCAG*GTCAACACCTTCATGTCCTTCATATTCCCCATGGT	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	11	3	23	12	28391411	+	20	62754685	+	3.6006	43.1641	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-05-4415-01A	ENSG00000106608	ENSG00000179869	URGCP	ABCA13	AGCATCAGAGAGACGAACAGCTGTGGCCATTGCAG*GTCCTTTTCCTTGCTGAATTCTTCTGGCCTTGTAT	exon-exon	BOWTIE	out-of-frame	0	6	4	24	7	43887415	-	7	48192959	+	5.6613	1.456	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-05-4415-01A	ENSG00000139083	ENSG00000111215	ETV6	PRR4	GGAGGAAGACTCGATCCGCCTGCCTGCGCACCTGC*GTTCTCCAGCATTTGGCTCAAGGCCCCAAGGGCAC	oncogene,cancer,tumor,exon-exon	BOWTIE	CDS(truncated)/UTR	0	5	6	22	12	11752579	+	12	11047188	-	3.9364	0.3553	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-05-4415-01A	ENSG00000064102	ENSG00000256654	INTS13	AC005906.2	TCACAAAGATGCACATGTAGATTTCCTGAAAAGTG*CCCAGCCCTGGCATTAGCCACAAGAAGATGAAGAT	exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	4	1	14	12	26922616	-	12	5010150	+	26.2447	0.2227	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-44-6145-01A	ENSG00000141127	ENSG00000122547	PRPSAP2	EEPD1	GGAAAAGATGTTTTCATCATCCAAACTGTTTCGAA*TTCTGCACGGAGCTAAACCAGCCGACCCTGCCCAA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	11	7	24	17	18872649	+	7	36281115	+	4.8574	2.464	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-05-4395-01A	ENSG00000141458	ENSG00000139132	NPC1	FGD4	CCTTGGGGCACATGAAAAGCTGTCGCAGGCTTCTG*GAGACTAATGAGCAAAAACTTCACAAAATAGCCAA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	17	12	24	18	23544960	-	12	32598497	+	7.5734	2.516	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-05-4395-01A	ENSG00000141458	ENSG00000139132	NPC1	FGD4	TATATATTTCCCTAGCCTTGGGGCACATGAAAAGCTGTCGCAGGCTTCTG*ATGGGACTGTCTAGTTGCAGGAAAACAAGATCAGGTCTCCCACTGATTCA	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	17	1	21	18	23544960	-	12	32594397	+	7.5734	2.516	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-05-4395-01A	ENSG00000141458	ENSG00000139132	NPC1	FGD4	AGTTCATTTATAGACCCTCTAGGGAGCTCATGGACCTCAGGTAAGAGCCT*CATTACATTTGTCACTCAGTTTGCAGGAACAATTTGGTTATTGTTGGTGG	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/intronic	0	17	1	19	18	23551264	-	12	32618215	+	7.5734	2.516	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-05-4395-01A	ENSG00000141458	ENSG00000139132	NPC1	FGD4	TATATATTTCCCTAGCCTTGGGGCACATGAAAAGCTGTCGCAGGCTTCTG*AGAAATAGTCCTGGAGAAGTACATGGAAGGGGCTGGGCGCATTGGCTCAT	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	17	1	15	18	23544960	-	12	32596624	+	7.5734	2.516	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-05-4395-01A	ENSG00000128973	ENSG00000205363	CLN6	C15ORF59	GGCGCGCAGCTGGGCGCCTCCTTCCTGCAGGCCAG*GTGGTGAGCCAGATCGATAAGCTAACCTCGGACTT	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	10	8	22	15	68229502	-	15	73740642	-	2.3491	1.4719	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-05-4395-01A	ENSG00000142655	ENSG00000054523	PEX14	KIF1B	TGGCGTCCTCGGAGCAGGCAGAGCAGCCGAGCCAG*GACCCCAGAAGCCAATTCCCGGGCCTCTAGTCCCT	cell_lines,chimerdb3seq,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	2	7	22	1	10475002	+	1	10374316	+	8.1319	3.9697	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-78-7158-01A	ENSG00000237669	ENSG00000271581	AL671277.2	AL671883.3	GCGGCCCGGCCAGGAAACGGCGGTGCTGAAATACCTCATGGAGTGGGAGC*CGGCCCAGGTCTCGGTCAGGGCCAGGGCCGCCGAGAGCAGCAGGAGGACG	pseudogene,m12	BOWTIE+BLAT	exonic(no-known-CDS)/exonic(no-known-CDS)	0	19	1	15	6	30006800	-	6	31357086	+	0.4736	0.0595	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	unprocessed_pseudogene	unprocessed_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-78-7158-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	GGAGCTTCTCAGAAGACAGAGGGTTTTCTTTTGAG*GTGTGTTTGTCAAAGTGTCTCTGATGAACCACAAC	antisense,m2,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	8	1	13	10	87288442	-	10	46585598	+	1.0531	0.0961	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-78-7158-01A	ENSG00000129515	ENSG00000183032	SNX6	SLC25A21	AGGAAGGCCTGGACGACGGCCCGGACTTCCTCTCAGAAGAGGACCGCGGA*TGAGAGAGCCATCTCAAGATTGTATGGAAACCCTGAATGTTCTGAGATCC	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	3	1	17	14	34629907	-	14	36753911	-	14.6921	0.3223	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-50-5941-01A	ENSG00000110841	ENSG00000123106	PPFIBP1	CCDC91	TTTGGAACTAGTGCCGGCGGCTCTCCACCCCCCAG*GCTTCTAACCCTCCTTTATGTGACTCAGAGAAAGG	cell_lines,cancer,exon-exon	BOWTIE	UTR/UTR	0	25	4	24	12	27524365	+	12	28225795	+	4.6881	9.5811	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-50-5941-01A	ENSG00000110841	ENSG00000123106	PPFIBP1	CCDC91	TTTGGAACTAGTGCCGGCGGCTCTCCACCCCCCAG*GTGCCACTTGAAGAATGGATGATGATGATTTTGGT	cell_lines,cancer,exon-exon	BOWTIE	UTR/UTR	0	25	4	22	12	27524365	+	12	28257202	+	4.6881	9.5811	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-50-5941-01A	ENSG00000110841	ENSG00000123106	PPFIBP1	CCDC91	TTTGGAACTAGTGCCGGCGGCTCTCCACCCCCCAG*GAAAAACATAAACAAGAATTGGAAGACATGAGGAA	cell_lines,cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	25	1	13	12	27524365	+	12	28362438	+	4.6881	9.5811	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-50-5941-01A	ENSG00000205133	ENSG00000227354	TRIQK	RBM26-AS1	AAAACTTCCTGTTGATCAGTACAGAAAACAAATTG*CATTCCCAGTTTACAGCTGAGGAAATTAAGCTTCA	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	5	3	22	8	92916929	-	13	79417835	+	12.2173	0.7577	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-50-5941-01A	ENSG00000102572	ENSG00000205133	STK24	TRIQK	ACTCCCCGGTGCAGTCGGGCCTGCCCGGCATGCAG*CAGGCATTTTGGAGATCAAAGATGGGTAGAAAAGA	known,tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	4	2	21	13	98576745	-	8	92917010	-	8.2103	12.2173	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-55-6642-01A	ENSG00000196914	ENSG00000149972	ARHGEF12	CNTN5	TGAGCGCATTGCATCACATGATTTTGACCCCACAG*ATCTGGGAAATTTTAGTGGCCGGACAAGAAGTGCA	tcga,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	4	2	21	11	120407823	+	11	99916054	+	10.6431	0.0529	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-75-5146-01A	ENSG00000124151	ENSG00000101049	NCOA3	SGK2	TAAACTGCTTGAACATCCTTTGACTGGTTAGCCAG*AGCTGCCTGATCATTGCTACAGAATGAACTCTAGC	known,oncogene,tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	57	11	22	20	47583261	+	20	43566473	+	4.8395	1.8214	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-75-5146-01A	ENSG00000122512	ENSG00000106305	PMS2	AIMP2	GGTGTTGCATCCATGGAGCGAGCTGAGAGCTCGAG*GAAGAGTCTAACCTGTCTCTGCAAGCTCTTGAGTC	oncogene,tcga,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	2	2	24	7	6008997	-	7	6015146	+	0.9324	5.0669	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-05-4422-01A	ENSG00000147676	ENSG00000066777	MAL2	ARFGEF1	GGACCTACTCGGGCGCCTTCGTCTGCCTGGAGATT*AAAGCTGAATGGATGACAACAACTTGCAATCATGC	18cancers,chimerdb3seq,exon-exon	BOWTIE	in-frame	0	144	19	24	8	119208604	+	8	67218138	-	28.7329	27.3224	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-05-4422-01A	ENSG00000147676	ENSG00000066777	MAL2	ARFGEF1	GGACCTACTCGGGCGCCTTCGTCTGCCTGGAGATT*ACAATGAGCAGTTAGCGCGATCTGGTACAAACTGT	18cancers,chimerdb3seq,exon-exon	BOWTIE	in-frame	0	144	2	22	8	119208604	+	8	67217920	-	28.7329	27.3224	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-05-4422-01A	ENSG00000165156	ENSG00000184672	ZHX1	RALYL	CGGCGTGGCGCTGAGAGGCGCGGCGGCCCCTGCAG*ATATCAACATGGCAGGAGAGCCCAAACCATACAGA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	67	18	24	8	123274217	-	8	84774579	+	4.8205	6.4489	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-05-4422-01A	ENSG00000165156	ENSG00000184672	ZHX1	RALYL	ACTGGAGCGCAGAGTCCGCGGCCGGCACGGGAAAG*ATATCAACATGGCAGGAGAGCCCAAACCATACAGA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	67	3	20	8	123274122	-	8	84774579	+	4.8205	6.4489	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-05-4422-01A	ENSG00000165156	ENSG00000184672	ZHX1	RALYL	TGAGGCCCCTTTGCGGGCCCGCCGAGCGGTTCCGGGTTTAGGGTTCACAG*ATATCAACATGGCAGGAGAGCCCAAACCATACAGACCAAAACCTGGAAAC	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	UTR/CDS(truncated)	0	67	1	15	8	123274304	-	8	84774579	+	4.8205	6.4489	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-05-4422-01A	ENSG00000104419	ENSG00000172164	NDRG1	SNTB1	CCATCACCGGCCTCCTGCAAGAGTTTGATGTCCAG*TGAAGTACATGCGAGAAGCCACGCCCTATGTGAAG	18cancers,chimerdb3seq,cancer,exon-exon	BOWTIE	out-of-frame	0	59	15	23	8	133280232	-	8	120693908	-	365.3031	18.7707	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-05-4422-01A	ENSG00000172164	ENSG00000104419	SNTB1	NDRG1	TTCCTCCAGGGAACCCGGGTGGAAAGGAGAGACAG*ATCTCAGGATGGACCCAAGCTCTGCCGGACATGGT	18cancers,chimerdb3seq,cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	59	1	13	8	120812605	-	8	133254595	-	18.7707	365.3031	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-05-4422-01A	ENSG00000156802	ENSG00000156795	ATAD2	WDYHV1	ACGGAGCAACTTGCTAATGGCAGGCATTTTACAAG*TGAAGAAAATATTTGGAAGCTCTGTGAATACATCA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	20	7	24	8	123380529	-	8	123427924	+	3.4224	3.4319	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-05-4422-01A	ENSG00000182197	ENSG00000253117	EXT1	OC90	CTGTGCCTGTCGTCGTCATTGAAGGAGAGAGCAAG*GATCTGCAGAGATAGTTGCAACAAGGGTTACAGCT	tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	18	2	23	8	117818435	-	8	132033164	-	3.5123	0	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-05-4422-01A	ENSG00000259305	ENSG00000184672	ZHX1-C8ORF76	RALYL	GCTTGGGGGCGGGGGGCTCTCTGGAGGGAACATCTCAGCCCCCTGCCTTG*ATATCAACATGGCAGGAGAGCCCAAACCATACAGACCAAAACCTGGAAAC	NA	BOWTIE+STAR	intronic/CDS(truncated)	0	7	1	18	8	123273858	-	8	84774579	+	0.0907	6.4489	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-05-4422-01A	ENSG00000165355	ENSG00000170289	FBXO33	CNGB3	GCTCTCAGCTCGTTGGCTGGAAGTGCTGCGCACCTACTTGGAGCTGGTGC*TTGTTTCTATTTAGGAGAAAAGGAAAGAACCTATATGAAGAAAATAATTG	NA	BOWTIE+BLAT	CDS(truncated)/intronic	0	2	6	24	14	39431595	-	8	86737451	-	6.296	0.364	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-71-6725-01A	ENSG00000147050	ENSG00000251192	KDM6A	ZNF674	AAGATGGCGCCAGGACGAAGGCCCTACTGGGCAAG*AAGTCTGGGAAGTTGACGAGCAGATAGATCACTA	tcga,chimerdb3seq,cancer,m9,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	14	7	22	X	44873987	+	X	46501335	-	1.5683	3.899	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-71-6725-01A	ENSG00000132824	ENSG00000079689	SERINC3	SCGN	CCATGCCTATGTTCTCAGGTGAAGAAGAATAATAGAAACCACATAGATGG*ATGAAGATTTTTGACAGAAATAAAGATGGTCGGTTGGATCTAAATGACTT	cancer	BOWTIE+STAR	UTR/CDS(truncated)	0	8	3	19	20	44496257	-	6	25681951	+	43.9477	0.9829	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-44-6778-01A	ENSG00000011426	ENSG00000122547	ANLN	EEPD1	AGCAAGTAACCAGCAGCCCCTCTCTGGTGGTGAAG*GAGAAAAGGATGTCATTATCTTAGGGGATTTTGGC	tcga,chimerdb3seq,cancer,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	20	5	24	7	36396419	+	7	36296993	+	4.1699	4.2454	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-44-6778-01A	ENSG00000110047	ENSG00000168062	EHD1	BATF2	GATCCTGTCTGGAGAGAAGCAGCGGATCAGCAGAG*CAGCACGAGTCTCTGGAAAAAGACAACCTCGCCCT	tcga,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	19	6	22	11	64874421	-	11	64989812	-	15.3819	10.6344	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-44-6778-01A	ENSG00000169683	ENSG00000078369	LRRC45	GNB1	AGAGGCTGGAGGCGGCGCGGCTGTCCCTGGAGGAG*GACGCCAGGAAAGCATGTGCAGATGCAACTCTCTC	tcga,chimerdb3seq,m17,tcga-cancer,exon-exon	BOWTIE	in-frame	0	19	6	23	17	82029185	+	1	1817875	-	4.168	121.3791	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-44-6778-01A	ENSG00000168038	ENSG00000160746	ULK4	ANO10	CAGCTGAGCTCCAGGAAAATACACCTGTTGTTGAG*CAAATGAAGCTCGTGACCGAGAACCTGAAGGAGGA	tcga,cell_lines,chimerdb3seq,m14,tcga-cancer,exon-exon	BOWTIE	in-frame	0	15	4	22	3	41883874	-	3	43366974	-	2.9202	6.6405	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-44-6778-01A	ENSG00000168038	ENSG00000160746	ULK4	ANO10	TAGTTCCAATTGCTAATCCAGCATTTGCGGATAGCTCCAAACTGGGATAT*GCCTACTGAAATGCTGTGGCCCCTGCAGAAAGAACCCTCTTACCCCCACC	tcga,cell_lines,chimerdb3seq,m14,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	15	1	16	3	41895518	-	3	43368335	-	2.9202	6.6405	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-44-6778-01A	ENSG00000002822	ENSG00000236708	MAD1L1	AC073316.3	ACGCCGAGCACCCAGGCGACTGCCTCATCTTCAAG*GTGGCAAAGGCAAAAGCTGGACTGCATTGTGTGGC	antisense,cancer,exon-exon	BOWTIE	CDS(complete)/exonic(no-known-CDS)	0	4	2	20	7	1898200	-	7	3264789	-	0.2545	0.6693	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-55-6986-01A	ENSG00000092820	ENSG00000047936	EZR	ROS1	GGACTATGAGGAGAAGACAAAGAAGGCAGAGAGAG*ATGATTTTTGGATACCAGAAACAAGTTTCATACTT	known,oncogene,cosmic,cgp,tcga,cell_lines,18cancers,chimerdb3kb,chimerdb3pub,chimerdb3seq,cancer,tumor,m182,tcga-cancer,exon-exon	BOWTIE	in-frame	0	183	22	24	6	158770764	-	6	117324415	-	192.587	48.1773	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-55-6986-01A	ENSG00000092820	ENSG00000047936	EZR	ROS1	CTGCAGGACTATGAGGAGAAGACAAAGAAGGCAGAGAGAGGTCAGGCGCC*AAAGTAGAAGATTGAGTGGATATATTCCAGTGGTTTGTTGCTCTCTGCAA	known,oncogene,cosmic,cgp,tcga,cell_lines,18cancers,chimerdb3kb,chimerdb3pub,chimerdb3seq,cancer,tumor,m182,tcga-cancer	BOWTIE+BLAT	intronic/intronic	0	183	1	21	6	158770754	-	6	117324671	-	192.587	48.1773	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-55-6986-01A	ENSG00000087470	ENSG00000123104	DNM1L	ITPR2	TCCAGCTGCCTCAAATCGTCGTAGTGGGAACGCAG*ATAACCCTGCACTGTTCTGGTTCTCGAGGCACATC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	9	2	22	12	32679465	+	12	26436346	-	7.2623	3.5745	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-05-4432-01A	ENSG00000152382	ENSG00000162706	TADA1	CADM3	TCTCACGCGTTGTCAGATTTTGGTTTCTACACCAG*ACCCCAGTCCGGTGCCCTCCTCCTCCAGCACCTAC	tcga,18cancers,chimerdb3seq,m126,tcga-cancer,exon-exon	BOWTIE	in-frame	0	153	21	24	1	166869445	-	1	159199751	+	8.2543	3.9083	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-05-4432-01A	ENSG00000141556	ENSG00000108557	TBCD	RAI1	AAACGACCCCCAGTAAGCTGGTGCATGTTCAATAG*ATAACCAGCCCGAGTCATGCAGTCTTTTCGAGAAA	exon-exon	BOWTIE	UTR/UTR	0	2	1	14	17	82895990	+	17	17792933	+	13.924	9.9229	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-50-6592-01A	ENSG00000138759	ENSG00000138771	FRAS1	SHROOM3	AAGGTGCTTGTGTCTATCAGGATTCCTTGTTGGCG*GTCGAAGAAGGGGGCAAAGCAGACACCCTGAGCTC	known,tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	17	3	18	4	78066016	+	4	76555609	+	1.3285	6.0964	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-50-6592-01A	ENSG00000203650	ENSG00000131724	LINC01285	IL13RA1	GGAAGCCCATGTGCCTTAATCGCTTCATCCTAGAG*CACTGGAAGAAGTACGACATCTATGAGAAGCAAAC	lincrna,10K<gap<100K,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	10	4	23	X	118855555	+	X	118791762	+	2.0868	48.4257	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-50-6592-01A	ENSG00000168175	ENSG00000237356	MAPK1IP1L	AL365295.1	TTGGCAGATGCACTACCTGAACACTCCCCTGCCAAAACCTCTGCTGTGAG*TTTGCAGGAACATGGATGAAGCTGGAAACTATCATCCTCAGCCAACTAAT	NA	BOWTIE+BLAT	CDS(truncated)/intronic	0	5	1	21	14	55062667	+	14	53522616	+	11.0809	0.2632	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-50-6592-01A	ENSG00000145362	ENSG00000073331	ANK2	ALPK1	AATTGGTATTTCAAATGACCACCATGTTGCAAAAG*GTATGTTGGGAAAGACTATAAGGAGCAGAAGGGGC	known,tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	2	3	23	4	112904514	+	4	112438484	+	0.4571	3.0723	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-50-6592-01A	ENSG00000145362	ENSG00000073331	ANK2	ALPK1	CTTAAAACAACTGTGCTTTATTCTAAAGGATACTGGTTGGTTTGTTTGGG*GTATGTTGGGAAAGACTATAAGGAGCAGAAGGGGCTCTGGCACCACTTCA	known,tcga,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	17	4	113014581	+	4	112438484	+	0.4571	3.0723	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-50-5930-01A	ENSG00000113593	ENSG00000123213	PPWD1	NLN	TCTGTACATCATTCAAAAAGAATAGATTTTATATG*GAAATCAAATCAATGAAGAAAAGAATGAGTGAGCT	cell_lines,18cancers,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	3	3	21	5	65579613	+	5	65780179	+	3.7923	2.6838	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-50-5930-01A	ENSG00000083844	ENSG00000174227	ZNF264	PIGG	GATGCTGGAAAACTGTGGGCTCCTGGTGTCTCTGG*ATCCTGGGTTTGAGCAGTTTAAAATGTCAGAAAGA	tcga,cell_lines,chimerdb3seq,m2,tcga-cancer,exon-exon	BOWTIE	in-frame	0	3	2	18	19	57194001	+	4	521056	+	2.012	3.1661	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-50-5930-01A	ENSG00000141232	ENSG00000170703	TOB1	TTLL6	GCGGGTCTGTGGTCCAAGCCGCCCCGAAGCAGCCC*GGGCCTGGTATTTCCCCAGAGCCTCCTCCCAGGCC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	2	1	14	17	50866058	-	17	48804991	-	22.7505	10.1261	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-55-6972-01A	ENSG00000104853	ENSG00000072958	CLPTM1	AP1M1	CCGTGGTGGCGGCCGGGGGAGGCAGCTCCGGTCAG*GTCAGCGCCAACGGCAATGTCCTGCGCAGCGAGAT	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	6	4	22	19	44955467	+	19	16226421	+	18.624	4.6733	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-55-6972-01A	ENSG00000122033	ENSG00000186184	MTIF3	POLR1D	CCGCTACAGTATGTCAATCGCTTGCCCCAGCACAG*CTTATTCAACATGAAGATGATGAGAATGAGGACTT	exon-exon	BOWTIE	UTR/CDS(truncated)	0	2	4	23	13	27450509	-	13	27738707	+	12.0513	11.3697	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-55-6972-01A	ENSG00000122033	ENSG00000186184	MTIF3	POLR1D	TCGCTACGTCCCGTCTCTAGCCCTGGCGCTCCGCCGGTCCCGTTCTGCAG*TGACCTCATGAGTACCCACAGCCTGGGAAGTCCAGGTGAGTTGGGTTACA	NA	BOWTIE+BLAT;BOWTIE+STAR	UTR/intronic	0	2	3	22	13	27450142	-	13	27722103	+	12.0513	11.3697	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-55-6972-01A	ENSG00000122033	ENSG00000186184	MTIF3	POLR1D	TCTAGCCCTGGCGCTCCGCCGGTCCCGTTCTGCAG*CTTATTCAACATGAAGATGATGAGAATGAGGACTT	exon-exon	BOWTIE	UTR/CDS(truncated)	0	2	2	19	13	27450142	-	13	27738707	+	12.0513	11.3697	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-44-6777-11A	ENSG00000111859	ENSG00000196616	NEDD9	ADH1B	CTCAATTACCTAGTCCATGATTTCTGGAAGTCAAAGTCAAAAGGTAAAAT*ATGGGGGCTTTCCAAAGAAATGGAAATTGATGGGAAATTATTTTTCAGGA	oncogene,m2	BOWTIE+STAR	UTR/UTR	0	3	1	14	6	11199533	-	4	99307719	-	23.4084	60.8801	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-55-6712-01A	ENSG00000146247	ENSG00000140718	PHIP	FTO	TAACTTTTGATCGAACTGGCAGACGGATATTTACT*GTGCCAGTCACGAATTGCCCGAACATTACCTGCTG	tcga,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	53	6	24	6	79042843	-	16	54111762	+	4.5255	3.4297	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-55-6712-01A	ENSG00000171100	ENSG00000155959	MTM1	VBP1	TCACGAGATACGCGTTTCCCCTGGCTCACAGTCTG*GAAGATGTAGATTCCTTCATGAAACAGCCTGGGAA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	32	6	24	X	150619139	+	X	155220183	+	8.3859	29.4964	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-44-3918-01A	ENSG00000196792	ENSG00000184304	STRN3	PRKD1	GGGCGCACTGGGAGGTGGAACGGGCCGAACTGCAG*TTCCCTGAATGTGGTTTCTACGGAATGTATGATAA	cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	2	3	22	14	31025904	-	14	29725674	-	23.5059	5.7226	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-44-2668-01B	ENSG00000100644	ENSG00000027075	HIF1A	PRKCH	AGCCCTAACGTGTTATCTGTCGCTTTGAGTCAAAG*AGATCTGAAACTGGACAATGTCCTGTTGGACCACG	tcga,chimerdb3seq,tcga-cancer,oesophagus,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	27	8	24	14	61741188	+	14	61529075	+	256.6307	14.0013	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-44-2668-01B	ENSG00000100644	ENSG00000027075	HIF1A	PRKCH	AAATCTCATCCAAGAAGCCCTAACGTGTTATCTGTCGCTTTGAGTCAAAG*CACCTCCTGCCAGGACCATGCTGGAGCTGCTAAGAAGGAAGACAGGTGCA	tcga,chimerdb3seq,tcga-cancer,oesophagus,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	27	1	24	14	61741188	+	14	61525052	+	256.6307	14.0013	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-44-2668-01B	ENSG00000198900	ENSG00000236772	TOP1	AL034550.1	GAGAAGGACCGGGAAAAGTCCAAGCATAGCAACAG*GACTTGAGGTACGTGCGGATGCGCTTGCGGGCCCG	antisense,cancer,tumor,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	4	3	24	20	41061490	+	20	32453338	+	34.4687	9.5586	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-44-2668-01B	ENSG00000198900	ENSG00000236772	TOP1	AL034550.1	GAGAAGGACCGGGAAAAGTCCAAGCATAGCAACAG*AGTAGCCTGGGGAGTTACCGGAAAAGCACCTACTG	antisense,cancer,tumor,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	4	2	19	20	41061490	+	20	32451568	+	34.4687	9.5586	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-44-3918-01B	ENSG00000145623	ENSG00000176771	OSMR	NCKAP5	AAGTGTCAATATCCTTTTTAACCTGACTCATCGAG*AAACTTCACTCACGTCTCTTGGATCTTTCATCTGG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	3	1	14	5	38886190	+	2	132796729	-	64.2946	2.2245	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-44-2668-01A	ENSG00000100644	ENSG00000027075	HIF1A	PRKCH	AGCCCTAACGTGTTATCTGTCGCTTTGAGTCAAAG*AGATCTGAAACTGGACAATGTCCTGTTGGACCACG	tcga,chimerdb3seq,tcga-cancer,oesophagus,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	35	10	24	14	61741188	+	14	61529075	+	238.3467	9.7237	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-44-2668-01A	ENSG00000257949	ENSG00000177728	TEN1	TMEM94	AGAAGAAATCCGAGGACCGGCGACGCCTAGAACAG*ATGTTGTGACTGTGACAGACTCACTGGGGTTTGTA	exon-exon	BOWTIE	UTR/UTR	0	2	2	22	17	75979511	+	17	75471800	+	0.0573	6.3771	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-44-2668-01A	ENSG00000198900	ENSG00000236772	TOP1	AL034550.1	GAGAAGGACCGGGAAAAGTCCAAGCATAGCAACAG*AGTAGCCTGGGGAGTTACCGGAAAAGCACCTACTG	antisense,cancer,tumor,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	2	3	22	20	41061490	+	20	32451568	+	26.2509	1.2296	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-50-6593-01A	ENSG00000180329	ENSG00000068650	CCDC43	ATP11A	TGGACGCTCTGCAGGGGATCCTCTCTGCTTTCCTG*AACATGCCCCCCCGCCATCCCAGGAGAAGCAGCAG	exon-exon	BOWTIE	CDS(truncated)/UTR	0	36	5	23	17	44689550	-	13	112717322	+	4.9017	30.6117	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-50-6593-01A	ENSG00000180329	ENSG00000068650	CCDC43	ATP11A	TGCAGGAAGTGCCCTTTTGATTCTTATATGGATGTAGGAGTCCATAAAAG*AACATGCCCCCCCGCCATCCCAGGAGAAGCAGCAGCTCTCTGCCTCCTTG	NA	BOWTIE+BLAT;BOWTIE+STAR	intronic/UTR	0	36	1	20	17	44689063	-	13	112717322	+	4.9017	30.6117	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-50-6593-01A	ENSG00000180329	ENSG00000068650	CCDC43	ATP11A	CTGTCTGTCCATCAAAGGCTTTATCCTCTGGCATTTATTACAATGGACAG*AACATGCCCCCCCGCCATCCCAGGAGAAGCAGCAGCTCTCTGCCTCCTTG	NA	BOWTIE+STAR	intronic/UTR	0	36	1	16	17	44688528	-	13	112717322	+	4.9017	30.6117	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-44-5643-01A	ENSG00000138777	ENSG00000145348	PPA2	TBCK	CCAGCCCTGCTCGCAGAATTACCGCCTCTTCTTTA*CTTTATTCGTGGTCACATTTCAGGAAGCATCAACA	known,exon-exon	BOWTIE	out-of-frame	0	13	3	24	4	105473894	-	4	106095641	-	7.4699	1.4398	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-44-5643-01A	ENSG00000138777	ENSG00000145348	PPA2	TBCK	CACTGAGGAGCGCGGCCAGCCCTGCTCGCAGAATTACCGCCTCTTCTTTA*GAAGCATCAACATTCCATTCAGTGCTGCCTTCACTGCAGAAGGGGAGCTT	known	BOWTIE+STAR	in-frame	0	13	1	15	4	105473894	-	4	106095618	-	7.4699	1.4398	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-05-4420-01A	ENSG00000138162	ENSG00000118960	TACC2	HS1BP3	GTTGGCCAGGTCTCTACGGATCTGATAGCCCAGAG*GTACCAGATCCCCAGGGGCTGCAGGGCTCACCAGC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	88	12	23	10	122132734	+	2	20638652	-	4.1587	7.2428	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-05-4420-01A	ENSG00000138162	ENSG00000118960	TACC2	HS1BP3	GTTGGCCAGGTCTCTACGGATCTGATAGCCCAGAG*GTCTCCAAAAAGTACAGCGAGATTGAGGAGTTTTA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	88	9	22	10	122132734	+	2	20641180	-	4.1587	7.2428	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-05-4420-01A	ENSG00000138162	ENSG00000118960	TACC2	HS1BP3	CCCTCCTGCCCAGATCCGGCCAAGGACCTCAGCAG*GTACCAGATCCCCAGGGGCTGCAGGGCTCACCAGC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	88	5	23	10	122143706	+	2	20638652	-	4.1587	7.2428	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-05-4420-01A	ENSG00000138162	ENSG00000118960	TACC2	HS1BP3	CCCTCCTGCCCAGATCCGGCCAAGGACCTCAGCAG*GTCTCCAAAAAGTACAGCGAGATTGAGGAGTTTTA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	88	5	21	10	122143706	+	2	20641180	-	4.1587	7.2428	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-05-4420-01A	ENSG00000138162	ENSG00000118960	TACC2	HS1BP3	GCTCCGTGCGGGCCATCCCCTATCTCCCCGGGCGG*GTACCAGATCCCCAGGGGCTGCAGGGCTCACCAGC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	88	4	22	10	122113233	+	2	20638652	-	4.1587	7.2428	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-05-4420-01A	ENSG00000100991	ENSG00000251033	TRPC4AP	AC113347.4	CCTGGACCGATTTGAAAACCAGGTGGATATGAAAG*GTTTTATTGGCGGTTTGAGACCATCCAGATATCTC	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	41	8	21	20	35005695	-	5	26712026	-	48.1336	5.0517	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-05-4420-01A	ENSG00000100991	ENSG00000251033	TRPC4AP	AC113347.4	AGAGATTCAATAAATATATCAACACCGATGCAAAG*GTTTTATTGGCGGTTTGAGACCATCCAGATATCTC	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	41	2	24	20	35006435	-	5	26712026	-	48.1336	5.0517	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-05-4420-01A	ENSG00000100991	ENSG00000251033	TRPC4AP	AC113347.4	GTCATGAAGAAGGAGCCAGCAGAGTCGTCTTTCAG*GTTTTATTGGCGGTTTGAGACCATCCAGATATCTC	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	41	2	19	20	35008664	-	5	26712026	-	48.1336	5.0517	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-05-4420-01A	ENSG00000100991	ENSG00000251033	TRPC4AP	AC113347.4	ATTTGAAAACCAGGTGGATATGAAAGGTACATGAAAGGCAGGCTGTCAAG*GTTTTATTGGCGGTTTGAGACCATCCAGATATCTCTCTCTGTGCACAGGA	lincrna	BOWTIE+BLAT	intronic/exonic(no-known-CDS)	0	41	1	24	20	35005671	-	5	26712026	-	48.1336	5.0517	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-05-4420-01A	ENSG00000165632	ENSG00000136770	TAF3	DNAJC1	GCTGGGCCGGGGCTGCCATCGGTACTCTGAGCTCT*GCACCTGAATGGACAGAAGAGGACCTCAGCCAACT	tcga,18cancers,chimerdb3seq,m6,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	14	8	24	10	7818875	+	10	21806099	-	3.3873	29.6476	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-05-4420-01A	ENSG00000165632	ENSG00000136770	TAF3	DNAJC1	GCTGGGCCGGGGCTGCCATCGGTACTCTGAGCTCT*GTGACAACCAAAGCCAAGCAACTGAAGGATTCAGT	tcga,18cancers,chimerdb3seq,m6,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	14	3	23	10	7818875	+	10	21766309	-	3.3873	29.6476	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-05-4420-01A	ENSG00000165632	ENSG00000136770	TAF3	DNAJC1	CCTTTCCCCGCCGCGGAAGCCCTAGAGGATGAATCGGGGACCCTGCTAAG*GCACCTGAATGGACAGAAGAGGACCTCAGCCAACTGACAAGAAGTATGGT	tcga,18cancers,chimerdb3seq,m6,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	14	1	19	10	7818648	+	10	21806099	-	3.3873	29.6476	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-05-4420-01A	ENSG00000146085	ENSG00000196284	MUT	SUPT3H	CCTGGCTGTGTGGATGTCTGACAG*TTACAGCAAGCTGCTGAAGTTTCTCAGCTGCGGGGAGCAAGGGTAATCAC	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	7	5	24	6	49463168	-	6	45020632	-	14.5824	4.0088	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-05-4420-01A	ENSG00000146085	ENSG00000196284	MUT	SUPT3H	CCTCTCCCACAGCGGAGTCCAAAACAGGCCTACCA*TTACAGCAAGCTGCTGAAGTTTCTCAGCTGCGGGG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	7	5	23	6	49463103	-	6	45020632	-	14.5824	4.0088	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-05-4420-01A	ENSG00000262583	ENSG00000166822	AC009163.5	TMEM170A	CAGGGATTTTCCTGGACGGGATTGTGAAGTAGCGG*AGATGTGGTATGGTGTATTCCTGTGGGCACTGGTG	pseudogene,10K<gap<100K,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	3	3	24	16	75516203	-	16	75451839	-	0.907	3.8657	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	transcribed_unprocessed_pseudogene	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-05-4420-01A	ENSG00000137713	ENSG00000258529	PPP2R1B	AP001781.3	GCACTGAGCCGAGATCGCGCCACTGCACTCTAGCCTGGGCCATAGAGCGA*GAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTC	10K<gap<100K	BOWTIE+BLAT	UTR/intronic	0	3	1	21	11	111740247	-	11	111793729	-	10.3676	0	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-05-4420-01A	ENSG00000109066	ENSG00000172794	TMEM104	RAB37	AAATTACAGAGACCGGGGAACTCTACTCTTCCTAC*GTGATGCTTCTGGGAGACACAGGCGTCGGCAAAAC	tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	3	2	21	17	74777375	+	17	74740768	+	8.4288	1.8888	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-05-4420-01A	ENSG00000067992	ENSG00000005889	PDK3	ZFX	CGATCCCACCTGTAACGTGGCGGATGTGGTGAAAG*TGGATGATGCTGGCAAAATAGAACACGATGGTTCT	exon-exon	BOWTIE	in-frame	0	2	2	17	X	24505298	+	X	24207326	+	3.097	3.8413	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-50-5946-01A	ENSG00000167232	ENSG00000115355	ZNF91	CCDC88A	TATGAAGCAACATGAGATGGTGGATGAACCCACAG*CAGGTGCAGTTAATAACCAAAGCAGGCCACAAAGC	tcga,chimerdb3seq,m23,tcga-cancer,exon-exon	BOWTIE	in-frame	0	48	12	23	19	23373742	-	2	55296523	-	8.0295	2.8515	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-50-5946-01A	ENSG00000132478	ENSG00000174652	UNK	ZNF266	CTGCAGGCACAGCCCGAGAAACCGCAGCACTACAC*GATACCGTTAACCCTGGATAAAGAGAATGGAGGTT	tcga,chimerdb3seq,m28,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	30	5	23	17	75784984	+	19	9420218	-	12.3277	22.0806	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-50-5946-01A	ENSG00000132478	ENSG00000174652	UNK	ZNF266	CTGCAGGCACAGCCCGAGAAACCGCAGCACTACAC*TAGAGATGGTTTCAGCATGTTGGCCAGTCTGGTCT	tcga,chimerdb3seq,m28,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	30	2	19	17	75784984	+	19	9433786	-	12.3277	22.0806	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-50-5946-01A	ENSG00000230453	ENSG00000148158	ANKRD18B	SNX30	CTTCAAAGAAGAAATTATTTCAAGTAGAAATTCAA*GACCTGAACGCCTACAAGAAGCAAGGGATAGCATT	tcga,cell_lines,chimerdb3seq,m2,tcga-cancer,exon-exon	BOWTIE	in-frame	0	17	3	23	9	33550579	+	9	112836214	+	4.1423	5.4991	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-78-7146-01A	ENSG00000275700	ENSG00000227906	AATF	SNAP25-AS1	AAGAAATCTTTGATGATGATGACTTTTACCACCAG*GATGCTCACCCTTGGAGACCAGCAACAATGTGTGC	antisense,18cancers,chimerdb3seq,cancer,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	101	12	24	17	36990857	+	20	10104394	-	51.16	0.8612	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-78-7146-01A	ENSG00000108510	ENSG00000198231	MED13	DDX42	CCTTATGAAAAAGATGAAAAACCTATAAATAAAAG*ATCCATGCAGAATGTAAGCGGTTTGGAAAAGCATA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	85	12	22	17	62052537	-	17	63808820	+	13.0007	39.8972	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-78-7146-01A	ENSG00000158769	ENSG00000198929	F11R	NOS1AP	ACTGTTGTGCCTCTTCATATTGGCGATCCTGTTGT*GCCGCCAGCTCACTGGAGCCGAGAGGGCCTCCACG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	64	14	24	1	161021010	-	1	162355187	+	140.5189	1.712	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-78-7146-01A	ENSG00000141562	ENSG00000055483	NARF	USP36	TGGCTCCCGGGGCGCTGACTGCGTGTTAACATCAG*ATGATCAAGCGGTGCTGATTCACGAGAGTGGAAGC	18cancers,exon-exon	BOWTIE	CDS(truncated)/UTR	0	64	16	24	17	82481211	+	17	78787658	-	18.5694	3.7745	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-78-7146-01A	ENSG00000160710	ENSG00000160818	ADAR	GPATCH4	GGCCACAGATGACATCCCAGATGACTTGAATAGTATCCGCGCAGCACCAG*AGGTCAAGAGTCGTGGGATGAAGTTTGCTGAGGAGCAGCTGCTAAAGCAT	tcga,chimerdb3seq,tcga-cancer	BOWTIE+STAR	in-frame	0	13	1	15	1	154601231	-	1	156599030	-	109.3853	10.6893	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-78-7146-01A	ENSG00000188878	ENSG00000198265	FBF1	HELZ	TGAGATGGCACCAAAAACCAAGAAAGGATGTAAAG*GTGTTTGAAGTGGTGGAACGTGTAGAAGAGTTAAG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	9	5	24	17	75937566	-	17	67138114	-	1.0117	10.2153	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-78-7146-01A	ENSG00000007314	ENSG00000132481	SCN4A	TRIM47	TCTTCCTCATGGTCATGGTCATCGGCAATCTTGTG*AGTGCAGCCGTAGCAGAGCGGGAGAGGGTGAGCCG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	3	1	13	17	63957162	-	17	75876492	-	1.7897	18.1976	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-78-7146-01A	ENSG00000146063	ENSG00000102048	TRIM41	ASB9	TGGTGCCATTGGAGGAGGTGGTGCAGGAGTACAAG*ATGCTGTGTCTGATTGGTCTCCTATGCATGAAGCT	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	3	3	23	5	181224812	+	X	15258945	-	2.1292	2.3177	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-05-4250-01A	ENSG00000133687	ENSG00000087502	TMTC1	ERGIC2	TCCCAGTGTCCCCACGAGCTGTGTGGTCCATGATGAG*CATGACTATATGAAGGAAGAGGAAGGTTTTCCTGAAG	100K<gap<200K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	14	5	25	12	29751666	-	12	29371670	-	0.5233	6.7264	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-05-4250-01A	ENSG00000185420	ENSG00000186197	SMYD3	EDARADD	GGAGTCGTGGCGTCGTCTGCGACCGCTGCCTTCTCGG*ATCATATGGTAAAGGAACCAGTGGAAGACACAGACCC	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	5	2	17	1	246507054	-	1	236409216	+	3.564	1.1316	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-64-1680-01A	ENSG00000019582	ENSG00000047936	CD74	ROS1	CTTGGAGCAAAAGCCCACTGACGCTCCACCGAAAG*ATGATTTTTGGATACCAGAAACAAGTTTCATACTT	known,oncogene,cosmic,chimerdb2,cgp,ticdb,tcga,cell_lines,18cancers,chimerdb3kb,chimerdb3pub,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE;BOWTIE+BLAT	in-frame	0	192	14	24	5	150404680	-	6	117324415	-	1318.3203	58.9226	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-64-1680-01A	ENSG00000256053	ENSG00000075413	APOPT1	MARK3	GCGGCGCCGAGCGCAGGGATACGGCGCCCAGCGGG*TCGCAATGTATCTGCTGAGCAAAAAGATGAAAACA	known,tcga,cell_lines,18cancers,chimerdb3seq,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	2	1	14	14	103563124	+	14	103502882	+	2.5755	1.556	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-44-5645-01A	ENSG00000136237	ENSG00000153774	RAPGEF5	CFDP1	CTTGCACCTGGAAGAAGTCCAGGACAAAGAAACAG*GTTAAAAAGATCAAGTGGCATGAGCAGCCTTTTGG	tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	7	5	24	7	22193367	-	16	75305182	-	14.226	23.2457	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-44-5645-01A	ENSG00000136237	ENSG00000153774	RAPGEF5	CFDP1	GGACTTCATGGCTTGACTCTCCTAGCACCAACCTAAGTGGGGAAGAAGGG*GCTGGAGTGCAGTGGCGCGCTGGAGTGCAGTGGCGCGATCTCGGCACACT	tcga-cancer	BOWTIE+STAR	UTR/intronic	0	7	1	23	7	22191529	-	16	75318111	-	14.226	23.2457	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-44-5645-01A	ENSG00000080845	ENSG00000019582	DLGAP4	CD74	GTGATCATGCCACTGCATTCCAGCCTGGGCAACATAGCAAGACCCCATCT*CCACCCTGTACCTCATCCCATGAGACCCTGGTGCCTGGCTCTTTCGTCAC	cancer	BOWTIE+BLAT	intronic/UTR	0	2	1	24	20	36380181	+	5	150402150	-	8.9665	3062.5566	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-44-5645-01A	ENSG00000080845	ENSG00000019582	DLGAP4	CD74	GCTGTCGCCATGGAGAGGCTGCTCCCACCCACCCAGCCCCAGGTGGCTGC*AGCTTTCTTGCTCCCTTCAGCCCCCAGCCCCTCCCCCATCTCCCACCCTG	cancer	BOWTIE+STAR	intronic/UTR	0	2	1	17	20	36394675	+	5	150402192	-	8.9665	3062.5566	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-44-4112-01A	ENSG00000178974	ENSG00000131981	FBXO34	LGALS3	AGCCCCGGGCCAGGCCGCGGCCGGGGCAGGAGCGCAG*ATTGTGCCTTATAACCTGCCTTTGCCTGGGGGAGTGG	tcga,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	39	14	24	14	55271537	+	14	55140275	+	23.2696	158.9296	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-44-4112-01A	ENSG00000178974	ENSG00000131981	FBXO34	LGALS3	GCTGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCAAG*ATTGTGCCTTATAACCTGCCTTTGCCTGGGGGAGTGGTGCCTCGCATGCT	tcga,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K	BOWTIE+STAR	intronic/CDS(truncated)	0	39	5	21	14	55316355	+	14	55140275	+	23.2696	158.9296	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-44-4112-01A	ENSG00000178974	ENSG00000131981	FBXO34	LGALS3	AACCAGAAGTCTGGGACATAATTCTTTATAAAAATAG*ATTGTGCCTTATAACCTGCCTTTGCCTGGGGGAGTGG	tcga,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	39	4	23	14	55318269	+	14	55140275	+	23.2696	158.9296	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-44-4112-01A	ENSG00000178974	ENSG00000131981	FBXO34	LGALS3	GTCGCGCCCTCCCGGGCTCGGCCACTCTGCCCTTCCCTGCCCCAGCGCAG*ATTGTGCCTTATAACCTGCCTTTGCCTGGGGGAGTGGTGCCTCGCATGCT	tcga,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	39	4	21	14	55271984	+	14	55140275	+	23.2696	158.9296	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-44-4112-01A	ENSG00000178974	ENSG00000131981	FBXO34	LGALS3	TGTTGAAACTTCCCTCACCACGCCCTCTGCTGAGTGTTTGTGAAACTCAG*ATTGTGCCTTATAACCTGCCTTTGCCTGGGGGAGTGGTGCCTCGCATGCT	tcga,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	39	3	24	14	55298105	+	14	55140275	+	23.2696	158.9296	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-44-4112-01A	ENSG00000101752	ENSG00000167088	MIB1	SNRPD1	ATCATGACATTGTAGTACAGTATCCAAGTGGCAATAG*ATTTTTGATGAAATTGAGTCATGAAACTGTAACCATT	m3,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	11	4	18	18	21779685	+	18	21622725	+	6.2978	13.2936	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-44-4112-01A	ENSG00000179583	ENSG00000175267	CIITA	VWA3A	GCCACCAGCAGCGCGCGCGGGAGCCCGGGGAACAGCG*AGCATTAAAGATGACCCTGACAGAGAGAAGAGCCCCC	cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	5	7	24	16	10879042	+	16	22140154	+	1.4778	7.9933	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-44-4112-01A	ENSG00000175267	ENSG00000179583	VWA3A	CIITA	GGCGTGGTGGCACATTCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAG*AAGACACTGATGGGCAACCCCCAGCCTGCTAATTCCCCAGATTGCAACAG	cancer	BOWTIE+BLAT	intronic/UTR	0	5	1	19	16	22132290	+	16	10924600	+	7.9933	1.4778	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-44-4112-01A	ENSG00000172932	ENSG00000173120	ANKRD13D	KDM2A	CCACCCACCTGGACACTCGTAATGTGGCCTTTGAGAG*ATGGTGGCAGATGAAAAAGCAGATTTTTTTCCCCTGA	oncogene,10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	2	2	20	11	67292180	+	11	67149055	+	4.8122	10.7117	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-44-4112-01A	ENSG00000051382	ENSG00000244578	PIK3CB	LINC01391	TAATGCCATCTGTTTTCCTAAAAGACTGAAATGGGGGCGACCATTCTTAG*AAGAGAAAAAAAGGAAATTCGACACATATTTTTAAAAATCTTCCCCCAAC	lincrna,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	UTR/intronic	0	2	1	23	3	138796463	-	3	138939256	-	11.395	4.4839	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-44-4112-01A	ENSG00000051382	ENSG00000244578	PIK3CB	LINC01391	TAATGCCATCTGTTTTCCTAAAAGACTGAAATGGGGGCGACCATTCTTAG*GATCGGGGGTCTTGAAACTGGAGCCGCTCACCGGCCGGCGGATGAGAGAT	lincrna,100K<gap<200K	BOWTIE+STAR	UTR/exonic(no-known-CDS)	0	2	1	15	3	138796463	-	3	138938012	-	11.395	4.4839	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-44-4112-01A	ENSG00000142186	ENSG00000126391	SCYL1	FRMD8	CTGCCTGGGCAAAATCGGCTCCTACCTCAGTGCTAGC*GCCGAACTGATGAGCAGTCTCATTGAGTACTGCATCG	known,tcga,cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	1	1	14	11	65535382	+	11	65404864	+	28.3685	13.1572	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-05-4384-01A	ENSG00000256612	ENSG00000269235	CYP2B7P	ZNF350-AS1	TGGACAGAAGAGGCCTACTCAAATCCTTTCTGAGG*TCTGTAAAATCGGATGGACCACCAATTGGAGAATG	pseudogene,antisense,chimerdb3seq,m7,exon-exon	BOWTIE	exonic(no-known-CDS)/exonic(no-known-CDS)	0	18	4	24	19	40924443	+	19	51980927	+	83.9371	22.249	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	transcribed_unprocessed_pseudogene	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-55-6543-01A	ENSG00000062650	ENSG00000238258	WAPL	AL121748.2	TCACATATTGGTGATTCCATCCACTTCTAGGCCAGTAGAAGATAATTGGC*CTTCGCCTTGCGTTTGCTGTCATCCATGATCATCTTCCAGTCCGAGCCGT	antisense,oncogene	BOWTIE+BLAT;BOWTIE+STAR	intronic/exonic(no-known-CDS)	0	40	8	24	10	86465965	-	10	33213386	+	9.3471	0.0692	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-55-6543-01A	ENSG00000062650	ENSG00000238258	WAPL	AL121748.2	TACCTCAGGAGCAGAGATTTGATATTCGAGTGCTG*AATCAAGGGTCTTACTGACCCCATCACACACCTCC	antisense,oncogene,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	40	7	24	10	86453220	-	10	33213238	+	9.3471	0.0692	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-55-6543-01A	ENSG00000062650	ENSG00000238258	WAPL	AL121748.2	GTCTGGCTGAACGTACTTCTTATTGTGCAAAAGAAAGCCATGAAAAGACC*CTTCGCCTTGCGTTTGCTGTCATCCATGATCATCTTCCAGTCCGAGCCGT	antisense,oncogene	BOWTIE+BLAT;BOWTIE+STAR	intronic/exonic(no-known-CDS)	0	40	2	22	10	86452716	-	10	33213386	+	9.3471	0.0692	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-55-6543-01A	ENSG00000062650	ENSG00000238258	WAPL	AL121748.2	AGGTTCCAAAGTACCTACCTCAGGAGCAGAGATTTGATATTCGAGTGCTG*GTCTATTTGGAGCCACTCATTGATGTAGGAATGAGGTGCGGGTGGAAGTG	antisense,oncogene	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	40	2	19	10	86453220	-	10	33213536	+	9.3471	0.0692	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-55-6543-01A	ENSG00000062650	ENSG00000238258	WAPL	AL121748.2	TGGGTGGGTGATCCAAAGAGTTGTTGAAGCTGAGCAGGTTCTGGCTGGGC*CTTCGCCTTGCGTTTGCTGTCATCCATGATCATCTTCCAGTCCGAGCCGT	antisense,oncogene	BOWTIE+BLAT;BOWTIE+STAR	intronic/exonic(no-known-CDS)	0	40	2	19	10	86485949	-	10	33213386	+	9.3471	0.0692	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-55-6543-01A	ENSG00000129595	ENSG00000173261	EPB41L4A	PLAC8L1	AGTTAACCCTTACCACCCAGCAGCAGGGCATCAAG*AGGCCATGTACCAGCCAGCGCTGTGGTGAAGCAGC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	36	8	21	5	112418941	-	5	146098292	-	2.5782	2.2166	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-55-6543-01A	ENSG00000197323	ENSG00000165731	TRIM33	RET	ACCTTCCATCGCTGCCAGATATTCCACCCATACAG*GAGGATCCAAAGTGGGAATTCCCTCGGAAGAACTT	known,oncogene,cosmic,chimerdb2,cgp,ticdb,tcga,chimerdb3kb,chimerdb3pub,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	22	8	22	1	114421436	-	10	43116584	+	3.6861	2.5613	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-55-6543-01A	ENSG00000197323	ENSG00000165731	TRIM33	RET	TTGGAGCCAGAGAGAAGACCCAGGACCAAAATGTG*GAGGATCCAAAGTGGGAATTCCCTCGGAAGAACTT	known,oncogene,cosmic,chimerdb2,cgp,ticdb,tcga,chimerdb3kb,chimerdb3pub,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	CDS(no-known-start-or-end)/CDS(truncated)	0	22	3	24	1	114420380	-	10	43116584	+	3.6861	2.5613	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-49-4486-01A	ENSG00000127663	ENSG00000011243	KDM4B	AKAP8L	AGTTCATCTCCTCCGTCACCAGCCACATCTACCAG*CTCATGATGGAGCAGTCCAAGAAGTCCTCCCTCAT	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	106	17	23	19	5144902	+	19	15380612	-	1.6228	1.8678	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-49-4486-01A	ENSG00000123815	ENSG00000105127	COQ8B	AKAP8	AGTTTGGGACAGAGTTCACAGACCATTACATCGAG*TTGGCTGCTGAACAGTTCAAGAAAACCAGTCTCCA	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	66	11	22	19	40695989	-	19	15359062	-	4.8748	8.903	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-49-4486-01A	ENSG00000237669	ENSG00000271581	AL671277.2	AL671883.3	CCCGCCTCGCTCTGGTTGTAGTAGCGGAGCAGGGTCCGCAGGTTCACTCG*GTCAGTCTGTGCCTGGGCCTTGTAGATCTGTGTGTTCCGGTCCCAATACT	pseudogene,m19	BOWTIE+BLAT	exonic(no-known-CDS)/exonic(no-known-CDS)	0	37	1	14	6	30007021	-	6	31356737	+	0.0503	0	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	unprocessed_pseudogene	unprocessed_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-49-4486-01A	ENSG00000099385	ENSG00000168878	BCL7C	SFTPB	GGGATTACAGACAAAGTACCTTCTTAAGGGCAGGGGAGAATATTACAAAG*CACCTTCCCCACCCTTGAGAAGGTGCTTTGTAATATTCTCCCCACCCACC	NA	BOWTIE+BLAT	intronic/UTR	0	2	1	18	16	30864869	-	2	85657955	-	7.0199	10211.4044	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-49-4486-01A	ENSG00000168878	ENSG00000099385	SFTPB	BCL7C	CCCGCACCCTTAAGAAGGTATTTTGTAATATTCTCTCCGCCATTGAGAAT*ATTACAAAGTACCTTCTTAAGGGTGGGGGGGTGGGGGTGGGGGGGAGAAT	NA	BOWTIE+BLAT	UTR/intronic	0	2	1	21	2	85657843	-	16	30864877	-	10211.4044	7.0199	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-44-2668-01A	ENSG00000100644	ENSG00000027075	HIF1A	PRKCH	AGCCCTAACGTGTTATCTGTCGCTTTGAGTCAAAG*AGATCTGAAACTGGACAATGTCCTGTTGGACCACG	tcga,chimerdb3seq,tcga-cancer,oesophagus,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	153	17	24	14	61741188	+	14	61529075	+	209.3086	8.3199	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-44-2668-01A	ENSG00000100644	ENSG00000027075	HIF1A	PRKCH	AAATCTCATCCAAGAAGCCCTAACGTGTTATCTGTCGCTTTGAGTCAAAG*CACCTCCTGCCAGGACCATGCTGGAGCTGCTAAGAAGGAAGACAGGTGCA	tcga,chimerdb3seq,tcga-cancer,oesophagus,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	153	2	22	14	61741188	+	14	61525052	+	209.3086	8.3199	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-44-2668-01A	ENSG00000100644	ENSG00000027075	HIF1A	PRKCH	CTTCCGATGGAAGCACTAGACAAAGTTCACCTGAG*AGATCTGAAACTGGACAATGTCCTGTTGGACCACG	tcga,chimerdb3seq,tcga-cancer,oesophagus,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	153	1	14	14	61738373	+	14	61529075	+	209.3086	8.3199	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-44-2668-01A	ENSG00000100644	ENSG00000027075	HIF1A	PRKCH	AAATCTCATCCAAGAAGCCCTAACGTGTTATCTGTCGCTTTGAGTCAAAG*ATGAGGAAACTGAGGCCCAGAAAGGTGACAGAGCTAAGACCAGAGTCCCT	tcga,chimerdb3seq,tcga-cancer,oesophagus,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/intronic	0	153	1	14	14	61741188	+	14	61513940	+	209.3086	8.3199	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-44-2668-01A	ENSG00000198900	ENSG00000236772	TOP1	AL034550.1	GAGAAGGACCGGGAAAAGTCCAAGCATAGCAACAG*AGTAGCCTGGGGAGTTACCGGAAAAGCACCTACTG	antisense,cancer,tumor,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	24	4	23	20	41061490	+	20	32451568	+	31.5562	0.5321	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-44-2668-01A	ENSG00000198900	ENSG00000236772	TOP1	AL034550.1	GAGAAGGACCGGGAAAAGTCCAAGCATAGCAACAG*GACTTGAGGTACGTGCGGATGCGCTTGCGGGCCCG	antisense,cancer,tumor,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	24	3	23	20	41061490	+	20	32453338	+	31.5562	0.5321	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-44-2668-01A	ENSG00000257949	ENSG00000177728	TEN1	TMEM94	AGAAGAAATCCGAGGACCGGCGACGCCTAGAACAG*ATGTTGTGACTGTGACAGACTCACTGGGGTTTGTA	exon-exon	BOWTIE	UTR/UTR	0	11	4	23	17	75979511	+	17	75471800	+	0	9.7944	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-44-2668-01A	ENSG00000155380	ENSG00000112701	SLC16A1	SENP6	ATCCTCCATAATGTTGGCTGTCATGTATGGTGGAG*CTTTGGCTAGATCAGAGTCTAAGAGAGATGGAGGT	cell_lines,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	7	3	21	1	112929092	-	6	75621532	+	4.9598	4.5584	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-44-2668-01A	ENSG00000090861	ENSG00000103051	AARS	COG4	AGGATGTGCAGAGGGAGATCGCTGACCTTGGAGAG*AAAGTGGTGGAGAGAGAGCTGGATGCTCTTTTGGA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	3	2	21	16	70254621	-	16	70519731	-	21.3601	16.1637	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-44-2668-01A	ENSG00000264772	ENSG00000115677	AC016876.2	HDLBP	CTCTACTAAAAATACAATTAGCCAGGTGTGGCGGCGTAATCCCAGCTGGC*CTGTGGTCCCAGCTGCTTGGGAGGCTGAGGCAGGAGAATGGCGTGAACCC	cancer	BOWTIE+STAR	exonic(no-known-CDS)/intronic	0	2	3	23	17	7581802	+	2	241254627	-	0	92.7951	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	processed_transcript	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-49-4506-01A	ENSG00000174243	ENSG00000272822	DDX23	AC073610.3	GTTGAGGCCGCGTTGGGCGGTTCAGACTCAGGGTG*GATGGGCACGATCTCGGCTCACTGCAACCTCCGCC	m13,10K<gap<100K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	15	7	22	12	48852084	-	12	48903908	-	19.2021	0.01	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-49-4506-01A	ENSG00000174243	ENSG00000272822	DDX23	AC073610.3	TCCATTCCCGCAATGCAACTGAAACAGCTCTTGTCAAGGTCACCAATAAT*CTCGTGATCCGCCATCCTCGGCCTCCTAAAGTGCTGGGATTACAGGTGTG	m13,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	intronic/intronic	0	15	1	23	12	48850824	-	12	48912044	-	19.2021	0.01	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-49-4507-01A	ENSG00000054118	ENSG00000077549	THRAP3	CAPZB	GCGAGCTGCAGCTGCGATCTCTGTGGTAGGCCCAG*GTCACCATGGAGTAACAAGTATGACCCTCCCTTGG	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	263	18	24	1	36224505	+	1	19378653	-	17.0738	16.796	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-49-4507-01A	ENSG00000054118	ENSG00000077549	THRAP3	CAPZB	CCAGTGGCAATCGGCGTGAGTTCTGCTTATATGAG*GTCACCATGGAGTAACAAGTATGACCCTCCCTTGG	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	263	2	22	1	36225102	+	1	19378653	-	17.0738	16.796	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-49-4507-01A	ENSG00000054118	ENSG00000077549	THRAP3	CAPZB	GACTCCTGATCCTGAGAGGATCGAGTGATCCTTCCACCTCAGCTTCACAA*GTCACCATGGAGTAACAAGTATGACCCTCCCTTGGAGGATGGGGCCATGC	tcga,chimerdb3seq,cancer,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	263	1	20	1	36238863	+	1	19378653	-	17.0738	16.796	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-05-4398-01A	ENSG00000138378	ENSG00000144476	STAT4	ACKR3	TACACAATCTAAAAAGAATTAGGAAGGTCCTTCAG*GTCATTTGATTGCCCGCCTCAGAACGATGGATCTG	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	95	14	24	2	191146613	-	2	236580440	+	4.3354	25.0869	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-05-4398-01A	ENSG00000179104	ENSG00000127720	TMTC2	METTL25	AACACCCTGAGTGCGGATTTCTGCTATGATGACAG*GTGATTGACTTGGGTTCCGGTAAAGGCTACCTAAG	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	23	2	22	12	82687669	+	12	82398795	+	2.0384	2.1891	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-05-4398-01A	ENSG00000058668	ENSG00000178568	ATP2B4	ERBB4	GCCTGAAGAAACCTGGATCTTTGCTAGAAAGAGAG*TGTGTGCAGGAACGGAGAATAAACTGAGCTCTCTC	oncogene,tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	14	6	24	1	203627219	+	2	212124903	-	68.836	2.5358	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-05-4398-01A	ENSG00000131558	ENSG00000169403	EXOC4	PTAFR	AGAAACATTACCGTCATATTCCACCCATTACTAAG*GCACCACCAGGACCAGCTGATCATTCCAGCCCACA	tcga,cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	11	4	23	7	133630141	+	1	28151059	-	13.3948	22.1142	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-05-4398-01A	ENSG00000259460	ENSG00000273749	AC078909.1	CYFIP1	GGACAGGCCCCTCTTAGGAGAGGATTTATATCTAG*GTATCCTGGAGTTCTTCCACCACCAGCTGAAGGAC	antisense,m6,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	7	4	22	15	37099429	+	15	22880043	-	0	11.9417	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-05-4398-01A	ENSG00000259460	ENSG00000273749	AC078909.1	CYFIP1	TTCATGGCTTTTTGCCACTCCAGCTGTCAATCAAAGCCCGGAATGTCAAG*GTATCCTGGAGTTCTTCCACCACCAGCTGAAGGACATCGTGGAGTACGCA	antisense,m6	BOWTIE+BLAT;BOWTIE+STAR	exonic(no-known-CDS)/CDS(truncated)	0	7	1	18	15	37099967	+	15	22880043	-	0	11.9417	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-05-4398-01A	ENSG00000273000	ENSG00000126522	AP000347.2	ASL	CATCTGGAATTTTGCCGATTTCATGACTAACCAGT*GTGGCTGAGGAGTGGGCCCAGGGCACCTTCAAACT	cancer,m2,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	4	5	22	22	23659865	-	7	66082368	+	NA	12.7757	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	processed_transcript	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-05-4398-01A	ENSG00000273000	ENSG00000126522	AP000347.2	ASL	CGTGGTTGGAGAGCTCATCTGGAATTTTGCCGATTTCATGACTAACCAGT*GTGGGTGCAGTGGACCCCATCATGGAGAAGTTCAACGCGTCCATTGCCTA	cancer,m2	BOWTIE+BLAT	exonic(no-known-CDS)/CDS(truncated)	0	4	1	20	22	23659865	-	7	66081830	+	NA	12.7757	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	processed_transcript	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-05-4398-01A	ENSG00000126012	ENSG00000017797	KDM5C	RALBP1	TGACAAACCAAGATGGCGGCGGCGGCGCTGAAGGCCGCGGCGTTTGGGAG*ATCAGCAATCGAGTCCTGTATGTGTTTTTCACACATGTGCAAGAACTCTT	cancer,m2	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	4	10	24	X	53225159	-	18	9524594	+	15.5812	11.5404	TRUE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-05-4398-01A	ENSG00000017797	ENSG00000126012	RALBP1	KDM5C	CGATGGTCTAACATGGCCACGATGCCCACGCTGCCAGAGACCCAGGCGGG*GACAAACCAAGATGGCGGCGGCGGCGCTGAAGGCCGCGGCGTTTGGGAGG	cancer,m2	BOWTIE+BLAT	CDS(truncated)/UTR	0	4	1	22	18	9524730	+	X	53225207	-	11.5404	15.5812	FALSE	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-49-6744-01A	ENSG00000116117	ENSG00000186153	PARD3B	WWOX	CCCGCCAAGAAGGACATTTTCTGCCCCGAGAGTTG*CAACAGGGAGCTGCCACCACCGTGTACTGTGCTGC	tcga,cell_lines,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	9	3	23	2	205125737	+	16	79211608	+	2.3771	2.2185	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-91-6847-01A	ENSG00000108641	ENSG00000128487	B9D1	SPECC1	CCCCAAGGTGGTGGCTCAGGGTGAAGGCCGGGAAG*AGACAGAGTTTTGCTATGTTGCTCAGGCTGGTCTT	cancer,tumor,m4,exon-exon	BOWTIE	CDS(truncated)/UTR	0	13	2	21	17	19343790	-	17	20057677	+	2.3917	2.018	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-91-6847-01A	ENSG00000145996	ENSG00000198663	CDKAL1	C6ORF89	TGGACAGCTAGCTGCTTATGGCTATAAAATTACAG*GAATCATTGTAGTCAATCATTTTCCAGTTCTCAGC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	11	3	21	6	20548705	+	6	36894504	+	10.2677	24.0842	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-91-6847-01A	ENSG00000184792	ENSG00000198089	OSBP2	SFI1	TTCGTGCTGGGCAATGGTTTGCTCTCTTACTACAG*ATTTTACTATGAGCAGCGATTACTACGGAAGGTCT	cell_lines,tcga-cancer,exon-exon	BOWTIE	in-frame	0	9	2	19	22	30695553	+	22	31546861	+	1.5292	7.9034	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-91-6847-01A	ENSG00000141376	ENSG00000108262	BCAS3	GIT1	AAGTCCATTCAATTTAAGACACCTATTTATGATCTCCATTGCAATAAACG*GCTGGTCTCCACCTCCTGGCCTCAAGCGAACCTCCCACCTTGGCCTCCCA	tcga,cell_lines,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	6	4	23	17	60868683	+	17	29579552	-	1.0207	15.7554	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-91-6847-01A	ENSG00000141376	ENSG00000108262	BCAS3	GIT1	AAGACACCTATTTATGATCTCCATTGCAATAAACG*CCTTGACTTATCCGAATTGGCCAAAGCTGCTAAGA	tcga,cell_lines,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	6	2	23	17	60868683	+	17	29578779	-	1.0207	15.7554	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-91-6847-01A	ENSG00000168872	ENSG00000121270	DDX19A	ABCC11	GATCAAGGAAGAGAAAGTCAAAGCAGATACCAATG*GTGTATTTGAATAAACCAGGTTGGCAAATCATACT	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	2	5	22	16	70350605	+	16	48235177	-	1.7869	0.8997	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-91-6847-01A	ENSG00000109171	ENSG00000224843	SLAIN2	LINC00240	CGCCTGTCAGGCTGGGAGGAGGAGGAGGAGAGCTG*GAGAAGCCAGCTCCCATGTTAAGAAGTTCAAATAC	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	2	1	13	4	48342128	+	6	27023254	+	7.0093	0.1739	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-64-5775-01A	ENSG00000123297	ENSG00000139266	TSFM	MARCH9	AGACCCTAAAGGATCAACCCTCTGCATACAGTAAA*TGGCAGGCCATCTCCCTGACGGTCATCGAGAAGGT	tcga,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	34	7	24	12	57787162	+	12	57758108	+	0.1188	4.1246	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-64-5775-01A	ENSG00000123297	ENSG00000139266	TSFM	MARCH9	AGACCCTAAAGGATCAACCCTCTGCATACAGTAAA*GCCTCATCATCCATGAAGGCTCCTCTGTCTACCGC	tcga,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	34	3	21	12	57787162	+	12	57758563	+	0.1188	4.1246	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-64-5775-01A	ENSG00000123297	ENSG00000139266	TSFM	MARCH9	CCATGATGCATTGTCAGACCCTAAAGGATCAACCCTCTGCATACAGTAAA*AGCACTTGCCCAATCCTGCCTTTCTAAAGTAAGACAAATGGTGTCAGACA	tcga,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	34	1	22	12	57787162	+	12	57757897	+	0.1188	4.1246	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-64-5775-01A	ENSG00000185483	ENSG00000116675	ROR1	DNAJC6	CTTGGGGCTTTCCAGAGAAATTTACTCCGCTGATTACTACAGGGTCCAGA*GTGCCTCATCTCCAGACATGGAGCCCAGCTATGGGGGAGGTCTCTTTGAC	known,tcga,cell_lines,chimerdb3pub,cancer	BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	8	3	20	1	64177989	+	1	65364635	+	5.466	3.8279	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-64-5775-01A	ENSG00000134744	ENSG00000253802	ZCCHC11	AC105999.2	TTCCCTGGTAAACAGTGGTGCAGTGGGGAATTCAG*AAGTAACCTGGCCAGGCGCAGTGGCATACACCTGT	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	8	6	22	1	52431013	-	8	40304783	-	2.5086	0.8866	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-64-5775-01A	ENSG00000134744	ENSG00000253802	ZCCHC11	AC105999.2	TACTGTGGCTCCAAATTCCCTGGTAAACAGTGGTGCAGTGGGGAATTCAG*GAAATACCTGGAGGAGGAAGACAGCGATGATCTGAAGGGCCTGAATTAGG	lincrna	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	8	5	22	1	52431013	-	8	40307468	-	2.5086	0.8866	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-64-5775-01A	ENSG00000134744	ENSG00000253802	ZCCHC11	AC105999.2	ACCAAAGAAGAATGTTATTTGTGAAGAAAGCAAAGCAGTTCAAGTTATAG*AAGTAACCTGGCCAGGCGCAGTGGCATACACCTGTAATTCCAACACAGTG	lincrna	BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	8	1	15	1	52526193	-	8	40304783	-	2.5086	0.8866	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-64-1678-01A	ENSG00000100345	ENSG00000149716	MYH9	ORAOV1	ACCTCAAGGAGCGTTACTACTCAGGGCTCATCTAC*GTTTCATGGGGAAGGGTATCGGGAAGGCTATGAAG	cell_lines,18cancers,chimerdb3seq,cancer,m49,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	61	9	24	22	36348904	-	11	69673321	-	34.6362	15.9048	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-64-1678-01A	ENSG00000100345	ENSG00000149716	MYH9	ORAOV1	ACCTCAAGGAGCGTTACTACTCAGGGCTCATCTAC*ATCGGGTGCTACCAAGGTTTTGCTTTTGCATGGAA	cell_lines,18cancers,chimerdb3seq,cancer,m49,tcga-cancer,exon-exon	BOWTIE	in-frame	0	61	7	23	22	36348904	-	11	69671819	-	34.6362	15.9048	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-64-1678-01A	ENSG00000100345	ENSG00000149716	MYH9	ORAOV1	CCTCGGTGCTGCACAACCTCAAGGAGCGTTACTACTCAGGGCTCATCTAC*AAAGATGAAGGTCTTAGAATCATTGATTGGAATGATCCAGAAATTCCCTT	cell_lines,18cancers,chimerdb3seq,cancer,m49,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	61	1	23	22	36348904	-	11	69668009	-	34.6362	15.9048	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-64-1678-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	GCCTGCCTCAGCCTCCAAAGTAGCTGAGACTACAG*CAGTTTAAGTATAGTGTGCCTGGGTTGGGTGCGGT	antisense,m2,exon-exon	BOWTIE	exonic(no-known-CDS)/UTR	0	17	5	24	10	87246115	-	10	46593287	+	1.0957	0.0279	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-64-1678-01A	ENSG00000279738	ENSG00000149716	AL022311.1	ORAOV1	TGGATGGTGAATTTCAGTCAGCCTCAGAGGTTGACTTCTACATTGATAAG*GGGACGGGAGCCAGTGGCACAGAGGAGAGACTGCCACGTGAAGACATGGG	cancer	BOWTIE+BLAT;BOWTIE+STAR	exonic(no-known-CDS)/intronic	0	8	4	21	22	37878171	+	11	69661602	-	2.0705	15.9048	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	sense_overlapping	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-64-1678-01A	ENSG00000100129	ENSG00000149716	EIF3L	ORAOV1	AGTCAGCCTCAGAGGTTGACTTCTACATTGATAAG*CGCCGCGGTGCAACCAGAAATGCACAGACCCAGCC	18cancers,cancer,exon-exon	BOWTIE	out-of-frame	0	8	3	16	22	37878171	+	11	69654384	-	94.6638	15.9048	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-64-1678-01A	ENSG00000100129	ENSG00000149716	EIF3L	ORAOV1	AGTCAGCCTCAGAGGTTGACTTCTACATTGATAAG*GCCGGTTACATGTTGGTGCTGGGAAGCGCCGCGGT	18cancers,cancer,exon-exon	BOWTIE	out-of-frame	0	8	2	21	22	37878171	+	11	69654410	-	94.6638	15.9048	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-05-4405-01A	ENSG00000171456	ENSG00000215529	ASXL1	EFCAB8	CCAAAACAGATTCTGCAGGTCATAGAGGCAGAAGGACTAAAGGAAATGAG*AGATAGGGTTTTCCTGTGTAGCCCAGGGTGGAGTGCAGTGGTGTGATGAT	cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	23	20	32366466	+	20	32871293	+	4.3213	0.1532	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-75-6205-01A	ENSG00000125872	ENSG00000125885	LRRN4	MCM8	GATACTCCACATCTACAGGTCCTTCTGTTCCAGAA*CATGCTAGGAACTTACTCTGATGAATTTGGGAACC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	8	2	18	20	6050779	-	20	5993506	+	1.8261	1.2011	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-75-6205-01A	ENSG00000104419	ENSG00000145623	NDRG1	OSMR	TTGGACCCAACAAAGACCACTCTCCTCAAGGTACAGGGAAAACAGTGGGG*GGTCTTGCTCAGTCTTCCCAGGATGCAGCACAATGTTGCCATCTTTGTTC	cancer	BOWTIE+STAR	intronic/intronic	0	3	1	18	8	133246596	-	5	38942475	+	44.532	38.4533	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000166272	ENSG00000107882	WBP1L	SUFU	CTTGCAGGATGCCTTTCCTTTTGGGTCTTAGACAG*AGAACACCTTCTGCAGTGGGGACCATGTGTCCTGG	known,tcga,prostates,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	148	15	23	10	102776417	+	10	102592582	+	13.0124	22.704	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000166272	ENSG00000107882	WBP1L	SUFU	CCAGCCCCTTGTCAGCCAGGGCTGAACCCCCGCAG*AGAACACCTTCTGCAGTGGGGACCATGTGTCCTGG	known,tcga,prostates,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	148	8	23	10	102744143	+	10	102592582	+	13.0124	22.704	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000185825	ENSG00000067840	BCAP31	PDZD4	GGTTCTCATTGTCATCCTTGTGCTGTTGGTCATCG*GTGAACGGGAAGGAGCTCTCCAAGCTGTCTCAGGA	tcga,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	110	18	24	X	153720872	-	X	153808595	-	94.5792	15.5243	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000166965	ENSG00000197299	RCCD1	BLM	GGCCGCGGGGGGCTGGCATTCTGTGTGTGTGAGTG*GTTTAGCATGAGCTTTAACAGACATAATCTGAAAT	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	110	11	24	15	90957725	+	15	90782822	+	13.2197	12.7343	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000166965	ENSG00000197299	RCCD1	BLM	GTCGGGTTTTGAGCTGCCGCGGTCCCGGGACTGAG*GTTTAGCATGAGCTTTAACAGACATAATCTGAAAT	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	110	8	24	15	90954948	+	15	90782822	+	13.2197	12.7343	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000166965	ENSG00000197299	RCCD1	BLM	GGCCGCGGGGGGCTGGCATTCTGTGTGTGTGAGTG*ATGATTCAGGGATAATTTACTGCCTCTCCAGGCGA	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	110	8	23	15	90957725	+	15	90784921	+	13.2197	12.7343	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000166965	ENSG00000197299	RCCD1	BLM	GTCGGGTTTTGAGCTGCCGCGGTCCCGGGACTGAG*ATGATTCAGGGATAATTTACTGCCTCTCCAGGCGA	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	110	6	22	15	90954948	+	15	90784921	+	13.2197	12.7343	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000166965	ENSG00000197299	RCCD1	BLM	TAAATGCTCGCTGGACGAATAAATGGCTAGATAAG*GTTTAGCATGAGCTTTAACAGACATAATCTGAAAT	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	110	4	20	15	90955883	+	15	90782822	+	13.2197	12.7343	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000166965	ENSG00000197299	RCCD1	BLM	GCTGCTGGCCAGGTGTTCTCCTGGGGCGGGGGCAG*GTTTAGCATGAGCTTTAACAGACATAATCTGAAAT	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	110	3	23	15	90957503	+	15	90782822	+	13.2197	12.7343	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000166965	ENSG00000197299	RCCD1	BLM	CCCGAGAGGGTAGAGGGCATAGGGTCAAGATCAAG*GTTTAGCATGAGCTTTAACAGACATAATCTGAAAT	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	110	2	15	15	90955452	+	15	90782822	+	13.2197	12.7343	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000166965	ENSG00000197299	RCCD1	BLM	AGTCATGGCTGAGGTGGCCGCGGGGGGCTGGCATTCTGTGTGTGTGAGTG*AATTGTACAACCATCCCCAATATCTAAGTTTACAGCATTTTTATCACCCC	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	110	1	20	15	90957725	+	15	90777759	+	13.2197	12.7343	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000119333	ENSG00000160445	WDR34	ZER1	GCTTCGAGGTGAACTGGACCGAGCAGCAGCAGATG*GTGCAGCGGAACTGCTGCCTGACGCTCTGCAACTT	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE;BOWTIE+BLAT	in-frame	0	101	15	24	9	128640691	-	9	128742745	-	15.6104	16.6974	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000006704	ENSG00000241135	GTF2IRD1	LINC00881	GGAGTGTGTGCAGATCCTGTTTAACAGCAGATATG*GAACAACGTGTGAAATGAAAGACCTCAGGTGCTGT	lincrna,18cancers,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	99	15	24	7	74524154	+	3	157099483	+	8.1311	1.6218	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000065526	ENSG00000090661	SPEN	CERS4	GTGCGGGAAGAGAAGATCATCGAGCATTTCAAACG*AATGCTGTCCAGTTTCAACGAGTGGTTTTGGCAGG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	97	18	23	1	15848150	+	19	8251076	+	8.9939	52.0128	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000065526	ENSG00000090661	SPEN	CERS4	AACTTACCCGAGAACGTGCGGGAAGAGAAGATCATCGAGCATTTCAAACG*GGTCTTGCTCTGTCCCTCAGGCTGGAGTATAGTGGTGTGATCGTAGCTCC	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	97	15	23	1	15848150	+	19	8247445	+	8.9939	52.0128	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000065526	ENSG00000090661	SPEN	CERS4	GTGCGGGAAGAGAAGATCATCGAGCATTTCAAACG*ATTCATTGGCCTGCCCCTGAGCCGGTGGCTGGGTG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	97	10	24	1	15848150	+	19	8254499	+	8.9939	52.0128	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000065526	ENSG00000090661	SPEN	CERS4	GTGCGGGAAGAGAAGATCATCGAGCATTTCAAACG*ACCTCCCAGCTAACTGGAACCTGTGTCCACAGAAT	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	97	4	23	1	15848150	+	19	8251044	+	8.9939	52.0128	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000256053	ENSG00000075413	APOPT1	MARK3	AAAAACTAAAGGCCTGGGCCTGAGAACTGAATCAG*CTGGACCAGCTATTCCTTCTGTTGTGGCGTATCCG	known,tcga,cell_lines,18cancers,chimerdb3seq,m83,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	86	6	23	14	103574170	+	14	103474993	+	5.4819	5.9294	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000256053	ENSG00000075413	APOPT1	MARK3	AGTAAAAATTTTCAGAAGCACATGTATTATAACAG*TCGCAATGTATCTGCTGAGCAAAAAGATGAAAACA	known,tcga,cell_lines,18cancers,chimerdb3seq,m83,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	86	4	19	14	103587364	+	14	103502882	+	5.4819	5.9294	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000256053	ENSG00000075413	APOPT1	MARK3	AAAAACTAAAGGCCTGGGCCTGAGAACTGAATCAG*CTGGATGCTAGTGATTCCAGTTCTAGCAGCAATCT	known,tcga,cell_lines,18cancers,chimerdb3seq,m83,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	86	4	19	14	103574170	+	14	103468033	+	5.4819	5.9294	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000256053	ENSG00000075413	APOPT1	MARK3	AAAAACTAAAGGCCTGGGCCTGAGAACTGAATCAG*TCGCAATGTATCTGCTGAGCAAAAAGATGAAAACA	known,tcga,cell_lines,18cancers,chimerdb3seq,m83,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	86	3	21	14	103574170	+	14	103502882	+	5.4819	5.9294	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000256053	ENSG00000075413	APOPT1	MARK3	TCCTGCCTCAGCCTTCTGAGTAGCTGGGACTACAG*CTGGATGCTAGTGATTCCAGTTCTAGCAGCAATCT	known,tcga,cell_lines,18cancers,chimerdb3seq,m83,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	86	2	22	14	103579491	+	14	103468033	+	5.4819	5.9294	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-38-4630-01A	ENSG00000256053	ENSG00000075413	APOPT1	MARK3	GCCGGATGTGGCTAACAGAAGTTCAGCAGGACTCACGAGGGCTATCTCAG*AAACATGTCATTCAGGTTTATCAAAAGGTAGGATTTATATATACACATTT	known,tcga,cell_lines,18cancers,chimerdb3seq,m83,10K<gap<100K	BOWTIE+STAR	intronic/CDS(truncated)	0	86	1	18	14	103593764	+	14	103498502	+	5.4819	5.9294	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000256053	ENSG00000075413	APOPT1	MARK3	AAAAACTAAAGGCCTGGGCCTGAGAACTGAATCAG*GTTAGGCCGAGCAGTGATCTCAACAACAGTACTGG	known,tcga,cell_lines,18cancers,chimerdb3seq,m83,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	86	1	14	14	103574170	+	14	103468081	+	5.4819	5.9294	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000256500	ENSG00000075413	AL139300.1	MARK3	GACTGCCAAGCGATCGGTGTGCTGGCCGTGGAGTCAGCACCACCCTCACT*GCTTCCAACTGAATATGAGAGGAACGGGAGATATGAGGGCTCAAGGTGAG	10K<gap<100K	BOWTIE+STAR	intronic/CDS(truncated)	0	75	1	18	14	103590977	+	14	103500156	+	0	5.9294	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000256500	ENSG00000075413	AL139300.1	MARK3	GAGGTGCGCGGTTGCTGTCACACACTAGAGAGGAAGAAACTGAGATGGAG*GTTAGGCCGAGCAGTGATCTCAACAACAGTACTGGCCAGTCTCCTCACCA	10K<gap<100K	BOWTIE+STAR	intronic/CDS(truncated)	0	75	1	17	14	103578971	+	14	103468081	+	0	5.9294	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000135503	ENSG00000260473	ACVR1B	AC068987.3	AAACATCCTTGGATTTATTGCTGCTGACAATAAAG*GTGTTGTTTGCTCCCCTTGGTTAGGCTGCCTGCAA	lincrna,cancer,100K<gap<200K,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	66	12	24	12	51981199	+	12	51837866	+	24.2074	3.8783	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000135503	ENSG00000260473	ACVR1B	AC068987.3	AAACATCCTTGGATTTATTGCTGCTGACAATAAAG*GTGAGGAAACTGAGGCTCGATTAACTTGTCTAAGT	lincrna,cancer,100K<gap<200K,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	66	10	23	12	51981199	+	12	51841393	+	24.2074	3.8783	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000177885	ENSG00000184402	GRB2	SS18L1	ACGAGCTGAGCTTCAAAAGGGGGGACATCCTCAAG*GAAACTCCCAGTACAGCCAGCAGCAGGCCGGGTAC	18cancers,cancer,exon-exon	BOWTIE	out-of-frame	0	51	9	23	17	75393551	-	20	62172682	+	32.944	17.6779	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000125503	ENSG00000105063	PPP1R12C	PPP6R1	GCCTGTTGGAGGAACTGGCCCGGAAACAGGAGGAC*GTGAACACCCACCACCTACACTCCTCCAGTGACGA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	50	12	24	19	55098784	-	19	55239683	-	7.6434	10.5761	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000125503	ENSG00000105063	PPP1R12C	PPP6R1	GGCCCTCCCAGTACAAAGGTGTGAAGACGGTGGTGAACTGCGCGGGGAAG*CTGCCTGCCCACCCTGGTCTGGGGGCTCCAGCAGGCCCTGACGCCCCCTC	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K	BOWTIE+BLAT	intronic/intronic	0	50	1	19	19	55097673	-	19	55239743	-	7.6434	10.5761	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000125503	ENSG00000105063	PPP1R12C	PPP6R1	GCGAACTGTGCGGGGTAGGGGTGAAGACGGTGGTGAACTGCGCGGGGAAG*CTGCCTGCCCACCCTGGTCTGGGGGCTCCAGCAGGCCCTGACGCCCCCTC	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K	BOWTIE+STAR	intronic/intronic	0	50	1	19	19	55097476	-	19	55239743	-	7.6434	10.5761	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000125503	ENSG00000105063	PPP1R12C	PPP6R1	GCGAACTGCGCGGGGTAGGGGTGAAGACGGTGGTGAACTGCGCGGGGAAG*CTGCCTGCCCACCCTGGTCTGGGGGCTCCAGCAGGCCCTGACGCCCCCTC	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K	BOWTIE+STAR	intronic/intronic	0	50	1	19	19	55097224	-	19	55239743	-	7.6434	10.5761	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000079215	ENSG00000171984	SLC1A3	C20ORF196	TTTTGTGCTGCTCACAGTCACCGCTGTCATTGTGG*GACTATGGCAGCCAGGGACGCCACTTCAGGCAGCC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	49	13	24	5	36608604	+	20	5772862	+	4.6187	8.1591	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000079215	ENSG00000171984	SLC1A3	C20ORF196	ATTTCAGATATTGAGGAAACAGAGCAGGCAATTTCAAATTTCTCTTTCAA*GACTATGGCAGCCAGGGACGCCACTTCAGGCAGCCTGTCAGAGGAGAGCA	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	49	1	22	5	36614979	+	20	5772862	+	4.6187	8.1591	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000132003	ENSG00000104957	ZSWIM4	CCDC130	TGAACTGGCTTCCACCATGTTGACGGCCGCCAAGG*ACACGCCGCTTTTTGGATGCCTCCTATGCCTGGCG	tcga,prostates,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	48	6	21	19	13823500	+	19	13751608	+	9.3782	19.1398	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000177302	ENSG00000196535	TOP3A	MYO18A	AGAGCAAGTGGCGGCCTCAAGCCTTGGACACTGTG*GCAGTGGAGGAGCTGCTGGAGTGCTTGGATCTGGA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	45	14	24	17	18299559	-	17	29103664	-	8.2475	6.9424	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000179364	ENSG00000182185	PACS2	RAD51B	TAGCGCTGCTGCGGAGGTTCAAAGTGTCCGACGAG*GCACTTCTGGATCCAGCTGTGTGATAGCCGCACTA	18cancers,cancer,exon-exon	BOWTIE	out-of-frame	0	44	6	19	14	105369900	+	14	68411424	+	16.459	1.2011	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000110066	ENSG00000132749	KMT5B	TESMIN	ACGGTTTTCGTACGGGCGGCCGTGCGCGAGGCGAG*GCATGTCTTGGTAGAAATCCAGAAGCTTTCCAGCC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	41	10	22	11	68213477	-	11	68713407	-	8.8553	9.0414	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000110066	ENSG00000132749	KMT5B	TESMIN	GACGCGCCCCGAGGAGGAGCGGGGCGGCGCAGGCG*GCATGTCTTGGTAGAAATCCAGAAGCTTTCCAGCC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	41	7	23	11	68213138	-	11	68713407	-	8.8553	9.0414	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000110066	ENSG00000132749	KMT5B	TESMIN	TTATTCCATTCTCTGCTCTATCACTGTTTGTATAAGTCATTGATAGGGCC*TCCCATTCTACCCTAGGCATGTCTTGGTAGAAATCCAGAAGCTTTCCAGC	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT	intronic/intronic	0	41	1	20	11	68210501	-	11	68713423	-	8.8553	9.0414	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000110066	ENSG00000132749	KMT5B	TESMIN	GGGGCGGCGACGCGGCGGCGGTGCGGGCGGCAGGGCAGCGGGGCGATGAG*GCATGTCTTGGTAGAAATCCAGAAGCTTTCCAGCCAAAAATTGGGAAGGG	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	UTR/CDS(truncated)	0	41	1	14	11	68213586	-	11	68713407	-	8.8553	9.0414	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000053328	ENSG00000004809	METTL24	SLC22A16	TGGGAAGCATTTTGAATGAATTTGGACATCACAAG*ATTCCAGAGAGTCCTCTATTTCATATGTGCCTTCC	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	40	7	24	6	110298922	-	6	110457017	-	11.7348	4.6891	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000163950	ENSG00000013810	SLBP	TACC3	GCAGAGCACCGCGGCGCCGAGCGCAGACCCGAGAG*GCAGCTGCATTCAGCCTCAGCGGAGGACACGCCTG	cell_lines,18cancers,cancer,exon-exon	BOWTIE	in-frame	0	39	6	23	4	1711874	-	4	1730887	+	91.9216	60.5081	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000123908	ENSG00000226807	AGO2	MROH5	GGAGGCGTGAACAACATCCTGCTGCCCCAGGGCAG*CCACCGGCTTCAAGATGCTGCAGGACATGAACAGT	pseudogene,18cancers,exon-exon	BOWTIE	in-frame	0	32	9	24	8	140547468	-	8	141495483	-	5.4857	7.3785	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	polymorphic_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000123908	ENSG00000226807	AGO2	MROH5	GGAGGCGTGAACAACATCCTGCTGCCCCAGGGCAG*AATCTCCCCCCCTGTCTCCACATCCATGAAGGACT	pseudogene,18cancers,exon-exon	BOWTIE	in-frame	0	32	3	24	8	140547468	-	8	141496501	-	5.4857	7.3785	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	polymorphic_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000123908	ENSG00000226807	AGO2	MROH5	ATCAACGTCAAGCTGGGAGGCGTGAACAACATCCTGCTGCCCCAGGGCAG*GGACAGATGGTCACACCCCACCACCATCCTGCTTCACAAGTCGCAGAGCA	pseudogene,18cancers	BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	32	1	21	8	140547468	-	8	141496429	-	5.4857	7.3785	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	polymorphic_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000262655	ENSG00000117461	SPON1	PIK3R3	CACCCGTGAAAATGGAGGAAGAAATTCGACAACAG*AATTATGATGAATTATGATAAATTGAAATCACGTC	18cancers,exon-exon	BOWTIE	out-of-frame	0	32	4	23	11	14135568	+	1	46055971	-	118.7385	9.0046	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000262655	ENSG00000117461	SPON1	PIK3R3	CACCCGTGAAAATGGAGGAAGAAATTCGACAACAG*ATGGCTCAATCACAAAGGAGTGAGACAGAAACGCC	18cancers,exon-exon	BOWTIE	out-of-frame	0	32	3	20	11	14135568	+	1	46046625	-	118.7385	9.0046	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000163638	ENSG00000168038	ADAMTS9	ULK4	TTTTTGGACCAGGTTCTCAGGTGTGCCCATATATG*GCAATTGTTCTCTTAACTGAATTAATTAGGGAAAA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	30	4	22	3	64649637	-	3	41835971	-	16.1357	3.7327	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000163638	ENSG00000168038	ADAMTS9	ULK4	AACAATGTGAATTGATTTTTGGACCAGGTTCTCAGGTGTGCCCATATATG*AAAAACCTCCAAAGTTTTCCGAGTGACTGTAGTGTTTTACATTCTCACCA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	30	1	21	3	64649637	-	3	41844788	-	16.1357	3.7327	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000148429	ENSG00000165309	USP6NL	ARMC3	CAAACTCTTCTCAGGCCCTAAACATGCCATGCATG*AAAAAATAGTTATCATTTTAGTGCTGGATTTGGAT	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	30	4	22	10	11489102	-	10	23008815	+	3.5979	0.7248	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000148429	ENSG00000165309	USP6NL	ARMC3	CAAACTCTTCTCAGGCCCTAAACATGCCATGCATG*TGCTGGATTTGGATCTCCCATAGAAGACAAATCAG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	30	3	24	10	11489102	-	10	23008836	+	3.5979	0.7248	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000148429	ENSG00000165309	USP6NL	ARMC3	CACACTCTGACCATGTGAGGATATTGTGTGTGTGTGGAAGAGTGAGGGGG*AAAAAATAGTTATCATTTTAGTGCTGGATTTGGATCTCCCATAGAAGACA	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	30	1	15	10	11487803	-	10	23008815	+	3.5979	0.7248	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000022567	ENSG00000226807	SLC45A4	MROH5	AACCGCTCTGGTCACACCAATACTGTTGCAGATTG*GAGCTGGAAGACATATACCAGGACGCGGCCAGCAA	pseudogene,18cancers,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	24	8	23	8	141253989	-	8	141490276	-	6.0271	7.3785	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	polymorphic_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000022567	ENSG00000226807	SLC45A4	MROH5	AACCGCTCTGGTCACACCAATACTGTTGCAGATTG*ATGGCCATCAAGTCAGTCCCGTTCCTGAGCACGGA	pseudogene,18cancers,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	24	4	19	8	141253989	-	8	141480448	-	6.0271	7.3785	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	polymorphic_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000135457	ENSG00000110934	TFCP2	BIN2	AGGCCATGGAGGCAGAATCCTGGCCCTCTGTGTTGGCCCAAGCTCTTGTG*GCAGAAGGCCACAAGCTGTACAAGGACCTGAAGAACTTCCTTAGTGCAGT	oncogene,18cancers,m21,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	23	5	24	12	51095060	-	12	51303141	-	23.2697	5.6244	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000135457	ENSG00000110934	TFCP2	BIN2	CACCTCTGAAAACGGCCCTCTTGAAGGGGGATATGAATGGAGATTTGAAG*GCAGAAGGCCACAAGCTGTACAAGGACCTGAAGAACTTCCTTAGTGCAGT	oncogene,18cancers,m21,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	23	4	24	12	51095153	-	12	51303141	-	23.2697	5.6244	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000135457	ENSG00000110934	TFCP2	BIN2	AGGCCATGGAGGCAGAATCCTGGCCCTCTGTGTTGGCCCAAGCTCTTGTG*ATGGAGTCTTGCTCTGTCACCGAGGCTGGAGTACAGTGGCGTGATCCGAT	oncogene,18cancers,m21,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	UTR/UTR	0	23	3	22	12	51095060	-	12	51304246	-	23.2697	5.6244	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000140553	ENSG00000197299	UNC45A	BLM	CTAACAAACCTGGCTGGGATCAGCGAGAGGCTCCG*TACGTTAAAGGACCTTGACACCTCTGACAGAAAAG	18cancers,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	23	6	23	15	90950615	+	15	90754811	+	47.5498	12.7343	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000183077	ENSG00000078687	AFMID	TNRC6C	AGCCTTGAGGACCTACTCACAGATAGGAATTGAAG*TTTCATCAGGCTGGGGAGAAATGCCTAATGTTCAC	tcga,cell_lines,prostates,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	22	7	24	17	78191060	+	17	78064722	+	10.62	4.1412	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000033327	ENSG00000159063	GAB2	ALG8	GGAAATCGCCTCCCGAGAAGAAGTTGAGGCGCTAT*GTTTGAAATTGAAATTTCTTGATCCCAACAATATT	oncogene,cell_lines,18cancers,chimerdb3seq,cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	19	4	20	11	78417646	-	11	78109581	-	2.2909	4.9173	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000033327	ENSG00000159063	GAB2	ALG8	GGAAATCGCCTCCCGAGAAGAAGTTGAGGCGCTAT*AAAAGGCATATGGAAGGAGCATTTCTCTTTGCTGT	oncogene,cell_lines,18cancers,chimerdb3seq,cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	19	3	23	11	78417646	-	11	78114392	-	2.2909	4.9173	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000033327	ENSG00000159063	GAB2	ALG8	GGAAATCGCCTCCCGAGAAGAAGTTGAGGCGCTAT*GGCCCAGAGGCTTTCTCCGATGTCTAACTCTTTGT	oncogene,cell_lines,18cancers,chimerdb3seq,cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	19	2	23	11	78417646	-	11	78106912	-	2.2909	4.9173	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000033327	ENSG00000159063	GAB2	ALG8	GGAAATCGCCTCCCGAGAAGAAGTTGAGGCGCTAT*CCCTCTATTTTCTGTCTTTGGTTTAAACCCCAAGG	oncogene,cell_lines,18cancers,chimerdb3seq,cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	19	2	19	11	78417646	-	11	78106946	-	2.2909	4.9173	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000033327	ENSG00000159063	GAB2	ALG8	GGCCAGGCTTCAGGGGAGATGGACTACAGCTGGTCTGAAATAGGAAGACG*CCTTTTGTCTGTGGGAAAAGCAGGAGACGCTTCGATTTTTCTGATTCTGA	oncogene,cell_lines,18cancers,chimerdb3seq,cancer,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	19	1	24	11	78350135	-	11	78104453	-	2.2909	4.9173	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000033327	ENSG00000159063	GAB2	ALG8	TCTATTAGATTGAAGATGCTGGAAGGCGAATGGCTTCAGCACAGGAAAAG*GTGCTGTAAATGCATTGATGGAAAAAAAGTGGGTAAAGAACTTACAGAAA	oncogene,cell_lines,18cancers,chimerdb3seq,cancer,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	19	1	22	11	78354734	-	11	78121174	-	2.2909	4.9173	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000033327	ENSG00000159063	GAB2	ALG8	GGCCAGGCTTCAGGGGAGATGGACTACAGCTGGTCTGAAATAGGAAGACG*AAAAGGCATATGGAAGGAGCATTTCTCTTTGCTGTTCTCCTACATTTCAA	oncogene,cell_lines,18cancers,chimerdb3seq,cancer,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	19	1	21	11	78350135	-	11	78114392	-	2.2909	4.9173	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000245532	ENSG00000255478	NEAT1	AP000944.1	GACTAGGTCTAGGGGGACCACAGTGGGGCAGGCTGCATGGAAAATATCCG*AGGCGGGGACTACATAAATTCTGGAGCACCAGCCTGCCACAGGGTAA	lincrna,antisense,oncogene,m18,10K<gap<100K	BOWTIE+BLAT	exonic(no-known-CDS)/exonic(no-known-CDS)	0	19	5	23	11	65422999	+	11	65367773	+	13.7677	4.4078	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	lincRNA	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000179832	ENSG00000183309	MROH1	ZNF623	CCTGCAGGTGGTCAGACATGTCATCAACTCAGCTG*ATTCTAATGTAGGAACTGGTGAGAAGAAGGTGACT	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	18	3	23	8	144200541	+	8	143649898	+	7.2244	9.2911	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000179832	ENSG00000183309	MROH1	ZNF623	AATCCAGAGCAGTCATCACCATCACCGAAGCTCAGATCGTCTCATCTTTG*ATTCTAATGTAGGAACTGGTGAGAAGAAGGTGACTGAAGCCTGGATTTCT	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT	intronic/CDS(truncated)	0	18	1	20	8	144211912	+	8	143649898	+	7.2244	9.2911	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000059122	ENSG00000197601	FLYWCH1	FAR1	AAGACGTGTTCTCCTGAAAGCCAGCAGATTTATGG*ACCTTCAATATTGATGTACGGCAGTTACATTGGGC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	12	5	23	16	2940092	+	11	13727556	+	4.8328	11.5519	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-38-4630-01A	ENSG00000182827	ENSG00000132680	ACBD3	KIAA0907	ACCCGGCTAATTTTTGTATTTTTAGTAGAGATGGGGTTTCTCCATGTTGG*CTAAGACTGGTCTAAAGCTATTAGTTTTCTCAGCCGGGCGCAGTGGCTCA	18cancers	BOWTIE+BLAT	intronic/CDS(truncated)	0	11	1	20	1	226179669	-	1	155915837	-	16.5337	32.2003	FALSE	FALSE	TRUE	TRUE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000132680	ENSG00000182827	KIAA0907	ACBD3	ATGCTGCAGATTCATCTGATGAAGAGGAGGAACATGGAGGTCATAAAAAT*AAAACATCGGTTGTGAAGAGAAAGCCAAAAAGAATGCCAACAAGCCTTTG	18cancers	BOWTIE+BLAT	out-of-frame	0	11	3	24	1	155914217	-	1	226146821	-	32.2003	16.5337	FALSE	FALSE	TRUE	TRUE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000176658	ENSG00000184381	MYO1D	PLA2G6	TCCATGCCCGAGTTCATGGCCAACCTCAGGCTCAG*ACAGAGGGGGAAGACGGTGGGGCCTCCCCACCTGC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	11	2	21	17	32876778	-	22	38169471	-	11.8109	11.6104	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000176658	ENSG00000184381	MYO1D	PLA2G6	TCCATGCCCGAGTTCATGGCCAACCTCAGGCTCAG*AGGGGGAAGACGGTGGGGCCTCCCCACCTGCCCCG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	11	2	19	17	32876778	-	22	38169467	-	11.8109	11.6104	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000121858	ENSG00000144959	TNFSF10	NCEH1	AGCTCACATAACTGGGACCAGAGGAAGAAGCAACACATTGTCTTCTCCAA*CGCGTGGTCTTCTGCCCAAGTGAAGGTGACCGACACAGACTTTGATGGTG	18cancers,cancer,tcga-cancer,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	11	3	21	3	172509217	-	3	172648034	-	1176.1305	65.9315	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000121858	ENSG00000144959	TNFSF10	NCEH1	TAACTTACGTGTACTTTACCAACGAGCTGAAGCAG*AGTAACCTGATCCACTACCTGGGACTGAGCCATCA	18cancers,cancer,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	11	2	22	3	172523253	-	3	172648114	-	1176.1305	65.9315	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000274272	ENSG00000144959	AC069281.2	NCEH1	AGGCAGGAGTGGGGTTGGTCCCCTTGGATAGCTGAGCAGGATCCGGGGAG*CTAGGCAGGCTCTCAATAAAGTCCTTAGTCACTTTTAAGCGTCAGTCATT	NA	BOWTIE+BLAT	intronic/intronic	0	9	3	24	7	100578557	-	3	172680903	-	0.0992	65.9315	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	processed_transcript	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000274272	ENSG00000144959	AC069281.2	NCEH1	TCCCTCTAATTCCCTTCTGTCTCTCCTCAGCGGCTCGCCTAAGTCCAGTG*TGACCACTCTGCTGTGCTGTCAGTCTCCACTCAGTGCGACGCTTAATCTA	NA	BOWTIE+BLAT	exonic(no-known-CDS)/intronic	0	9	2	21	7	100576986	-	3	172680824	-	0.0992	65.9315	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	processed_transcript	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000077454	ENSG00000144959	LRCH4	NCEH1	TCCCTCTAATTCCCTTCTGTCTCTCCTCAGCGGCTCGCCTAAGTCCAGTG*TGACCACTCTGCTGTGCTGTCAGTCTCCACTCAGTGCGACGCTTAATCTA	18cancers	BOWTIE+BLAT	CDS(truncated)/intronic	0	9	3	22	7	100576986	-	3	172680824	-	1.5577	65.9315	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000144959	ENSG00000077454	NCEH1	LRCH4	TCTTTGCGCAGCCTAGGGCACTCTGCTGTCTGACCACTCTGCTGTGCTGT*CAGCATCCCCTCCCCACTCCTCTTCCTATGACCATCATCCCTCTAATTCC	18cancers	BOWTIE+BLAT	intronic/UTR	0	9	1	22	3	172680805	-	7	100577072	-	65.9315	1.5577	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000130560	ENSG00000165661	UBAC1	QSOX2	TGGACCGGGCCGCGGTCCAGACCAACATGAGAGAC*ACTGGGCCAGTGCCATTCGCGTCGCAGCTCTGGAC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	9	5	20	9	135947798	-	9	136226874	-	10.8742	19.7368	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000100478	ENSG00000250365	AP4S1	AL139353.2	CCGTTGAGAGGACCATCACAACCTGAGCAGCACAG*AAATAAGAAGAAAAAAAAGGATATTACCAACAATG	antisense,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	8	2	20	14	31025787	+	14	31439672	+	2.0105	0.2895	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000134775	ENSG00000257267	FHOD3	ZNF271P	CGGGGGTCCATAGGCTGCTGCAGGCGCCGCACAAG*GGCCAGAATTTTCTGCTCTTACGATGCTGATGATT	pseudogene,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	8	5	22	18	36298000	+	18	35326797	+	0.6917	3.1295	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	transcribed_unitary_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000144959	ENSG00000223387	NCEH1	LINC02068	GCTGAGGAATTGAATGCTGTCATTGTTTCCATTGA*GCTTCACTCATTACAGGAGAAGAGAGTCTGGGTTG	lincrna,10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	8	3	22	3	172645623	-	3	172574340	-	65.9315	2.8217	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000144959	ENSG00000223387	NCEH1	LINC02068	GCTGAGGAATTGAATGCTGTCATTGTTTCCATTGA*GGAGAGGCGGGCAGTAACGTGCATGGAGCTGTCAC	lincrna,10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	8	2	22	3	172645623	-	3	172561069	-	65.9315	2.8217	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000180900	ENSG00000251136	SCRIB	AF117829.1	GCAAGGGCTCCACACCCTATAAGGGGGACGACGAG*TTCATTGGAAATTTCTGCTTCTTTGAGACTGAGGT	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	7	1	14	8	143806924	-	8	89725641	-	52.4119	0.8724	TRUE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000142920	ENSG00000162521	AZIN2	RBBP4	CCCAGCTGGGGCTGGGCTTTAGCTGTGCCAACAAG*AATTTGGAGGTTTTGGTTCAGTTAGTGGAAAAATT	exon-exon	BOWTIE	out-of-frame	0	6	2	21	1	33084127	+	1	32668225	+	0.8193	23.1851	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000133961	ENSG00000156030	NUMB	ELMSAN1	GCAGTGGCGCTTGAGTTGGTCGGGGGCAGCGGCAG*GGTGTTTTACAAGGTGAAGAGCCGCAGTGCGCATA	prostates,exon-exon	BOWTIE	UTR/CDS(truncated)	0	6	2	17	14	73458493	-	14	73719008	-	8.4943	6.516	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000124208	ENSG00000101417	TMEM189-UBE2V1	PXMP4	CTCACCCCACGAGACCTACTTCTGCATCACCACAG*CTATGGAGCCAAAATCCGGGCCCCTCACGCGCTGG	18cancers,exon-exon	BOWTIE	out-of-frame	0	6	6	23	20	50127975	-	20	33714736	-	0	1.6056	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000172992	ENSG00000225190	DCAKD	PLEKHM1	CTCAAGTACATGAAGCACACCGTGGTAGTATACTG*ATCTGCAGGCAGGCCCTGAAGTTTCTGACACAGAT	exon-exon	BOWTIE	out-of-frame	0	5	1	13	17	45030092	-	17	45445663	-	22.5229	2.9606	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000166548	ENSG00000179044	TK2	EXOC3L1	CCAAGTGGAGAAATGTCCGTGGCCACAATCCTCTG*GACCTGAGTGGCCAGAGCAGGAGCGGGCAGAGCAG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	5	3	19	16	66536964	-	16	67189180	-	0.8372	2.8832	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000182185	ENSG00000184990	RAD51B	SIVA1	CCTTGAAGTATTTGGCTGAGGAGTTTTCAATCCCA*GCCGGCCTTGTGCTGGAAAGAGCATGATGTGGGCA	18cancers,cancer,exon-exon	BOWTIE	out-of-frame	0	4	2	24	14	67887204	+	14	104766790	+	1.2011	17.4521	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000141293	ENSG00000120093	SKAP1	HOXB3	CAAAGCCAGGTACTATTGGGATTTTCAGCCCCAAG*GAGGGGAGATTTGTCGCCTGCCGCTCGCTCTGGGG	tcga,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	4	2	17	17	48363789	-	17	48555618	-	3.5296	13.5772	TRUE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000173442	ENSG00000142186	EHBP1L1	SCYL1	CTGAGAATGTGGACATCTCTGTGACCCTCTACAGG*GTGGGCAAGTTCCTGAGCGCTGAGGAGTATCAGCA	cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	3	2	21	11	65579436	+	11	65531576	+	14.9487	77.6029	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-38-4630-01A	ENSG00000100284	ENSG00000100099	TOM1	HPS4	GAACCCGTTCAGCTCTCCAGTGGGACAGCGCATCG*GTGCTGGGCTGTGCTGTGGAGCTCCCTGATGTCAG	exon-exon	BOWTIE	out-of-frame	0	3	2	19	22	35299980	+	22	26472939	-	8.4411	6.468	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000088538	ENSG00000173473	DOCK3	SMARCC1	GTGGACCCCCACGGAGGAGGAGAAATACGGCGTAG*CACCTGGCTGCAGTGGAAGAAAGAAAGATCAAGTC	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	2	8	23	3	50675300	+	3	47622341	-	0.6804	34.3422	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000205209	ENSG00000153896	SCGB2B2	ZNF599	CGGACACATAACAAGCAGCAGTGAGGACACCAAAG*GCATTAGTATCATTTGAAGACGTGGTTGTGACCTT	10K<gap<100K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	2	3	21	19	34675630	-	19	34769555	-	0.4794	3.0865	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000205209	ENSG00000153896	SCGB2B2	ZNF599	TGTTGAAGCCACTTGCCTGTGACTTCTGTCACCTGACTGGACCCTGATTG*GCATTAGTATCATTTGAAGACGTGGTTGTGACCTTCACTGGAGAGGAATG	10K<gap<100K	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	18	19	34667949	-	19	34769555	-	0.4794	3.0865	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000185739	ENSG00000126602	SRL	TRAP1	GCTGAATGAGGACAAGCCATCCGATGACTACTCTG*TTCTGGAGTGTTTGAAATCGCCGAAGCTTCGGGAG	cancer,exon-exon	BOWTIE	in-frame	0	2	2	22	16	4204533	-	16	3676145	-	1.8873	8.5926	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-38-4630-01A	ENSG00000121858	ENSG00000137573	TNFSF10	SULF1	AAGTCAAGTGGCAACTCCGTCAGCTCGTTAGAAAG*AGGACAGTTATGGGATGGATGGGAAGGTTAATCAG	cancer,exon-exon	BOWTIE	out-of-frame	0	2	1	14	3	172514861	-	8	69658505	+	1176.1305	15.8773	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-73-4676-01A	ENSG00000221823	ENSG00000196141	PPP3R1	SPATS2L	TGAGGCAAGTTATCCTTTGGAAATGTGCTCACACT*GCCCAAATATTGAGAAATCAGTGAAGGATTTGCAA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	17	5	23	2	68217092	-	2	200440649	+	13.0304	19.2315	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-73-4676-01A	ENSG00000146143	ENSG00000112200	PRIM2	ZNF451	ATTTCTTAAAGGATAGCCAATTGCAGTTTGAGGCT*AATGTGACAGTGATGATAACATGGGTGCCAAAAAT	chimerdb3seq,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	4	3	23	6	57326045	+	6	57161084	+	4.0988	2.1509	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-73-4676-01A	ENSG00000146143	ENSG00000112200	PRIM2	ZNF451	ATTTCTTAAAGGATAGCCAATTGCAGTTTGAGGCT*AGGAAGAAATTGTTGAGCTTCCAGATTTGGATTAC	chimerdb3seq,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	4	1	14	6	57326045	+	6	57150719	+	4.0988	2.1509	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-55-8299-01A	ENSG00000169223	ENSG00000131187	LMAN2	F12	CGAGCCCAGCGTCAACTTCCTCAAGTCGCCCAAAG*CCTTGCCGGCGAAGCGGGAGCAGCCGCCTTCCCTG	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	53	17	24	5	177334284	-	5	177404090	-	137.9861	6.0884	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-55-8299-01A	ENSG00000169223	ENSG00000131187	LMAN2	F12	CGAGCCCAGCGTCAACTTCCTCAAGTCGCCCAAAG*GCCCGCACCCGAGGATCTGACGGTGGTGCTCGGCC	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	53	1	13	5	177334284	-	5	177403617	-	137.9861	6.0884	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-49-4488-01A	ENSG00000126267	ENSG00000167614	COX6B1	TTYH1	GAACCAGACTAGAAACTGCTGGCAGAACTACCTGG*GTGGCTGGCCTACGTCCTCCTGCTGCTCCTGGAGC	chimerdb3seq,exon-exon	BOWTIE	out-of-frame	0	11	6	19	19	35651349	+	19	54426673	+	104.02	0.1491	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-49-4488-01A	ENSG00000272333	ENSG00000213892	KMT2B	CEACAM16	CCCCATGGGGCTGCTCGGGCAGAGGTCTATCTCCG*CCCTGGGGTAACAGCGTGACCCTGGAGACGTCCAG	exon-exon	BOWTIE	out-of-frame	0	5	2	18	19	35737263	+	19	44710496	+	6.3042	1.4568	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-49-4488-01A	ENSG00000272333	ENSG00000213892	KMT2B	CEACAM16	GAGCCGCCCCTGAATCCCCATGGGGCTGCTCGGGCAGAGGTCTATCTCCG*CAGACAGAGCATTCTCAGAAGCCATGTCCCTGAGTCCGGGATGGTGCCTC	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	5	1	17	19	35737263	+	19	44710072	+	6.3042	1.4568	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-55-6982-01A	ENSG00000117385	ENSG00000117419	P3H1	ERI3	CCGACTTCAAGGATCTTGAGACTCAACCCCATATG*ACGACTGCAAGAACATTGCCAACATCATGAAGACA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	29	11	23	1	42762323	-	1	44221640	-	8.1248	22.6899	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-55-6982-01A	ENSG00000113504	ENSG00000139173	SLC12A7	TMEM117	GCTTCTTTGAAGGGAAGAACATGGCACTTTTCGAG*GACAGTTCTTTTTACTCTGACGTCTGTGGTTGTAC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	21	6	22	5	1094154	-	12	44299580	+	108.5094	11.45	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-64-5774-01A	ENSG00000075539	ENSG00000145247	FRYL	OCIAD2	TACAAACTCTGTGCCTCAACAACCATTTCTAAGTG*GTTATTTGGCAGCTAATTCTAGATTTGGATCATTG	known,tcga,cell_lines,chimerdb3seq,cancer,m70,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	71	13	22	4	48710519	-	4	48894053	-	2.8137	52.0809	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-64-5774-01A	ENSG00000153162	ENSG00000216863	BMP6	LY86-AS1	CGACGCGGACATGGTCATGAGCTTTGTGAACCTGG*TGTGAAGAAGGTCCTTGCTTCCCCTTCACCTTCTG	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	2	2	16	6	7727619	+	6	6564388	-	3.4326	0.2461	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-50-6591-01A	ENSG00000173480	ENSG00000087088	ZNF417	BAX	GATGCTAGAGAACCTGGCTCTCATATCCTCGCTGG*GCCCTGTGCACCAAGGTGCCGGAACTGATCAGAAC	oncogene,18cancers,chimerdb3seq,cancer,tumor,m43,exon-exon	BOWTIE	in-frame	0	387	20	24	19	57912060	-	19	48960810	+	2.9313	39.7814	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-50-6591-01A	ENSG00000106571	ENSG00000106049	GLI3	HIBADH	GGACCCCAGGAATGGTTACATGGAGCCCCACTACC*GTAGTATCTTCCCCAGCAGATGTTGCTGAAAAAGC	oncogene,tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	29	6	21	7	42148226	-	7	27632445	-	44.0979	21.3785	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-50-6591-01A	ENSG00000106571	ENSG00000106049	GLI3	HIBADH	ATCTTTTCTCAGTCAACCTCAGTAGATCGACTATAACTTTTTTCTGTTTT*GTAGTATCTTCCCCAGCAGATGTTGCTGAAAAAGCTGACAGAATTATTAC	oncogene,tcga,18cancers,chimerdb3seq,cancer,tcga-cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	29	1	18	7	42145438	-	7	27632445	-	44.0979	21.3785	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-50-6591-01A	ENSG00000127616	ENSG00000215483	SMARCA4	LINC00598	AAGATTGTGGATGCCGTGATCAAGTACAAGGACAG*ATCCTAGTCCACTGCCTGGAACATGGAAGATGCTC	lincrna,18cancers,cancer,m15,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	18	2	16	19	11041560	+	13	40466677	-	28.7178	0.4137	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-50-6591-01A	ENSG00000127616	ENSG00000150907	SMARCA4	FOXO1	AAGATTGTGGATGCCGTGATCAAGTACAAGGACAG*GCTGGAGCACAGTGGCATGATCTCGGCTAACTGCA	oncogene,cancer,tumor,m12,exon-exon	BOWTIE	CDS(truncated)/UTR	0	15	5	23	19	11041560	+	13	40474095	-	28.7178	2.6013	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-50-6591-01A	ENSG00000143786	ENSG00000155816	CNIH3	FMN2	TGACTTGTGGTCACTGATGAGTGGACCAAGTGAAG*AGAGCACAGTCAGACGAACTCGAAAAAATAGAAAA	exon-exon	BOWTIE	UTR/CDS(truncated)	0	2	1	14	1	224515876	+	1	240329076	+	1.3867	0.1395	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-05-4389-01A	ENSG00000254004	ENSG00000205209	ZNF260	SCGB2B2	AGAAGGTTCTCTTTGTGTGAGTAAGCAAGAACCTG*AAGAAGATCCTTCAGAGCAACGATTGCATAGAAGC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	56	10	23	19	36525155	-	19	34593599	-	5.1749	0.5203	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-38-4632-01A	ENSG00000137501	ENSG00000101134	SYTL2	DOK5	GCGAGGCGCGCTCCCTGCCCGGCAGCGACTCGGAG*CTCCAGATGAAGATGAGTGAGCGGGCCGCCTCGCT	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	32	4	24	11	85810954	-	20	54643458	+	5.1513	22.0029	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-38-4632-01A	ENSG00000137501	ENSG00000101134	SYTL2	DOK5	GCGAGGCGCGCTCCCTGCCCGGCAGCGACTCGGAG*GATGTGTGAGACTGGTGAAGGGCTGTTTATCTTTC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	32	4	20	11	85810954	-	20	54610388	+	5.1513	22.0029	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-38-4632-01A	ENSG00000137501	ENSG00000101134	SYTL2	DOK5	TGTGCTGTGTGCCACACAAGATTATTATGATAGAAGTAAAGCAACCAAAT*GATGTGTGAGACTGGTGAAGGGCTGTTTATCTTTCAGACCCGAGACGGGG	tcga,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	32	1	21	11	85788874	-	20	54610388	+	5.1513	22.0029	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-38-4632-01A	ENSG00000182985	ENSG00000095139	CADM1	ARCN1	GTTGCTCTTCTCCGCCGCGGCACTGATCCCCACAG*GTCTGGTGTCGGCGCGCCTGTTATCGGTGAGATCG	tcga,chimerdb3seq,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	16	8	23	11	115504271	-	11	118597707	+	11.110900000000001	139.7087	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-38-4632-01A	ENSG00000182985	ENSG00000095139	CADM1	ARCN1	TCGGCTCACTGCAGCCTCGGCCTTCCCGTGCTCAG*GTCTGGTGTCGGCGCGCCTGTTATCGGTGAGATCG	tcga,chimerdb3seq,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	16	3	18	11	115445761	-	11	118597707	+	11.110900000000001	139.7087	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-38-4632-01A	ENSG00000154856	ENSG00000153339	APCDD1	TRAPPC8	GCTCAGATACCTGTTCCCGGCCCTCCTGCTTCACG*GCACAGAATATTAAGACACACTGCAATTATTTGTA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	6	3	19	18	10455039	+	18	31855807	-	10.9853	5.2035	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-44-2659-01A	ENSG00000162591	ENSG00000116213	MEGF6	WRAP73	AGGTGGCCGCGTGGCTGGCACCTCACCTGCTTCTCCCCTCGCAGATGTGG*GCTTCCTGTGTCCAGTACCGGTTAGTGGTCCGGGATGTGAACACCCTTCA	tcga,chimerdb3seq,tcga-cancer,oesophagus,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	8	1	23	1	3547118	-	1	3647560	-	8.0614	5.5062	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-75-6203-01A	ENSG00000108091	ENSG00000165731	CCDC6	RET	AGAACCGCGACCTGCGCAAAGCCAGCGTGACCATC*GAGGATCCAAAGTGGGAATTCCCTCGGAAGAACTT	known,oncogene,cosmic,chimerdb2,cgp,ticdb,tcga,cell_lines,18cancers,chimerdb3kb,chimerdb3pub,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	17	3	23	10	59906122	-	10	43116584	+	10.821	2.352	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-75-6203-01A	ENSG00000107798	ENSG00000168878	LIPA	SFTPB	GCCAGGTGCAGTGGCTCATGCCTGGCTCATGCCTTGGGAGGCCGAGGCGG*GAGGATCCTTGAGGTCAGGAGTTCGAGACCAGCCTCGCCAACATGGTGAA	18cancers	BOWTIE+STAR	intronic/UTR	0	5	3	20	10	89360639	-	2	85658767	-	135.7491	4888.7875	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-97-8171-01A	ENSG00000169398	ENSG00000251003	PTK2	ZFPM2-AS1	AAGATAAGCCAACTTTGAATTTCTTCTATCAACAG*GTGGCTCAAAGAGGTCAGGAGGCACCTTCAACACT	18cancers,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	62	18	24	8	140864312	-	8	105927717	-	6.225	0.4626	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-97-8171-01A	ENSG00000169398	ENSG00000251003	PTK2	ZFPM2-AS1	TAAACCAGTTTACTGAAGATAAGCCAACTTTGAATTTCTTCTATCAACAG*TTGATTAAATTTGATTGGACACTCTGGAATGAAATTATTTGTCCTCAAAT	18cancers	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	62	1	22	8	140864312	-	8	105964420	-	6.225	0.4626	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-97-8171-01A	ENSG00000169398	ENSG00000251003	PTK2	ZFPM2-AS1	TAAACCAGTTTACTGAAGATAAGCCAACTTTGAATTTCTTCTATCAACAG*AGCAGGGAGAAGATGGAAATGGTGGCGAAGGAGGTTGGAGCTCAGCTAAG	18cancers	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	62	1	21	8	140864312	-	8	105912840	-	6.225	0.4626	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-97-8171-01A	ENSG00000142507	ENSG00000108515	PSMB6	ENO3	CTCCAGACTGGGAAAGCCGAGAAGTTTCCACTGGG*CCATGGCCATGCAGAAAATCTTTGCCCGGGAAATC	18cancers,100K<gap<200K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	32	9	24	17	4796296	+	17	4951828	+	35.7827	7.4448	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-97-8171-01A	ENSG00000198846	ENSG00000253377	TOX	AC068672.2	AGGATGGAACACTGCTTTCTAATTCCATTTCTGTG*CTCCTACAGCAAAAGAAGTACTAAGAGGAAAGTTT	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	29	4	23	8	58939302	-	8	31384157	+	1.0104	2.8531	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-97-8171-01A	ENSG00000164684	ENSG00000253507	ZNF704	AC104257.1	GTTGTTTCCTCCAACATTGATGTTCCTCCAGCAAG*GGACATGCATGAAATTTGGTGCCGTGACTCAGATC	lincrna,m8,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	19	12	24	8	80821374	-	8	131310553	+	1.1203	2.1631	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-97-8171-01A	ENSG00000132549	ENSG00000185053	VPS13B	SGCZ	TGAAGCTTTGATAAATGAAATCTTCCTAAGTATAG*GATGGTATGGGAAATCTGAGAGTCACCAAGAAGGG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	3	4	22	8	99193057	+	8	14324204	-	1.1023	0.5007	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-05-4402-01A	ENSG00000157368	ENSG00000157350	IL34	ST3GAL2	AAATCCTAGGAGACCGAGTCTTGGCACGTGAACAG*GGTCGTGCTGCGGCAGCCTGGCGCCCGACATGTGA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/UTR	0	3	2	22	16	70580049	+	16	70399533	-	1.7779	2.8622	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-05-4402-01A	ENSG00000157368	ENSG00000157350	IL34	ST3GAL2	CTTAAGGCCACCAGCAAATCCTAGGAGACCGAGTCTTGGCACGTGAACAG*CCACCCTGATGGGCAGGAAGTGGTATCTGATTGTGGTTTTGATTTGCATT	tcga,chimerdb3seq,tcga-cancer	BOWTIE+STAR	UTR/intronic	0	3	1	18	16	70580049	+	16	70404520	-	1.7779	2.8622	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-49-6767-01A	ENSG00000185989	ENSG00000249203	RASA3	LINC02224	GCTCCGGGTCTTCCAGAGCGTGAAGATCAAGATCG*GCCATTGGGAGACACACTTCTGAACACCACCACTG	lincrna,cancer,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	6	4	24	13	114132435	-	5	44504472	-	6.9817	2.9799	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-67-6217-01A	ENSG00000011304	ENSG00000065000	PTBP1	AP3D1	TCTGCTGTCTCTAAAGAGAGTCACACCCCAAAGCCTCTTTATTCTTTTCG*CACCCTTAGGAAGGCCCAGGCAGGGCCTGGAAGCAGCGGACCTGGGCTGT	chimerdb3seq,cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	285	18	24	19	807902	+	19	2101400	-	48.8913	27.273	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-67-6217-01A	ENSG00000011304	ENSG00000065000	PTBP1	AP3D1	TGGCGGGGGCAGGAAATTCTGTATTGCTGGTCAGCAACCTCAACCCAGAG*CACCCTTAGGAAGGCCCAGGCAGGGCCTGGAAGCAGCGGACCTGGGCTGT	chimerdb3seq,cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	285	13	24	19	806556	+	19	2101400	-	48.8913	27.273	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-67-6217-01A	ENSG00000011304	ENSG00000065000	PTBP1	AP3D1	TGGTCCCGTAGATACGTACGCATGGTTTATCGCCCTGCATGCTTTTCAGA*GGACTCCCCCACCTGGGTCTGTGCCCTGCCCCGCGCTGGGGGCCGAGTCC	chimerdb3seq,cancer	BOWTIE+STAR	UTR/UTR	0	285	8	23	19	808104	+	19	2101926	-	48.8913	27.273	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-67-6217-01A	ENSG00000173273	ENSG00000173295	TNKS	FAM86B3P	AGCTGCTATTAAAGGGAAGATCGATGTGTGCATTG*GTTTTTGCTTGTCTGATGACTGATGGCTCCACCCA	pseudogene,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	15	4	22	8	9580383	+	8	8244099	+	3.1791	0.5149	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	transcribed_unprocessed_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-67-6217-01A	ENSG00000171634	ENSG00000141376	BPTF	BCAS3	CCATGGCTCAACTTACTCAGTTAACACAGGGCCAC*GTACCTTTGACAGGAGCGTGACCCTGCTGGAGGTG	tcga,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	6	2	21	17	67940656	+	17	61368327	+	8.4598	3.307	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-67-6217-01A	ENSG00000171634	ENSG00000141376	BPTF	BCAS3	GACAAGTGAAGCTCACCATGGCTCAACTTACTCAGTTAACACAGGGCCAC*GTCAGAGCTTCAAGGAACTCTGTAATCTTCCCACCAGCTTTATTCTCTCC	tcga,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	6	1	23	17	67940656	+	17	61260550	+	8.4598	3.307	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-67-6217-01A	ENSG00000182400	ENSG00000150527	TRAPPC6B	CTAGE5	CTGGAGTGTACAAGTCCGCGGAGCAGGGGGAGGTG*TTAGTGAAGAGAGTAGAATATCTCCAGTTTTGGCT	chimerdb3seq,m4,exon-exon	BOWTIE	CDS(truncated)/UTR	0	5	1	13	14	39170015	-	14	39234015	+	2.4771	3.4989	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-67-6217-01A	ENSG00000158528	ENSG00000227117	PPP1R9A	HORMAD2-AS1	TGGACACAAGCAAGCTCAGTCACAAGTTCAAAGAG*TTCAAGGAAAGAAGCAAACTTATTATTTAAGAGCA	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	3	4	23	7	95226116	+	22	30009196	-	3.5328	0.0379	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-67-6217-01A	ENSG00000105401	ENSG00000055609	CDC37	KMT2C	TCGACACGGCCAGTCTCTTCCGCTGGCGGCATCAG*GGGCTGGGCCTGTATGCTGCTCGAGACATTGAGAA	cell_lines,cancer,exon-exon	BOWTIE	in-frame	0	2	2	21	19	10403378	-	7	152139791	-	54.2662	10.2298	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-49-4512-01A	ENSG00000177830	ENSG00000125844	CHID1	RRBP1	TGCGTTTGTGGCCGTCCGGCCTCCCTGACATGCAG*GCGTCCCACAGGGAGAGTGAGGAGGCCCTGCAGAA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	9	3	22	11	910775	-	20	17629961	-	13.7631	23.273	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-49-4512-01A	ENSG00000125844	ENSG00000177830	RRBP1	CHID1	CAGCTGCCTTCGAGAAGCAGGTCCTGCAGCTGCAG*GGGCCTCATCCACATGCTCACCCACTTGGCCGAGG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	9	3	22	20	17633460	-	11	893519	-	23.273	13.7631	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-49-4512-01A	ENSG00000125844	ENSG00000177830	RRBP1	CHID1	CAGCTGCCTTCGAGAAGCAGGTCCTGCAGCTGCAG*GACCGACCAGCTGGGCATGTTCACGCACAAGGAGT	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	9	2	14	20	17633460	-	11	884169	-	23.273	13.7631	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-55-1594-01A	ENSG00000124201	ENSG00000277022	ZNFX1	AL031663.3	TGCCAGGCCCAGGAATTCCCATACCAACCACAGAG*GTCCACCTGGTGCCCCTGGCTTCATCACCAATGGG	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	45	12	24	20	49275779	-	20	45435971	-	8.7127	3.6073	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-55-1594-01A	ENSG00000124201	ENSG00000277022	ZNFX1	AL031663.3	AAGACCTCATCTGGATGCCAGGCCCAGGAATTCCCATACCAACCACAGAG*GCCCTTGTGTCACTCTCTCCCATGCTGACCAGCTCTGGCCACAAAGCTGC	lincrna	BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	45	1	16	20	49275779	-	20	45435906	-	8.7127	3.6073	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-55-1594-01A	ENSG00000108219	ENSG00000133665	TSPAN14	DYDC2	AGTACCTCCTTTTCAGCTACAACATCATCTTCTGG*GCTGCCAGGATGGAAACTAACTACCTGAAGAGGTG	known,tcga,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	40	7	22	10	80489314	+	10	80362435	+	5.9018	5.8424	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-55-1594-01A	ENSG00000165678	ENSG00000175893	GHITM	ZDHHC21	TCAGCAGAACGCCTGTTCTCATGAACTTCATGATGAGAGGCTCTTGGGTG*ACATAATGCTGTTGTACACTTCATAGAGTATAGCATAAACATAACATTTA	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	19	1	15	10	84145016	+	9	14629581	-	116.1508	2.2017	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-55-1594-01A	ENSG00000151338	ENSG00000229415	MIPOL1	SFTA3	TGTCGACTCCCCGGTCTATGCCAGGCGCATCTCAG*ATGTTAATTATTCATACTGCATGACTGAGGATTTT	exon-exon	BOWTIE	UTR/CDS(truncated)	0	15	2	19	14	37198104	+	14	36473881	-	4.1586	16.4262	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-55-1596-01A	ENSG00000171495	ENSG00000112996	MROH2B	MRPS30	TGCTAGCTCAACTATTGGTCTGTTCTATATAAAAG*GCTCAAAAACTGCAGATCCTTGCTGTTACGGTCAC	ribosomal,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	62	11	23	5	41017850	-	5	44813106	+	1.1641	6.8202	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-55-1596-01A	ENSG00000010292	ENSG00000110799	NCAPD2	VWF	ACTGCCGGAATCAGAGCCGCGGGTGAGATCCCCAG*GTGAGGAGCCTGAGTGCAACGACATCACTGCCAGG	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	30	20	24	12	6494154	+	12	5949883	-	17.9898	10.5691	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-55-1596-01A	ENSG00000107968	ENSG00000171495	MAP3K8	MROH2B	AGCGCTCGGCCGGCGTGGGAGCGCCAAGGCCGCAG*TAAACTGAAACCTCAGCTCTCACTACAAGACCACC	known,oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	21	7	22	10	30434378	+	5	41019018	-	6.0005	1.1641	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-55-1596-01A	ENSG00000221983	ENSG00000151067	UBA52	CACNA1C	TGGCCGCACTCTCTCAGACTACAACATCCAGAAAG*CACTACGGCCAGAGCTGCCTGTTCAAAATCGCCAT	ribosomal,18cancers,m3,exon-exon	BOWTIE	out-of-frame	0	8	4	19	19	18573748	+	12	2611903	+	79.8226	0.2434	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-44-2665-01B	ENSG00000047936	ENSG00000141367	ROS1	CLTC	GAACCGAGAAGGGTTAAACTATATGGTACTTGCTACAGAATGTGGCCAAG*GTCAGCCCCAGTTGATGCTGACAGCAGGACCCAGTGTTGCCGTCCCTCCC	known,oncogene,tcga,cell_lines,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+STAR	in-frame	0	10	1	15	6	117288686	-	17	59693728	+	67.8661	45.6097	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-67-3771-01A	ENSG00000155962	ENSG00000166887	CLIC2	VPS39	CTCAAGTGGACCCTGAGATTGAGCTTTTTGTAAAG*ATCAAACATTATCTATGTGGCCAGCAATCATTTTG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	50	9	24	X	155334371	-	15	42178338	-	22.0516	3.3467	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-67-3771-01A	ENSG00000177600	ENSG00000177156	RPLP2	TALDO1	GAATGGAAAAAACATTGAAGACGTCATTGCCCAGG*CCATCGACGAGTACAAGCCCCAGGATGCTACCACC	ribosomal,oncogene,tcga,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	27	10	24	11	811645	+	11	755879	+	237.8129	173.1153	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-67-3771-01A	ENSG00000157540	ENSG00000182670	DYRK1A	TTC3	ATGATATGAGACTTGAAAGAAGACGATGCATACAG*GTATCCGTACTTGAAAACTGGAAGGAGAGTGAAGT	known,tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	17	4	21	21	37420384	+	21	37188495	+	2.9409	13.0886	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-67-3771-01A	ENSG00000157540	ENSG00000182670	DYRK1A	TTC3	CGCTATACTGCACATTGGCTATACCAAGTAGATGCTCACTTTCGACTGAG*GTATCCGTACTTGAAAACTGGAAGGAGAGTGAAGTGTATAAGCTACAGAT	known,tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	17	3	22	21	37421866	+	21	37188495	+	2.9409	13.0886	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-67-3771-01A	ENSG00000157540	ENSG00000182670	DYRK1A	TTC3	TCCAGTCATAGGAGAAATGTTACCACTGGATTGAG*GTATCCGTACTTGAAAACTGGAAGGAGAGTGAAGT	known,tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	17	2	21	21	37430400	+	21	37188495	+	2.9409	13.0886	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-67-3771-01A	ENSG00000157540	ENSG00000182670	DYRK1A	TTC3	GACCTCAGGTTATCCTGCTGCCTTGGGCTCCCAAAGTGCTGGGATTACAG*GTATCCGTACTTGAAAACTGGAAGGAGAGTGAAGTGTATAAGCTACAGAT	known,tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K	BOWTIE+STAR	intronic/CDS(truncated)	0	17	1	23	21	37428908	+	21	37188495	+	2.9409	13.0886	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-67-3771-01A	ENSG00000157540	ENSG00000182670	DYRK1A	TTC3	ATTGTCAAAACTTTGGTCACTAGCAAAGCCCTGGTTACCAGGGAGGTAAG*GTATCCGTACTTGAAAACTGGAAGGAGAGTGAAGTGTATAAGCTACAGAT	known,tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	17	1	21	21	37450217	+	21	37188495	+	2.9409	13.0886	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-67-3771-01A	ENSG00000108510	ENSG00000136492	MED13	BRIP1	TGCTATGTCATTATTTAGTCCCTCTATCAAGCAAG*ATGTATTAGACACAGAAATGATTGGGGAGCTCTTA	18cancers,cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	12	4	24	17	61992540	-	17	61693512	-	5.6015	2.0027	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-44-2665-01A	ENSG00000141367	ENSG00000047936	CLTC	ROS1	AGAACAAGCTACAGAGACACAACCCATTGTTTATG*TCTGGCATAGAAGATTAAAGAATCAAAAAAGTGCC	known,oncogene,tcga,cell_lines,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	141	8	24	17	59690711	+	6	117321394	-	30.8985	22.6548	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-44-2665-01A	ENSG00000141367	ENSG00000047936	CLTC	ROS1	AAGCATTTGCCATTTTCCGGAAATTTGATGTCAATACTTCAGCAGTTCAG*CACTTAAATGATCATTTTGACTACTTATGAGAGCAGCAACTGTTTATTAA	known,oncogene,tcga,cell_lines,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	141	1	15	17	59681478	+	6	117311602	-	30.8985	22.6548	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-44-2665-01A	ENSG00000141367	ENSG00000047936	CLTC	ROS1	AAGCATTTGCCATTTTCCGGAAATTTGATGTCAATACTTCAGCAGTTCAG*GAATTAAATGATCATAGGCCTTGCTTTCAGAAATTTATAATGCAAGGTGT	known,oncogene,tcga,cell_lines,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	141	1	15	17	59681478	+	6	117320739	-	30.8985	22.6548	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Lung	TCGA-44-2665-01A	ENSG00000047936	ENSG00000141367	ROS1	CLTC	GAACCGAGAAGGGTTAAACTATATGGTACTTGCTACAGAATGTGGCCAAG*GTCAGCCCCAGTTGATGCTGACAGCAGGACCCAGTGTTGCCGTCCCTCCC	known,oncogene,tcga,cell_lines,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	141	9	23	6	117288686	-	17	59693728	+	22.6548	30.8985	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-44-2665-01A	ENSG00000044115	ENSG00000139329	CTNNA1	LUM	CCTCCCGAGTCTGGCCTCTACCTACCTCAGCAGCTCCCAAATCACAGAAA*GATCTGCAGCTTACTCATAACAAGATCACAAAGCTGGGCTCTTTTGAAGG	cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	14	5	138745007	+	12	91108559	-	65.6812	1247.5048	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-73-4668-01A	ENSG00000179195	ENSG00000187109	ZNF664	NAP1L1	TGGAATGTCTTGGGGGTTTTGATCCTGTCACTGTG*CCTGCCTAGGGTAGTTAAAAGACGAGTGAATGCTC	m15,exon-exon	BOWTIE	UTR/CDS(truncated)	0	42	6	23	12	123988138	+	12	76060279	-	21.2872	15.1473	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-73-4668-01A	ENSG00000135124	ENSG00000179195	P2RX4	ZNF664	GCCGTGCAACTGCTCATCCTGGCCTACGTCATCGG*ACCTGCAAATCCAAGAGACACATCTTTGGAAGATA	exon-exon	BOWTIE	CDS(truncated)/UTR	0	6	1	14	12	121210298	+	12	124011381	+	5.9534	21.2872	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Lung	TCGA-73-4666-01A	ENSG00000170421	ENSG00000178209	KRT8	PLEC	CTCCCTGGACATGGACAGCATCATTGCTGAGGTCAAGGCACAGTACGAGG*GCGGCCACCGGTTACGTCATCGACCCCATCAAGGGACTGAAGCTGACGGT	NA	BOWTIE+BLAT	out-of-frame	0	3	1	22	12	52899951	-	8	143917910	-	287.3829	45.3644	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-73-4670-01A	ENSG00000179151	ENSG00000160172	EDC3	FAM86C2P	TCAGTCCAAAAGTTTCCGTCGTCGGCACAACTCCT*ACGTGCTGTATAGCCCAGAAGCCATCGTGTCGCTG	pseudogene,m4,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	17	4	24	15	74671455	-	11	67796833	-	9.9526	2.4708	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	transcribed_unprocessed_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Lung	TCGA-73-4670-01A	ENSG00000179151	ENSG00000160172	EDC3	FAM86C2P	TCAGTCCAAAAGTTTCCGTCGTCGGCACAACTCCT*CACGAGGCTGTCCACACAGAGCCTTTGGACGAGCT	pseudogene,m4,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	17	4	23	15	74671455	-	11	67799475	-	9.9526	2.4708	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	transcribed_unprocessed_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-44-3917-01B	ENSG00000060749	ENSG00000150477	QSER1	KIAA1328	TCCTGAGATCCATACTAGTAGTAGTGACGATGAGG*GAAGTCATTTGGGACCTTTCAGAAGTGTAGTATCC	m18,exon-exon	BOWTIE	CDS(truncated)/UTR	0	19	4	18	11	32958086	+	18	36924912	+	98.6647	15.9991	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-44-3917-01B	ENSG00000060749	ENSG00000150477	QSER1	KIAA1328	TCCTGAGATCCATACTAGTAGTAGTGACGATGAGG*TTGACCAAAACAGATAAAATAAACACAGAAAGACA	m18,exon-exon	BOWTIE	CDS(truncated)/UTR	0	19	3	22	11	32958086	+	18	36946249	+	98.6647	15.9991	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-44-3917-01B	ENSG00000060749	ENSG00000150477	QSER1	KIAA1328	TCCCAATCTGACTCATCTCCTGAGATCCATACTAGTAGTAGTGACGATGA*GCTACAGTATAGAGAATGCCAAGAACTTCTAAGCCTGTATCAGAAATATT	m18	BOWTIE+BLAT	in-frame	0	19	1	20	11	32958084	+	18	36959315	+	98.6647	15.9991	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Lung	TCGA-44-3917-01B	ENSG00000060749	ENSG00000267039	QSER1	AC016493.1	TCCTGAGATCCATACTAGTAGTAGTGACGATGAGG*GAGCTTCTGCTTCCACCCAAGATGAATAAATTGGG	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	5	4	21	11	32958086	+	18	36921207	-	98.6647	29.5304	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-44-3917-01B	ENSG00000114861	ENSG00000113805	FOXP1	CNTN3	TTGTTTGTTTTTTGTTTTTGAGTTGGAGTCTCGCTCTGTCGCCCAGGCTG*GCAGTGGCTCAATCTCAGCTCACTGCAACCTCTGCCTTCCAGGCTCAAGA	oncogene,cancer	BOWTIE+BLAT	intronic/intronic	0	2	1	21	3	71178853	-	3	74439471	-	10.7056	9.8183	TRUE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-44-3917-01A	ENSG00000060749	ENSG00000267039	QSER1	AC016493.1	TCCTGAGATCCATACTAGTAGTAGTGACGATGAGG*GAGCTTCTGCTTCCACCCAAGATGAATAAATTGGG	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	6	5	22	11	32958086	+	18	36921207	-	25.7487	5.9745	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Lung	TCGA-44-3917-01A	ENSG00000196517	ENSG00000070785	SLC6A9	EIF2B3	GGACCCAGCACGCCTGGGCCGGGGGCTGCAGCATG*GCATCCTAGAATACGTTTCCACACGGGTCTTGTGG	tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	3	3	18	1	44031306	-	1	44897444	-	1.2285	19.4025	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Lung	TCGA-44-3917-01A	ENSG00000143614	ENSG00000160789	GATAD2B	LMNA	TAAAGAAACTGAGACAGAGTCAGCTACAGAAAGAGAATGTGGTCCAGAAG*AGACAGTGTTTCACCATGTTGGCCAGGCTGGTTCGAACTCCTGACTTCAG	NA	BOWTIE+BLAT	CDS(truncated)/intronic	0	2	1	23	1	153818791	-	1	156093075	+	3.0066	24.2718	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-FU-A3WB-01A	ENSG00000136068	ENSG00000283148	FLNB	AC137936.1	CGCCTATGGCACGGGACTCGAAGGGGGCACCACAG*ATGGAATCTCACTCTGTTGCCTAGGCCAGATGGAG	lincrna,cancer,m986,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	1072	21	24	3	58163330	+	3	58174975	-	57.0706	100.462	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-FU-A3WB-01A	ENSG00000136068	ENSG00000283148	FLNB	AC137936.1	GATAAATCCAGAGTGAGAGCTCGATGGCCGTGTTATCACACCTCATTACT*ATGGAATCTCACTCTGTTGCCTAGGCCAGATGGAGTGCAGTAGCACGATC	lincrna,cancer,m986	BOWTIE+BLAT;BOWTIE+STAR	intronic/exonic(no-known-CDS)	0	1072	5	22	3	58163559	+	3	58174975	-	57.0706	100.462	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-FU-A3WB-01A	ENSG00000136068	ENSG00000283148	FLNB	AC137936.1	TCTGAACAAAGCAAACCTCCCTCTGTTTTTAATGG*ATGGAATCTCACTCTGTTGCCTAGGCCAGATGGAG	lincrna,cancer,m986,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	1072	2	22	3	58165580	+	3	58174975	-	57.0706	100.462	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-FU-A3WB-01A	ENSG00000136068	ENSG00000283148	FLNB	AC137936.1	CCCGAGCAGGTCCAGGGACATTATCCGTCACCATCGAAGGCCCATCCAAG*ATGGAATCTCACTCTGTTGCCTAGGCCAGATGGAGTGCAGTAGCACGATC	lincrna,cancer,m986	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	1072	2	22	3	58168519	+	3	58174975	-	57.0706	100.462	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-FU-A3WB-01A	ENSG00000136068	ENSG00000283148	FLNB	AC137936.1	ATCGAAGGCCCATCCAAGGTTAAAATGGATTGCCAGGAAACACCTGAAGG*ATGGAATCTCACTCTGTTGCCTAGGCCAGATGGAGTGCAGTAGCACGATC	lincrna,cancer,m986	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	1072	2	22	3	58168551	+	3	58174975	-	57.0706	100.462	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-FU-A3WB-01A	ENSG00000136068	ENSG00000283148	FLNB	AC137936.1	ATTGCCAGGAAACACCTGAAGGGTACAAAGTCATGTACACCCCCATGGCT*TAAGCGAGTCCAAAATACAAAACACCCTTGGATATGTGGATCCGTGCCAC	lincrna,cancer,m986	BOWTIE+BLAT	CDS(truncated)/intronic	0	1072	1	21	3	58168579	+	3	58175624	-	57.0706	100.462	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Cervix	TCGA-FU-A3TQ-01A	ENSG00000233836	ENSG00000268362	AC139769.1	AC092279.1	ACGCACAGCCAGGACATCCTGGAACCTGGGAAAGG*AAGGCATTGAGACATGGCTGGGCTCAGCACTAAGA	pseudogene,lincrna,m5,exon-exon	BOWTIE	exonic(no-known-CDS)/exonic(no-known-CDS)	0	6	1	14	19	23763134	+	19	24063816	+	2.658	0.1891	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	transcribed_unprocessed_pseudogene	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-EK-A2RL-01A	ENSG00000127603	ENSG00000174574	MACF1	AKIRIN1	GCAGGCGTACGAGGATGTGCTGGAGCGGTACAAAG*AGCAAATTTTTCAGAACATAAAACAAGAATATAGT	known,tcga,chimerdb3seq,cancer,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	3	2	16	1	39105717	+	1	38998171	+	2.2676	22.851	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Cervix	TCGA-JX-A3Q8-01A	ENSG00000050748	ENSG00000198939	MAPK9	ZFP2	AAACCAATTGGCTCTGGGGCCCAAGGGATTGTTTG*ACTGGGAGACAAGACTTGAAACCAAAGAGCCAACT	cancer,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	7	1	13	5	180280440	-	5	178931237	+	1.4108	7.7056	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Cervix	TCGA-JX-A3Q8-01A	ENSG00000239523	ENSG00000074416	MYLK-AS1	MGLL	AGGATAAGCCCATTGGGCTGTCGGCTGAGAGTGAG*GACCTGAAGACCCTTCCAGCATGCCAGAGGAAAGT	antisense,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	5	1	14	3	123585794	+	3	127821838	-	0.0865	4.4199	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-JX-A3Q8-01A	ENSG00000239523	ENSG00000074416	MYLK-AS1	MGLL	GCCCATTGGGCTGTCGGCTGAGAGTGAGGTGCGGG*GACCTGAAGACCCTTCCAGCATGCCAGAGGAAAGT	antisense,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	5	1	13	3	123585801	+	3	127821838	-	0.0865	4.4199	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-JX-A3Q8-01A	ENSG00000165138	ENSG00000136874	ANKS6	STX17	CACTACGGCTGGAGCGCGCTCATGCAGGCGGCCAG*GTTTTTCTATATGAGTGGAGAAGACAGCTGTTACC	tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	4	2	22	9	98796133	-	9	99915178	+	0.0618	4.8753	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Cervix	TCGA-IR-A3LC-01A	ENSG00000075275	ENSG00000235091	CELSR1	BX324167.1	GTGTGAGTGACGGGCGGTGGCACTCTGTGCAGGTGCAGTACTACAACAAG*GCTGTGAGCTCCCCGAGGACGACGCCCCCTCTGCTTACACCACCTGCAGG	lincrna	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	2	2	22	22	46433393	-	22	45879204	-	4.4146	0.263	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-IR-A3LA-01A	ENSG00000131626	ENSG00000131620	PPFIA1	ANO1	CCTTGCAGAGACAGCTCAACACGGCACTTCCACAG*GGAGACTACAACGGTGAAAACGTCGAGTTCAACGA	chimerdb3seq,m697,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	897	23	24	11	70272436	+	11	70116458	+	18.9141	389.8248	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	TRUE	Cervix	TCGA-IR-A3LA-01A	ENSG00000131626	ENSG00000131620	PPFIA1	ANO1	TGAGAGAGACTCAAGAAACGCTGGCCTTAACCCAGGGGAAGTTACACGAG*GAATGTCACTGTTGGACAATTATTTTAAAAGTGTATAAAACCAAGTCTCA	chimerdb3seq,m697,tcga-cancer,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	897	1	23	11	70272382	+	11	70189069	+	18.9141	389.8248	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	TRUE	Cervix	TCGA-IR-A3LA-01A	ENSG00000131626	ENSG00000131620	PPFIA1	ANO1	TGAGAGAGACTCAAGAAACGCTGGCCTTAACCCAGGGGAAGTTACACGAG*GGAGACTACAACGGTGAAAACGTCGAGTTCAACGACAGAAAAGTAAGTTG	chimerdb3seq,m697,tcga-cancer,10K<gap<100K	BOWTIE+STAR	in-frame	0	897	1	17	11	70272382	+	11	70116458	+	18.9141	389.8248	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	FALSE	Cervix	TCGA-IR-A3LA-01A	ENSG00000100227	ENSG00000100266	POLDIP3	PACSIN2	TCCTAGGCTGGGCACAATGGCTCACTCCTGTAATCCGCCAGGCGGATCAC*AAGCGGACTGTGAAGCGGATCGACGATGGCCACCGCCTGTGCAGCGACCT	cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	41	15	23	22	42588862	-	22	42893601	-	66.2716	24.7411	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Cervix	TCGA-EK-A3GJ-01A	ENSG00000262583	ENSG00000166822	AC009163.5	TMEM170A	CAGGGATTTTCCTGGACGGGATTGTGAAGTAGCGG*AGATGTGGTATGGTGTATTCCTGTGGGCACTGGTG	pseudogene,10K<gap<100K,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	2	2	19	16	75516203	-	16	75451839	-	0.1938	7.2296	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	transcribed_unprocessed_pseudogene	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Cervix	TCGA-EK-A3GJ-01A	ENSG00000100345	ENSG00000160710	MYH9	ADAR	TTGCCAGGCTTGACCAAGGGGAAGTGTATTGAGAGTCCAGAGAGCAGCAT*GGAAGAGCCCAAGCATAGACTTGGTGCCGTGGTGATGGCTGCAGTCCAGT	cancer	BOWTIE+STAR	intronic/UTR	0	2	1	14	22	36347275	-	1	154583292	-	138.6817	55.9283	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-C5-A2M1-01A	ENSG00000249859	ENSG00000249375	PVT1	CASC11	ATGTTGGCGGTCCCTGTGACCTGTGGAGACACGGCCAGATCTGCCCTCCA*GTTGGAGTGCAGTGGTGTGATCACGACTCACTGCAGTCTTGAACTTGCCA	known,lincrna,oncogene,18cancers,chimerdb3seq,cancer	BOWTIE+BLAT;BOWTIE+STAR	exonic(no-known-CDS)/exonic(no-known-CDS)	0	6	1	20	8	127794734	+	8	127716148	-	6.3301	0.3818	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Cervix	TCGA-DG-A2KJ-01A	ENSG00000247556	ENSG00000178279	OIP5-AS1	TNP2	AAGATTCACCAAAATTTGAGAGTGATAAAAATGGCCTAAAATGGGAAATG*GATGGAAATCCAACTAATGAGACCGCACTCCTTGGCTTGTTCCTGCGTGT	NA	BOWTIE+STAR	exonic(no-known-CDS)/CDS(truncated)	0	5	1	16	15	41299758	+	16	11268012	-	3.7295	0.1446	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	processed_transcript	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Cervix	TCGA-DG-A2KJ-01A	ENSG00000247556	ENSG00000178279	OIP5-AS1	TNP2	TTATAAAGACATCATTTTGCAAGCAGAAGGCTGAGTTTCATTTGAAACAG*GATGGAAATCCAACTAATGAGACCGCACTCCTTGGCTTGTTCCTGCGTGT	NA	BOWTIE+STAR	exonic(no-known-CDS)/CDS(truncated)	0	5	1	14	15	41298334	+	16	11268012	-	3.7295	0.1446	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	processed_transcript	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Cervix	TCGA-IR-A3LH-01A	ENSG00000105053	ENSG00000105329	VRK3	TGFB1	CAGGACCACAGAAGCAAAAGTTCTCACTCAAACTG*CTCCACGGAGAAGAACTGCTGCGTGCGGCAGCTGT	oncogene,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	119	10	22	19	50000790	-	19	41332281	-	4.0202	31.5042	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Cervix	TCGA-IR-A3LH-01A	ENSG00000213024	ENSG00000104946	NUP62	TBC1D17	GTCCAGAGAAGGTGGAGGAATCCTGATACTGAGCG*CTCCCCGCAGGACTCCCGCCTCTACCTTGTCTTCC	chimerdb3seq,exon-exon	BOWTIE	UTR/CDS(truncated)	0	86	14	22	19	49927694	-	19	49882041	+	21.7106	13.0661	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Cervix	TCGA-IR-A3LH-01A	ENSG00000104951	ENSG00000104946	IL4I1	TBC1D17	GTCCAGAGAAGGTGGAGGAATCCTGATACTGAGCG*CGCTTCCTCCAGGATCCCTACTCCACCACCTTCAG	tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	72	2	21	19	49927694	-	19	49882242	+	38.231	13.0661	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Cervix	TCGA-IR-A3LH-01A	ENSG00000070404	ENSG00000233452	FSTL3	STXBP5-AS1	CGTGAGCTCCATGGGCTCGGGGAACCCCGCGCCCG*CCCCTGGCAAACACCATTCTACTTTCCGTCTCTAT	antisense,cancer,tumor,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	48	4	18	19	676526	+	6	147119477	-	45.0553	3.5719	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Cervix	TCGA-IR-A3LH-01A	ENSG00000070404	ENSG00000233452	FSTL3	STXBP5-AS1	CGTGAGCTCCATGGGCTCGGGGAACCCCGCGCCCG*GTGAAATGTTGGTGCCAAATGAACTTTTCTGGTTC	antisense,cancer,tumor,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	48	3	20	19	676526	+	6	147074847	-	45.0553	3.5719	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Cervix	TCGA-IR-A3LH-01A	ENSG00000070404	ENSG00000233452	FSTL3	STXBP5-AS1	CTTCTTGGGCCTTGTCCACTGCCTTCCCTGCAAAG*CCCCTGGCAAACACCATTCTACTTTCCGTCTCTAT	antisense,cancer,tumor,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	48	2	23	19	677977	+	6	147119477	-	45.0553	3.5719	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Cervix	TCGA-IR-A3LH-01A	ENSG00000196961	ENSG00000105053	AP2A1	VRK3	CTGCCTCTCCACGTCGGCCTTCCTCACCGTGGGGAAGCCGGCTGACCCAG*AGACCCTGCAGAAGTACCTGAAGGTGGTGATGGCCCTCACGTATGAGGAG	tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	19	4	23	19	49803453	+	19	49979242	-	14.0655	4.0202	TRUE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Cervix	TCGA-IR-A3LH-01A	ENSG00000196961	ENSG00000105053	AP2A1	VRK3	CCAGGCCCTCACCCTGAAGCTCCCAGTGACCATCAACAAGTTCTTCCAGC*CCAAGTAGCTGGGGTTATAGGCGTGCGTCACCATACCTGGCTAGTTTTTT	tcga-cancer	BOWTIE+BLAT	CDS(truncated)/intronic	0	19	1	21	19	49805725	+	19	49980611	-	14.0655	4.0202	TRUE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Cervix	TCGA-IR-A3LH-01A	ENSG00000173064	ENSG00000135148	HECTD4	TRAFD1	AAGTTGAGCCCGAGAAGACACTGGCCTTCCCCGGCACAGACAGCATGGAG*GTGCAGCTGACGAGATCATGTTGCCTTGTGAATTTTGTGAGGAGCTCTAC	NA	BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	13	1	23	12	112184556	-	12	112145586	+	1.2403	24.3022	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Cervix	TCGA-IR-A3LH-01A	ENSG00000104946	ENSG00000105722	TBC1D17	ERF	CTCCTGTAGAGGAGGCTGGAGATTCCACCCAAATCCTCTTCTCCAAGAAG*TTTAAGCTCCAGCCGCCCCCACTCGGACGCCGGCAGCGGGCAGCTGGGGA	NA	BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	10	1	18	19	49878572	+	19	42248983	-	13.0661	23.9054	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Cervix	TCGA-IR-A3LH-01A	ENSG00000105767	ENSG00000121413	CADM4	ZSCAN18	GCTGCTGCTGCTGTGGGCGGCCGCGGCGGGGCCAG*GTCTGTGGGTTCTGGCACCACCTGAGCCCACTGGG	tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	2	2	17	19	43639727	-	19	58090386	-	16.078	0.936	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Cervix	TCGA-IR-A3LH-01A	ENSG00000186020	ENSG00000268423	ZNF529	AC093503.1	TGGAAGACAGCATTGGTACTAATGGCCAACTCAAG*GTGGGGATTACAATTTGAGATGAGATTTCGGTGGG	exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	2	1	13	19	36572333	-	19	46576717	-	1.5719	NA	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	sense_intronic	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-C5-A3HF-01A	ENSG00000065526	ENSG00000116138	SPEN	DNAJC16	GTGCGGGAAGAGAAGATCATCGAGCATTTCAAACG*GCCCGAGGTATGAAGAAGCAAATCATTGACGACTT	tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	11	5	22	1	15848150	+	1	15559526	+	9.9352	7.9708	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Cervix	TCGA-EA-A3Y4-01A	ENSG00000143862	ENSG00000077152	ARL8A	UBE2T	CTCAGTTCTTATATCATCCTAAGGCCCTGATGAATAGGTGGTTCCTGCAG*AGAGCTTCACGTCTGAAGAGAGAGCTGCACATGTTAGCCACAGAGCCACC	tcga-cancer,100K<gap<200K	BOWTIE+BLAT	intronic/CDS(truncated)	0	13	1	23	1	202140455	-	1	202335748	-	16.8005	15.1432	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Cervix	TCGA-EA-A3Y4-01A	ENSG00000143862	ENSG00000077152	ARL8A	UBE2T	ACTCGGGCAAGACCACCTTCGTCAACGTGATCGCG*AAATATTAGGTGGAGCCAACACACCTTATGAGAAA	tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	13	1	14	1	202144450	-	1	202335058	-	16.8005	15.1432	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Cervix	TCGA-C5-A2LY-01A	ENSG00000215241	ENSG00000226711	LINC02449	FAM66C	TCCTGAGACAACGGAATTCTGGCGATGGAGCACAG*ATATAATACGTAAGTTTGGAGGTGGATGCTTTCAG	lincrna,antisense,m2,10K<gap<100K,exon-exon	BOWTIE	exonic(no-known-CDS)/exonic(no-known-CDS)	0	6	2	22	12	8235999	+	12	8215806	+	1.4059	0.9397	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	lincRNA	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Cervix	TCGA-FU-A3TX-01A	ENSG00000154845	ENSG00000177425	PPP4R1	PAWR	TCTAGAGCCCCACATTGATGATCCAGATGTTAAAG*TGCTTAGATGAGTACGAAGATGATGAAGCAGGGCA	cancer,m59,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	60	5	23	18	9570157	-	12	79621207	-	9.1713	3.6805	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Cervix	TCGA-FU-A3TX-01A	ENSG00000154845	ENSG00000177425	PPP4R1	PAWR	TCTAGAGCCCCACATTGATGATCCAGATGTTAAAG*AGGTAAAGAGTTCAGAAGTAAGATAAAAGAAGACC	cancer,m59,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	60	4	23	18	9570157	-	12	79668408	-	9.1713	3.6805	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Cervix	TCGA-FU-A3TX-01A	ENSG00000154845	ENSG00000177425	PPP4R1	PAWR	TCTAGAGCCCCACATTGATGATCCAGATGTTAAAG*TTAAAAATATGAAGATTAAGGGGAAATTGAAGACA	cancer,m59,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	60	2	21	18	9570157	-	12	79688465	-	9.1713	3.6805	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Cervix	TCGA-FU-A3TX-01A	ENSG00000154845	ENSG00000177425	PPP4R1	PAWR	AGAAATGATAGAAAATCTAGAGCCCCACATTGATGATCCAGATGTTAAAG*GGGTCCCCAGCTCCTGGGCCGTAGACCCGTACTGGTCCATGACTTGTTAG	cancer,m59,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	60	1	20	18	9570157	-	12	79668843	-	9.1713	3.6805	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Cervix	TCGA-FU-A3TX-01A	ENSG00000154845	ENSG00000177425	PPP4R1	PAWR	AGAAATGATAGAAAATCTAGAGCCCCACATTGATGATCCAGATGTTAAAG*GAGGGGGAGAGAGAGACCAAGGATGCACACACACAGAAAAAAGGCCAAAT	cancer,m59,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	60	1	20	18	9570157	-	12	79642612	-	9.1713	3.6805	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Cervix	TCGA-FU-A3TX-01A	ENSG00000102910	ENSG00000129521	LONP2	EGLN3	GGAGTATGTGATCAGTCTGACATTCGAGGACACAG*CAGCTACCAGGAGGCAGCCTGAACGTGTCAGGGCC	tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	7	2	17	16	48270274	+	14	34169646	-	3.1901	26.513	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Cervix	TCGA-FU-A3TX-01A	ENSG00000102910	ENSG00000129521	LONP2	EGLN3	AGGATTGCACTTGGAGGAGTATGTGATCAGTCTGACATTCGAGGACACAG*GTGACTCTACACTGAGTACTAGGCAGTGAGCTCCTTCCGGACCAGCCCCT	tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	7	1	22	16	48270274	+	14	34362005	-	3.1901	26.513	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Cervix	TCGA-FU-A3TX-01A	ENSG00000184465	ENSG00000231720	WDR27	AL353747.3	GACGATTCGCGGCTTGTGGGGCCGAGGACAGACAC*GTACCAGAGCAATGAGGAAGCAGGACCCAGACCCC	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	5	1	13	6	169602219	-	6	167237805	-	0.558	0.0951	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Cervix	TCGA-C5-A2LV-01A	ENSG00000137693	ENSG00000164733	YAP1	CTSB	GCCTGGCTAATTTTTTGGTATTTTTAGTAGAGATGGGGTTTCACCGTGTT*GCCAAGCATGCTGGCACATGCCTGTAATCCCAGCTACTCGGGAGGCTGAG	oncogene,cancer,tumor	BOWTIE+BLAT	intronic/UTR	0	3	1	20	11	102161268	+	8	11842800	-	889.6173	453.1739	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Cervix	TCGA-IR-A3LL-01A	ENSG00000168214	ENSG00000249699	RBPJ	LINC02261	TTTTTTTCCAGGAAATTTGGTGAGCGGCCTCCACCTAAACGACTTACTAG*GGAAGCAAACGCTCGTCACCATGTTTTCTCATCAAGCAACAGGAACCATC	lincrna	BOWTIE+STAR	CDS(truncated)/intronic	0	13	1	17	4	26386391	+	4	27273349	+	6.3233	0.6892	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Cervix	TCGA-IR-A3LL-01A	ENSG00000171862	ENSG00000166167	PTEN	BTRC	ATTTCTATGGGGAAGTAAGGACCAGAGACAAAAAG*GGGACAGTATTTATTCAAAAACAAACCTCCTGACG	cancer,tumor,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	2	1	13	10	87933251	+	10	101531237	+	1.227	5.7416	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	FALSE	Cervix	TCGA-EA-A1QS-01A	ENSG00000121775	ENSG00000284702	TMEM39B	AL136115.3	TACTCCTTCCTGAACCTCCTGTTCCTCTGCTATCC*ATGGAGTCTCTCTCTGTAGCCCAGACTGGAATGCA	lincrna,m3,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	6	4	24	1	32077318	+	1	31973878	-	13.5698	1.651	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Cervix	TCGA-EK-A2PM-01A	ENSG00000164548	ENSG00000240583	TRA2A	AQP1	TGAGTGATGTGGAGGAAAACAACTTCGAGGGCAGA*CTGGCTGATGGTGTGAACTCGGGCCAGGGCCTGGG	oncogene,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	144	18	24	7	23531789	-	7	30922066	+	8.844	42.9152	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Cervix	TCGA-EK-A2PM-01A	ENSG00000164548	ENSG00000240583	TRA2A	AQP1	TGAGTGATGTGGAGGAAAACAACTTCGAGGGCAGA*GAGTGCTCCTGACCATCACCTTCATGCCTGGGGCT	oncogene,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	144	2	23	7	23531789	-	7	30921681	+	8.844	42.9152	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Cervix	TCGA-EK-A2PM-01A	ENSG00000164548	ENSG00000240583	TRA2A	AQP1	CTTGAGGTTGAAGGTGGGACGAGCCTAATGAAGTG*GAGTGCTCCTGACCATCACCTTCATGCCTGGGGCT	oncogene,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	144	1	13	7	23531181	-	7	30921681	+	8.844	42.9152	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Cervix	TCGA-EK-A2PM-01A	ENSG00000164548	ENSG00000250424	TRA2A	AC004691.2	TGAGTGATGTGGAGGAAAACAACTTCGAGGGCAGA*CATCGGTTCTGCCCTGGGCTTCAAATACCCGGTGG	exon-exon	BOWTIE	CDS(truncated)/CDS(no-known-start-or-end)	0	129	6	24	7	23531789	-	7	30911993	+	8.844	0	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-EK-A2PM-01A	ENSG00000103021	ENSG00000140848	CCDC113	CPNE2	AAAAAATTGAAAAAGAAACACTACAAGTAGAGGAG*CAGTACTTCATCCTCCTCATCATCACGGACGGGGT	tcga-cancer,exon-exon	BOWTIE	in-frame	0	14	7	20	16	58267586	+	16	57146085	+	0.8655	3.0654	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Cervix	TCGA-EK-A2PM-01A	ENSG00000115183	ENSG00000136536	TANC1	MARCH7	CCTTTTCCTGGTGCATGTGAAGTTATCAAAAACAG*AAAAATCTTTAAGAATGGAGTCTAAACCTTCAAGG	exon-exon	BOWTIE	UTR/UTR	0	5	3	18	2	159001189	+	2	159729009	+	1.457	12.1032	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Cervix	TCGA-EK-A2PM-01A	ENSG00000100490	ENSG00000214900	CDKL1	LINC01588	GAATATTGTGACCACACAGTTCTCCATGAGTTGGACAGATACCAAAGAGG*ATTCATTTCAAATGTCACCACAGACCAGGCGTGGTGGCTCACTCCTGTAA	lincrna	BOWTIE+STAR	CDS(truncated)/intronic	0	4	3	17	14	50359028	-	14	49973506	-	0.2971	0.0489	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-C5-A2LT-01A	ENSG00000170006	ENSG00000109670	TMEM154	FBXW7	GAATGTTTACCTACCTTGAAGGAAGAGAAGGAATCAAATCACAACCCAAG*GGTCTTGCTCTGTCGTCCAAGCTGGAGTGCGGTCACAGCTCACTGCAGCC	tcga,chimerdb3seq,cancer,tcga-cancer,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	3	1	18	4	152640928	-	4	152451776	-	0.1782	0.8287	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-C5-A2LT-01A	ENSG00000170006	ENSG00000109670	TMEM154	FBXW7	GAATGTTTACCTACCTTGAAGGAAGAGAAGGAATCAAATCACAACCCAAG*TCTCACTCTGTTGCCCAGGCTGGAGTGCAATGGTGCGATCTTGGCTCACT	tcga,chimerdb3seq,cancer,tcga-cancer,10K<gap<100K	BOWTIE+STAR	CDS(truncated)/intronic	0	3	1	16	4	152640928	-	4	152453174	-	0.1782	0.8287	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-C5-A2LT-01A	ENSG00000170006	ENSG00000109670	TMEM154	FBXW7	GAATGTTTACCTACCTTGAAGGAAGAGAAGGAATCAAATCACAACCCAAG*TCTCACTCTGTTGCCCAGGCTGGGATGCAGTGGAATGATCATAGCTCACT	tcga,chimerdb3seq,cancer,tcga-cancer,10K<gap<100K	BOWTIE+STAR	CDS(truncated)/intronic	0	3	1	16	4	152640928	-	4	152335458	-	0.1782	0.8287	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Cervix	TCGA-EA-A3HR-01A	ENSG00000179134	ENSG00000166750	SAMD4B	SLFN5	CATCCACCTGCTGGAGTCGGAGGCCAACAGTGCTG*TATTTTCAGACAGAGTGGTATATACTCCAGAAAGC	tcga-cancer,exon-exon	BOWTIE	in-frame	0	25	5	23	19	39357089	+	17	35264183	+	63.6536	10.242	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Cervix	TCGA-DS-A0VL-01A	ENSG00000110330	ENSG00000152558	BIRC2	TMEM123	GGAGAAGGAAAAACAAGCTGAAGAAATGGCATCAG*AGACTCTCCAACATGTGCCTTCTGACCATACAAAT	oncogene,cell_lines,18cancers,chimerdb3seq,cancer,m308,tcga-cancer,exon-exon	BOWTIE	in-frame	0	309	20	24	11	102368548	+	11	102402206	-	110.7968	101.7234	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Cervix	TCGA-DS-A0VL-01A	ENSG00000110330	ENSG00000152558	BIRC2	TMEM123	TGAAAAAAGAGAAGAGGAGAAGGAAAAACAAGCTGAAGAAATGGCATCAG*GCCATATTTTATGCAAAAAGAAGGAAACCTTTGCTGGATGAAAACAAAAG	oncogene,cell_lines,18cancers,chimerdb3seq,cancer,m308,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	309	2	23	11	102368548	+	11	102403386	-	110.7968	101.7234	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Cervix	TCGA-DS-A0VL-01A	ENSG00000110330	ENSG00000152558	BIRC2	TMEM123	TGAAAAAAGAGAAGAGGAGAAGGAAAAACAAGCTGAAGAAATGGCATCAG*TACTGTGAAACCACCAACTTCAGTTGCCTCAGACTCCAGTAATACAACGG	oncogene,cell_lines,18cancers,chimerdb3seq,cancer,m308,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	309	1	19	11	102368548	+	11	102402157	-	110.7968	101.7234	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Cervix	TCGA-DS-A0VL-01A	ENSG00000155313	ENSG00000166265	USP25	CYYR1	TACATTCAGAGAATTCAGGAAAATCAGGCCAAGAG*GACCACCACCCTACGGTCACGACCACGAGATGGAA	18cancers,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	22	5	21	21	15818846	+	21	26468631	-	5.136	6.1934	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Cervix	TCGA-DS-A0VL-01A	ENSG00000157540	ENSG00000142192	DYRK1A	APP	ACACTGGAGAACCTCTGTTCAGTGGTGCCAATGAG*ATGAGCTGCTTCAGAAAGAGCAAAACTATTCAGAT	18cancers,chimerdb3seq,cancer,exon-exon	BOWTIE	out-of-frame	0	16	8	24	21	37493163	+	21	25911962	-	3.6284	86.7961	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Cervix	TCGA-IR-A3LI-01A	ENSG00000242852	ENSG00000104774	ZNF709	MAN2B1	ACAGAACACCAGGACATCCCAGAGTCTGGGAAATG*TTCTCAGGGCTGCGCAGGGACCTGCCGCCCTCGGT	chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	204	20	23	19	12484655	-	19	12647598	-	0.1511	14.9902	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	TRUE	Cervix	TCGA-IR-A3LI-01A	ENSG00000242852	ENSG00000104774	ZNF709	MAN2B1	ACAGAACACCAGGACATCCCAGAGTCTGGGAAATG*GACCTGTTCTCCACCTTCACCATCACCCGCCTGCA	chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	204	3	21	19	12484655	-	19	12647335	-	0.1511	14.9902	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	TRUE	Cervix	TCGA-EK-A2R7-01A	ENSG00000090060	ENSG00000151322	PAPOLA	NPAS3	GACTGGGCGGTGCCGGCGCCGGAGACGATGCCGTT*GTGGAGCTGACAGGCAGCAGTGTCTTTGACTATGT	tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	3	3	16	14	96502600	+	14	33676211	+	16.1102	3.1687	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Cervix	TCGA-EK-A3GM-01A	ENSG00000150712	ENSG00000145526	MTMR12	CDH18	GCTGCAACCATCTCCGCCAGAACGACAAAGAGGAG*ATAATCCTGATTTGCTGAGCCATGTCACAGTGGGT	exon-exon	BOWTIE	out-of-frame	0	4	4	19	5	32239001	-	5	19520778	-	9.1552	0.4389	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Cervix	TCGA-EK-A3GM-01A	ENSG00000150712	ENSG00000145526	MTMR12	CDH18	ACTGTTTCTTGGATCGCTGCAACCATCTCCGCCAGAACGACAAAGAGGAG*AGACAGGCTTTCACCATGTTGGCCAGACTGGTCTCGAACTCCTGATCTCA	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	4	3	22	5	32239001	-	5	19531764	-	9.1552	0.4389	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Cervix	TCGA-EK-A3GM-01A	ENSG00000150712	ENSG00000145526	MTMR12	CDH18	ACTGTTTCTTGGATCGCTGCAACCATCTCCGCCAGAACGACAAAGAGGAG*TGAGTTTTTCAAAGAACATTTTCTTGAAAATTACAATTTATTGGAGGTGG	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	4	1	14	5	32239001	-	5	19531146	-	9.1552	0.4389	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Cervix	TCGA-EK-A3GM-01A	ENSG00000142544	ENSG00000161558	CTU1	TMEM143	GGCGCGCCGCGTGGGAGCCACGCACATCGTGACAG*ATGTTCGGGCAGCGGCGCAGCGCGCAGGCGTTGGA	tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	2	3	23	19	51104062	-	19	48334197	-	1.1212	3.1781	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	TRUE	Cervix	TCGA-C5-A1M8-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	GCCTGCCTCAGCCTCCAAAGTAGCTGAGACTACAG*CAGTTTAAGTATAGTGTGCCTGGGTTGGGTGCGGT	antisense,m2,exon-exon	BOWTIE	exonic(no-known-CDS)/UTR	0	35	6	24	10	87246115	-	10	46593287	+	1.0698	0.1571	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-C5-A1M8-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	GCCTGCCTCAGCCTCCAAAGTAGCTGAGACTACAG*ATTCCAGTTCTTTGATGAAAGTCTCTATTCCACCC	antisense,m2,exon-exon	BOWTIE	exonic(no-known-CDS)/UTR	0	35	5	23	10	87246115	-	10	46593989	+	1.0698	0.1571	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-C5-A1M8-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	GGAGCTTCTCAGAAGACAGAGGGTTTTCTTTTGAG*ATTCCAGTTCTTTGATGAAAGTCTCTATTCCACCC	antisense,m2,exon-exon	BOWTIE	exonic(no-known-CDS)/UTR	0	35	4	23	10	87288442	-	10	46593989	+	1.0698	0.1571	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-C5-A1M8-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	GGAGCTTCTCAGAAGACAGAGGGTTTTCTTTTGAG*GTGTGTTTGTCAAAGTGTCTCTGATGAACCACAAC	antisense,m2,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	35	2	16	10	87288442	-	10	46585598	+	1.0698	0.1571	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-C5-A1M8-01A	ENSG00000176697	ENSG00000254560	BDNF	BBOX1-AS1	TTAACAAACTGATCCCTGAAAATGGTTTCATAAAG*GTTTGAATGAGAGAGGCAGAAGCACATTTCCAATC	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	13	2	16	11	27674060	-	11	27047312	-	0.0254	1.2775	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-C5-A1M8-01A	ENSG00000176697	ENSG00000254560	BDNF	BBOX1-AS1	TCCCGGAGCAGCTGCCTTGATGGTTACTTTGACAAGTAGTGACTGAAAAG*GGATAGCCCAGAGCTATTCCATGTATTCCATGGATGGGCACATTTGGAAG	antisense,exon-exon	BOWTIE+BLAT	UTR/exonic(no-known-CDS)	0	13	1	21	11	27701297	-	11	27066662	-	0.0254	1.2775	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-C5-A1M8-01A	ENSG00000176697	ENSG00000254560	BDNF	BBOX1-AS1	CGCCGGGGACCCGTGAGGTTTGTGTGGACCCCGAG*GTTTGAATGAGAGAGGCAGAAGCACATTTCCAATC	antisense,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	13	1	14	11	27700164	-	11	27047312	-	0.0254	1.2775	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Cervix	TCGA-C5-A1MI-01A	ENSG00000170421	ENSG00000087460	KRT8	GNAS	TCACCGCAGTTACGGTCAACCAGAGCCTGCTGAGCCCCCTTGTCCTGGAG*CTGGCCAACCCCGAGAACCAGTTCAGAGTGGACTACATCCTGAGTGTGAT	oncogene,cancer,tumor	BOWTIE+BLAT	in-frame	0	4	1	16	12	52904745	-	20	58903714	+	947.8229	173.1167	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-C5-A3HD-01B	ENSG00000116793	ENSG00000134242	PHTF1	PTPN22	TATGGGAAAAGTCAATCGAACAGACTCAGATTAAG*GTATCTGTAATTCTTGCCCACCAAACAAGCCTGCA	tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	2650	23	24	1	113757699	-	1	113819654	-	15.0909	111.6917	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Cervix	TCGA-C5-A3HD-01B	ENSG00000116793	ENSG00000134242	PHTF1	PTPN22	CTCCCACCTTAGCCTCCTGAGTAACTGGGACCACAGGCATGCACCAACAG*GTATCTGTAATTCTTGCCCACCAAACAAGCCTGCAGAATCTGTTCAGTCA	tcga-cancer,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	2650	11	24	1	113754272	-	1	113819654	-	15.0909	111.6917	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Cervix	TCGA-C5-A3HD-01B	ENSG00000116793	ENSG00000134242	PHTF1	PTPN22	TATGGGAAAAGTCAATCGAACAGACTCAGATTAAG*GTTTTGCAAACCGTTTTTCAAAACCCAAAGGACCA	tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	2650	9	22	1	113757699	-	1	113814969	-	15.0909	111.6917	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Cervix	TCGA-C5-A3HD-01B	ENSG00000116793	ENSG00000134242	PHTF1	PTPN22	CCTACGATCAGCAGATATGGGAAAAGTCAATCGAACAGACTCAGATTAAG*ACAGGGTCTTGCTCTGTCACCCAGTCTGGATGGAGTGCAGTGGCGCAATC	tcga-cancer,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	2650	7	23	1	113757699	-	1	113820459	-	15.0909	111.6917	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Cervix	TCGA-C5-A3HD-01B	ENSG00000116793	ENSG00000134242	PHTF1	PTPN22	TATGGGAAAAGTCAATCGAACAGACTCAGATTAAG*GGTCTTGCTCTGTCACCCAGGCTGGAGTGCCGTGG	tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	2650	7	22	1	113757699	-	1	113864382	-	15.0909	111.6917	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Cervix	TCGA-C5-A3HD-01B	ENSG00000116793	ENSG00000134242	PHTF1	PTPN22	CCTACGATCAGCAGATATGGGAAAAGTCAATCGAACAGACTCAGATTAAG*GATGTATATAACTTTCAGCTCCTATGCAGTATACAGATTACTGATATCTC	tcga-cancer,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	2650	2	19	1	113757699	-	1	113821174	-	15.0909	111.6917	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Cervix	TCGA-C5-A3HD-01B	ENSG00000116793	ENSG00000134242	PHTF1	PTPN22	TCTACTCAGATAACAAGACCATCAGGAAACAATGGAAATCGAAGAAGAAG*CATGGACCAAAGAGAAATTCTGCAGAAGTTCCTGGATGAGGCCCAAAGCA	tcga-cancer,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	2650	1	24	1	113726418	-	1	113871624	-	15.0909	111.6917	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Cervix	TCGA-C5-A3HD-01B	ENSG00000116793	ENSG00000134242	PHTF1	PTPN22	AGACTCCGTCTCAAAAATAAAAAAAAAAAAAGAAGAACCTAATTAAGAAG*GTATCTGTAATTCTTGCCCACCAAACAAGCCTGCAGAATCTGTTCAGTCA	tcga-cancer,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	2650	1	19	1	113753408	-	1	113819654	-	15.0909	111.6917	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Cervix	TCGA-C5-A3HD-01B	ENSG00000116793	ENSG00000134242	PHTF1	PTPN22	CCTACGATCAGCAGATATGGGAAAAGTCAATCGAACAGACTCAGATTAAG*ACAGGGTCTTGCTCTGTTGCCCATGCTAGAGTGCAGTGGCATAAATATGG	tcga-cancer,10K<gap<100K	BOWTIE+STAR	CDS(truncated)/intronic	0	2650	1	17	1	113757699	-	1	113826341	-	15.0909	111.6917	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Cervix	TCGA-C5-A3HD-01B	ENSG00000278311	ENSG00000078114	GGNBP2	NEBL	GGCAGATTCCCCTCTACATAGACGACACCCTGACG*GTAAAATACCATGAAGATTTTGAAAAAACAAAGGG	tcga-cancer,exon-exon	BOWTIE	in-frame	0	127	20	24	17	36545817	+	10	20812940	-	12.5492	16.4933	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Cervix	TCGA-C5-A3HD-01B	ENSG00000278311	ENSG00000078114	GGNBP2	NEBL	GTGAAGGTCGGAACCGACAGCCTCCTCCGAGAAGG*GTAAAATACCATGAAGATTTTGAAAAAACAAAGGG	tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	127	2	21	17	36545097	+	10	20812940	-	12.5492	16.4933	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Cervix	TCGA-C5-A3HD-01B	ENSG00000133895	ENSG00000149177	MEN1	PTPRJ	GGCCCACATCCAGTCCCTCTTCAGCTTCATCACAG*ATGCTATTCAGGTTTTTGACGTCACCGCTGTGAAC	cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	47	9	23	11	64809665	-	11	48127780	+	12.574	2.2885	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Cervix	TCGA-C5-A3HD-01B	ENSG00000078114	ENSG00000273611	NEBL	ZNHIT3	CGTGGAGATGGACAGGAGACCTGGAATCATTGTTG*ATGGACTCTCGTCCTGTCACCCAGGCTGGAGTGCA	m18,exon-exon	BOWTIE	in-frame	0	22	3	22	10	20812769	-	17	36497606	+	16.4933	6.2442	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Cervix	TCGA-C5-A1M9-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	GCCTGCCTCAGCCTCCAAAGTAGCTGAGACTACAG*CAGTTTAAGTATAGTGTGCCTGGGTTGGGTGCGGT	antisense,m3,exon-exon	BOWTIE	exonic(no-known-CDS)/UTR	0	22	5	21	10	87246115	-	10	46593287	+	1.023	0.0091	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-C5-A1M9-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	GGAGCTTCTCAGAAGACAGAGGGTTTTCTTTTGAG*ATTCCAGTTCTTTGATGAAAGTCTCTATTCCACCC	antisense,m3,exon-exon	BOWTIE	exonic(no-known-CDS)/UTR	0	22	1	14	10	87288442	-	10	46593989	+	1.023	0.0091	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-EK-A2R9-01A	ENSG00000114346	ENSG00000206120	ECT2	EGFEM1P	CACCAGTTGTATTAAATTGTTCACAAAAAGGAGAG*CTATCGCTGCAGTGGGAACTTGTTTCAATGGAAGA	pseudogene,oncogene,18cancers,chimerdb3seq,cancer,m69,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	70	10	22	3	172757165	+	3	168314071	+	9.5223	7.3173	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	transcribed_unitary_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-EK-A2R9-01A	ENSG00000114346	ENSG00000206120	ECT2	EGFEM1P	CTGGAAAACAAGAAGAACTTATAAAAGCCTTAAAG*CTATCGCTGCAGTGGGAACTTGTTTCAATGGAAGA	pseudogene,oncogene,18cancers,chimerdb3seq,cancer,m69,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	70	7	22	3	172755374	+	3	168314071	+	9.5223	7.3173	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	transcribed_unitary_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-EK-A2R9-01A	ENSG00000114346	ENSG00000206120	ECT2	EGFEM1P	GTAGAGTTATTGGACCACCAGTTGTATTAAATTGTTCACAAAAAGGAGAG*AGATAGGGCCTTGCTCTGTTACCCAGGCTGGAGTATGGTGCCATAATCAT	pseudogene,oncogene,18cancers,chimerdb3seq,cancer,m69	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	70	2	22	3	172757165	+	3	168310327	+	9.5223	7.3173	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	transcribed_unitary_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-EK-A2R9-01A	ENSG00000114346	ENSG00000206120	ECT2	EGFEM1P	GTAGAGTTATTGGACCACCAGTTGTATTAAATTGTTCACAAAAAGGAGAG*TTGATTCAAAAGTCTGGAGGGAAATCATCGTACTAAATCTAAATGGGATT	pseudogene,oncogene,18cancers,chimerdb3seq,cancer,m69	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	70	2	22	3	172757165	+	3	168312697	+	9.5223	7.3173	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	transcribed_unitary_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-EK-A2R9-01A	ENSG00000114346	ENSG00000206120	ECT2	EGFEM1P	TATTGGTTCAAGAAGCTGGAAAACAAGAAGAACTTATAAAAGCCTTAAAG*ATGACATGCTGAGGTGAAGAGAAGTTAAGTAACTTATCTGAGATCATACA	pseudogene,oncogene,18cancers,chimerdb3seq,cancer,m69	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	70	2	20	3	172755374	+	3	168322628	+	9.5223	7.3173	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	transcribed_unitary_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-EK-A2R9-01A	ENSG00000114346	ENSG00000206120	ECT2	EGFEM1P	CTGGAAAACAAGAAGAACTTATAAAAGCCTTAAAG*GTCCTCTTTTCCGTCTTCTCATTCCTGTGGATCTG	pseudogene,oncogene,18cancers,chimerdb3seq,cancer,m69,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	70	2	18	3	172755374	+	3	168519536	+	9.5223	7.3173	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	transcribed_unitary_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-EK-A2R9-01A	ENSG00000114346	ENSG00000206120	ECT2	EGFEM1P	GTTGTCCTGGAAAATCGGATGAAAAATTAATAAAAAGTGTTATTAATATG*TCTTCTTTTACAGATGACATGCTGAGGTGAAGAGAAGTTAAGTAACTTAT	pseudogene,oncogene,18cancers,chimerdb3seq,cancer,m69	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	70	1	21	3	172755575	+	3	168322615	+	9.5223	7.3173	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	transcribed_unitary_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-EK-A2R9-01A	ENSG00000114346	ENSG00000206120	ECT2	EGFEM1P	CGGATGAAAAATTAATAAAAAGTGTTATTAATATG*GTCCTCTTTTCCGTCTTCTCATTCCTGTGGATCTG	pseudogene,oncogene,18cancers,chimerdb3seq,cancer,m69,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	70	1	13	3	172755575	+	3	168519536	+	9.5223	7.3173	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	transcribed_unitary_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-EK-A2R9-01A	ENSG00000008952	ENSG00000163584	SEC62	RPL22L1	CTGTTTTGTAGCCAGTATTCTTCTCCTTGCTGTTG*CAGAAAGACAGGAAGCCCAAGAGGTCAACCTGGAG	ribosomal,oncogene,18cancers,m17,exon-exon	BOWTIE	out-of-frame	0	45	18	24	3	169988359	+	3	170868390	-	179.1696	404.7286	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Cervix	TCGA-EK-A2R9-01A	ENSG00000008952	ENSG00000163584	SEC62	RPL22L1	CTGTTTTGTAGCCAGTATTCTTCTCCTTGCTGTTG*AAAGACAGGAAGCCCAAGAGGTCAACCTGGAGGTT	ribosomal,oncogene,18cancers,m17,exon-exon	BOWTIE	out-of-frame	0	45	1	13	3	169988359	+	3	170868387	-	179.1696	404.7286	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Cervix	TCGA-EK-A2R9-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	GCCTGCCTCAGCCTCCAAAGTAGCTGAGACTACAG*CAGTTTAAGTATAGTGTGCCTGGGTTGGGTGCGGT	antisense,m2,exon-exon	BOWTIE	exonic(no-known-CDS)/UTR	0	11	5	24	10	87246115	-	10	46593287	+	1.0414	0.2351	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-EK-A2R9-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	GGAGCTTCTCAGAAGACAGAGGGTTTTCTTTTGAG*CAGTTTAAGTATAGTGTGCCTGGGTTGGGTGCGGT	antisense,m2,exon-exon	BOWTIE	exonic(no-known-CDS)/UTR	0	11	2	23	10	87288442	-	10	46593287	+	1.0414	0.2351	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-EK-A2R9-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	GCCTGCCTCAGCCTCCAAAGTAGCTGAGACTACAG*ATTCCAGTTCTTTGATGAAAGTCTCTATTCCACCC	antisense,m2,exon-exon	BOWTIE	exonic(no-known-CDS)/UTR	0	11	2	19	10	87246115	-	10	46593989	+	1.0414	0.2351	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-EK-A2R9-01A	ENSG00000215241	ENSG00000226711	LINC02449	FAM66C	TCCTGAGACAACGGAATTCTGGCGATGGAGCACAG*ATATAATACGTAAGTTTGGAGGTGGATGCTTTCAG	lincrna,antisense,m2,10K<gap<100K,exon-exon	BOWTIE	exonic(no-known-CDS)/exonic(no-known-CDS)	0	6	2	24	12	8235999	+	12	8215806	+	0.4427	0.4772	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-EK-A2R9-01A	ENSG00000215241	ENSG00000226711	LINC02449	FAM66C	ATTCCAGCAGGATCAATGAAGAGAATTCACCAGAGGAACTAGTTCCAAAG*ATATAATACGTAAGTTTGGAGGTGGATGCTTTCAGCCATTAAGTTCAAAA	lincrna,antisense,m2,10K<gap<100K	BOWTIE+STAR	intronic/exonic(no-known-CDS)	0	6	1	17	12	8238252	+	12	8215806	+	0.4427	0.4772	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-EK-A2R9-01A	ENSG00000008952	ENSG00000085276	SEC62	MECOM	CTGTTTTGTAGCCAGTATTCTTCTCCTTGCTGTTG*ATAATGAGTGTGTATATGGCAACTACCCTGAAATA	oncogene,cancer,tumor,exon-exon	BOWTIE	in-frame	0	2	4	22	3	169988359	+	3	169381524	-	179.1696	32.6764	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Cervix	TCGA-EK-A2R9-01A	ENSG00000008952	ENSG00000085276	SEC62	MECOM	CAGTGTGGGTGCAGGCTGTTTTGTAGCCAGTATTCTTCTCCTTGCTGTTG*AATCATGGATGCTGCCAATTTTGAGCAGTTTTTGCAAGAAAGGATCAAAG	oncogene,cancer,tumor	BOWTIE+BLAT	CDS(truncated)/intronic	0	2	2	17	3	169988359	+	3	169483962	-	179.1696	32.6764	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Cervix	TCGA-C5-A1MQ-01A	ENSG00000197111	ENSG00000135409	PCBP2	AMHR2	AGACTACTTCTCATGAACTCACCATTCCAAACGAT*ACAGCAGTCCACCACCCTTCCAACTGGCCTATGAG	18cancers,m249,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	459	22	24	12	53468832	+	12	53430146	+	25.2496	16.0654	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Cervix	TCGA-C5-A1MQ-01A	ENSG00000197111	ENSG00000135409	PCBP2	AMHR2	AGACTACTTCTCATGAACTCACCATTCCAAACGAT*GACCCTGATGGGCTGAGGGAGCTCCTAGAAGACTG	18cancers,m249,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	459	20	24	12	53468832	+	12	53431177	+	25.2496	16.0654	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Cervix	TCGA-C5-A1MQ-01A	ENSG00000197111	ENSG00000135409	PCBP2	AMHR2	AGACTACTTCTCATGAACTCACCATTCCAAACGAT*CAGTCCACCACCCTTCCAACTGGCCTATGAGGCAG	18cancers,m249,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	459	2	24	12	53468832	+	12	53430150	+	25.2496	16.0654	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Cervix	TCGA-C5-A1MQ-01A	ENSG00000197111	ENSG00000135409	PCBP2	AMHR2	GCCTGGCATGGTGTTGCATCTCTGTAATCCCAGCTATTTGGGAGGCTAAG*GACCCTGATGGGCTGAGGGAGCTCCTAGAAGACTGTTGGGATGCAGACCC	18cancers,m249,tcga-cancer,10K<gap<100K	BOWTIE+STAR	intronic/CDS(truncated)	0	459	1	15	12	53469629	+	12	53431177	+	25.2496	16.0654	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Cervix	TCGA-C5-A1MQ-01A	ENSG00000216331	ENSG00000183166	HIST1H1PS1	CALN1	GGTTGCAAGTCCGAAGTTGCAGTGAAGTGCAAGATGTCCAGGCCCCTCCG*TTTGACATGCAAAGGATAACTCTGGAAGAGTTGAAGCACATTCTCTATCA	pseudogene	BOWTIE+STAR	exonic(no-known-CDS)/CDS(truncated)	0	2	3	22	6	26195683	+	7	71810492	-	0.0445	0.3452	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	unprocessed_pseudogene	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Cervix	TCGA-FU-A3HZ-01A	ENSG00000166272	ENSG00000107882	WBP1L	SUFU	CCAGCCCCTTGTCAGCCAGGGCTGAACCCCCGCAG*GAGCCGCAAAGACAGCCTGGAAAGTGACAGCTCCA	known,tcga,prostates,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	15	2	16	10	102744143	+	10	102615268	+	7.8462	7.3978	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Cervix	TCGA-IR-A3LK-01A	ENSG00000137812	ENSG00000166035	KNL1	LIPC	TGCGCAAAATTTGTCGAGGAGGTTTGCCGCGGCAG*GGGCAAAGGAATTGCTAGTAATAAAACGTATTCCT	chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	386	11	24	15	40594392	+	15	58563505	+	3.4667	6.6476	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Cervix	TCGA-IR-A3LK-01A	ENSG00000137812	ENSG00000166035	KNL1	LIPC	GACCCCAAACAAGTCTGCGCAAAATTTGTCGAGGAGGTTTGCCGCGGCAG*TTCAAGATCCAGTTCATCAACCAAACTGAGACACCAATACAAACAACTTT	chimerdb3seq,cancer,tcga-cancer	BOWTIE+BLAT	UTR/CDS(truncated)	0	386	2	19	15	40594392	+	15	58560878	+	3.4667	6.6476	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Cervix	TCGA-IR-A3LK-01A	ENSG00000137812	ENSG00000166035	KNL1	LIPC	TGCGCAAAATTTGTCGAGGAGGTTTGCCGCGGCAG*AATGACATTTTGTTCAGAAAACACAGATGACCTAC	chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	386	2	15	15	40594392	+	15	58568716	+	3.4667	6.6476	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Cervix	TCGA-IR-A3LK-01A	ENSG00000177380	ENSG00000182264	PPFIA3	IZUMO1	CCCAGCTCCGCCCGCAGCCGCCGCGGACCAGGCAG*ATGAGGCCACACTGCAAAAGGGGTCCTGGAGTTTG	tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	3	4	21	19	49119722	+	19	48745288	-	4.9643	0.9432	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-LN-A49S-01A	ENSG00000130024	ENSG00000080839	PHF10	RBL1	GGGAACGCATGGAAGAAAGAAGAGCTTATTTTGACTTGCAGACACAT*GTTATATTCCCAAATAACTTTGAAACAGGAAATGGAGGAAATGTGCA	cancer,tumor,m3,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	4	7	30	6	169715708	-	20	37040285	-	15.1308	9.0047	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49S-01A	ENSG00000130024	ENSG00000080839	PHF10	RBL1	TACCCAGTGGCTCTCATCCCCGGACAGTTCCAGGAATATTATAAGAG*GTTATATTCCCAAATAACTTTGAAACAGGAAATGGAGGAAATGTGCA	cancer,tumor,m3,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	4	3	28	6	169714733	-	20	37040285	-	15.1308	9.0047	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OH-01A	ENSG00000121067	ENSG00000259753	SPOP	AC068234.1	TTCAAGCGATTCTTCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAG*ATTTGAAACATCAATAATCTTTTGTGGAGAAGAAAAGTCCTCTGATT	cancer,exon-exon	BOWTIE	UTR/UTR	0	4	2	24	17	49675895	-	17	47341921	+	5.1484	0	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OH-01A	ENSG00000121067	ENSG00000259753	SPOP	AC068234.1	GAGGCAAGCGCAGGGGGACGGGGACCAGCAGCTGTCGCCGCCGCTCTCAG*GGCCCAACATCTGTACCACGCGAGGTGTGAGCTCCTGCCAGCAGTGCCTG	cancer,exon-exon	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(no-known-start-or-end)	0	4	1	17	17	49677933	-	17	47274419	+	5.1484	0	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OH-01A	ENSG00000121067	ENSG00000259207	SPOP	ITGB3	GCAAGCGCAGGGGGACGGGGACCAGCAGCTGTCGCCGCCGCTCTCAG*GGCCCAACATCTGTACCACGCGAGGTGTGAGCTCCTGCCAGCAGTGC	chimerdb3seq,cancer,oesophagus,exon-exon	BOWTIE	UTR/CDS(truncated)	0	4	4	29	17	49677933	-	17	47274419	+	5.1484	2.723	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OH-01A	ENSG00000121067	ENSG00000259207	SPOP	ITGB3	TTCCTGTTAGACAAGACAAATTAGAGTTTTCCTACTGACTTAACTTG*GGCCCAACATCTGTACCACGCGAGGTGTGAGCTCCTGCCAGCAGTGC	chimerdb3seq,cancer,oesophagus,exon-exon	BOWTIE	UTR/CDS(truncated)	0	4	3	25	17	49636759	-	17	47274419	+	5.1484	2.723	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OH-01A	ENSG00000121067	ENSG00000259207	SPOP	ITGB3	TTCAAGCGATTCTTCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAG*GGCCCAACATCTGTACCACGCGAGGTGTGAGCTCCTGCCAGCAGTGC	chimerdb3seq,cancer,oesophagus,exon-exon	BOWTIE	UTR/CDS(truncated)	0	4	2	23	17	49675895	-	17	47274419	+	5.1484	2.723	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OH-01A	ENSG00000086062	ENSG00000161013	B4GALT1	MGAT4B	GATTTCTTGGTCTGCAGAGGGTAGGAGCAAGCCTTGAAGGCTGCTGGAGT*GGTAAGATGTTCAAGTCGCTGGACCTGAGCCTGATTGTAGAGTTCATTCT	NA	BOWTIE+STAR	intronic/UTR	0	2	1	16	9	33158296	-	5	179799637	-	105.7527	337.1277	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OH-01A	ENSG00000086062	ENSG00000161013	B4GALT1	MGAT4B	ACTTTGCGGCTTGGCCTCAGCCCGCCCCTTCCCTGCACAAATGAAGGCCA*GCAGGGAGAAAGGAAGTAGGCAGAGCAGCACTGCCCACTCAGGCCCCTCC	NA	BOWTIE+STAR	intronic/UTR	0	2	1	15	9	33161180	-	5	179799693	-	105.7527	337.1277	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OH-01A	ENSG00000086062	ENSG00000161013	B4GALT1	MGAT4B	AGGGCGCCTTGGCTCGGCTTGAGGCCTGTCATGAAGCCCTCAGCCCTCTG*GAAGCACTGTGACCGGCAGAAAGCCAACCTGCGGATCCGCTTCAAACCGT	NA	BOWTIE+STAR	intronic/intronic	0	2	1	15	9	33139774	-	5	179799311	-	105.7527	337.1277	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OH-01A	ENSG00000086062	ENSG00000161013	B4GALT1	MGAT4B	AGGTTTTCATCTGCCTTGGGGCAGAGTCAAGAGAAAGAAGAGGAAGAGGC*TCAAGAGGGCCGTGTCAGAAAGGCAGGCGCTGCGAGACGGAGACGGCAAT	NA	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	15	9	33155689	-	5	179801855	-	105.7527	337.1277	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OH-01A	ENSG00000086062	ENSG00000161013	B4GALT1	MGAT4B	GCTTCTTCCCCCGTCATGTTTATCTCTGCTCAGATTGGGCAGCAGCTCAA*CAGACAAGGAGGCCCTGCAGGAGGGCCGCACCGCCACCCTCCGGTACCCT	NA	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	14	9	33163630	-	5	179798424	-	105.7527	337.1277	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OH-01A	ENSG00000086062	ENSG00000161013	B4GALT1	MGAT4B	CTCAACACAGTAGATTTCTGAATGTCCTCTGCCAGCTACATGCTCCTGCC*GCAGAGGTGAGCACGAGCCTGAAGACATACCAGCACTTCACCCTGGAGAA	NA	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	14	9	33132620	-	5	179799070	-	105.7527	337.1277	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OH-01A	ENSG00000086062	ENSG00000161013	B4GALT1	MGAT4B	AAACCTGGTCGCAGGTCTGCATGATTCTGAACAGAGGTAGTCGTTGCCTT*TGGAGGATGACATCGTGGCCAAGCCCAACTACCTGAGCACCATGAAGAAC	NA	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	14	9	33139680	-	5	179800067	-	105.7527	337.1277	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OH-01A	ENSG00000086062	ENSG00000161013	B4GALT1	MGAT4B	ATGAATTTGTGTTGAGCTGCATTCAAAGCCATCCTGGCCGCATGTGGCCC*CCCTGGGTCCGGCTCTTCCAGATCTTCCTGAAAAAGGCCGACTAAGCTGC	NA	BOWTIE+STAR	intronic/intronic	0	2	1	14	9	33154767	-	5	179798089	-	105.7527	337.1277	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OH-01A	ENSG00000086062	ENSG00000161013	B4GALT1	MGAT4B	TATACATCCTAGATATTAATCCCTTCCTGGTCTCAGACATTGCAGATATC*CGGGACGCGGGGTTGGGGGACATTCAGAGGAGCCCCCGCGGTGCAGAACT	NA	BOWTIE+STAR	intronic/intronic	0	2	1	14	9	33148079	-	5	179801323	-	105.7527	337.1277	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OH-01A	ENSG00000161013	ENSG00000086062	MGAT4B	B4GALT1	TGGCTCTCTAGGCCTCTGCACCTCCAGTCCCATCCCTGTGGGCGAGTGCT*CACCCACAGGGCTGTCTGTCACAAACCCACCTCTGTTGGGAGCTATTGAG	NA	BOWTIE+STAR	UTR/UTR	0	2	1	14	5	179803441	-	9	33111857	-	337.1277	105.7527	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OE-01A	ENSG00000109756	ENSG00000163694	RAPGEF2	RBM47	AAACTATCAGATTATTTACTAATTTGGGGAGTTGAATATAATGTTTCCAA*GACTCTTTTCAGCAGAAAGTTATGCTTCTAGTTGCCTTACCATGTTTCTT	chimerdb3seq,oesophagus	BOWTIE+STAR	intronic/UTR	0	3	1	18	4	159148500	+	4	40424770	-	7.2601	66.7794	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OE-01A	ENSG00000109756	ENSG00000163694	RAPGEF2	RBM47	TCCTTTCTCCCACACCTCCTCTAGGCAACTCTGCCTCAAGTTTGCTTTCT*TAATATATCAACTATATATTAAAAAAGCACACTTGAGGAGCTAGGGAACT	chimerdb3seq,oesophagus	BOWTIE+STAR	intronic/UTR	0	3	1	17	4	159197832	+	4	40425525	-	7.2601	66.7794	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OE-01A	ENSG00000109756	ENSG00000163694	RAPGEF2	RBM47	TGGGTATGTATTTTTACTTTGGTTGTTTGAACATGAGTATTGTTCCTTGT*CCAGGGGCGGCGGCGCGGCTGAGGCAGCGCAGCAGCCCAGCTACGTGTAC	chimerdb3seq,oesophagus	BOWTIE+STAR	intronic/CDS(truncated)	0	3	1	16	4	159213764	+	4	40437902	-	7.2601	66.7794	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OE-01A	ENSG00000109756	ENSG00000163694	RAPGEF2	RBM47	GGTTAAAGAAACCCAGATACCATTAATGTTACCATCTTAACATTTTTATG*AATTTTCCACTCACGGGATTTTTGTTGATGGCTGAATTCTTGTGGATTCA	chimerdb3seq,oesophagus	BOWTIE+STAR	intronic/UTR	0	3	1	16	4	159249878	+	4	40424230	-	7.2601	66.7794	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OE-01A	ENSG00000109756	ENSG00000163694	RAPGEF2	RBM47	TTATAAAGATAATAGGCTAAGATCTTCTTAATATTCTTAACATTTGGCTA*TACTTTTGTTTTGTTTTAAATTAAGAGATTCCCAAATGCCTTTTTCCCCC	chimerdb3seq,oesophagus	BOWTIE+STAR	intronic/UTR	0	3	1	15	4	159128546	+	4	40424156	-	7.2601	66.7794	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OE-01A	ENSG00000109756	ENSG00000163694	RAPGEF2	RBM47	GATCCTTATCCCATGGGCAAACCTCCTTTGCCTAGAGGCTATCACACGGT*CACTGCAGTTTTGTGCTCTTTTGTCTTAATTTCAAGAAGTAGCTTTGGTA	chimerdb3seq,oesophagus	BOWTIE+STAR	intronic/intronic	0	3	1	15	4	159241370	+	4	40563789	-	7.2601	66.7794	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OE-01A	ENSG00000109756	ENSG00000163694	RAPGEF2	RBM47	TGAGCCACCATGCCTGGCCGGGAATACAGTCATTCTGTACTATTTAACAA*ACTGGATCTCTCCTTAAGCCAACATTGAAAAGACTTGCCGCACTTCTGAG	chimerdb3seq,oesophagus	BOWTIE+STAR	intronic/UTR	0	3	1	14	4	159181869	+	4	40425279	-	7.2601	66.7794	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OE-01A	ENSG00000109756	ENSG00000163694	RAPGEF2	RBM47	TTGACAAATAGGATCTAATTAAACTAAAGAGCCTCTGCACAGCAAAAAAA*AGGAGGAGGAGAGACCTGTAGAAGTTTAAAGATAGTTTGTAAATATCTTC	chimerdb3seq,oesophagus	BOWTIE+STAR	intronic/UTR	0	3	1	14	4	159116127	+	4	40424606	-	7.2601	66.7794	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OE-01A	ENSG00000109756	ENSG00000163694	RAPGEF2	RBM47	AGAAAGATATTTAATTGGACTCACAGTGCCACCTGGCTGGGGAAACCTCA*CCTGGCCGCATCCAGCTGTGGGGCCACCAGATCGCCGTGGACTGGGCCGA	chimerdb3seq,oesophagus	BOWTIE+STAR	intronic/CDS(truncated)	0	3	1	14	4	159257312	+	4	40438248	-	7.2601	66.7794	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OE-01A	ENSG00000109756	ENSG00000163694	RAPGEF2	RBM47	TCCCCACGTTTATTTCTTTTCAAGAGAAAGTTGTTCGAAATGTGAACGTT*TTTTTTTTTTTTTAGTGTTAAGAACAAACTATATAAATGTAAAAAAAAAG	chimerdb3seq,oesophagus	BOWTIE+STAR	intronic/UTR	0	3	1	14	4	159106349	+	4	40423471	-	7.2601	66.7794	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OE-01A	ENSG00000163694	ENSG00000109756	RBM47	RAPGEF2	AAAACATCTCAGAAAGAGCCAGTCTGAGAAGCAGTGTGCAATGGCCTCAG*CTTCCTGCAGATTTCACAAAACTGCATCTTACTGACAGTCTCCACCCACA	chimerdb3seq,oesophagus	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	intronic/CDS(truncated)	0	3	3	36	4	40594258	-	4	159304342	+	66.7794	7.2601	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OE-01A	ENSG00000163694	ENSG00000109756	RBM47	RAPGEF2	GGTGTTAATTTCTGAAGTGGGCGGCTCCAAAAACTTAACAAGGAAAG*CTTCCTGCAGATTTCACAAAACTGCATCTTACTGACAGTCTCCACCC	chimerdb3seq,oesophagus,exon-exon	BOWTIE	UTR/CDS(truncated)	0	3	3	29	4	40629396	-	4	159304342	+	66.7794	7.2601	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OE-01A	ENSG00000163694	ENSG00000109756	RBM47	RAPGEF2	CACTACTGAGGTAAGTTTATAACTTGAAATGTGAACTTTTTTTTTTTTTA*TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT	chimerdb3seq,oesophagus	BOWTIE+STAR	UTR/intronic	0	3	1	35	4	40423458	-	4	159273627	+	66.7794	7.2601	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OE-01A	ENSG00000163694	ENSG00000109756	RBM47	RAPGEF2	AAAGAAAAGAAAGAAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG*AAAAAAAAAAAAAAAAAGAAAGAAAAACCATAGGTTTTAGAGAAACATAC	chimerdb3seq,oesophagus	BOWTIE+STAR	UTR/intronic	0	3	1	23	4	40423680	-	4	159337897	+	66.7794	7.2601	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OE-01A	ENSG00000163694	ENSG00000109756	RBM47	RAPGEF2	GACCTCAAGTGATCTGCCCACCTTGGCCTCCTCAAGTGCTGGGATTACAG*CTTCCTGCAGATTTCACAAAACTGCATCTTACTGACAGTCTCCACCCACA	chimerdb3seq,oesophagus	BOWTIE+STAR	intronic/CDS(truncated)	0	3	1	21	4	40598995	-	4	159304342	+	66.7794	7.2601	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OE-01A	ENSG00000163694	ENSG00000109756	RBM47	RAPGEF2	ATCTTCTAATGCTTGTTTTTAGTCCTTTTATGTTGGAGAAGTTCATGGTA*CTTCTTTAAAGATAGTTTAGCATTTCCTCATTTGAACTATTTTTTGGGGG	chimerdb3seq,oesophagus	BOWTIE+STAR	UTR/intronic	0	3	1	18	4	40424513	-	4	159332891	+	66.7794	7.2601	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OE-01A	ENSG00000163694	ENSG00000109756	RBM47	RAPGEF2	TTATTTTAAAGGTTATACTGGAAAGTGCAATTTTAAAATGAGTAAAACCT*TTTGCATAATGCTTTATATTACCAGAATTCTTTCACATCTGTTTTCCATT	chimerdb3seq,oesophagus	BOWTIE+STAR	UTR/intronic	0	3	1	17	4	40425360	-	4	159287940	+	66.7794	7.2601	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OE-01A	ENSG00000163694	ENSG00000109756	RBM47	RAPGEF2	TGTACACTACTGAGGTAAGTTTATAACTTGAAATGTGAACTTTTTTTTTT*ATATATTTTATTCTTAATAAAGAACACTTATATGCCATTGTGATGAGATT	chimerdb3seq,oesophagus	BOWTIE+STAR	UTR/intronic	0	3	1	16	4	40423462	-	4	159323641	+	66.7794	7.2601	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OE-01A	ENSG00000163694	ENSG00000109756	RBM47	RAPGEF2	TGTAGTTTAATGCAAAATGAAACCATTTTATTTCAATGTTATTAAAAAGG*ACTTAAAATAAGCATTTATAGACATTTTTATATACTCCTCGTAGGATTGT	chimerdb3seq,oesophagus	BOWTIE+STAR	UTR/intronic	0	3	1	16	4	40424463	-	4	159310244	+	66.7794	7.2601	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OE-01A	ENSG00000163694	ENSG00000109756	RBM47	RAPGEF2	CTAGTGAAGGATTGTCACAGAGTTTCACTGGATGAAACTATGACCCAGTA*AAATGTGAAGATTATACTAAATGAATCCTCAAGCTCTTCCAGGTCTATGA	chimerdb3seq,oesophagus	BOWTIE+STAR	UTR/intronic	0	3	1	15	4	40423790	-	4	159287866	+	66.7794	7.2601	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OE-01A	ENSG00000163694	ENSG00000109756	RBM47	RAPGEF2	TCCCCCAATCTCTGCCATCAAGGCCGATTTTCTTTGAACCTTCAGCAAAG*CTTCCTGCAGATTTCACAAAACTGCATCTTACTGACAGTCTCCACCCACA	chimerdb3seq,oesophagus,exon-exon	BOWTIE+STAR	UTR/CDS(truncated)	0	3	1	15	4	40630108	-	4	159304342	+	66.7794	7.2601	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OE-01A	ENSG00000163694	ENSG00000109756	RBM47	RAPGEF2	AAGAAAGAAAGAAAAAGAAAGAAAGAATAAAAAAAAATGATAACATGGCA*CCAGTGTTTGTTTTTATTTATTTTACATAATGCCTAAGAATTTTTCTGCC	chimerdb3seq,oesophagus	BOWTIE+STAR	UTR/intronic	0	3	1	15	4	40423617	-	4	159352981	+	66.7794	7.2601	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OE-01A	ENSG00000163694	ENSG00000109756	RBM47	RAPGEF2	CGCGTGACGCTCCTGCCTGCGCGCGGCCAAGCCATGCTCGGCCCCAG*CTTCCTGCAGATTTCACAAAACTGCATCTTACTGACAGTCTCCACCC	chimerdb3seq,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	UTR/CDS(truncated)	0	3	1	14	4	40630463	-	4	159304342	+	66.7794	7.2601	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OE-01A	ENSG00000163694	ENSG00000109756	RBM47	RAPGEF2	ATTCTTGTGGATTCATAAGAGGATCATGCCCTTAGCAAGTACTTTTGTTT*AAAACAAAACAAAAAATACCACCACCATCACCACACACACACACACACAC	chimerdb3seq,oesophagus	BOWTIE+STAR	UTR/intronic	0	3	1	14	4	40424146	-	4	159340749	+	66.7794	7.2601	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OE-01A	ENSG00000163694	ENSG00000109756	RBM47	RAPGEF2	CATGTTAGAGATCCATACAATTTTCCACTCACGGGATTTTTGTTGATGGC*CTGTTCCTCTTATGAACTGCTGCTTCTACTTAAAATCTATTGATTATGCG	chimerdb3seq,oesophagus	BOWTIE+STAR	UTR/UTR	0	3	1	14	4	40424199	-	4	159328521	+	66.7794	7.2601	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OE-01A	ENSG00000163694	ENSG00000109756	RBM47	RAPGEF2	CTGTCCCCTCCTCCCCAGATTCCCAATCCCACCGCAATGTTTGGCAAGCC*GGGGCTTCTTCTCCCCTTCTTCCTTTCCCCTTTGCATGTGAAATACTGTG	chimerdb3seq,oesophagus	BOWTIE+STAR	UTR/UTR	0	3	1	14	4	40425083	-	4	159358277	+	66.7794	7.2601	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OE-01A	ENSG00000163694	ENSG00000109756	RBM47	RAPGEF2	TTTTGAAAAATATATACAATATTTAAAGATACAAACAGTAGTGCTTAAAA*CCTTGTATATATTTCTCAGATCTGTGTTTCCCTGATGGCCTTGGGTTTAA	chimerdb3seq,oesophagus	BOWTIE+STAR	UTR/intronic	0	3	1	14	4	40425425	-	4	159300809	+	66.7794	7.2601	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OE-01A	ENSG00000163694	ENSG00000109756	RBM47	RAPGEF2	ATTCTTGTGGATTCATAAGAGGATCATGCCCTTAGCAAGTACTTTTGTTT*AAAACAAAACAAAAAATACCACCACCATCACCACACACACACACACACAC	chimerdb3seq,oesophagus	BOWTIE+STAR	UTR/intronic	0	3	1	14	4	40424146	-	4	159340637	+	66.7794	7.2601	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000113732	ENSG00000113719	ATP6V0E1	ERGIC1	GTCGGCTTCTTGGTGCCTTGGTTCATCCCTAAGGGTCCTAACCGGGG*GTTTGACATCTACAGGAAGGTGCCCAAGGACCTTACGCAGCCAACGT	oncogene,chimerdb3seq,tcga-cancer,oesophagus,10K<gap<100K,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	35	35	30	5	172983964	+	5	172888699	+	76.1356	18.8521	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000260083	ENSG00000168734	MIR762HG	PKIG	CGCCATTACCAACTGCAAATCCACAGGCAAATGCAAGAGGACAGAAA*AATTCCCGTACTGATTAGTCAACAGTGGAAAATCTGAAGAGATGCAA	antisense,cancer,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	exonic(no-known-CDS)/UTR	0	35	23	29	16	30876118	+	20	44589797	+	1.4094	9.6685	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000260083	ENSG00000168734	MIR762HG	PKIG	CGCCATTACCAACTGCAAATCCACAGGCAAATGCAAGAGGACAGAAA*GAGACACGGGGAAGAGACAGAGAGGAGGGTAAAGTGAGAATCCTGCC	antisense,cancer,exon-exon	BOWTIE;BOWTIE+STAR	exonic(no-known-CDS)/UTR	0	35	13	30	16	30876118	+	20	44582585	+	1.4094	9.6685	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000260083	ENSG00000168734	MIR762HG	PKIG	GAACGCCATTACCAACTGCAAATCCACAGGCAAATGCAAGAGGACAGAAA*GTCTGGACTGCTAACCTTGAATCCTGGTTTCTTAAATTCTGCCTCCGCTT	antisense,cancer	BOWTIE+BLAT;BOWTIE+STAR	exonic(no-known-CDS)/UTR	0	35	1	26	16	30876118	+	20	44582642	+	1.4094	9.6685	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000260083	ENSG00000168734	MIR762HG	PKIG	GAACGCCATTACCAACTGCAAATCCACAGGCAAATGCAAGAGGACAGAAA*GTGGTGGTGAGGAGGTGATGTTCTGGAAGGAAGGTACCTAGACTTTGTGG	antisense,cancer,exon-exon	BOWTIE+STAR	exonic(no-known-CDS)/UTR	0	35	1	18	16	30876118	+	20	44585100	+	1.4094	9.6685	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000099814	ENSG00000127423	CEP170B	AUNIP	ACCAAGCCGGGGACTAAGGCGAGCCGGAGACCGAGCCCGAACAGCAG*ACACATTTAATCAAACCAGGCACCAAAATGCTAACACTCCTTCCTGG	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	30	32	30	14	104865513	+	1	25837554	-	10.899	18.4415	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000115760	ENSG00000115484	BIRC6	CCT4	GTACAATCACATCTAGCAGTCCTACTGCCCAACCAGCTGAAGTGCTATTG*AAACACTCGATAATCTGGATAACTGACTAGCACCATTATGATCACCAGTA	chimerdb3seq,cancer,tcga-cancer,oesophagus	BOWTIE+STAR	out-of-frame	0	24	1	14	2	32505054	+	2	61868704	-	6.3588	22.8277	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000115484	ENSG00000115760	CCT4	BIRC6	CATTGCTGGCTCCCTCTTAGATTCTTGTACCAAGCTTCTTCAGAAAG*ATCATGGAGACTTACTTGCTAGCTGTCCAGAAGATGAGGCTCTCACT	chimerdb3seq,cancer,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	24	24	29	2	61880286	-	2	32531355	+	22.8277	6.3588	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000176095	ENSG00000182179	IP6K1	UBA7	CCAGCTCCCGTAGGGAGCCGTGGGCGCTCGGTGCCCGGGCCGGGCAG*GGCGCTATGTGGCTGCTCGTTGCACCCACTATCTGAAGCCACTGCTG	chimerdb3seq,cancer,tcga-cancer,oesophagus,10K<gap<100K,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	19	17	29	3	49786354	-	3	49810183	-	16.1692	15.7363	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000176095	ENSG00000182179	IP6K1	UBA7	TGTGTTAGCCAGGATGGTTTCGATCTCTTGACCTCAGGCAATCCATCCAC*CAGTCGCCCTAAGCAGTGCAGGTGTCTTGAGCCCTATGGTGGCCATGCTG	chimerdb3seq,cancer,tcga-cancer,oesophagus,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	19	9	37	3	49777331	-	3	49811352	-	16.1692	15.7363	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000176095	ENSG00000182179	IP6K1	UBA7	CCAGCTCCCGTAGGGAGCCGTGGGCGCTCGGTGCCCGGGCCGGGCAG*TGGGCCCGGCATGAGTTTGAAGAACTCTTCCGACTGTCTGCAGAGAC	chimerdb3seq,cancer,tcga-cancer,oesophagus,10K<gap<100K,exon-exon	BOWTIE;BOWTIE+STAR	UTR/CDS(truncated)	0	19	9	30	3	49786354	-	3	49809879	-	16.1692	15.7363	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000176095	ENSG00000182179	IP6K1	UBA7	CCTCCACCTCCCGGGTTCAAGCGATTATCCTGCCTCAGCCTCCCGAGTAG*GGCGCTATGTGGCTGCTCGTTGCACCCACTATCTGAAGCCACTGCTGGAG	chimerdb3seq,cancer,tcga-cancer,oesophagus,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	19	3	36	3	49785393	-	3	49810183	-	16.1692	15.7363	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000176095	ENSG00000182179	IP6K1	UBA7	ACTTTTTGGAGAGTGGTAATGTCTTCCTCTTTTTGCTTTAGGAGAAA*GCAATCTCCAGGAAGTTCATGCCTCTGGACCAGTGGCTTTACTTTGA	chimerdb3seq,cancer,tcga-cancer,oesophagus,10K<gap<100K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	19	3	26	3	49785670	-	3	49811091	-	16.1692	15.7363	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000176095	ENSG00000182179	IP6K1	UBA7	CCAGCTCCCGTAGGGAGCCGTGGGCGCTCGGTGCCCGGGCCGGGCAG*GCAATCTCCAGGAAGTTCATGCCTCTGGACCAGTGGCTTTACTTTGA	chimerdb3seq,cancer,tcga-cancer,oesophagus,10K<gap<100K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	19	3	20	3	49786354	-	3	49811091	-	16.1692	15.7363	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000176095	ENSG00000182179	IP6K1	UBA7	CCAGCTCCCGTAGGGAGCCGTGGGCGCTCGGTGCCCGGGCCGGGCAG*GTGGGCGCTGGTGCCATTGGTTGTGAGCTGCTCAAAGTCTTTGCCCT	chimerdb3seq,cancer,tcga-cancer,oesophagus,10K<gap<100K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	19	2	29	3	49786354	-	3	49810672	-	16.1692	15.7363	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000176095	ENSG00000182179	IP6K1	UBA7	CCAGCTCCCGTAGGGAGCCGTGGGCGCTCGGTGCCCGGGCCGGGCAG*AGAGGCAGCCGCTATGATGGGCAAATTGCAGTGTTTGGGGCTGGTTT	chimerdb3seq,cancer,tcga-cancer,oesophagus,10K<gap<100K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	19	2	24	3	49786354	-	3	49810832	-	16.1692	15.7363	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000176095	ENSG00000182179	IP6K1	UBA7	CCTCCACCTCCCGGGTTCAAGCGATTATCCTGCCTCAGCCTCCCGAGTAG*TGGGCCCGGCATGAGTTTGAAGAACTCTTCCGACTGTCTGCAGAGACCAT	chimerdb3seq,cancer,tcga-cancer,oesophagus,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	19	2	21	3	49785393	-	3	49809879	-	16.1692	15.7363	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000176095	ENSG00000182179	IP6K1	UBA7	ACTTTTTGGAGAGTGGTAATGTCTTCCTCTTTTTGCTTTAGGAGAAA*GGCGCTATGTGGCTGCTCGTTGCACCCACTATCTGAAGCCACTGCTG	chimerdb3seq,cancer,tcga-cancer,oesophagus,10K<gap<100K,exon-exon	BOWTIE;BOWTIE+STAR	UTR/CDS(truncated)	0	19	1	14	3	49785670	-	3	49810183	-	16.1692	15.7363	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000166689	ENSG00000006611	PLEKHA7	USH1C	GGCTGGGAGGAGGGCTTCACGGAGGAGGGCGCCAGCTACTTCATCGA*GATTTCCGGAAATATGAGGAAGGCTTTGACCCCTACTCTATGTTCAC	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE	out-of-frame	0	19	15	29	11	17013989	-	11	17501980	-	2.2714	18.2789	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000166689	ENSG00000006611	PLEKHA7	USH1C	GACAGGGCTGGCCAGTCCTTGCAGAACATTATAACCGCCAGAGACCTCAG*GATTTCCGGAAATATGAGGAAGGCTTTGACCCCTACTCTATGGTAAGAGA	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	19	5	34	11	16956807	-	11	17501980	-	2.2714	18.2789	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000166689	ENSG00000006611	PLEKHA7	USH1C	GACAGGGCTGGCCAGTCCTTGCAGAACATTATAACCGCCAGAGACCTCAG*AAAGGAAAAGATAAGAAGAAAGCCAAGTATGGCAGCCTGCAGGACTTGAG	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	intronic/CDS(truncated)	0	19	2	32	11	16956807	-	11	17512054	-	2.2714	18.2789	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000166689	ENSG00000006611	PLEKHA7	USH1C	GGGCTGGGCACGCCTCCCCTCTAGGGTCTGGGGCTGCGCCCCGCCGGGAG*AGGATTTCCGGAAATATGAGGAAGGCTTTGACCCCTACTCTATGGTAAGA	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/UTR	0	19	2	28	11	17013654	-	11	17501982	-	2.2714	18.2789	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000166689	ENSG00000006611	PLEKHA7	USH1C	GGCTGGAATGTGGTGCACAAGGGAGAAAGTGGCATGAGGAGAGGTCACAG*GATTTCCGGAAATATGAGGAAGGCTTTGACCCCTACTCTATGGTAAGAGA	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	19	2	25	11	17012296	-	11	17501980	-	2.2714	18.2789	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000166689	ENSG00000006611	PLEKHA7	USH1C	GGCTGGGAGGAGGGCTTCACGGAGGAGGGCGCCAGCTACTTCATCGA*GACCTTCTTCTGAAGTCCAAAAGGGGAAACCAAATTCACCGTTAG	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE	in-frame	0	19	2	24	11	17013989	-	11	17494376	-	2.2714	18.2789	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000166689	ENSG00000006611	PLEKHA7	USH1C	AGGTCCAGAGATGGGAAGTGGGTTTCCTAGCAGGGATAGGGTAAGCAAAG*GATTTCCGGAAATATGAGGAAGGCTTTGACCCCTACTCTATGGTAAGAGA	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	19	1	35	11	16987530	-	11	17501980	-	2.2714	18.2789	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000166689	ENSG00000006611	PLEKHA7	USH1C	ATCCAGGACTATGAGGATTTCCCTTTATCCCTGTCACAGACCTGGATTAG*GATTTCCGGAAATATGAGGAAGGCTTTGACCCCTACTCTATGGTAAGAGA	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	19	1	30	11	16956624	-	11	17501980	-	2.2714	18.2789	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000166689	ENSG00000006611	PLEKHA7	USH1C	GCTGGGCACGCCTCCCCTCTAGGGTCTGGGGCTGCGCCCCGCCGGGAGAG*CCACAGGAGATGTTGAAGAGGATGGTGGTTTATCAGACAGCATTCAGACA	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+BLAT;BOWTIE+BOWTIE2	intronic/CDS(truncated)	0	19	1	28	11	17013652	-	11	17504697	-	2.2714	18.2789	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000166689	ENSG00000006611	PLEKHA7	USH1C	AAGGGCTTCACAGACACAGCCTCCTTTAATCCTCATGCCAACCTTATAAG*GATTTCCGGAAATATGAGGAAGGCTTTGACCCCTACTCTATGGTAAGAGA	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	19	1	28	11	16998092	-	11	17501980	-	2.2714	18.2789	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000166689	ENSG00000006611	PLEKHA7	USH1C	CGCGGCTGGGAGGAGGGCTTCACGGAGGAGGGCGCCAGCTACTTCATCGA*CTAAAGGGCCAACCTGCGCTCCGCAGAATCTGGGGAGGCCTCTTACCTTC	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/intronic	0	19	1	22	11	17013989	-	11	17502624	-	2.2714	18.2789	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000166689	ENSG00000006611	PLEKHA7	USH1C	GGCTGGAATGTGGTGCACAAGGGAGAAAGTGGCATGAGGAGAGGTCACAG*AAAGGAAAAGATAAGAAGAAAGCCAAGTATGGCAGCCTGCAGGACTTGAG	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	intronic/CDS(truncated)	0	19	1	22	11	17012296	-	11	17512054	-	2.2714	18.2789	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000166689	ENSG00000006611	PLEKHA7	USH1C	GTACCTACTATGTGCCAGCCACTGTGCTAGGGGCCAGAGACACAGGGCTG*CACACCAGATGGCATCCTTGGGACCTGAATCTATCACCCAGGAATCTCAA	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/UTR	0	19	1	16	11	16940165	-	11	17494260	-	2.2714	18.2789	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000131626	ENSG00000166435	PPFIA1	XRRA1	ATGAAAGAGATTCCTTGCAGAGACAGCTCAACACGGCACTTCCACAG*GTGAAAAGCGAAATCCCAAAGGTGCCGAAGCAGCCTCTGGTGCTCCA	chimerdb3seq,oesophagus,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	15	23	27	11	70272436	+	11	74848462	-	6.5943	2.7964	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000131626	ENSG00000166435	PPFIA1	XRRA1	ATGAAAGAGATTCCTTGCAGAGACAGCTCAACACGGCACTTCCACAG*GTGAGTGAACTGCCTTCCTCCGTCATCCATAAGGATGATTTAGAGTT	chimerdb3seq,oesophagus,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	15	5	29	11	70272436	+	11	74845271	-	6.5943	2.7964	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000131626	ENSG00000166435	PPFIA1	XRRA1	ATGAAAGAGATTCCTTGCAGAGACAGCTCAACACGGCACTTCCACAG*ATCGCAAAAGAGGATGCTGTCCTACCAGTAGCTCTCTTCCCATCTCT	chimerdb3seq,oesophagus,exon-exon	BOWTIE	in-frame	0	15	5	27	11	70272436	+	11	74852082	-	6.5943	2.7964	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000131626	ENSG00000166435	PPFIA1	XRRA1	ATGAAAGAGATTCCTTGCAGAGACAGCTCAACACGGCACTTCCACAG*GGGTCCCTCCACTGCTGAAGAGCTTCCTCCAGGAGCGACTGGGAATC	chimerdb3seq,oesophagus,exon-exon	BOWTIE	out-of-frame	0	15	2	29	11	70272436	+	11	74851203	-	6.5943	2.7964	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000128789	ENSG00000141447	PSMG2	OSBPL1A	CCTGCGGGGAGTCGGCCCCCGACCTTGCCGGCTTCACCCTCCTAATG*CTGTAGAAAGGACTCAACAAAGAAAGCTTGAAGAATTACTTTTAGCA	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	13	21	30	18	12703164	+	18	24334330	-	9.4953	9.6949	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000164327	ENSG00000113600	RICTOR	C9	GCGGAATGACAGCGGCGAGGAGAACGTCCCGCTGGATCTGACCCGAG*TTATGACCCAGAGCTAACAGAAAGCAGTGGCTCTGCATCACACATAG	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	12	14	30	5	39074111	-	5	39342196	-	3.8966	5.7389	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000164327	ENSG00000113600	RICTOR	C9	AGGGCGGAATGACAGCGGCGAGGAGAACGTCCCGCTGGATCTGACCCGAG*GTGGCTTCGTACACAGTGGTGAAAGGCTTTCAAGCAAATATCTTTAGATA	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+BLAT	CDS(truncated)/intronic	0	12	1	23	5	39074111	-	5	39357946	-	3.8966	5.7389	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000182095	ENSG00000075624	TNRC18	ACTB	GCCGCCCGGGAAGTACATGGCCGGCCTGAATCTCCATCCGCACCCGG*CTCACCATGGATGATGATATCGCCGCGCTCGTCGTCGACAACGGCTC	prostates,chimerdb3seq,cancer,oesophagus,100K<gap<200K,exon-exon	BOWTIE;BOWTIE+STAR	CDS(truncated)/CDS(no-known-start-or-end)	0	12	9	29	7	5421060	-	7	5529663	-	46.1633	1397.5255	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000182095	ENSG00000075624	TNRC18	ACTB	TTCACGGTTTTAAACCCCGGAGCATTTGACGCCTAGGAATAAAATAGGAG*CTCACCATGGATGATGATATCGCCGCGCTCGTCGTCGACAACGGCTCCGG	prostates,chimerdb3seq,cancer,oesophagus,100K<gap<200K	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	intronic/CDS(no-known-start-or-end)	0	12	7	25	7	5421830	-	7	5529663	-	46.1633	1397.5255	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000182095	ENSG00000075624	TNRC18	ACTB	GCTGCCGCCCGGGAAGTACATGGCCGGCCTGAATCTCCATCCGCACCCGG*AGATGGAGTTTCAACATGTTGTCCAGGCTGGTCTTGAACTCGTGACCACA	prostates,chimerdb3seq,cancer,oesophagus,100K<gap<200K	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/UTR	0	12	5	35	7	5421060	-	7	5540768	-	46.1633	1397.5255	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000182095	ENSG00000075624	TNRC18	ACTB	GGAGTCGTTGTCGCCGGAGCCTGGAGCCGTGAACCCAGCCGCGCCAG*CTCACCATGGATGATGATATCGCCGCGCTCGTCGTCGACAACGGCTC	prostates,chimerdb3seq,cancer,oesophagus,100K<gap<200K,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(no-known-start-or-end)	0	12	4	22	7	5423441	-	7	5529663	-	46.1633	1397.5255	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000182095	ENSG00000075624	TNRC18	ACTB	GCCGCCCGGGAAGTACATGGCCGGCCTGAATCTCCATCCGCACCCGG*TAGAGATGGAGTTTCAACATGTTGTCCAGGCTGGTCTTGAACTCGTG	prostates,chimerdb3seq,cancer,oesophagus,100K<gap<200K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	12	3	27	7	5421060	-	7	5540771	-	46.1633	1397.5255	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000182095	ENSG00000075624	TNRC18	ACTB	GCTGCCGCCCGGGAAGTACATGGCCGGCCTGAATCTCCATCCGCACCCGG*ATGGAGTCTCCCTCTGTCGCCCAGGCTGGAGTGCAGTGGTGTGATCTCGG	prostates,chimerdb3seq,cancer,oesophagus,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	12	2	34	7	5421060	-	7	5561949	-	46.1633	1397.5255	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000182095	ENSG00000075624	TNRC18	ACTB	CCGGCCACCACGCCTGGCTAATTTTTTGTATTTTTTTTTTTTTTTTTTTT*TTTTGGTTTTTTTTTTTTTTTTGGCTTGACTCAGGATTTAAAAACTGGAA	prostates,chimerdb3seq,cancer,oesophagus,100K<gap<200K	BOWTIE+STAR	intronic/UTR	0	12	2	22	7	5409813	-	7	5527645	-	46.1633	1397.5255	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000182095	ENSG00000075624	TNRC18	ACTB	TGATCATTCAGCCCCGCCGAGGGGAGCCTGGAAACTGCTGGAGCCCCTAG*CTCACCATGGATGATGATATCGCCGCGCTCGTCGTCGACAACGGCTCCGG	prostates,chimerdb3seq,cancer,oesophagus,100K<gap<200K	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	intronic/CDS(no-known-start-or-end)	0	12	1	29	7	5424047	-	7	5529663	-	46.1633	1397.5255	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000182095	ENSG00000075624	TNRC18	ACTB	GCCGGAGTCGTTGTCGCCGGAGCCTGGAGCCGTGAACCCAGCCGCGCCAG*ATGGAGTCTCCCTCTGTCGCCCAGGCTGGAGTGCAGTGGTGTGATCTCGG	prostates,chimerdb3seq,cancer,oesophagus,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	12	1	19	7	5423441	-	7	5561949	-	46.1633	1397.5255	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000182095	ENSG00000075624	TNRC18	ACTB	GCCGGAGTCGTTGTCGCCGGAGCCTGGAGCCGTGAACCCAGCCGCGCCAG*TCAGGGTGGTCTCGAACTTTCGACCTCAGGTGATCCGCTCACCTTGGCCT	prostates,chimerdb3seq,cancer,oesophagus,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	12	1	19	7	5423441	-	7	5557399	-	46.1633	1397.5255	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000182095	ENSG00000075624	TNRC18	ACTB	GTGTGAGCCATCGTGCCGGCTGTGTGTTTTAGGTTTTTTTGTTTTTGTTT*GTTTTTTTTTTTTTTTTGGCTTGACTCAGGATTTAAAAACTGGAACGGTG	prostates,chimerdb3seq,cancer,oesophagus,100K<gap<200K	BOWTIE+STAR	intronic/UTR	0	12	1	17	7	5399708	-	7	5527640	-	46.1633	1397.5255	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000182095	ENSG00000075624	TNRC18	ACTB	GGGCATGAGCCACTGTGCCTGGGCTAATTTCTGTATACTTTTTATTTTTA*AGGATTTAAAAACTGGAACGGTGAAGGTGACAGCAGTCGGTTGGAGCGAG	prostates,chimerdb3seq,cancer,oesophagus,100K<gap<200K	BOWTIE+STAR	intronic/UTR	0	12	1	15	7	5405756	-	7	5527613	-	46.1633	1397.5255	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000159069	ENSG00000054179	FBXW5	ENTPD2	TCGCGGAGGAGATTGACCTGCTGGTGTTCGACCTCAAGACCATGCGGGAG*TATGGCATCGTCCTGGACGCTGGTTCTTCACACACGTCCATGTTTATCTA	oesophagus,100K<gap<200K	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	in-frame	0	10	15	37	9	136941343	-	9	137052348	-	71.3753	47.2714	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000100413	ENSG00000177757	POLR3H	FAM87B	GGAGGATGCCTATGTATTCCCTGGGGATGGCGCATCACACACCAAAG*GGCAACGTCGGCTGCAGCTGAGATGGCTGCTCCCCGGTGGGGTGTGT	lincrna,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	10	22	29	22	41540699	-	1	818723	+	1.5324	4.8634	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000188522	ENSG00000108641	FAM83G	B9D1	TCCTGCACATGTGTGAGCGGGCCTGCATGCACCTGGGGCACCTCAAG*GGTCTGGAGGAGGGGATCTCACAGATCACATCCAAGAGCCAAGATGT	tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	9	17	29	17	18988247	-	17	19357951	-	22.6605	2.9849	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000162032	ENSG00000167969	SPSB3	ECI1	AAAGTGGGTCAGGGCCGGGCCGGCGGAGCGCGCAGCGGGGGCTGCAG*GTTGAAAGACACCCTGGAGAACACCATCGGGCACCGGGCGGCGGAGC	chimerdb3seq,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	UTR/CDS(truncated)	0	7	20	30	16	1782502	-	16	2243224	-	1.0851	23.3701	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000162032	ENSG00000167969	SPSB3	ECI1	GCGCCGCGATCCGCCCCGGCCTCCCTGGAACCCCACCCGGGGCCCAGCGG*GGAGGCTGCCTGGTGGCCCTGACCTGTGACTACCGCATCCTGGCGGACAA	chimerdb3seq,oesophagus	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	7	10	37	16	1782194	-	16	2243424	-	1.0851	23.3701	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000162032	ENSG00000167969	SPSB3	ECI1	GAAAGTGGGTCAGGGCCGGGCCGGCGGAGCGCGCAGCGGGGGCTGCAGGT*ACTGCATAGGACTCAATGAGACCCAGCTGGGCATCATCGCCCCTTTCTGG	chimerdb3seq,oesophagus	BOWTIE+BOWTIE2	UTR/CDS(truncated)	0	7	4	37	16	1782500	-	16	2243366	-	1.0851	23.3701	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000160963	ENSG00000006704	COL26A1	GTF2IRD1	GGAGTGGAGATGCTGCCCTGGCTTCACCGGGAGCAACTGTGATGAGG*CGGAAGCCCTGGGCCTGGACCACATGGTCCCCGTGCCCTACCGGAAG	chimerdb3seq,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	6	7	29	7	101447787	+	7	74529734	+	0.1683	6.676	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000160963	ENSG00000006704	COL26A1	GTF2IRD1	CTGCATTTGGACCCTATTTTTATTATTATTTATTTTTGAGACGGAGTCTC*AATCGCTTGAACCTGGGAGGCAGAGGTTGCAATGAGCCGAGGTCGCGCCA	chimerdb3seq,oesophagus	BOWTIE+STAR	intronic/UTR	0	6	1	24	7	101391590	+	7	74601693	+	0.1683	6.676	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000067900	ENSG00000176194	ROCK1	CIDEA	GGGAGAGTGAGGCTGTCCTGCGTGGACCAGCTCGTGGCCGAGACTGATCG*GCCCCTGACATTTATGGGATCACAGACTAAGCGAGTCCTGTTCACCCCGC	oncogene,oesophagus	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	6	20	37	18	21111475	-	18	12262825	+	8.9511	4.8626	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000067900	ENSG00000176194	ROCK1	CIDEA	CGCGGCTGCGAACCCACCGCGGAGGAAGTTGGTTGAAATTGCTTTCCGCT*GTGGAAGCCGGAGCTGGATTCAGACCCTGGTCTAGCCTTTGCTGCCCTGA	oncogene,oesophagus	BOWTIE+STAR	UTR/intronic	0	6	1	16	18	21110951	-	18	12258664	+	8.9511	4.8626	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000178537	ENSG00000225697	SLC25A20	SLC26A6	GCGGCGTGTGCCTGGTGTTCGTCGGTCACCCTCTGGACACGGTCAAG*ATTTTCCATGACTTCCGGGAGATTGAGGTGGAGGTGTACATGGCGGC	chimerdb3seq,exon-exon	BOWTIE	in-frame	0	6	12	25	3	48898690	-	3	48626685	-	8.0974	3.1983	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000178537	ENSG00000225697	SLC25A20	SLC26A6	TGAGAAGCAATGATGACCTCAGTGACCGAGCCCCTTCCACGGAAAGCAAG*ATTTTCCATGACTTCCGGGAGATTGAGGTGGAGGTGTACATGGCGGCCTG	chimerdb3seq	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	intronic/CDS(truncated)	0	6	2	24	3	48898087	-	3	48626685	-	8.0974	3.1983	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000225697	ENSG00000178537	SLC26A6	SLC25A20	TCACCTTTGCCCTCCAACACCCGAGGCCTGTCCCCGACAGCCCTGTTTCG*GAGACGGGGTTTCACCATGTTGGGCAGGATGGTCTCGATCTCCTGACCTC	chimerdb3seq	BOWTIE+BLAT	CDS(truncated)/intronic	0	6	1	30	3	48626218	-	3	48873442	-	3.1983	8.0974	TRUE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000067798	ENSG00000153233	NAV3	PTPRR	TCGCAAACCTGAGGATTTCCGCGGCCCGCCGGCAAGACCTCGGCCAG*ACACTGCAAATGGATGTAAACAAGCTGAACATAACCTTGCTTCGGAT	18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE;BOWTIE+STAR	UTR/CDS(truncated)	0	4	2	19	12	77325214	+	12	70764778	-	0.0366	1.0219	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000112339	ENSG00000135541	HBS1L	AHI1	GAAGGACAAGAATGAGGCAACAGTATCTACAGGAAAGATAGCAAAAG*CCTGACACTATTAGAAGCAATCTTCACTATATGAAAGAAACTACAAG	known,oncogene,chimerdb3seq,cancer,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	2	7	23	6	135039573	-	6	135467634	-	3.9436	4.2714	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000112339	ENSG00000135541	HBS1L	AHI1	GAAGGACAAGAATGAGGCAACAGTATCTACAGGAAAGATAGCAAAAG*CCCGACACTATTAGAAGCAATCTTCCCCATATTAAAGAAACTACAAG	known,oncogene,chimerdb3seq,cancer,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	2	2	23	6	135039573	-	6	135466373	-	3.9436	4.2714	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000112339	ENSG00000135541	HBS1L	AHI1	CACTTTATATTATGGGATTCAAATTCTGATTTTTATGAAAATTGTCGTAG*CCTGACACTATTAGAAGCAATCTTCACTATATGAAAGAAACTACAAGTGA	known,oncogene,chimerdb3seq,cancer,100K<gap<200K	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	UTR/CDS(truncated)	0	2	1	32	6	135036443	-	6	135467634	-	3.9436	4.2714	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000112339	ENSG00000135541	HBS1L	AHI1	GGGTTCAAGCGATTCTCCTGTGTCAGCCCCCCGAGTAGCTGGGATTACAG*CCTGACACTATTAGAAGCAATCTTCACTATATGAAAGAAACTACAAGTGA	known,oncogene,chimerdb3seq,cancer,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	27	6	135034519	-	6	135467634	-	3.9436	4.2714	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000112339	ENSG00000135541	HBS1L	AHI1	TGAATTATTTTTATACATTTTTAAAAACCATTTGTCCTAAGTATACACTT*TTTATATATTTATTTTAATCTCAGATTCTACCATGGCCTGGGTAACAGAA	known,oncogene,chimerdb3seq,cancer,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	2	1	18	6	135035887	-	6	135434694	-	3.9436	4.2714	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000112339	ENSG00000135541	HBS1L	AHI1	GGTTTCACCACGTTGGCCAGGCTGATCTCAAACTCCTGACCTCAGATGAT*GAAAAATGAAATAAACAATACAAATACTTTCAGAGTTTTACCTCATCCTT	known,oncogene,chimerdb3seq,cancer,100K<gap<200K	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	14	6	135034421	-	6	135433250	-	3.9436	4.2714	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000110422	ENSG00000143622	HIPK3	RIT1	GTATCAAAGACTGTTTGTTCAACATATCTACAATCTCGGTACTACAG*CCATGACCATGCAGTTCATCAGCCACCGATTCCCAGAAGATCATGAT	oncogene,exon-exon	BOWTIE	out-of-frame	0	2	2	25	11	33287511	+	1	155910506	-	8.9948	6.3224	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000110422	ENSG00000143622	HIPK3	RIT1	CATGTATCAAAGACTGTTTGTTCAACATATCTACAATCTCGGTACTACAG*GTCAGTGCCGGAGCCTCCGCGAGTGAAGGAAGACGAAGTGCGTGACCCGA	oncogene	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	2	1	18	11	33287511	+	1	155911352	-	8.9948	6.3224	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000110422	ENSG00000143622	HIPK3	RIT1	TGTATCAAAGACTGTTTGTTCAACATATCTACAATCTCGGTACTACAGGT*TACTGAGTATGGTGCTTGCTCTTTCACTTAACTGATAAGAGGGACATGCC	oncogene	BOWTIE+STAR	intronic/UTR	0	2	1	15	11	33287513	+	1	155900321	-	8.9948	6.3224	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000084764	ENSG00000084733	MAPRE3	RAB10	CACCTGTCCCCTCCCCCTCCGCCTCCGCCGGAGCCGCCTCGTGCACT*GAATAGACTTCAAGATCAAAACAGTTGAATTACAAGGAAAGAAGATC	oesophagus,exon-exon	BOWTIE	UTR/CDS(truncated)	0	2	4	25	2	26970802	+	2	26098662	+	1.566	71.2072	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000084764	ENSG00000084733	MAPRE3	RAB10	CGCCACCTGTCCCCTCCCCCTCCGCCTCCGCCGGAGCCGCCTCGTGCACT*GAGCAAAACTGAATCTCGAAAGATAAATGAAGTTTACCAGGAAAAGAAAA	oesophagus	BOWTIE+STAR	UTR/intronic	0	2	1	18	2	26970802	+	2	26093591	+	1.566	71.2072	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NE-01A	ENSG00000155034	ENSG00000011275	FBXL18	RNF216	TTGACAAGAGCCTCATCCACACCGTGTTGCTGCAAAAGGACTATCAG*TGAAGAAAAAATGACTGCTGCCCGCATTAGAAAATGCCACAAGTGTG	known,cosmic,chimerdb3kb,cancer,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	1	2	22	7	5505412	-	7	5641376	-	4.074	9.1785	TRUE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-V5-A7RC-06A	ENSG00000131196	ENSG00000215474	NFATC1	SKOR2	GGGGCCCGCGCCGCGCGCCGGCGGCACCATGAAGTCAGCGGAGGAAG*ATCCCCTATGCAGCAAGTTTGATCAGGAAAGAAAAGCTTGGCGCCCA	cancer,exon-exon	BOWTIE	out-of-frame	0	6	9	25	18	79396351	+	18	47212151	-	9.7126	0.7511	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-V5-A7RC-06A	ENSG00000131196	ENSG00000215474	NFATC1	SKOR2	CTTCGAGTTTAACCAGCGCGACGAGGGCGCCGCCGCGGCCGCCCCAG*ATCCCCTATGCAGCAAGTTTGATCAGGAAAGAAAAGCTTGGCGCCCA	cancer,exon-exon	BOWTIE	out-of-frame	0	6	5	29	18	79400479	+	18	47212151	-	9.7126	0.7511	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-V5-A7RC-06A	ENSG00000122490	ENSG00000215421	PQLC1	ZNF407	GGTCCGTGTGGCCAACGAGCTCAACGCCAGGCGCCGCTCCTTTACAG*GTTATGAGTGCCAGTGAGCCGCCTTAGATAGAAGCATCGTCAGCACT	oesophagus,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	6	9	29	18	79943329	-	18	74630967	+	6.3222	4.1387	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-V5-A7RC-06A	ENSG00000122490	ENSG00000215421	PQLC1	ZNF407	CGAGGTCCGTGTGGCCAACGAGCTCAACGCCAGGCGCCGCTCCTTTACAG*CATGAGGAATTGCTGCGGGAGGTGAATAAGTATATAGTGGAAGACACTGA	oesophagus	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	out-of-frame	0	6	1	32	18	79943329	-	18	74635544	+	6.3222	4.1387	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-V5-A7RC-06A	ENSG00000215474	ENSG00000131196	SKOR2	NFATC1	TTCAAACCAGTTTTTTTCTACAGTCTTAGATATGTTTGAGGCTGGGCTTC*CTCACCCCACCACTCGCCCACGCCGTCCCCGCACGGCTCCCCGCGGGTCA	cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	6	1	15	18	47234961	-	18	79411106	+	0.7511	9.7126	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OJ-01A	ENSG00000136436	ENSG00000146733	CALCOCO2	PSPH	TTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAG*GATGCTTTCATTGGATTTGGAGGAAATGTGATCAGGCAACAAGTCAA	m80,exon-exon	BOWTIE	out-of-frame	0	368	6	27	17	48844026	+	7	56011869	-	21.2902	109.7419	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OJ-01A	ENSG00000136436	ENSG00000146733	CALCOCO2	PSPH	GGTTGTATCAGACATTTTCCCATATGTATTTGTCATAAGTGAAAAATAAA*TAGGATGCTTTCATTGGATTTGGAGGAAATGTGATCAGGCAACAAGTCAA	m80	BOWTIE+STAR	intronic/intronic	0	368	1	19	17	48847586	+	7	56011872	-	21.2902	109.7419	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OJ-01A	ENSG00000136436	ENSG00000146733	CALCOCO2	PSPH	TTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAG*GGAGCTGGTAAGTCGCCTACAGGAGCGAAATGTTCAGGTTTTCCTAA	m80,exon-exon	BOWTIE	out-of-frame	0	368	1	13	17	48844026	+	7	56017379	-	21.2902	109.7419	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OJ-01A	ENSG00000136574	ENSG00000173334	GATA4	TRIB1	CAGCCTGCCCGGCCGGGCCAACCCGGCCGCCCGACACCCCAATCTCG*AACCCAGCTTAGACTAGAAAGTCTAGAAGACACACACATAATGAAGG	oncogene,chimerdb3seq,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	8	13	30	8	11708928	+	8	125436006	+	126.1491	44.8518	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OJ-01A	ENSG00000136574	ENSG00000173334	GATA4	TRIB1	TCCGGGGGCTCCCAGGGGAGCGTGCGCGGAACCTCCAGGCCCAGCAG*AACCCAGCTTAGACTAGAAAGTCTAGAAGACACACACATAATGAAGG	oncogene,chimerdb3seq,oesophagus,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	8	4	28	8	11704304	+	8	125436006	+	126.1491	44.8518	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OJ-01A	ENSG00000136574	ENSG00000173334	GATA4	TRIB1	GCACAGCCTGCCCGGCCGGGCCAACCCGGCCGCCCGACACCCCAATCTCG*GACTTTGGGGACATGCACTCCTATGTGCGAAGCCGGAAGAGGCTGCGGGA	oncogene,chimerdb3seq,oesophagus	BOWTIE+STAR	out-of-frame	0	8	1	18	8	11708928	+	8	125433443	+	126.1491	44.8518	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OJ-01A	ENSG00000136574	ENSG00000173334	GATA4	TRIB1	TTACCCTTGCCTCAGGGGAACACCTGGACCAAACTCAGTTTCCAAGGACT*CAAATATGTTAGTACCTACCCTTTACTTTTTCCCCAAGACCATCTCAGGG	oncogene,chimerdb3seq,oesophagus	BOWTIE+STAR	intronic/UTR	0	8	1	15	8	11695628	+	8	125437290	+	126.1491	44.8518	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OJ-01A	ENSG00000155313	ENSG00000232193	USP25	AL157359.2	CCATGACCGTGGAGCAGAACGTGCTGCAGCAGAGCGCGGCGCAGAAG*ATGAAGAAACTAAGGATCAAGCACCAAGTCAACTGCACAAGATGTTA	lincrna,exon-exon	BOWTIE;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	4	11	29	21	15730438	+	21	18918217	-	5.9177	0.8642	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OJ-01A	ENSG00000171105	ENSG00000169894	INSR	MUC3A	AGTCGTCTCCCTTTTGTCACGATGGAATGTGAAATAGGTGCATTTTCCTT*GTGGCCACTTGGTGTCCCCCAGCTCGCCTCTCCTGCTCCTGGCCACAGGG	NA	BOWTIE+STAR	intronic/CDS(truncated)	0	2	2	22	19	7203775	-	7	100951944	+	13.9968	63.1779	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OJ-01A	ENSG00000171105	ENSG00000169894	INSR	MUC3A	TGATGCCGTGTTACAGCCAGGCTGGGTTCCTCACGCCTGTGATGGCAGCG*TAGCACACATTCCTCCACCCTTCAAACAACTCCTTCTACTCCCTCATTGC	NA	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	16	19	7199663	-	7	100959675	+	13.9968	63.1779	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OJ-01A	ENSG00000171105	ENSG00000169894	INSR	MUC3A	GGCTCAAGCAACTCTCCTGCCTCAGCCTTTCTAGTAGCTGGGGTTACAGG*TGTGGGCACCACCTCTCCCACCATGTCCACTGTGAGAATGACCCTCAGAA	NA	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	16	19	7285324	-	7	100959399	+	13.9968	63.1779	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OJ-01A	ENSG00000171105	ENSG00000169894	INSR	MUC3A	GTTTCACCATGTTGGCCAGGATGGTCTCAATCTCTTGACCTTGTGATCTG*CCTGCCTCCCCCACTGATCCATGTGTTGAAATGGATCCCAGCACTGAAGC	NA	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	16	19	7252890	-	7	100960114	+	13.9968	63.1779	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OJ-01A	ENSG00000171105	ENSG00000169894	INSR	MUC3A	AGTCCTCAGATTCATAGAGACAGAAAGTAGAATGGGGAGTGCCAGGGACT*ATGGTCACCTGTCCTACCTCCATCAGTATCCAAACTACTCTTACTACATA	NA	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	15	19	7159340	-	7	100960213	+	13.9968	63.1779	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OJ-01A	ENSG00000171105	ENSG00000169894	INSR	MUC3A	TGCTTCCATGAACAAGCACAGACTCAGAGCCCATGGTCCTGGGTTCGAAT*CCTCACACAATACTCGCAGCTTCACTTCTTCGATCACCACCACCGAGACC	NA	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	14	19	7215176	-	7	100958780	+	13.9968	63.1779	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A5S3-01A	ENSG00000133019	ENSG00000155816	CHRM3	FMN2	TGTCACTGTTTTGCATCCTTGTTACATAACTCAGTTCCTGGTAGATT*GGCGAACGCTGTTGGAGAAGCTGTTCAGCCAGCAGGAGAACGGGCCT	tcga,chimerdb3seq,10K<gap<100K,exon-exon	BOWTIE;BOWTIE+STAR	UTR/CDS(truncated)	0	3	7	27	1	239827378	+	1	240123179	+	3.186	1.5615	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A5S3-01A	ENSG00000133019	ENSG00000155816	CHRM3	FMN2	ACAATTCTGGACACATTGTATTGGTTTGATGCTCCTACCTGGAACAG*GGCGAACGCTGTTGGAGAAGCTGTTCAGCCAGCAGGAGAACGGGCCT	tcga,chimerdb3seq,10K<gap<100K,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	3	2	19	1	239678288	+	1	240123179	+	3.186	1.5615	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4ON-01A	ENSG00000149474	ENSG00000101310	KAT14	SEC23B	ACTGGTCTAGCTGGACTCCAAGAGGGAGAAAGTGGAAGCAAGCCACCAGT*AATGGTCACTGCATTGATATTTATGCTTGTGCCCTTGATCAAACTGGACT	chimerdb3seq,cancer,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/CDS(truncated)	0	30	1	14	20	18177347	+	20	18527529	+	7.6865	25.9277	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4ON-01A	ENSG00000101310	ENSG00000149474	SEC23B	KAT14	CTGCCGAATTGATGCCCCAGTTTTCTACAATTGAGTACGTGATACAG*ACTTCCTTGCCGTCCAGGAAGGGATTTCGACACCAGACCACCAAGTT	chimerdb3seq,cancer,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	30	30	30	20	18515736	+	20	18181710	+	25.9277	7.6865	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-L5-A4ON-01A	ENSG00000011114	ENSG00000100605	BTBD7	ITPK1	GCTTGTTGGACTACTTGAATGGCAAAAAGTGTGCATATTTCAGTACCTTA*TTTTGGAAACTGAGGACCCAACAACTAACCACGTTTACACGACTTGAGTT	tcga,18cancers,chimerdb3seq,tcga-cancer,oesophagus,100K<gap<200K	BOWTIE+STAR	intronic/UTR	0	17	1	14	14	93332162	-	14	92940038	-	10.2076	28.2742	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4ON-01A	ENSG00000011114	ENSG00000100605	BTBD7	ITPK1	TTACATGTGTTATTATGATGTCGTCCTTAGTTTTTCTTCAGACTCTGAAC*AGTTCTGAACTCCAAGCGCCACACAGAGCAGGATCCAGCATGGGCCCTGC	tcga,18cancers,chimerdb3seq,tcga-cancer,oesophagus,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/intronic	0	17	1	14	14	93294245	-	14	93020113	-	10.2076	28.2742	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4ON-01A	ENSG00000011114	ENSG00000100605	BTBD7	ITPK1	GAATTGAAGACCAGTCTGGGCAACATAGCGAGATCACACCTCTACAAAAA*AGCTGGGCTGCAGGATGCCCACTTTGAGGAGGGAGGCACAGGGCTTGGGC	tcga,18cancers,chimerdb3seq,tcga-cancer,oesophagus,100K<gap<200K	BOWTIE+STAR	intronic/UTR	0	17	1	14	14	93322295	-	14	92940120	-	10.2076	28.2742	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4ON-01A	ENSG00000100605	ENSG00000011114	ITPK1	BTBD7	AGGCCTTCGCCGAGCTGTGCAGGAAGCGAGGGATGGAGGTTGTGCAG*GCTGTGAGGATATCATTGCTGAGAGCATCTCATTAGATACCTTAATT	tcga,18cancers,chimerdb3seq,tcga-cancer,oesophagus,100K<gap<200K,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	17	22	29	14	93076595	-	14	93263993	-	28.2742	10.2076	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4ON-01A	ENSG00000100605	ENSG00000011114	ITPK1	BTBD7	CCTCCCCCACACGTGTGGGCCTACCCGATGCTGGCGACTGGAGGTCTCGG*CTGTGAGGATATCATTGCTGAGAGCATCTCATTAGATACCTTAATTGCCA	tcga,18cancers,chimerdb3seq,tcga-cancer,oesophagus,100K<gap<200K	BOWTIE+BOWTIE2	intronic/CDS(truncated)	0	17	2	30	14	93050778	-	14	93263992	-	28.2742	10.2076	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4ON-01A	ENSG00000100605	ENSG00000011114	ITPK1	BTBD7	TCTTGAAATAGGTACTTATTCTTGGCATTTCTTAGCCAAAAACTGCAGAG*GCTGTGAGGATATCATTGCTGAGAGCATCTCATTAGATACCTTAATTGCC	tcga,18cancers,chimerdb3seq,tcga-cancer,oesophagus,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	17	2	26	14	93051885	-	14	93263993	-	28.2742	10.2076	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4ON-01A	ENSG00000100605	ENSG00000011114	ITPK1	BTBD7	TTGGCTGACCCAGTGGACATCAGCCAGGACCACATTAGGCCCAGCTTTGG*GAGTGTGAAAGCTGCACCGCCTGATTGTACCAGCACTGCAGGACTGGGCA	tcga,18cancers,chimerdb3seq,tcga-cancer,oesophagus,100K<gap<200K	BOWTIE+STAR	intronic/CDS(truncated)	0	17	1	14	14	93092711	-	14	93245954	-	28.2742	10.2076	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4ON-01A	ENSG00000100605	ENSG00000011114	ITPK1	BTBD7	AGGCCTTCGCCGAGCTGTGCAGGAAGCGAGGGATGGAGGTTGTGCAG*GCAAGTGAACAAGATATCCTTAAATATCTGATTAAATGGGGAGAGCA	tcga,18cancers,chimerdb3seq,tcga-cancer,oesophagus,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	17	1	13	14	93076595	-	14	93261677	-	28.2742	10.2076	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4ON-01A	ENSG00000104866	ENSG00000146122	PPP1R37	DAAM2	GGATATCGTGTCTGGAGCAGTGGAGCCCAAAGACCCCTGGAGACATG*CCATCCTGTTGGCCTCCCGGGAGCTGGTCCGCAGCAAGCGTCTTAGA	tcga-cancer,oesophagus,exon-exon	BOWTIE	in-frame	0	4	6	26	19	45093527	+	6	39896812	+	3.176	1.3597	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4ON-01A	ENSG00000104866	ENSG00000146122	PPP1R37	DAAM2	GGATATCGTGTCTGGAGCAGTGGAGCCCAAAGACCCCTGGAGACATG*AAACATCTCTCTGCTCCATTACCTGATCATGATCCTGGAGAAGCATT	tcga-cancer,oesophagus,exon-exon	BOWTIE	out-of-frame	0	4	4	23	19	45093527	+	6	39897175	+	3.176	1.3597	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4ON-01A	ENSG00000123104	ENSG00000121210	ITPR2	TMEM131L	GAGAAATAGGGGAAAGTCAAGTGAAAGGTGGTGAAGAGCCAATTGAG*GCAGAAACCACTAATACTAGCCTCTTGCAGGTGCAACTGGAATGCAG	chimerdb3seq,oesophagus,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	3	5	28	12	26621123	-	4	153580826	+	3.2096	1.7438	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4ON-01A	ENSG00000123104	ENSG00000121210	ITPR2	TMEM131L	GTGTGTGTCGGATGAGAGCCTGCCGTTCGACCTCCGAGCGTCCTTCTGTC*CAGTGCCTGGCATATAAGAACCATTTAATAGAGGTGCTGTTTTTACTATA	chimerdb3seq,oesophagus	BOWTIE+STAR	CDS(truncated)/intronic	0	3	1	15	12	26656403	-	4	153595300	+	3.2096	1.7438	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4ON-01A	ENSG00000149179	ENSG00000088726	C11ORF49	TMEM40	GATGCTGAGTCCGGAGCGCCTAGCCCTACCGGACTACGAGTATCTGG*GAAAAGCCATGGAGACTTCAGCATCCTCCTCCCAGCCTCAGGACAAC	exon-exon	BOWTIE	CDS(truncated)/UTR	0	2	2	22	11	46936851	+	3	12749840	-	6.4956	0.6652	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4ON-01A	ENSG00000145113	ENSG00000132549	MUC4	VPS13B	TCCATCAATGGTGGTCGTGTGATTGAAGCCTACAAGGGGCAGACCACGCT*CCTGGGCTGGAGTGCAGTAGTGCGATCTCAGCCCACTGTAACTTCCACCT	oncogene,cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	17	3	195759198	-	8	99579438	+	35.5331	7.7246	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4ON-01A	ENSG00000145113	ENSG00000132549	MUC4	VPS13B	TGAAGGAGTCTCCACGGGAATCATGACTCCCAGAGCGAGGCTGGGGCTTG*TGACAGGGGCCAGAACATTTCTGAGAATGAAAGGAACGCCATTAAATATT	oncogene,cancer	BOWTIE+STAR	UTR/intronic	0	2	1	16	3	195809968	-	8	99823649	+	35.5331	7.7246	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-LN-A49Y-01A	ENSG00000006453	ENSG00000054654	BAIAP2L1	SYNE2	TTGCTTTTTTTGTCCCTGGGTTTAAAAATAACATGTACTTCAGCTAAAAT*CTAATGTAAAGTAAATGCCAAACTACCGACTTGATAGGGATGTTTTTGTA	oncogene,cancer	BOWTIE+STAR	intronic/UTR	0	2	1	14	7	98370858	-	14	64226220	+	65.2562	7.6452	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49Y-01A	ENSG00000068305	ENSG00000051382	MEF2A	PIK3CB	TTTATTTCTTTGAATATAGATATCATATTGTTCCAGCAGTTTTTTTGAAA*GGTTCCGCCAGTGTTGTGAGGATGCATATCTGATTTTACGACGGCATGGG	NA	BOWTIE+STAR	intronic/intronic	0	2	1	14	15	99600655	+	3	138656275	-	7.6602	11.602	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49Y-01A	ENSG00000127922	ENSG00000227646	SEM1	STEAP2-AS1	TAAAAAAATGTGTTTATTTCATTATCTGCTTGGATTTATTTGTGTTTTTG*TACAACAAAAACACAAAGGACAGTGCTTGTTTTGTTGGACATTTTCAATG	NA	BOWTIE+STAR	UTR/intronic	0	2	3	17	7	96688796	-	7	89908322	-	121.6344	4.9621	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49Y-01A	ENSG00000127922	ENSG00000227646	SEM1	STEAP2-AS1	TTGGATTTATTTGTGTTTTTGTAACACAAAAAATAAATGTTTTGATATAA*TCTAAAAAAAAGAAAAAAAAAGTTTCATTTAAGATTTTCTCTTTACTTGG	NA	BOWTIE+STAR	UTR/intronic	0	2	2	15	7	96688767	-	7	89974465	-	121.6344	4.9621	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49Y-01A	ENSG00000127922	ENSG00000227646	SEM1	STEAP2-AS1	TACAATATTCTTCTTTATGCATATTTATGTTTATTCTTCCTTTAAAAATA*AAAATGTTTCAAAATTTATATTGCATATATTCTTGCTCACCTTCTCCCTA	NA	BOWTIE+STAR	UTR/intronic	0	2	1	22	7	96695367	-	7	90008843	-	121.6344	4.9621	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49Y-01A	ENSG00000127922	ENSG00000227646	SEM1	STEAP2-AS1	ATTTCATTATCTGCTTGGATTTATTTGTGTTTTTGTAACACAAAAAATAA*ATATTTGTAAAAAAAAAAAAAAAAAAAAAAAAAAAGTCAGTGTCCTTGGA	NA	BOWTIE+STAR	UTR/intronic	0	2	1	19	7	96688781	-	7	89948393	-	121.6344	4.9621	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49Y-01A	ENSG00000127922	ENSG00000227646	SEM1	STEAP2-AS1	TCATTATCTGCTTGGATTTATTTGTGTTTTTGTAACACAAAAAATAAATG*TTTTGATTTCCAAACATTCATCATTAACAGTCAACAACAGGAAAAGAACA	NA	BOWTIE+STAR	UTR/intronic	0	2	1	17	7	96688778	-	7	90040401	-	121.6344	4.9621	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49Y-01A	ENSG00000127922	ENSG00000227646	SEM1	STEAP2-AS1	TAATACATTCTAGGGCAGAGAACCCAGGATGGGACACTAAAAAAATGTGT*TTTTATATATATCAAAATATAATATATACATATTATATATATTTATAATA	NA	BOWTIE+STAR	UTR/intronic	0	2	1	17	7	96688833	-	7	89959253	-	121.6344	4.9621	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49Y-01A	ENSG00000127922	ENSG00000227646	SEM1	STEAP2-AS1	ATTATCTGCTTGGATTTATTTGTGTTTTTGTAACACAAAAAATAAATGTT*TTGATATGGACAATAATGTCAGGTGTATTTAGCTTGTAGAATCCATTAAG	NA	BOWTIE+STAR	UTR/intronic	0	2	1	17	7	96688776	-	7	89952006	-	121.6344	4.9621	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49Y-01A	ENSG00000127922	ENSG00000227646	SEM1	STEAP2-AS1	ATATAGACATATGGCCTGCAGAATTGTAAGATAATACATTTTTGTTGTTT*TGAAACAACAAAAATGCAAATATCTTTGGGGTATATTAAAAAATCTTACA	NA	BOWTIE+STAR	UTR/intronic	0	2	1	16	7	96664178	-	7	90033722	-	121.6344	4.9621	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49Y-01A	ENSG00000127922	ENSG00000227646	SEM1	STEAP2-AS1	TTATTTCATTATCTGCTTGGATTTATTTGTGTTTTTGTAACACAAAAAAT*AGATGTCTATTTCATTCTTTTCTCTATGCTTAGCACTGAGCTTTATTATG	NA	BOWTIE+STAR	UTR/intronic	0	2	1	16	7	96688783	-	7	89942208	-	121.6344	4.9621	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49Y-01A	ENSG00000127922	ENSG00000227646	SEM1	STEAP2-AS1	TAGATGAAGATGAAGATGCACATGTCTGGGAGGATAATTGGGATGATGAC*AATATAGAAAAGTCATGGTAAAAACACACTATAAAAGATAAAAAATGGTA	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	16	7	96694830	-	7	90065525	-	121.6344	4.9621	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49Y-01A	ENSG00000127922	ENSG00000227646	SEM1	STEAP2-AS1	TCGTCTTTCTCTTTCCGTGTAATTACCTTTAACAGAAGTAGAAAGAATAA*ATATGCCTTATTCTTATGGCAATCTCATGAGATAGAGTATTTGTGAATAA	NA	BOWTIE+STAR	intronic/intronic	0	2	1	15	7	96691220	-	7	89978176	-	121.6344	4.9621	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49Y-01A	ENSG00000127922	ENSG00000227646	SEM1	STEAP2-AS1	TTTATTTCATTATCTGCTTGGATTTATTTGTGTTTTTGTAACACAAAAAA*ATCTAAACAGATAATAAAGTAACTGAAGATAATTTTCAACTGTCAGCAAT	NA	BOWTIE+STAR	UTR/intronic	0	2	1	15	7	96688784	-	7	89903607	-	121.6344	4.9621	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49Y-01A	ENSG00000127922	ENSG00000227646	SEM1	STEAP2-AS1	ATACCAAAATAGGGGTTGGTGGCCTGAAATACAAGTTATACTTCAAAATG*TTCTTTGGTGTTCCTTGGTCTGTAGCTTCGTGAACCCAGTCTCTGCCTTC	NA	BOWTIE+STAR	UTR/intronic	0	2	1	15	7	96687952	-	7	90041631	-	121.6344	4.9621	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49Y-01A	ENSG00000127922	ENSG00000227646	SEM1	STEAP2-AS1	AGTGTTGAAGTAACCTAAACTTGACCTGCTTAATACATTCTAGGGCAGAG*GCTATAGATGAGTCTTGTCTGTTCTTAATAAAAAAAAAATACATTTTCTT	NA	BOWTIE+STAR	UTR/intronic	0	2	1	14	7	96688863	-	7	90030093	-	121.6344	4.9621	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49Y-01A	ENSG00000054654	ENSG00000006453	SYNE2	BAIAP2L1	AATGATAAAGAGAAATTTACTTCCAGTTTATGACTTAAACACTCTAAGTT*AAAATACTATATAAATGTAATTTAACTTAAAATGTTTAAGTGTAGAGCTT	oncogene,cancer	BOWTIE+STAR	intronic/UTR	0	2	1	17	14	63980028	+	7	98293035	-	7.6452	65.2562	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49Y-01A	ENSG00000054654	ENSG00000006453	SYNE2	BAIAP2L1	GCCCCGGTGAACTCATTTCAAAACACAAGGTGGGAATCTTTTCAACCATC*TGCAAAGAGGCTCTGCTTGAAGAGAAGAGGCGCTTCTGCTTTCTGGTTGA	oncogene,cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	15	14	63991136	+	7	98315555	-	7.6452	65.2562	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-LN-A49P-01A	ENSG00000089177	ENSG00000166960	KIF16B	CCDC178	ATCGTGTGATTAGTGAAGGCTGCAGTACATCTGCAGACACGATGAAG*CTCTGTCAGCTGCAGAGAAGGATGCACACACTGTGGCAGGAGCACTT	oesophagus,exon-exon	BOWTIE	in-frame	0	3	11	29	20	16371665	-	18	32974681	-	9.4425	0.4183	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Esophagus	TCGA-LN-A49P-01A	ENSG00000089177	ENSG00000166960	KIF16B	CCDC178	TGCATCGTGTGATTAGTGAAGGCTGCAGTACATCTGCAGACACGATGAAG*ACGGATTCTCACTCTGTCTCCCAGGCTGGAGAGGAATGGCGCGATCTCTG	oesophagus	BOWTIE+STAR	CDS(truncated)/intronic	0	3	1	17	20	16371665	-	18	32979033	-	9.4425	0.4183	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Esophagus	TCGA-LN-A49X-01A	ENSG00000169288	ENSG00000184305	MRPL1	CCSER1	AGGTAGATGAAGAAAGGGAGAACTTTCTCCAGACCAAAATAGCAACA*GGTTTAAACTTGAAAAGACTAGAGACAGTACAAGGAGGGAGAGAGGT	ribosomal,chimerdb3seq,oesophagus,exon-exon	BOWTIE	in-frame	0	2	10	29	4	77909372	+	4	91085950	+	10.3363	0.4964	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-LN-A49X-01A	ENSG00000169398	ENSG00000167632	PTK2	TRAPPC9	GATTGGAGTCATCACAGAGAATCCTGTCTGGATAATCATGGAGCTGTGCA*TGTGTGCTCAGCTCCATCTAGGAAGAAGCACAAGAGCCTCTGGCTTCTGC	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	17	8	140746771	-	8	139901764	-	15.244	5.4991	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-LN-A49X-01A	ENSG00000169398	ENSG00000167632	PTK2	TRAPPC9	GAAGACAAGGACAGAAAAGGAATGCTACAACTAAAAATAGCAGGTGCACC*TGCTACTTTTAGTGGCAAAAACTGCAGTTACTTTTGCACCAAGCCAATAG	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	15	8	140803547	-	8	140147056	-	15.244	5.4991	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-LN-A49X-01A	ENSG00000169398	ENSG00000167632	PTK2	TRAPPC9	TATGACCCCAGCAGGCGGCCCAGGTTTACTGAACTTAAAGCTCAGCTCAG*ATCTCTCTTCCTCCATAGACATTTCATGAGCATTTCCTGTGCCCCGGGTG	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	15	8	140735251	-	8	140050693	-	15.244	5.4991	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-LN-A49X-01A	ENSG00000169398	ENSG00000167632	PTK2	TRAPPC9	TATGACCCCAGCAGGCGGCCCAGGTTTACTGAACTTAAAGCTCAGCTCAG*GGATCTCTTCCTCCAATTCCTGGGCGCCCCTGCTTCCTGTACACTCAGGA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	15	8	140735251	-	8	140007078	-	15.244	5.4991	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-LN-A49X-01A	ENSG00000167632	ENSG00000169398	TRAPPC9	PTK2	ATAGGGTTTTGGAGATGAAGAAACTCTTGAGGGTAGTGTTTGAGACCATT*CCCCTCCTACTGCCAACCTGGACCGGTCGAATGATAAGGTGTACGAGAAT	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	15	8	140295664	-	8	140668402	-	5.4991	15.244	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-LN-A49X-01A	ENSG00000167632	ENSG00000169398	TRAPPC9	PTK2	ACCATTGGAGAAACTGGAGGTCACCTCGAAAGTTCTCACCACTAAAG*CACAATCCTGGAGGAAGAGAAGGCTCAGCAAGAAGAGCGCATGAGGA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	2	1	13	8	140275658	-	8	140717709	-	5.4991	15.244	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-LN-A49U-01A	ENSG00000127947	ENSG00000273341	PTPN12	AC004921.1	ATGTTGTGATCATTGTAATGGCCTGCCGAGAATTTGAGATGGGAAGG*GCTAGAGTGCAGTGGTGCGATCTCGGCTCACTACAACTCCTACCTCC	lincrna,100K<gap<200K,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	153	35	30	7	77585581	+	7	77421767	+	53.514	31.3604	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49U-01A	ENSG00000127947	ENSG00000273341	PTPN12	AC004921.1	TCACTTTTTAGATCATTGTAATGGCCTGCCGAGAATTTGAGATGGGAAGG*ATGGTGTCTCTCGCCCTGTCTCCAGGCTAGAGTGCAGTGGTGCGATCTCG	lincrna,100K<gap<200K	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/intronic	0	153	8	37	7	77585581	+	7	77421742	+	53.514	31.3604	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49U-01A	ENSG00000127947	ENSG00000273341	PTPN12	AC004921.1	AGGGACGTGCTGGGGGAACGAGCTGGGGAAGACGGAGCGGGCTCTGTGCC*AGACCCCAGCTCCCACTTTCCCTGAAAGCTCCCTTTAATGAAGCTGAACG	lincrna,100K<gap<200K	BOWTIE+BOWTIE2	UTR/exonic(no-known-CDS)	0	153	1	22	7	77537493	+	7	77425263	+	53.514	31.3604	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49U-01A	ENSG00000127947	ENSG00000273341	PTPN12	AC004921.1	TCACTTTTTAGATCATTGTAATGGCCTGCCGAGAATTTGAGATGGGAAGG*AGCAGAGACCTCACCAAGATGCAGTAGGCAAGAGGGGAGAGGAATATGAG	lincrna,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	153	1	20	7	77585581	+	7	77419538	+	53.514	31.3604	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49U-01A	ENSG00000127947	ENSG00000273341	PTPN12	AC004921.1	TATATCCCACAGCCACTGGAGAAAAAGAAGAAAATGTTAAAAAGAACAGA*AGACCTACTGTCACCACCTCTGGAGGGGCAATTCCTGGAGGAACCAAGTC	lincrna,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	153	1	14	7	77571167	+	7	77425338	+	53.514	31.3604	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-LN-A49U-01A	ENSG00000127947	ENSG00000186088	PTPN12	GSAP	GTCATATTTATACTGTATTATAGTCTGTTAAATGTTCAGTAGCATTATAC*TTAGAGATGAAGAAATGGAGGCTCAGAAAGGCTTAGTTGCCTGCAGCTGG	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/UTR	0	9	1	14	7	77585929	+	7	77315352	-	53.514	6.911	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-LN-A49U-01A	ENSG00000256500	ENSG00000224186	AL139300.1	C5ORF66	GATGCAGCTAACCTACTGAATGATGCCTTGGCTATTCGTGAGAAAACTTT*TTCTGGGATTTTCAGCTTTTTACTCTCCTCAAGGAGCAGTTACAAACCTG	antisense	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	15	14	103669579	+	5	135329774	+	0	0.2031	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-LN-A49U-01A	ENSG00000224186	ENSG00000126214	C5ORF66	KLC1	TGATTTAGTGAGGATCATGTTGTGGGTGGTTCTTCCATACTTCCCAGTCT*ATGGTTCCCTGAGCAGGCGTGACTGTCACAGACAGGCTGGGCCTGGGGGC	antisense	BOWTIE+STAR	intronic/UTR	0	2	1	14	5	135075137	+	14	103712643	+	0.2031	2.8188	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-LN-A49U-01A	ENSG00000224186	ENSG00000126214	C5ORF66	KLC1	TGCCAAAGCTGCCATCATCCTCTCCCACATGCTTTGGGCCAGCTGGCCAG*CTGCTCTCCTTCTGCCATGGTTTCACCCTCTCCCCCTCACAGGTCAGCAG	antisense	BOWTIE+STAR	intronic/intronic	0	2	1	14	5	135047590	+	14	103699904	+	0.2031	2.8188	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OF-11A	ENSG00000126777	ENSG00000023287	KTN1	RB1CC1	GAGACTAAACAAGAAAGTGGATCAGGGAAGAAGAAAGCTTCATCAAAGAA*GACATTTTCTGTATTATCAGTCTTCTTAAAGCTTCTATTTGATTACATTC	cancer,tumor	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	16	14	55616637	+	8	52677579	-	12.8589	13.5406	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-IG-A4P3-01A	ENSG00000147799	ENSG00000071894	ARHGAP39	CPSF1	GGACCAGTGGAAGGTGCCCACAGGCCTGGAAGACCCCCACGTCCCTG*CCCCACAGTGGATGACGAGGAGGAGATGCTGTATGGGGATTCGGGCT	tcga-cancer,100K<gap<200K,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	out-of-frame	0	2	4	26	8	144532305	-	8	144397661	-	2.2521	9.3664	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-IG-A4P3-01A	ENSG00000147799	ENSG00000071894	ARHGAP39	CPSF1	GAGCCCTTCCTGGCGCAGGCTCGGCTGGCCTGGGAGGCGCAGCAGGCCCA*TGCCCCCACCCCCACCCCACCAGGGACCTTCTGGGCCTGGCCGGGCCACT	tcga-cancer,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	15	8	144547386	-	8	144395431	-	2.2521	9.3664	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-LN-A4MQ-01A	ENSG00000143614	ENSG00000143552	GATAD2B	NUP210L	GCCGCCTGAGGAGGCGAGCTAGCCGGGAGTTACACCGCCACCGCCAG*GTCATCAGATCCTTAAAGTACATCAGATAAAAGGGACTGTACTGATT	known,tcga,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	1	2	24	1	153922733	-	1	154061674	-	16.8408	0.7942	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-V5-A7RC-01B	ENSG00000043514	ENSG00000284719	TRIT1	AL033527.5	GGGTGGCGGCCGGGCAGAGGCTGCAATCTCGGCACTTTGGGAGGCCAAGG*ATCCAATTCAGTCGCCTTCAAGGAGTCTCTTCAGTCTAATTTATTCTAGA	lincrna	BOWTIE+BOWTIE2	intronic/exonic(no-known-CDS)	0	16	1	36	1	39869477	-	1	39809069	+	320.7302	27.7531	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-V5-A7RC-01B	ENSG00000043514	ENSG00000284719	TRIT1	AL033527.5	GGACAATAGTGGAGGGAAGGTCAGCAGATAAACATGTGAACAAGGGTCTC*CCAAATTACCTTTACAGGCCCAGCATCCAATTCAGTCGCCTTCAAGGAGT	lincrna	BOWTIE+BOWTIE2	intronic/intronic	0	16	1	31	1	39870407	-	1	39809045	+	320.7302	27.7531	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-V5-A7RC-01B	ENSG00000043514	ENSG00000284719	TRIT1	AL033527.5	CTTCCCAGACGGGGTGGCGGCCGGGCAGAGGCTGCAATCTCGGCACTTTG*GGAGTCTCTTCAGTCTAATTTATTCTAGAACAATTCTTCAGGCTTCCCTT	lincrna	BOWTIE+STAR	intronic/exonic(no-known-CDS)	0	16	1	31	1	39869488	-	1	39809090	+	320.7302	27.7531	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-V5-A7RC-01B	ENSG00000043514	ENSG00000284719	TRIT1	AL033527.5	AAAACCGCCATCGTCATCATGGCCCGTTCTCAATGAGCTGCTGGGTACAC*CGCCCGGCAGCCACCCCGTCTGCCAAGTGAGGAGCCCCTCCGCCCGGCAG	lincrna	BOWTIE+BLAT	intronic/intronic	0	16	1	26	1	39870008	-	1	39808290	+	320.7302	27.7531	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-V5-A7RC-01B	ENSG00000043514	ENSG00000284719	TRIT1	AL033527.5	CCCAGACGGGGTGGCGGCCGGGCAGAGGCTGCAATCTCGGCACTTTGGGA*GGCCAAGTTTCAGGAGTCAATAATACCTTGGAAAAATTTAAAAGTTCATT	lincrna	BOWTIE+STAR	intronic/exonic(no-known-CDS)	0	16	1	23	1	39869485	-	1	39804713	+	320.7302	27.7531	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-V5-A7RC-01B	ENSG00000043514	ENSG00000284719	TRIT1	AL033527.5	CAGGCGGCTGGGAGGTGGAGGTTGTAGCGAGCCAAGATCACAACACTGCA*CTCTCCCCTCTCCCTCGTCCCTCGTCTCCCTCGTCTCCCTCATCTCCCTC	lincrna	BOWTIE+STAR	intronic/intronic	0	16	1	20	1	39869427	-	1	39807622	+	320.7302	27.7531	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-V5-A7RC-01B	ENSG00000043514	ENSG00000284719	TRIT1	AL033527.5	TCCACTAAAAATACAAAAAAATTAGTCAAGCATGGTGGTGCATGCCTGTA*GCCTCAGCCTCCCAAAGTGCTGGGATTATAGGTGTGAGTCATTGTGCCTG	lincrna	BOWTIE+STAR	intronic/exonic(no-known-CDS)	0	16	1	16	1	39874804	-	1	39804567	+	320.7302	27.7531	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-V5-A7RC-01B	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	CCGAAATGATCCGCCTGCCTCAGCCTCCAAAGTAGCTGAGACTACAG*ATTCCAGTTCTTTGATGAAAGTCTCTATTCCACCCATCAAGTCTGTG	antisense,m2,exon-exon	BOWTIE	exonic(no-known-CDS)/UTR	0	8	4	28	10	87246115	-	10	46593989	+	1.1464	0.0783	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-V5-A7RC-01B	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	CCGAAATGATCCGCCTGCCTCAGCCTCCAAAGTAGCTGAGACTACAG*CAGTTTAAGTATAGTGTGCCTGGGTTGGGTGCGGTGGCTCACGCCTA	antisense,m2,exon-exon	BOWTIE	exonic(no-known-CDS)/UTR	0	8	2	26	10	87246115	-	10	46593287	+	1.1464	0.0783	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-V5-A7RC-01B	ENSG00000158435	ENSG00000043514	CNOT11	TRIT1	ATTGTGAACCTTTAAACTATTGGGTATTAACAATATAACAATGGGGCCAG*GTCTATGGCTTAGAGGTATCTGATGTCTCGAAGTGGGAAGAGTCTGTTCT	NA	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	14	2	101259761	+	1	39844617	-	24.7337	320.7302	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-V5-A7RC-01B	ENSG00000122490	ENSG00000215421	PQLC1	ZNF407	GGTCCGTGTGGCCAACGAGCTCAACGCCAGGCGCCGCTCCTTTACAG*GTTATGAGTGCCAGTGAGCCGCCTTAGATAGAAGCATCGTCAGCACT	oesophagus,exon-exon	BOWTIE	CDS(truncated)/UTR	0	2	8	29	18	79943329	-	18	74630967	+	7.393	4.4609	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-V5-A7RC-01B	ENSG00000122490	ENSG00000215421	PQLC1	ZNF407	CCGCAGTATCGGGACATTCGCAGGACGCAGAACGCCGACGGCTTCTCCAC*AGCAGCACCAGGCCTGTGCCTCGTCTCCCGGTGACCTGTACAGACACCG	oesophagus	BOWTIE+STAR	CDS(truncated)/intronic	0	2	2	15	18	79950775	-	18	75048158	+	7.393	4.4609	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A43C-01A	ENSG00000103126	ENSG00000129925	AXIN1	TMEM8A	ATTGAGGGGGAAAAGGAGATCAGCAGGCACCGCAGGACCGGCCACGG*GTGCTGTTTCTTCTGGGTACACTGGTCATCGCCATGTCCTTGCAGCT	chimerdb3seq,cancer,tumor,tcga-cancer,oesophagus,10K<gap<100K,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	11	17	30	16	297056	-	16	372727	-	5.0591	21.0501	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A43C-01A	ENSG00000103126	ENSG00000129925	AXIN1	TMEM8A	ATTGAGGGGGAAAAGGAGATCAGCAGGCACCGCAGGACCGGCCACGG*GCTTACCGCTGCGGGCACCGGCGCCAGTGCTACCCCACCTCGTGGCA	chimerdb3seq,cancer,tumor,tcga-cancer,oesophagus,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	11	5	29	16	297056	-	16	372283	-	5.0591	21.0501	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A43C-01A	ENSG00000136758	ENSG00000230445	YME1L1	LRRC37A6P	ACCAGCATCGAGATGTAGTTCCTGAGCATGAGGCTCCCAGCAGTGAG*GAACCTGAAGAAAGATCTAGCTCAGCATTGGAGCATTGCTGATATTG	pseudogene,m3,oesophagus,10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	4	5	29	10	27148906	-	10	27251180	-	25.729	3.8924	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	transcribed_processed_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A43C-01A	ENSG00000136758	ENSG00000230445	YME1L1	LRRC37A6P	TCTTCACCAGGCTGATCTCGAACTCCTGGCCTGAAGCAGTCCTCCCACCT*CAGCCCAGACAGGGGCTCCCACAGTGCAACGGCGGGCTGAAGGGCTCCTC	pseudogene,m3,oesophagus,10K<gap<100K	BOWTIE+STAR	UTR/intronic	0	4	3	24	10	27147261	-	10	27256419	-	25.729	3.8924	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	transcribed_processed_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A43C-01A	ENSG00000136758	ENSG00000230445	YME1L1	LRRC37A6P	AAAACCAGCATCGAGATGTAGTTCCTGAGCATGAGGCTCCCAGCAGTGAG*AGCCTGAAACTCAAAATCCAGAGACCCTTGAAGATATCCAGTCCTCTTCA	pseudogene,m3,oesophagus,10K<gap<100K	BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	4	1	14	10	27148906	-	10	27250962	-	25.729	3.8924	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	transcribed_processed_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A43C-01A	ENSG00000111196	ENSG00000060138	MAGOHB	YBX3	AAGAAGATGATGCTTTGTGGCCTCCCCCTGATAGGGTTGGCCGACAG*GGTGCAGAAGCTGCCAATGTGACTGGCCCGGATGGAGTTCCTGTGGA	chimerdb3seq,oesophagus,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	3	13	29	12	10609831	-	12	10713333	-	2.5855	31.5618	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A43C-01A	ENSG00000111196	ENSG00000060138	MAGOHB	YBX3	GTAACTTAAGTCTTCTGCTTAAAGAAGCATTATTTAGAAAAGCAAAG*GGTGCAGAAGCTGCCAATGTGACTGGCCCGGATGGAGTTCCTGTGGA	chimerdb3seq,oesophagus,10K<gap<100K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	3	1	13	12	10609098	-	12	10713333	-	2.5855	31.5618	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A43J-01A	ENSG00000100241	ENSG00000158526	SBF1	TSR2	ACGCAACACGCTTAGCGGCTTCTCCTCAGCCCACATGGGCAGTCACG*CTGACTTGGAGCTAGATGAGGTGGAAGACTTCCTTGGAGAGCTGTTG	oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	4	5	28	22	50459255	-	X	54443400	+	25.1921	9.7635	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A43J-01A	ENSG00000100241	ENSG00000158526	SBF1	TSR2	GCTAGACTGGCCCCAGGACGGGGTGGCAGATAGGCCCCACACTCACTCCT*CCCCTGCCCAGAACTTGGAACCTCCCAGGAATGCTGCCTTCCTTCAGCCC	oesophagus	BOWTIE+STAR	intronic/UTR	0	4	1	16	22	50458634	-	X	54445074	+	25.1921	9.7635	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A43J-01A	ENSG00000100241	ENSG00000158526	SBF1	TSR2	AGCCGCCTACTTCGGGAGCGTGCCGGGCTGGGCGACCTGGAGAGCGCCAG*ACAGTGTCTTTTGGGTGCGGTCATTGTGAGGAAGGGGATGAGTGAGTGTG	oesophagus	BOWTIE+STAR	CDS(truncated)/UTR	0	4	1	15	22	50462226	-	X	54444803	+	25.1921	9.7635	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-IG-A3YA-01A	ENSG00000115392	ENSG00000233891	FANCL	AC007179.2	ATTATTTTGTGGATTTTCCTGTTCCATTTTGTGCCTCCTGGACACCTCAG*ACGGAGTTTCACTCTTGTCCCCCAGGCTGGAGTGCAATGGCGCGATTTCG	lincrna	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	27	2	58198594	-	2	59363616	-	5.057	0.0822	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A43E-01A	ENSG00000108010	ENSG00000198964	GLRX3	SGMS1	GTCGGCTCAGCCGGGCAGTTTGAGGAGCTGCTGCGCCTCAAAGCCAA*GTAAAGCTTCAGCGACTGAAGGAGTGTGGACTTTTTGAATTTCAAGA	chimerdb3seq,cancer,tcga-cancer,oesophagus,exon-exon	BOWTIE	CDS(truncated)/UTR	0	9	10	26	10	130136512	+	10	50519921	-	7.763	9.8005	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L7-A56G-01A	ENSG00000076321	ENSG00000117593	KLHL20	DARS2	AGTTGCTAAGGATAGCAGACAAGTTCACCCAACATAACTTTCAAGAG*AAATACTTAAAAAGGAAAGACATTGAATCCATTAGAAACTTTGCAGC	chimerdb3seq,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	2	9	26	1	173734286	+	1	173845229	+	4.1717	4.1745	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OT-01A	ENSG00000104375	ENSG00000164919	STK3	COX6C	AAATGGCTGAAGGAAAACCTCCTTATGCTGATATACATCCAATGAGG*TTTCGTGTGGCTGATCAAAGAAAGAAGGCATACGCAGATTTCTACAG	chimerdb3seq,cancer,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	26	30	30	8	98706467	-	8	99887618	-	3.2717	25.8608	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A4OT-01A	ENSG00000104375	ENSG00000164919	STK3	COX6C	TTGTTATAGGGATTAAATAAGAAAATGCTTGTTTGGCCAGGTGTGGTGGC*CCACACCTGGCTAACTTCTTTATTTTTAGTAGAGACAGGGTTTCACCATA	chimerdb3seq,cancer,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/UTR	0	26	1	17	8	98804286	-	8	99886254	-	3.2717	25.8608	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-L5-A4OT-01A	ENSG00000089022	ENSG00000135148	MAPKAPK5	TRAFD1	GTGACTTGATGACACCCCAGTTCACCCCTTATTATGTAGCACCCCAG*GAAGAGCTAAAGATGGCTGAATTTCTAGATGACCAGGAAACTCGACT	prostates,chimerdb3seq,tumor,exon-exon	BOWTIE	CDS(truncated)/UTR	0	10	16	29	12	111871180	+	12	112130511	+	1.7501	9.4962	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OT-01A	ENSG00000089022	ENSG00000135148	MAPKAPK5	TRAFD1	GTGACTTGATGACACCCCAGTTCACCCCTTATTATGTAGCACCCCAG*CAAAAAAGAAATTCCTGTGTTTAACTTTACCATCCATGAGATCCACT	prostates,chimerdb3seq,tumor,exon-exon	BOWTIE	out-of-frame	0	10	2	24	12	111871180	+	12	112134738	+	1.7501	9.4962	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OT-01A	ENSG00000148655	ENSG00000035403	LRMDA	VCL	GTCAAACTCCTACATGTTCCAGGCTCACTCTGAATCAAACACCTACATGT*TTTTTAAATTCAGTCCTAAGAAAGAGGAGTGCTTGTCCCCTAAGAGTGTT	tcga,chimerdb3seq,cancer,tcga-cancer	BOWTIE+STAR	intronic/UTR	0	7	1	14	10	75477506	+	10	74119250	+	0.7351	23.7641	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-L5-A4OT-01A	ENSG00000035403	ENSG00000148655	VCL	LRMDA	ACTGAGGATCAGATTTTGAAGAGAGATATGCCACCAGCATTTATTAA*GTCACTGGAAGGACTGAGCGCATTCAGGAGCCTGGAGGAACTCATCT	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	7	11	30	10	74043153	+	10	76036008	+	23.7641	0.7351	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OT-01A	ENSG00000035403	ENSG00000148655	VCL	LRMDA	ACCACTGAGGATCAGATTTTGAAGAGAGATATGCCACCAGCATTTATTAA*GAGGAAGAGTGAAGAGGTTCCTTCTGGACACTGGGCCCTTGAACTTGAAG	tcga,chimerdb3seq,cancer,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	7	1	19	10	74043153	+	10	75814106	+	23.7641	0.7351	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OT-01A	ENSG00000035403	ENSG00000148655	VCL	LRMDA	ACCACTGAGGATCAGATTTTGAAGAGAGATATGCCACCAGCATTTATTAA*ATAATGCTTTTGGTGTTACATATAAGAAATCCCTGCCGAGGTCATGAAGA	tcga,chimerdb3seq,cancer,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	7	1	16	10	74043153	+	10	75798354	+	23.7641	0.7351	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Esophagus	TCGA-LN-A4A3-01A	ENSG00000120029	ENSG00000181904	C10ORF76	C5ORF24	CACTCACGCCACTGCACTCCAGCCTGGGTGACAGAGTGAGACTCCGTCTC*AAATAAATAAATAAATAAATAAATAAATAAAACCATTTATTGATGTTGCT	NA	BOWTIE+STAR	intronic/UTR	0	2	9	37	10	102030800	-	5	134856653	+	10.2714	14.8366	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-LN-A4A3-01A	ENSG00000120029	ENSG00000181904	C10ORF76	C5ORF24	TAGCTTGGGCAAGAGTGAGACCCTATCTCAAAAAAAAGAAAAAAAAAAAA*TAAATTTCTCCTTTATATTCTAAGAAGCTTTAAAAGAACAATTCAGGGGT	NA	BOWTIE+STAR	intronic/UTR	0	2	1	14	10	102038739	-	5	134859111	+	10.2714	14.8366	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A3-01A	ENSG00000105677	ENSG00000269416	TMEM147	LINC01224	GCTCTTGCCTACTTCCCCTACTTCATCACCTACAAGTGCAGCGGCCT*CACCTGAGTAATTTGACTCTCCTGCCTGGACCCAGCGTACAGATGGG	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	2	5	28	19	35545816	+	19	23405335	-	17.2263	1.4058	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A3-01A	ENSG00000105677	ENSG00000269416	TMEM147	LINC01224	GCTCTTGCCTACTTCCCCTACTTCATCACCTACAAGTGCAGCGGCCT*GAGGAGACTGTAACGTATCCCTAATTGAGCACCCAGGTGGTGTGACA	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	2	3	28	19	35545816	+	19	23406105	-	17.2263	1.4058	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A8I1-01A	ENSG00000177565	ENSG00000043093	TBL1XR1	DCUN1D1	CTCCATTCCCGGGAGGGGGGAGCGGCGTTGGAGGCCACCGTTTCCAG*AACAAGTTGAAATCATCGCAGAAGGATAAAGTTCGTCAGTTTATGAT	oncogene,chimerdb3seq,tumor,m24,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	30	25	29	3	177197121	-	3	182965753	-	55.1909	39.2992	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-LN-A8I1-01A	ENSG00000177565	ENSG00000043093	TBL1XR1	DCUN1D1	GTTGGGTTCAGGAGTGTAGAATTGGCAAAGTTATTGCCAGCTTCCTG*AACAAGTTGAAATCATCGCAGAAGGATAAAGTTCGTCAGTTTATGAT	oncogene,chimerdb3seq,tumor,m24,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	UTR/CDS(truncated)	0	30	6	28	3	177196340	-	3	182965753	-	55.1909	39.2992	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-LN-A8I1-01A	ENSG00000177565	ENSG00000043093	TBL1XR1	DCUN1D1	CTCCATTCCCGGGAGGGGGGAGCGGCGTTGGAGGCCACCGTTTCCAG*ACCCTCAAGATGAGAATAAAATTGGAATAGATGGCATACAGCAGTTC	oncogene,chimerdb3seq,tumor,m24,tcga-cancer,oesophagus,exon-exon	BOWTIE	UTR/CDS(truncated)	0	30	2	26	3	177197121	-	3	182964049	-	55.1909	39.2992	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-LN-A8I1-01A	ENSG00000177565	ENSG00000043093	TBL1XR1	DCUN1D1	TGCCTCCATTCCCGGGAGGGGGGAGCGGCGTTGGAGGCCACCGTTTCCAG*TTTATTTTCTGGTTTCAATAGAACAAGTTGAAATCATCGCAGAAGGATAA	oncogene,chimerdb3seq,tumor,m24,tcga-cancer,oesophagus	BOWTIE+BLAT;BOWTIE+STAR	UTR/intronic	0	30	1	21	3	177197121	-	3	182965774	-	55.1909	39.2992	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-LN-A8I1-01A	ENSG00000053524	ENSG00000177565	MCF2L2	TBL1XR1	AAACACAAAAATTAGCTGGGCATGGTGGCAGGCACCTGTAATCCCAGCTA*CTTAGGAGGTGGAGGCGGGAGGATCACTCTAGCCCAGGAGTTAGAAGGTG	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+BOWTIE2	intronic/UTR	0	15	1	35	3	183316473	-	3	177027123	-	3.4303	55.1909	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A8I1-01A	ENSG00000053524	ENSG00000177565	MCF2L2	TBL1XR1	ACAGGATAAAAAGGTTTGTGGGTTTTTTTTTGTTTTTTTTTTTTTTTTTT*TTTTTTTTTTTTTTTTTCTTTTTTGTTTTTTGGTGATGTGGCTTAAATGC	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/UTR	0	15	1	23	3	183326499	-	3	177024730	-	3.4303	55.1909	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A8I1-01A	ENSG00000053524	ENSG00000177565	MCF2L2	TBL1XR1	CCCTTGTTTTTGTTTGTTTGTTTGCTTGTTTGTTTTTTTTTTTTTTTTTG*TTTTTTTTTTTTTTTTTCTTTTTTGTTTTTTGGTGATGTGGCTTAAATGC	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/UTR	0	15	1	19	3	183280845	-	3	177024730	-	3.4303	55.1909	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A8I1-01A	ENSG00000053524	ENSG00000177565	MCF2L2	TBL1XR1	AAGAGACAAGTGGAGCTCCGTAAAGGCATCCTTGACACGAATAGCTGTAA*GTTTCCTGGAATTGCTATTATTTCAGCTTAGTATTGTAAGTTTATTTGTC	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/intronic	0	15	1	17	3	183341536	-	3	177101811	-	3.4303	55.1909	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A8I1-01A	ENSG00000053524	ENSG00000177565	MCF2L2	TBL1XR1	TAGAAAAAAATTAAAATTTCTGTAAACATTAAAAAGCTACCTGCTAAAAA*AGTTTTTTTTTTCTTTTGAGACGGAGTCTCACTCCGTTGCCCAGGCTGGA	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+STAR	UTR/intronic	0	15	1	17	3	183272483	-	3	177078965	-	3.4303	55.1909	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A8I1-01A	ENSG00000053524	ENSG00000177565	MCF2L2	TBL1XR1	CGAGAGGCATTAAAAACTGTGCAGATCCTGGGGTGTAGAAGTATACCTGG*CTCTTCACAGTTTTTTTTTAAAACTATACTTTGATACTTGGGCTGTTATC	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+STAR	UTR/intronic	0	15	1	15	3	183299830	-	3	177071621	-	3.4303	55.1909	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A8I1-01A	ENSG00000177565	ENSG00000053524	TBL1XR1	MCF2L2	CTCCATTCCCGGGAGGGGGGAGCGGCGTTGGAGGCCACCGTTTCCAG*ATGAAATTATGCAGCAGGAAGTCAGACCCCTGATGGCGGTGGAGATA	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	UTR/CDS(truncated)	0	15	19	30	3	177197121	-	3	183389779	-	55.1909	3.4303	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-LN-A8I1-01A	ENSG00000177565	ENSG00000053524	TBL1XR1	MCF2L2	AGATATACAGTCACTGAAAAAAACAATGCAGTGCTGCCATTGTAGTGCTA*TCTTTTTTAAAAGGTTGGAACCCTTTTATTTACAGATACTCTTCTCAGTA	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/intronic	0	15	3	14	3	177145311	-	3	183273099	-	55.1909	3.4303	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-LN-A8I1-01A	ENSG00000177565	ENSG00000053524	TBL1XR1	MCF2L2	GAAGTTGGGTTCAGGAGTGTAGAATTGGCAAAGTTATTGCCAGCTTCCTG*GACAAGAGGGAAGATTGCTGTCACAATTATCAATAAATCAACAAATTGTG	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+STAR	UTR/intronic	0	15	1	23	3	177196340	-	3	183289084	-	55.1909	3.4303	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-LN-A8I1-01A	ENSG00000177565	ENSG00000053524	TBL1XR1	MCF2L2	TGCCTCCATTCCCGGGAGGGGGGAGCGGCGTTGGAGGCCACCGTTTCCAG*GACAAGAGGGAAGATTGCTGTCACAATTATCAATAAATCAACAAATTGTG	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+STAR	UTR/intronic	0	15	1	18	3	177197121	-	3	183289084	-	55.1909	3.4303	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-LN-A8I1-01A	ENSG00000177565	ENSG00000053524	TBL1XR1	MCF2L2	TAATTTGCATTTCTCTTGCAAGGAGGTTGAGCACTTTTTAATGTTTTAAG*AAACATTAAAAAGCTACCTGCTAAAAATTGTAAGTATCATCATTCAGTTG	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/UTR	0	15	1	17	3	177129362	-	3	183272509	-	55.1909	3.4303	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-LN-A8I1-01A	ENSG00000177565	ENSG00000053524	TBL1XR1	MCF2L2	GCTAAAGCAGCCATAAATAGTACATAAATGAGCTTTTCTGTTCAATTAAA*AAAACTTAAACTGTAATGATCTAAAACCCTGTATCTACTCTGAAAGTAAC	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/UTR	0	15	1	16	3	177145265	-	3	183272672	-	55.1909	3.4303	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-LN-A8I1-01A	ENSG00000177565	ENSG00000053524	TBL1XR1	MCF2L2	ATTGTTGAGTATCGTTCAGTTTAGGTACCACGAAGGTGGTATCTCCTGCT*AGGGAGGTAGTGTGTATTATAGCCACATTTTTATCCTGCTTTGTAAAATA	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/UTR	0	15	1	15	3	177194159	-	3	183272259	-	55.1909	3.4303	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-LN-A8I1-01A	ENSG00000177565	ENSG00000053524	TBL1XR1	MCF2L2	GTATGTGGCTGGTCAGTATAAGTAAGTGATTGTACAGCAACATGCTGTGT*TGTTGGTGAATGTTAATCTCTCCATATTGTTACAATTGTCTGACCTTCCA	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/intronic	0	15	1	15	3	177202147	-	3	183318268	-	55.1909	3.4303	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-LN-A8I1-01A	ENSG00000177565	ENSG00000053524	TBL1XR1	MCF2L2	GATACTGCCCTGCTAGCCTGTCCTGTCCTGTAGCTTTCTCTGTAAACACA*ACTGAGAAATCTTTTTTCGTTTTGTTTTGCGTGTTTCCGACATCACCTTA	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/UTR	0	15	1	14	3	177111036	-	3	183272454	-	55.1909	3.4303	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-LN-A8I1-01A	ENSG00000177565	ENSG00000053524	TBL1XR1	MCF2L2	GGGCTGCAAGGGTCAGAGATGGTCATTACGGTATCTTAATAGAGTAATTT*ACATCTCTTTGATTACAAGGAACATGCAGCTTTAAAAATGCTTTAACCCC	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/UTR	0	15	1	14	3	177188555	-	3	183272180	-	55.1909	3.4303	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-LN-A8I1-01A	ENSG00000177565	ENSG00000053524	TBL1XR1	MCF2L2	TTGGCAGAGCCATTCTCATTTCTATTGGAAATGTGTTCAACTGAATGATT*ATACTGAGAAATCTTTTTTCGTTTTGTTTTGCGTGTTTCCGACATCACCT	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/UTR	0	15	1	14	3	177105585	-	3	183272456	-	55.1909	3.4303	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-LN-A8I1-01A	ENSG00000050344	ENSG00000103544	NFE2L3	C16ORF62	CGGAACCGACGGCTCAGGTGCCGGACGCTGGCGGATGTGCGAGCGAG*CTGATGCTTTTTTCAAAGCCGCTATAAGCCTTGTTCCGGAAGTTCCA	chimerdb3seq,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	8	11	28	7	26153068	+	16	19669160	+	3.8283	22.6886	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A8I1-01A	ENSG00000050344	ENSG00000103544	NFE2L3	C16ORF62	CGGAACCGACGGCTCAGGTGCCGGACGCTGGCGGATGTGCGAGCGAG*GATCATCCTGAACATGGGGTCCTGTTTCTTGTTCGAGAGCTTCTCAA	chimerdb3seq,oesophagus,exon-exon	BOWTIE	in-frame	0	8	5	26	7	26153068	+	16	19682225	+	3.8283	22.6886	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A8I1-01A	ENSG00000102781	ENSG00000179141	KATNAL1	MTUS2-AS1	TTTGCGAAGAAGGTTAGAAAAAAGGATATATATACCTCTCCCAACAG*GTTTACCAAGAAGCTCACTGAGAGGCGACACAAACGGCCAAGAACAT	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	6	18	29	13	30227412	-	13	29476939	-	3.4872	0.8979	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A8I1-01A	ENSG00000173898	ENSG00000173599	SPTBN2	PC	CAGCTCGGCCCGCCTCTTTGAGAGGTCTCGCATTAAGGCTCTGGCAG*ATGCTGAAGTTCCGAACAGTCCATGGGGGCCTGAGGCTCCTGGGAAT	chimerdb3seq,tcga-cancer,oesophagus,100K<gap<200K,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	5	6	28	11	66721084	-	11	66872159	-	8.8504	3.7094	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-IG-A3QL-01A	ENSG00000008382	ENSG00000167670	MPND	CHAF1A	GGCTCCGGCTGCACCAGCTGCACACGCCTGCCACGGCTGCTGATGAG*ATAACTAAGAAATTCGTCAAAGGCTCTACAGAGAAGAACAAGCTCAG	10K<gap<100K,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	10	23	29	19	4345981	+	19	4418020	+	5.5065	13.2949	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3QL-01A	ENSG00000008382	ENSG00000167670	MPND	CHAF1A	GGCTCCGGCTGCACCAGCTGCACACGCCTGCCACGGCTGCTGATGAG*GATCAGGAGCGTCTGGGCAAGCAGCTCAAGTTACGTGCAGAAAGGGA	10K<gap<100K,exon-exon	BOWTIE	in-frame	0	10	3	25	19	4345981	+	19	4422566	+	5.5065	13.2949	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3QL-01A	ENSG00000008382	ENSG00000167670	MPND	CHAF1A	CCTGGCTCCGGCTGCACCAGCTGCACACGCCTGCCACGGCTGCTGATGAG*GCTGCTGCCGCTTTGCAAAATTTCGTCCTGTGATGTGAGCCATTTAGCAA	10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	10	2	32	19	4345981	+	19	4412198	+	5.5065	13.2949	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000173801	ENSG00000178502	JUP	KLHL11	CCATCGTGAAGCTGCTCAACCAGCCCAACCAGTGGCCACTGGTCAAG*GTTCCTACTCATTCGTTTAAAAGAATTTTGTGGAGAATTTCTCAAGA	oncogene,chimerdb3seq,oesophagus,10K<gap<100K,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	32	28	29	17	41762983	-	17	41855321	-	717.4112	18.6988	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000173801	ENSG00000178502	JUP	KLHL11	CGCCAGTACACGCTCAAGAAAACCACCACTTACACCCAGGGGGTGCCCCC*ATTATCTGGGTGGCCAGGCACAGTGGCTCACGCCTGTAATCCCAGCACTT	oncogene,chimerdb3seq,oesophagus,10K<gap<100K	BOWTIE+STAR	CDS(truncated)/intronic	0	32	1	17	17	41771655	-	17	41858744	-	717.4112	18.6988	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000131473	ENSG00000166483	ACLY	WEE1	GAGATGGGCATTGGCGGGGTCCTCGGCCTCCTCTGGTTCCAGAAAAG*AGAACTCAAGAAAGCACAGATGGCAAAAGCTGCAGCTGAGGAAAGAG	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	25	26	30	17	41873811	-	11	9588449	+	227.9234	20.9781	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000131473	ENSG00000166483	ACLY	WEE1	CTGTACATGGAACTTTGTGTAAAATGCCTTGGGTGACAGAAGTCAGACTC*GTAGGATGTGTCACTGTTGGATGTTACACCAGCCTTTCCAGGGTTAACCA	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/UTR	0	25	1	14	17	41902622	-	11	9588806	+	227.9234	20.9781	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000157388	ENSG00000163938	CACNA1D	GNL3	GGGAAGGCATCCGGACATTGCTGTGGACTTTTATTAAGTCCTTTCAG*ATCTGGTACCAAAGGAGAATTTGGAGAGCTGGCTAAATTATTTGAAG	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	14	8	30	3	53770552	+	3	52690592	+	2.8408	62.496	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000157388	ENSG00000163938	CACNA1D	GNL3	GGGAAGGCATCCGGACATTGCTGTGGACTTTTATTAAGTCCTTTCAG*CGTGTGAAGGCAAAGAAGAATGCTGCTCCATTCAGAAGTGAAGTCTG	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	14	3	27	3	53770552	+	3	52690945	+	2.8408	62.496	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000157388	ENSG00000163938	CACNA1D	GNL3	TTAAGTCCTTTCAGGTAAGAGCCATGCCAAGGACTTCTCTCTTTGTCTTT*GGAATTGAAATAGAGAAGTGCAGATGCTGAGCTCTGTTAAGATACGGGCA	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+BLAT;BOWTIE+STAR	intronic/intronic	0	14	1	20	3	53770588	+	3	52690069	+	2.8408	62.496	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000157388	ENSG00000163938	CACNA1D	GNL3	TAGAAAGTAGTAATTTCCAGACATTTGAGATCTGATTCACCAACATTACT*CATCTGAAAGGCAATGTAGTTATCTTAAGAGCTGGGCTCTGGAGCCTGAT	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/UTR	0	14	1	16	3	53633922	+	3	52690830	+	2.8408	62.496	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000117148	ENSG00000161533	ACTL8	ACOX1	CTGTTTCTGAGAGCAGCTTTTGTGGCATCTTACAGGGCAGATTTCTG*AGAACATGATCCTGAACGACCCAGACTTCCAGCATGAGGACTTGAAC	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	UTR/CDS(complete)	0	11	15	29	1	17755504	+	17	75978693	-	15.2418	16.6741	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000117148	ENSG00000161533	ACTL8	ACOX1	CTGTTTCTGAGAGCAGCTTTTGTGGCATCTTACAGGGCAGATTTCTG*TTTTGTGCACCGAGGGCGGCCTGAGCCTCTGGATCTTCACTTGGGCA	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE	UTR/CDS(truncated)	0	11	3	24	1	17755504	+	17	75960375	-	15.2418	16.6741	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000117148	ENSG00000161533	ACTL8	ACOX1	CTGTTTCTGAGAGCAGCTTTTGTGGCATCTTACAGGGCAGATTTCTG*ACTACATTTGGTCAATTTTGTGGAACCTGTGGGCCTCAATTACTCCA	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE	UTR/CDS(truncated)	0	11	2	25	1	17755504	+	17	75973785	-	15.2418	16.6741	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000117148	ENSG00000161533	ACTL8	ACOX1	GGGTTCAATCAATTCTCCTGCTTCAGCCTCCCGAGTAGCTAGGACTAAAG*AGAACATGATCCTGAACGACCCAGACTTCCAGCATGAGGACTTGAACTTC	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(complete)	0	11	1	25	1	17800737	+	17	75978693	-	15.2418	16.6741	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000117148	ENSG00000161533	ACTL8	ACOX1	CTGTTTCTGAGAGCAGCTTTTGTGGCATCTTACAGGGCAGATTTCTG*GAACTCACCTTCGAGGCTTGGAAACCACAGCCACGTATGACCCTGAA	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE	UTR/CDS(truncated)	0	11	1	13	1	17755504	+	17	75957566	-	15.2418	16.6741	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000132155	ENSG00000187753	RAF1	C9ORF153	GGAGTGGTTCTCAGCAGGTTGAACAACCTACTGGCTCTGTCCTCTGGATG*GTCAGCAATTTGCCCTGTGACCTTACTTCTCTGCCAGATCTAAGAAGAGT	oncogene,tcga,cancer,tumor,tcga-cancer,oesophagus	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	10	14	37	3	12585681	-	9	86234992	-	7.9094	2.9417	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000132155	ENSG00000187753	RAF1	C9ORF153	CAGCTATTTGCATGCAAAGAACATCATCCATAGAGACATGAAATCCAACA*CCGAACATGATTCCTGTACTGGCTCTTCTGGAGGCTTCTGCCCTGTTCTC	oncogene,tcga,cancer,tumor,tcga-cancer,oesophagus	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/intronic	0	10	4	32	3	12587591	-	9	86235107	-	7.9094	2.9417	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000132155	ENSG00000187753	RAF1	C9ORF153	CAGCTATTTGCATGCAAAGAACATCATCCATAGAGACATGAAATCCAACA*TTTGGAACGTTCTGTTGAGATATCCTCAAGCTCGGACATTCTGTCCTCAG	oncogene,tcga,cancer,tumor,tcga-cancer,oesophagus	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/intronic	0	10	4	29	3	12587591	-	9	86235452	-	7.9094	2.9417	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000132155	ENSG00000187753	RAF1	C9ORF153	ATGTTCCAGCTAATTGACATTGCCCGGCAGACGGCTCAGGGAATGGA*GAATTAGAGAATAAAATCCCAGCACGATGTTCCTCACTGGAGACACC	oncogene,tcga,cancer,tumor,tcga-cancer,oesophagus,exon-exon	BOWTIE	CDS(truncated)/UTR	0	10	4	25	3	12590798	-	9	86229629	-	7.9094	2.9417	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000132155	ENSG00000187753	RAF1	C9ORF153	GTGGTTCTCAGCAGGTTGAACAACCTACTGGCTCTGTCCTCTGGATG*GAATTAGAGAATAAAATCCCAGCACGATGTTCCTCACTGGAGACACC	oncogene,tcga,cancer,tumor,tcga-cancer,oesophagus,exon-exon	BOWTIE	CDS(truncated)/UTR	0	10	3	27	3	12585681	-	9	86229629	-	7.9094	2.9417	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000132155	ENSG00000187753	RAF1	C9ORF153	CAGCTATTTGCATGCAAAGAACATCATCCATAGAGACATGAAATCCAACA*TTTCAGATATTTCTTTAGAGCAATTCAAGAATGGACTAATACAGGTATAA	oncogene,tcga,cancer,tumor,tcga-cancer,oesophagus	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/intronic	0	10	1	30	3	12587591	-	9	86229798	-	7.9094	2.9417	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000185022	ENSG00000089902	MAFF	RCOR1	GAGACGCGCGTGTGTGAGCGCGCCGGACCAAGCGGGCCCAGAAGCGG*CCAAACTGGCAAGACGCAGTCAAGAACGGGACAATCTTGGCATGTTG	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	UTR/CDS(truncated)	0	9	16	30	22	38202212	+	14	102681895	+	5.3896	21.1419	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000185022	ENSG00000089902	MAFF	RCOR1	ACCAAGCGGGCCCAGAAGCGGGTGAGGAACGCGGGACCAGGAGGACG*CCAAACTGGCAAGACGCAGTCAAGAACGGGACAATCTTGGCATGTTG	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE	UTR/CDS(truncated)	0	9	1	13	22	38202238	+	14	102681895	+	5.3896	21.1419	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000089902	ENSG00000185022	RCOR1	MAFF	AGGTTCAAGGGATTCTCCTGCCTCAGGCTCCCAAGTAGCTGGGACTACAG*GCAGGAGGATCACTTAAGCCCAGAAGGCAGAGGTTGTAGTGAGCTGAGAT	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/UTR	0	9	1	21	14	102617732	+	22	38216279	+	21.1419	5.3896	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000089902	ENSG00000185022	RCOR1	MAFF	ATCCCCTGCGCTCAAGTAATCCTTAGCCTCCCAAGTAGCTGGGACTACAG*GCAGGAGGATCACTTAAGCCCAGAAGGCAGAGGTTGTAGTGAGCTGAGAT	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/UTR	0	9	1	21	14	102625007	+	22	38216279	+	21.1419	5.3896	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000007545	ENSG00000187535	CRAMP1	IFT140	CGCTGTGGGGAGCGGCAACGCCGGTGGCTCGGGGCCCCGCGGAAAAG*GGGACTGTCAAACAACTCCTCCTTTTCTCGGAGACTGAGGGGAATCC	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	8	11	29	16	1614985	+	16	1571534	-	1.8655	3.8966	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000007545	ENSG00000187535	CRAMP1	IFT140	CATTCTCAACCGAAGAAGGCTGGCCTCCGGAATCATGGCCTTACTCATTG*GGGACTGTCAAACAACTCCTCCTTTTCTCGGAGACTGAGGGGAATCCCTG	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	8	4	33	16	1616067	+	16	1571534	-	1.8655	3.8966	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000007545	ENSG00000187535	CRAMP1	IFT140	CGCTGTGGGGAGCGGCAACGCCGGTGGCTCGGGGCCCCGCGGAAAAG*GCTGACAACAGCCCTGATTCCAAAATCTGCTTCTACGATGTTGAAAT	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE	out-of-frame	0	8	2	23	16	1614985	+	16	1566291	-	1.8655	3.8966	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000007545	ENSG00000187535	CRAMP1	IFT140	CCCGGGGAGGCCCCGGGAAGCCAGGCTGCCGCCCGGCGTTGATGAAAAAG*GGGACTGTCAAACAACTCCTCCTTTTCTCGGAGACTGAGGGGAATCCCTG	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	8	1	36	16	1612657	+	16	1571534	-	1.8655	3.8966	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000177885	ENSG00000142623	GRB2	PADI1	CCAGAAACCAGCAGATATTCCTGCGGGACATAGAACAGGTGCCACAG*GTTAACATGGTGGTCTTAGGCAAGTACCTGGGCATCCCCAAGCCCTA	chimerdb3seq,cancer,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	8	11	29	17	75321659	-	1	17244010	+	56.7694	1.9434	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000177885	ENSG00000142623	GRB2	PADI1	ACCGGAACGTCTAAGAGTCAAGAAGCAATTATTTAAAGAAAGTGAAAAAT*GTTAACATGGTGGTCTTAGGCAAGTACCTGGGCATCCCCAAGCCCTACGG	chimerdb3seq,cancer,tcga-cancer,oesophagus	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	8	2	28	17	75320332	-	1	17244010	+	56.7694	1.9434	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000177885	ENSG00000142623	GRB2	PADI1	AAAATAAGTTAAAGGCAGTCCAGAGCTTTTCAGCCAATTTGTCTCCTACT*AAATGTTCCATATCGGTACAATACAGTCCAGTAGCCACTCAGCTACCACC	chimerdb3seq,cancer,tcga-cancer,oesophagus	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	UTR/intronic	0	8	1	30	17	75319252	-	1	17242311	+	56.7694	1.9434	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000133943	ENSG00000198752	C14ORF159	CDC42BPB	TCCCCAGAAGAGACCCAGCAGGTCACAGCCAGGCGGGTGCATACAAG*AGACATTAAACCTGACAATGTCCTTTTGGACGTGAATGGTCATATCC	chimerdb3seq,oesophagus,exon-exon	BOWTIE	in-frame	0	4	3	25	14	91170201	+	14	102986580	-	9.2503	23.5235	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000133943	ENSG00000198752	C14ORF159	CDC42BPB	TCCTGGACATCTGTTGGTAAAGTCTGAGAGTTCACTCTGCTCCATCAGTG*GACTCCATCCATCAGCTTCATTACGTGCACAGGTAACCGGCTTCTGATAT	chimerdb3seq,oesophagus	BOWTIE+BLAT	intronic/CDS(truncated)	0	4	1	32	14	91170827	+	14	102999596	-	9.2503	23.5235	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000133943	ENSG00000198752	C14ORF159	CDC42BPB	GCTCCCCAGAAGAGACCCAGCAGGTCACAGCCAGGCGGGTGCATACAAGG*GACTGTTGTCATGTACAGGATCACCATGGGCTTGGGTCTGTTTCTGGATC	chimerdb3seq,oesophagus	BOWTIE+STAR	intronic/intronic	0	4	1	14	14	91170202	+	14	102960732	-	9.2503	23.5235	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000119487	ENSG00000167112	MAPKAP1	TRUB2	CTCGGCCTCCTAAAGTGCTGGGATTACAGGCATGAGCCACCACACCCAGC*CTGTTTTTGTTTTTTAGACAGGGTCTTGCTCTGTCACCCAGGCTGGAGTG	chimerdb3seq,oesophagus	BOWTIE+BOWTIE2	intronic/UTR	0	4	1	34	9	125664444	-	9	128307915	-	6.2401	7.7482	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000119487	ENSG00000167112	MAPKAP1	TRUB2	CCTGTCTCTACTAAAAATACAAAAAATTAGCCAGGCGTGGTGGCGGGCGC*TTGTAATCCCAGCTACTCCCAAGGCTGAGGCAGGAGAATTGCTTGAGCCC	chimerdb3seq,oesophagus	BOWTIE+STAR	intronic/UTR	0	4	1	16	9	125678386	-	9	128309304	-	6.2401	7.7482	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000138758	ENSG00000136895	SEPT11	GARNL3	TTCCCACTGATGAAGAAACGGTGGCAGAGATTAACGCAACAATGAGT*GACAGCTGCCCAGCCTCCAGGCCCACTGATGGACCCGTTAACGAAGG	exon-exon	BOWTIE	CDS(truncated)/UTR	0	4	10	30	4	77015017	+	9	127243079	+	17.6149	1.9896	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000167112	ENSG00000119487	TRUB2	MAPKAP1	GACCCTCACAGCCACCAGCGTACCCTCTTTCATCAACCATCCACTGG*GGTCATGTAGGTACAACAGCAACCAAGAAGATCGATGTCTACCTCCC	chimerdb3seq,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	4	6	30	9	128321599	-	9	125585727	-	7.7482	6.2401	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000105372	ENSG00000007129	RPS19	CEACAM21	TTTAGTACCGCAGCACAAACCACCTGGAGGATAGGTGGGTCCTGTGTCCC*TCTCTGTTTTTACAGGAATTGCTACACTCTGACACAAACATTTACTGCTG	ribosomal	BOWTIE+STAR	intronic/UTR	0	3	21	37	19	41865499	+	19	41586449	+	98.3426	3.3135	TRUE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000105372	ENSG00000007129	RPS19	CEACAM21	CAAAGAGCTTGCTCCCTACGATGAGAACTGGTTCTACACGCGAGCTG*GAATTGCTACACTCTGACACAAACATTTACTGCTGGATCGACCACAA	ribosomal,exon-exon	BOWTIE	CDS(truncated)/UTR	0	3	5	30	19	41861212	+	19	41586464	+	98.3426	3.3135	TRUE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000105372	ENSG00000007129	RPS19	CEACAM21	TCAAAAGCTGGGGCTGGAACCTTGGTCTCCAGGGGGTGAGGAAAAAG*GAATTGCTACACTCTGACACAAACATTTACTGCTGGATCGACCACAA	ribosomal,exon-exon	BOWTIE	UTR/UTR	0	3	4	30	19	41864899	+	19	41586464	+	98.3426	3.3135	TRUE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000105372	ENSG00000007129	RPS19	CEACAM21	GCACAAAGAGCTTGCTCCCTACGATGAGAACTGGTTCTACACGCGAGCTG*GTTCCTCTGGGAGCTGCTCCTGTGGGTTGATGGAGCGTCCCTGAAGCCCC	ribosomal	BOWTIE+STAR	CDS(truncated)/UTR	0	3	1	15	19	41861212	+	19	41586530	+	98.3426	3.3135	TRUE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000072786	ENSG00000137216	STK10	TMEM63B	AGATCGTGGGCGAGCTGGGCGACGGCGCCTTCGGCAAGGTTTACAAG*CATCAGGCCTACGAGTTCCAGTTTGGCGCAGCCTACGCCTGGATGAT	exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	3	3	28	5	172187887	-	6	44152593	+	8.2979	19.8229	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000072786	ENSG00000137216	STK10	TMEM63B	GGGAGATCGTGGGCGAGCTGGGCGACGGCGCCTTCGGCAAGGTTTACAAG*ATTGAGCACACGGAGACAGATACTGTGGACCCCAGAAGCAATGGACGGCC	exon-exon	BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	3	1	20	5	172187887	-	6	44154365	+	8.2979	19.8229	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000137216	ENSG00000072786	TMEM63B	STK10	GGTCATCAATGTCGTCCTCTTCATCCTCCTCTTCTTCCTCACCACTCCAG*GGTGATGATGATGATGGTAATGGTAATGATGGTGGTGATGGTAATGATGG	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	3	1	17	6	44148886	+	5	172099024	-	19.8229	8.2979	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000137216	ENSG00000072786	TMEM63B	STK10	GGTCATCAATGTCGTCCTCTTCATCCTCCTCTTCTTCCTCACCACTCCAG*GGTGGTGGTGATGATGGTAATGGTAATGATGGTGGTGATGGTGGTGGTGA	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	3	1	17	6	44148886	+	5	172098946	-	19.8229	8.2979	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000137216	ENSG00000072786	TMEM63B	STK10	TTGTTCCAACCCCGTGCCACCAACCAGCTCCCAAAAACCCCTGTGTGCAC*CTCTGGGTTTTTGGGGTTTTGTGGTTTTTTGGGTTTTGGGGATTTTTGTT	NA	BOWTIE+STAR	UTR/intronic	0	3	1	15	6	44149093	+	5	172060472	-	19.8229	8.2979	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000137216	ENSG00000072786	TMEM63B	STK10	ACACTTTCCTCATCTTCATGGTGCTGCTCCTACCCTCGCTGGGACTGAGC*CAGCGGAAGGAAAGCATGAAGCAGAAGATGGAGGAGCACACGCAGAAAAA	NA	BOWTIE+STAR	in-frame	0	3	1	14	6	44150308	+	5	172064779	-	19.8229	8.2979	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000137216	ENSG00000072786	TMEM63B	STK10	CAAAGCTGGAGCAGAAGCTGAAGGAAGACTACAAGCGGGAGAAGGAGAAG*AATGTTTATTCTGCTTCTCCCGTGTTTCATGCCATCTCGCGTCCCCCTTC	NA	BOWTIE+STAR	CDS(truncated)/UTR	0	3	1	14	6	44148323	+	5	172044267	-	19.8229	8.2979	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000137216	ENSG00000072786	TMEM63B	STK10	CTCTTCATCCTCCTCTTCTTCCTCACCACTCCAGCCATCATCATCACCAC*AGGCTGGGTGAGGTCGGTGTGTCCACAACAGTGTTCTGAGGGCTGTGCAC	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	3	1	14	6	44148902	+	5	172104370	-	19.8229	8.2979	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000183117	ENSG00000138768	CSMD1	USO1	TCAAAATTCACATAGAAAGTATAGATTACAAAGAAAACCAATTATATTAA*CACACAGTGATGTGGAGGGCATTCCGGAGAAACTTTTGCAACAGTGTATT	NA	BOWTIE+STAR	intronic/UTR	0	2	1	19	8	4198714	-	4	75813901	+	1.025	26.5166	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000185507	ENSG00000099991	IRF7	CABIN1	CCTAGAGCTGGCCGCGGCCGCCCAGTCTAATAAAAAGAACTCCAGAACAC*TCAGCCATCCTTTCTGCCCAGTCTGCTGCCAACGTGAGGAAGGAGAGCCT	oncogene	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	UTR/CDS(truncated)	0	2	3	24	11	612554	-	22	24178053	+	38.509	16.5193	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000185507	ENSG00000099991	IRF7	CABIN1	ACCTGTCAGCTGGGAGGCCCAAGGAGAAGAGCCTGGTCCTGGTGAAG*TCAGCCATCCTTTCTGCCCAGTCTGCTGCCAACGTGAGGAAGGAGAG	oncogene,exon-exon	BOWTIE	in-frame	0	2	1	14	11	612999	-	22	24178053	+	38.509	16.5193	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000171360	ENSG00000131473	KRT38	ACLY	AATGAGATTGCCACGTACCGGAACCTTCTGGAAAGCGAGGACTGCAA*ACGCCAGCCCCCAGCAGGACAGCATCTTTTTCTGAGTCCAGGGCCGA	oesophagus,exon-exon	BOWTIE	out-of-frame	0	2	2	26	17	41438093	-	17	41897839	-	0.1997	227.9234	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000189050	ENSG00000062725	RNFT1	APPBP2	ATATATTTTGATTCTGAGCGTCAAACTTGTTATGCAGCATATAACAG*GTTGCTTCATGTGCGAAATGGAAACTGCAAATATCATTTGGGTGAAG	exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	2	4	21	17	59962827	-	17	60466459	-	6.1194	6.8615	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000138768	ENSG00000183117	USO1	CSMD1	CTGGCCTTGGCCTCCCAAGGATTACAGGCATGAGCCACCGCACCCAGCCT*AGAACCAGCCCTCCCCAGCAACAGCATCAAAATCGGAGATCGGTACATGG	NA	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	25	4	75806285	+	8	3162255	-	26.5166	1.025	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000138768	ENSG00000183117	USO1	CSMD1	ATGTAGAACACACATCTTTTATTTAAATCCATCTGAACTGTCCCAAAATG*CACACACACACACACATACACACATATATTTATACATTTAATCATATATA	NA	BOWTIE+STAR	UTR/intronic	0	2	1	23	4	75813524	+	8	3342915	-	26.5166	1.025	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000138768	ENSG00000183117	USO1	CSMD1	TGGTTTACCTCCATGGAAAATAAAGATTTAGAAACCAGGTGGAAAACATT*ACAAAAATATATAAGTATAATTATAAAAATTATATTTATAGTATAATTAT	NA	BOWTIE+STAR	UTR/intronic	0	2	1	17	4	75813406	+	8	3237918	-	26.5166	1.025	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000138768	ENSG00000183117	USO1	CSMD1	AGAAACTTTTGCAACAGTGTATTAATGTGATTGGTTTTCTTTTTGTTTTA*AATTACTAGCTTAAAACTAACCCTATACCCCCTACTGTCTTCCACTCTTG	NA	BOWTIE+STAR	UTR/intronic	0	2	1	17	4	75813977	+	8	3045956	-	26.5166	1.025	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000138768	ENSG00000183117	USO1	CSMD1	ACTTCTCATGTCCATGGTTAATGAAAGGCAGCCATTTGTTTTGCGCTGTG*TCTTATTTATTGTTTTTCTTGAAAAGTGTTTTGTTTAAATCAATTATATA	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	16	4	75790707	+	8	3403218	-	26.5166	1.025	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OS-01A	ENSG00000138768	ENSG00000183117	USO1	CSMD1	AGTTAACAGTTCATACAACTCAGATTTAGTAGTATTGTTTATCATAAAAC*TGGGAACATAATATAACTAACTGAATTAATTTCTGCAGTTCGCTGTGCTG	NA	BOWTIE+STAR	UTR/intronic	0	2	1	14	4	75814052	+	8	3174186	-	26.5166	1.025	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3YB-01A	ENSG00000132879	ENSG00000177674	FBXO44	AGTRAP	CAGACCCGGCGACCATCCAGCAGAAGAGCGATGCCAAGTGGAGGGAG*GGGCTGCATTGTATTCTCAGGCTCCTATGCCTGGGCCAACTTCACCA	chimerdb3seq,10K<gap<100K,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	15	23	28	1	11658871	+	1	11747440	+	9.7287	13.8699	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3YB-01A	ENSG00000132879	ENSG00000177674	FBXO44	AGTRAP	AACTCCATCTCAACAAAAAAAGAAAAGAAAAGAAAAAAAATTCCAAAAGG*GGCTGCATTGTATTCTCAGGCTCCTATGCCTGGGCCAACTTCACCATCCT	chimerdb3seq,10K<gap<100K	BOWTIE+BOWTIE2	intronic/CDS(truncated)	0	15	1	24	1	11659417	+	1	11747441	+	9.7287	13.8699	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3YB-01A	ENSG00000132879	ENSG00000177674	FBXO44	AGTRAP	AGCCAGACCCGGCGACCATCCAGCAGAAGAGCGATGCCAAGTGGAGGGAG*GCGGAGCCCATGGGATTTGCTGGCACACAGCCGGGTGGCCTCGAAGACTA	chimerdb3seq,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	15	1	22	1	11658871	+	1	11747291	+	9.7287	13.8699	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3YB-01A	ENSG00000168280	ENSG00000198648	KIF5C	STK39	ACAAATTCATCCCCAAATTTAAAGGCGATGAGACCGTGGTGATCGGG*GCAGTGGAGCTACTGCTGTGGTTCAGGCAGCCCTATGCAAACCCAGG	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	8	9	28	2	148875743	+	2	168182090	-	0.1095	6.5268	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3YB-01A	ENSG00000115904	ENSG00000163214	SOS1	DHX57	CTGAAAATGATTCGACATACCACCAACCTCACTCTGTGGTTTGAGAA*GGGTTAGCAAGTCAGTCATCAAAACAATGTCCATCATGGATTTTGAA	tcga,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	7	14	29	2	39010584	-	2	38837947	-	2.746	1.5577	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3YB-01A	ENSG00000115904	ENSG00000163214	SOS1	DHX57	CTTCTGAAAATGATTCGACATACCACCAACCTCACTCTGTGGTTTGAGAA*GGAAGATCAACCACTTATCATTTTCTCAAAGGAACCTAAAGGTTCAGCGA	tcga,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/intronic	0	7	1	16	2	39010584	-	2	38838773	-	2.746	1.5577	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3YB-01A	ENSG00000149179	ENSG00000149418	C11ORF49	ST14	GCCTCGACCTCCCAAAATGCTGGGATTACAGGTGTGAGCCACCGCTCCTG*CACCCCTTCTTCAATGACTTCACCTTCGACTATGACATCGCGCTGCTGGA	NA	BOWTIE+STAR	intronic/CDS(truncated)	0	3	1	15	11	47044283	+	11	130208513	+	3.9969	63.9476	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3YB-01A	ENSG00000149179	ENSG00000149418	C11ORF49	ST14	AGGGAAGATATTAGCCAATATGGAATTGCCAGGTTCTTCACTGAATA*AAAGTGAATGGCTTGGAGGAAGGCGTGGAGTTCCTGCCAGTCAACAA	exon-exon	BOWTIE	out-of-frame	0	3	1	14	11	46987310	+	11	130188114	+	3.9969	63.9476	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3YB-01A	ENSG00000163694	ENSG00000183783	RBM47	KCTD8	GGTGTTAATTTCTGAAGTGGGCGGCTCCAAAAACTTAACAAGGAAAG*GACCACCTCAGAAAATAGTATCACCTAAACAAGAACATGAAGATAGG	oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	UTR/CDS(truncated)	0	3	6	27	4	40629396	-	4	44175250	-	25.5838	1.1175	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3YB-01A	ENSG00000163694	ENSG00000183783	RBM47	KCTD8	CGCGTGACGCTCCTGCCTGCGCGCGGCCAAGCCATGCTCGGCCCCAG*GACCACCTCAGAAAATAGTATCACCTAAACAAGAACATGAAGATAGG	oesophagus,exon-exon	BOWTIE	UTR/CDS(truncated)	0	3	3	18	4	40630463	-	4	44175250	-	25.5838	1.1175	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3YB-01A	ENSG00000163694	ENSG00000183783	RBM47	KCTD8	AATGGTGTTAATTTCTGAAGTGGGCGGCTCCAAAAACTTAACAAGGAAAG*AACCTGAATCACTTGCATCTCAGCTCCACACTATAAAGACCATTTGTTAT	oesophagus	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	UTR/intronic	0	3	1	35	4	40629396	-	4	44311727	-	25.5838	1.1175	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-IG-A3YB-01A	ENSG00000278540	ENSG00000133392	ACACA	MYH11	ACGCCATTCTCCTGCCTCAGCCTCCCTAGTAGCTGGGACTACAGATGCCT*ACCACCACCCCTACTACCCCTGTATTCAAGGTAAAAATTGAAGTTTGTAT	cancer,tumor	BOWTIE+STAR	intronic/UTR	0	2	4	22	17	37394758	-	16	15703597	-	10.5631	341.5466	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-IG-A3YB-01A	ENSG00000278540	ENSG00000133392	ACACA	MYH11	CTCAAGCAATCCTCCCACCTCAGCCACCCAAGTAGCTGGGACTACAG*AGGGCCCCCCCCACAGGAAACTTCGCAGTGATGCACCAGGCGAGGAA	cancer,tumor,exon-exon	BOWTIE	UTR/CDS(truncated)	0	2	3	20	17	37369370	-	16	15708841	-	10.5631	341.5466	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-IG-A3YB-01A	ENSG00000278540	ENSG00000133392	ACACA	MYH11	ACGCCATTCTCCTGCCTCAGCCTCCCTAGTAGCTGGGACTACAGATGCCT*ACCACCACCCTCCAGCCTGGGCAACGTAGTAAAACCTCATCTATACAAGA	cancer,tumor	BOWTIE+STAR	intronic/UTR	0	2	2	35	17	37394758	-	16	15703814	-	10.5631	341.5466	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-IG-A3YB-01A	ENSG00000278540	ENSG00000133392	ACACA	MYH11	CATGCAATTCTTCTGTCTCAGCCTCCCAAGTAGCTGGGACTACAGGTGTG*AACCACCACCCTCCAGCCTGGGCAACGTAGTAAAACCTCATCTATACAAG	cancer,tumor	BOWTIE+BOWTIE2	intronic/UTR	0	2	2	34	17	37281736	-	16	15703815	-	10.5631	341.5466	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-IG-A3YB-01A	ENSG00000278540	ENSG00000133392	ACACA	MYH11	GGAGTCTTGCTCTTGTCACCCAGGCTGGAGTGCAATGGCGCAATTTTGGC*TCATTGCACTCCAGCCTGGGCAACAGAGACCCTGTCTCAACCACCACCAC	cancer,tumor	BOWTIE+STAR	intronic/UTR	0	2	1	30	17	37368527	-	16	15703648	-	10.5631	341.5466	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-IG-A3YB-01A	ENSG00000278540	ENSG00000133392	ACACA	MYH11	GCCTGCTGGTGTCTGCTGGTCTGTTCCTCTGCTCCTCTTGATGTTCAATC*GTGCCCGGCAGCAGCTCGAGCGGCAGAACAAGGAGCTCCGGAGCAAGCTC	cancer,tumor	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	21	17	37322657	-	16	15717290	-	10.5631	341.5466	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-IG-A3YB-01A	ENSG00000278540	ENSG00000133392	ACACA	MYH11	GGAAGGGGGCGTTGCGGGTTGGGTCTGATTGCATTGAAAGTCCTTTCTCT*CAGCCTGCAAGACCAGCTGGACGAGGAGATGGAGGCCAAGCAGAACCTGG	cancer,tumor	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	17	17	37358544	-	16	15724725	-	10.5631	341.5466	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-IG-A3YB-01A	ENSG00000278540	ENSG00000133392	ACACA	MYH11	AGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCTAGTA*GCTGAGCCAGGAAGAACGCTCCAGCCCAGGACTTCGAGGCTGCAATGAGC	cancer,tumor	BOWTIE+STAR	intronic/UTR	0	2	1	16	17	37394777	-	16	15703708	-	10.5631	341.5466	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-IG-A3YB-01A	ENSG00000278540	ENSG00000133392	ACACA	MYH11	GAGCTTGCAGTGAGCTGAGATCGCACCACTGCACTCCAGCCTGGGCAACG*AAGCAAAACCCAGCAGACTGTACTTAGCATTGTCTAAATCCATTCTCAAA	cancer,tumor	BOWTIE+STAR	intronic/UTR	0	2	1	15	17	37381663	-	16	15703905	-	10.5631	341.5466	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-IG-A3YB-01A	ENSG00000278540	ENSG00000133392	ACACA	MYH11	GAGGTTACAATGAGCCAAGATCTTGCCATTCCACTCCAGCCTGGGCAACG*AAGCAAAACCCAGCAGACTGTACTTAGCATTGTCTAAATCCATTCTCAAA	cancer,tumor	BOWTIE+STAR	intronic/UTR	0	2	1	15	17	37405588	-	16	15703905	-	10.5631	341.5466	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-IG-A3YB-01A	ENSG00000278540	ENSG00000133392	ACACA	MYH11	TAGCAGGAAAAACCTGAACCTGATATAGGAATGATGGAGACACTAGGGAA*ATGCGGGTGCGGCTGGCGGCCAAGAAGCAGGAGCTGGAGGAGATACTGCA	cancer,tumor	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	14	17	37366202	-	16	15741597	-	10.5631	341.5466	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-IG-A3YB-01A	ENSG00000278540	ENSG00000133392	ACACA	MYH11	TAAAAAAAAAAAAGAATTTAGGGAAGTTATTATCTTCCTGCATCTCCTTT*TGCTGCAGGTGACACGGCAGGAGGAGGAGATGCAGGCCAAGGAGGATGAA	cancer,tumor	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	14	17	37398949	-	16	15741881	-	10.5631	341.5466	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-IG-A3YB-01A	ENSG00000278540	ENSG00000133392	ACACA	MYH11	AATTCCAGTTGTACTGTCTTAAAGACACAGCTCTTTGCTCATTCTCTGCC*ATGAACTGCAGAAGACCAAGGAGCGGCAGCAGAAGGCAGAGAATGAGCTT	cancer,tumor	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	14	17	37361628	-	16	15741836	-	10.5631	341.5466	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3YB-01A	ENSG00000133392	ENSG00000278540	MYH11	ACACA	CGGTGTCTGGACTTTTTCTTGGTACTTTTCAACGCTTATCCCATTTTCTG*AAAGTGGTGGGGGACAATTCTCAGTCCAGGAAAATGCATTGACCATTGCT	cancer,tumor	BOWTIE+STAR	intronic/UTR	0	2	1	15	16	15814233	-	17	37085595	-	341.5466	10.5631	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-IG-A50L-01A	ENSG00000171940	ENSG00000088888	ZNF217	MAVS	CGACCAAATGACAAAAAAACTTGATTCACTAATTAGGGGGAAAAAAG*GGACCTCGGACCGTCCCCCAGACCCACTGGAGCCACCGTCACTTCCT	oncogene,chimerdb3seq,cancer,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	UTR/CDS(truncated)	0	16	12	29	20	53571721	-	20	3861332	+	12.7526	18.6365	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-IG-A50L-01A	ENSG00000171940	ENSG00000088888	ZNF217	MAVS	CACTTGTGTGCCTGCTGGTAGTCCAGCATCCAGCTCGACGTTAGAAG*GGACCTCGGACCGTCCCCCAGACCCACTGGAGCCACCGTCACTTCCT	oncogene,chimerdb3seq,cancer,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	16	5	29	20	53575727	-	20	3861332	+	12.7526	18.6365	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-IG-A50L-01A	ENSG00000171940	ENSG00000088888	ZNF217	MAVS	CGACCAAATGACAAAAAAACTTGATTCACTAATTAGGGGGAAAAAAG*AATTCAGAGCAAGCCCTGCAGACGCTCAGCCCCAGAGCCATCCCAAG	oncogene,chimerdb3seq,cancer,tcga-cancer,oesophagus,exon-exon	BOWTIE	UTR/CDS(truncated)	0	16	3	25	20	53571721	-	20	3862254	+	12.7526	18.6365	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-IG-A50L-01A	ENSG00000171940	ENSG00000088888	ZNF217	MAVS	CACTTGTGTGCCTGCTGGTAGTCCAGCATCCAGCTCGACGTTAGAAG*AATTCAGAGCAAGCCCTGCAGACGCTCAGCCCCAGAGCCATCCCAAG	oncogene,chimerdb3seq,cancer,tcga-cancer,oesophagus,exon-exon	BOWTIE	out-of-frame	0	16	3	23	20	53575727	-	20	3862254	+	12.7526	18.6365	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-IG-A50L-01A	ENSG00000171940	ENSG00000088888	ZNF217	MAVS	GCCTGAGTGCAGTGGCACGATCTCGGCTCACTGAAACCTCCTTCTCCTGG*GTTCAAGTGATTCTCCTGCTTCAGCCTCTCAAGTAGCTGGGATTACAGAT	oncogene,chimerdb3seq,cancer,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/UTR	0	16	1	37	20	53574718	-	20	3870976	+	12.7526	18.6365	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-IG-A50L-01A	ENSG00000171940	ENSG00000088888	ZNF217	MAVS	TATTTTTAGTAGAGATGGGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAA*CTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGAGGCCTGCCACCAC	oncogene,chimerdb3seq,cancer,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/UTR	0	16	1	21	20	53603537	-	20	3869712	+	12.7526	18.6365	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-IG-A50L-01A	ENSG00000171940	ENSG00000088888	ZNF217	MAVS	TTATTGCAGCCTCAACCTCCCTGGCTCAAGTGATCCTCCCACCTCATCCT*GCTTCCTTTGAGCAACATTATTTATTATGAACTTTCAAACACAAAAAAGT	oncogene,chimerdb3seq,cancer,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/UTR	0	16	1	18	20	53600411	-	20	3870721	+	12.7526	18.6365	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-IG-A50L-01A	ENSG00000171940	ENSG00000088888	ZNF217	MAVS	AACCTCCTGAGTAGCTGGGACTACAGGTGCCCGCCACCACGCCTGGCTAA*TTGGGAGGCTGAGGTGGGAGGATCACTTGAGCCCAGAAGCTTGAAGCTGC	oncogene,chimerdb3seq,cancer,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/UTR	0	16	1	17	20	53602032	-	20	3867487	+	12.7526	18.6365	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-IG-A50L-01A	ENSG00000171940	ENSG00000088888	ZNF217	MAVS	TTTGGAACCCAGGGCTGTTAGAGGGGTGAGTGACAAGTCTTACAAGTGGC*TTCCTCCATCTCCGTCCTGCCTCCCCCATCCCCAGGTGCCATTCCCACAC	oncogene,chimerdb3seq,cancer,tcga-cancer,oesophagus	BOWTIE+STAR	UTR/UTR	0	16	1	16	20	53582871	-	20	3875790	+	12.7526	18.6365	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-IG-A50L-01A	ENSG00000171940	ENSG00000088888	ZNF217	MAVS	TGCCAACCACCATGCCCAGCTAATTTTTTTTTTTTTTTTTGAGACAGTCT*CACTCCAACCTGGGTGAGAGAGCGAGACCCTGTCTCAAGAAAAAGAAAAA	oncogene,chimerdb3seq,cancer,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/UTR	0	16	1	16	20	53602168	-	20	3867560	+	12.7526	18.6365	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-IG-A50L-01A	ENSG00000171940	ENSG00000088888	ZNF217	MAVS	GGGCATGTCAGCACCTGGAAGTCAAAGAAGAGAGTCTAAAGAAGGAGCCA*AGACTCAGACCCTCCTGCCTCACAGCTTTATCTTTGTATTTGCCCCTTAC	oncogene,chimerdb3seq,cancer,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/UTR	0	16	1	16	20	53599834	-	20	3867648	+	12.7526	18.6365	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-IG-A50L-01A	ENSG00000171940	ENSG00000088888	ZNF217	MAVS	CGATTTTGTTCCCAATCAGTATCTGGCAATGTCTGGAGGCATTTTGGTTG*GTGCCTTCTAATGCGCTCACCAATCCAGCACCATCCAAATTGCCCATCAA	oncogene,chimerdb3seq,cancer,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/CDS(truncated)	0	16	1	14	20	53581072	-	20	3864636	+	12.7526	18.6365	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-L5-A4OM-01A	ENSG00000100554	ENSG00000072121	ATP6V1D	ZFYVE26	GTCAGAATGTCGGGCAAAGACCGAATTGAAATCTTTCCCTCGCGAAT*GTAACAGCACTAACATTGTTGAAAGAAGAAGACTTCCCAAATCTTGG	chimerdb3seq,cancer,tcga-cancer,oesophagus,exon-exon	BOWTIE	out-of-frame	0	2	12	30	14	67359658	-	14	67805618	-	8.2323	6.7503	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OM-01A	ENSG00000100554	ENSG00000072121	ATP6V1D	ZFYVE26	TCAGAATGTCGGGCAAAGACCGAATTGAAATCTTTCCCTCGCGAATGTAA*CAGCAACCCCATACCAAAGAGAGATCTGTTGTATCATTTACACGGTGGAG	chimerdb3seq,cancer,tcga-cancer,oesophagus	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	intronic/intronic	0	2	1	30	14	67359654	-	14	67804267	-	8.2323	6.7503	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OM-01A	ENSG00000100554	ENSG00000072121	ATP6V1D	ZFYVE26	GCTGCACCTTGTTCAGACCTGTGTTAATACCGGTCATCACGCTGTAAAGT*CACATAGCTGCCTATAACAGCTTTCTTTGACTTACAGGTAACAGCACTAA	chimerdb3seq,cancer,tcga-cancer,oesophagus	BOWTIE+BOWTIE2	intronic/intronic	0	2	1	28	14	67359004	-	14	67805655	-	8.2323	6.7503	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OM-01A	ENSG00000072121	ENSG00000100554	ZFYVE26	ATP6V1D	TACCTATGCAGAGAAGGTCACAGAAAAGCCACCGAGGGCTACAGCCTCGG*TGGCTTTTCTTTTACAGAATTCCAGATTCTGCATGAATAGCAGGAAAAAA	chimerdb3seq,cancer,tcga-cancer,oesophagus	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	15	14	67807404	-	14	67305650	-	6.7503	8.2323	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A8NN-01A	ENSG00000174547	ENSG00000136153	MRPL11	LMO7	TTTAAAAGTGTGTAGCACCTACCTCATTTCTCTTTCTCCTGCTCTGGTTG*ATATTTTTCTTCCTTGCCCATGTGCTGCAACACAGGAAGCTCTGATTCGG	ribosomal,cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	15	11	66450531	-	13	75840050	+	19.0456	3.4713	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000130479	ENSG00000086548	MAP1S	CEACAM6	GGTCTTTGTGTCCCGACACTCTGCCACCTTCTCCAGCATTGTGAAAG*GAAGTGCTCCTGTCCTCTCAGCTGTGGCCACCGTCGGCATCACGATT	oncogene,chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	813	35	30	19	17721037	+	19	41766183	+	26.0243	288.5029	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000130479	ENSG00000086548	MAP1S	CEACAM6	AGACCCTGGTCCTCCTGAACCCATCAGACAAGTCCCTGTATGATGAG*ATTGGACCAGACCCTGAATTCTTCTAGCTCCTCCAATCCCATTTTAT	oncogene,chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	CDS(truncated)/UTR	0	813	27	29	19	17724208	+	19	41770802	+	26.0243	288.5029	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000130479	ENSG00000086548	MAP1S	CEACAM6	TGGAGACCCTGGTCCTCCTGAACCCATCAGACAAGTCCCTGTATGATGAG*GAAGTGCTCCTGTCCTCTCAGCTGTGGCCACCGTCGGCATCACGATTGGA	oncogene,chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	813	10	19	19	17724208	+	19	41766183	+	26.0243	288.5029	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000130479	ENSG00000086548	MAP1S	CEACAM6	GGTCTTTGTGTCCCGACACTCTGCCACCTTCTCCAGCATTGTGAAAG*ATTGGACCAGACCCTGAATTCTTCTAGCTCCTCCAATCCCATTTTAT	oncogene,chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	CDS(truncated)/UTR	0	813	7	28	19	17721037	+	19	41770802	+	26.0243	288.5029	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000130479	ENSG00000086548	MAP1S	CEACAM6	GCGGGCGCCGAGAACGCCGGGGCGGCCCGAAGATGGCGGCGGTGGCTGGA*GATGGACAACTCAATGAAAATTTAAAGGGAAAACCCTCAGGCCTGAGGTG	oncogene,chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+BOWTIE2	CDS(truncated)/UTR	0	813	1	24	19	17719520	+	19	41770905	+	26.0243	288.5029	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000170919	ENSG00000177359	TPT1-AS1	AC024940.1	CAGATTTGAGCTTTCTTCTTGGACACCTAATACCCAGAGTCCTCCAG*GCCACCCTTAAGTACAATGTTCTCCTACCTAAGAAGGCATCTGGATT	m61,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	158	34	30	13	45377215	+	12	31116469	-	1.0919	45.3433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	processed_transcript	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000170919	ENSG00000177359	TPT1-AS1	AC024940.1	CAGATTTGAGCTTTCTTCTTGGACACCTAATACCCACAGTCCTCCAG*GCCACCCTTAAGTACAATGTTCTCCTACCTAAGAAGGCATCTGGATT	m61,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	158	28	30	13	45378671	+	12	31116469	-	1.0919	45.3433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	processed_transcript	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000170919	ENSG00000177359	TPT1-AS1	AC024940.1	CGGCAGATTTGAGCTTTCTTCTTGGACACCTAATACCCAGAGTCCTCCAG*TAAGGTACCTGCCGTGGGCAGATCTGAGCTTTCTTCTTGGACACCCCATA	m61	BOWTIE+BLAT;BOWTIE+BOWTIE2	exonic(no-known-CDS)/intronic	0	158	16	37	13	45377215	+	12	31117484	-	1.0919	45.3433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	processed_transcript	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000170919	ENSG00000177359	TPT1-AS1	AC024940.1	CAGATTTGAGCTTTCTTCTTGGACACCTAATACCCACAGTCCTCCAA*GCCACCCTTAAGTACAATGTTCTCCTACCTAAGAAGGCATCTGGATT	m61,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	158	5	18	13	45381217	+	12	31116469	-	1.0919	45.3433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	processed_transcript	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000170919	ENSG00000177359	TPT1-AS1	AC024940.1	TGGCAGATTTGAGCTTTCTTCTTGGACACCTAATACCCACAGTCCTCCAG*TAAGGTACCTGCCGTGGGCAGATCTGAGCTTTCTTCTTGGACACCCCATA	m61	BOWTIE+STAR	exonic(no-known-CDS)/intronic	0	158	4	37	13	45378671	+	12	31117484	-	1.0919	45.3433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	processed_transcript	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000170919	ENSG00000177359	TPT1-AS1	AC024940.1	CAGCAGATTTGAGCTTTCTTCTTGGACACCTAATACCCACAGTCCTCCAG*TAAGGTACCTGCCGTGGGCAGATCTGAGCTTTCTTCTTGGACACCCCATA	m61	BOWTIE+STAR	exonic(no-known-CDS)/intronic	0	158	4	37	13	45380001	+	12	31117484	-	1.0919	45.3433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	processed_transcript	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000170919	ENSG00000177359	TPT1-AS1	AC024940.1	TGGCAGATTTGAGCTTTCTTCTTGGACACCTAATACCCACAGTCCTCCAG*TAAGGTACCTGCCGTGGGCAGATCTGAGCTTTCTTCTTGGACACCCCATA	m61	BOWTIE+STAR	exonic(no-known-CDS)/intronic	0	158	4	37	13	45379335	+	12	31117484	-	1.0919	45.3433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	processed_transcript	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000170919	ENSG00000177359	TPT1-AS1	AC024940.1	TCAGCAGATTTGAGCTTTCTTCTTGGACACCTAATACCCACAGTCCTCCA*GTAAGGTACCTGCCGTGGGCAGATCTGAGCTTTCTTCTTGGACACCCCAT	m61	BOWTIE+BLAT	exonic(no-known-CDS)/intronic	0	158	1	32	13	45381216	+	12	31117485	-	1.0919	45.3433	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	processed_transcript	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000116017	ENSG00000105618	ARID3A	PRPF31	AGCCGCCTGACCACGGCGACTGGACTTACGAGGAGCAGTTTAAGCAG*GGCCTGGAGATTGTGAACCCACAGGCGGCAGAGAAGAAGGTGGCTGA	oncogene,chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	157	35	30	19	932742	+	19	54131307	+	11.6617	16.4427	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000116017	ENSG00000105618	ARID3A	PRPF31	GGGCCAGGAGAGGAGCACTTTGAGGACATGGCCTCCGACGAGGACAT*GGCCTGGAGATTGTGAACCCACAGGCGGCAGAGAAGAAGGTGGCTGA	oncogene,chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE	in-frame	0	157	8	29	19	929896	+	19	54131307	+	11.6617	16.4427	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000116017	ENSG00000105618	ARID3A	PRPF31	GAGGAGGATTACGAGGATGAGGAGGAGGAGGAGGACGAGGAGGGGCTGGG*GATTGTGAACCCACAGGCGGCAGAGAAGAAGGTGGCTGAGGCCAACCAGA	oncogene,chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+BOWTIE2	in-frame	0	157	1	35	19	932528	+	19	54131315	+	11.6617	16.4427	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000173276	ENSG00000160182	ZBTB21	TFF1	AGTGTGAGCGGAAAGGGGCCCGGCGTCTGCCTCGAGACTGAAGACCG*AGACGTGTACAGTGGCCCCCCGTGAAAGACAGAATTGTGGTTTTCCT	chimerdb3seq,cancer,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	91	21	27	21	42010252	-	21	42363407	-	2.158	24.0679	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000173276	ENSG00000160182	ZBTB21	TFF1	AATCCAGGAAGGCTTTGGGAAGCTATTTGTGTGCGAGGATCAAAGTG*AGACGTGTACAGTGGCCCCCCGTGAAAGACAGAATTGTGGTTTTCCT	chimerdb3seq,cancer,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	UTR/CDS(truncated)	0	91	20	29	21	42002897	-	21	42363407	-	2.158	24.0679	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000173276	ENSG00000160182	ZBTB21	TFF1	CCCTTTTTACTTACATTCTTGATGGATGGAGCATTTTATATTTTTAG*AGACGTGTACAGTGGCCCCCCGTGAAAGACAGAATTGTGGTTTTCCT	chimerdb3seq,cancer,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	UTR/CDS(truncated)	0	91	14	29	21	42002350	-	21	42363407	-	2.158	24.0679	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000123810	ENSG00000115255	B9D2	REEP6	CGGTTTCTCGGAAAGTAGCCTCTTCTGCAAGTGGGGCATTCACACAG*GAGCCGTCACTCTGCTAAGCCTGTATCTGCTGTTCGGCTACGGAGCG	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	75	32	30	19	41363432	-	19	1495294	+	1.553	26.0392	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000163331	ENSG00000130702	DAPL1	LAMA5	TGACTCTTCTCAGTTTGTTTGTCTAAGGATGTTCAAGTTTTCACTTGAGG*CCTCAGGACCACCCGAGACTCCTACCAGTTTGGGGGTTCCCTGTCCAGTC	m2	BOWTIE+STAR	intronic/CDS(truncated)	0	46	1	14	2	158816280	+	20	62311251	-	2.3894	62.5886	FALSE	TRUE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000130702	ENSG00000163331	LAMA5	DAPL1	CACGGCCACGCGGATGCCTGCGATGCCAAAGACCCCACGGACCCGTTCAG*CTCAGAGGATCCAGAACGGCTGTTCCTGTCCATGTGCCTGGTCACGG	m2,exon-exon	BOWTIE;BOWTIE+STAR	CDS(truncated)/CDS(no-known-start-or-end)	0	46	27	37	20	62351704	-	2	158862409	+	62.5886	2.3894	TRUE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000130702	ENSG00000163331	LAMA5	DAPL1	TGGGCCATCTCATGGGGAAGGCGCTGCGGGACCCCACGGTCACCCGCCGG*AGATGGGGTGTCCCTATGTTGTCCGAGCTGATCTTGAGGTCCTGGCTCCT	m2	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/intronic	0	46	2	25	20	62351909	-	2	158838755	+	62.5886	2.3894	TRUE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000130702	ENSG00000163331	LAMA5	DAPL1	CACGGCCACGCGGATGCCTGCGATGCCAAAGACCCCACGGACCCGTTCAG*GAGTGCTAAGAAAGTTCATTGGTGGAAAAGCAGCCTTTTCAAGAAATGGT	m2	BOWTIE+STAR	CDS(truncated)/intronic	0	46	1	15	20	62351704	-	2	158857119	+	62.5886	2.3894	TRUE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000071626	ENSG00000167380	DAZAP1	ZNF226	CACGGAGGTAGTCATGATCTATGACGCCGAGAAGCAGAGGCCCCGAG*ATACCTTACTTGTAAAAGCTCTTTTGCTCTATGACCTGGCTCAAACT	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	44	28	28	19	1422396	+	19	44174984	+	16.1436	3.0671	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000071626	ENSG00000167380	DAZAP1	ZNF226	TCAGACACTCCTGCAGTTTGCGAAAATGTCTACTTCTAAATACGTTGTTT*CAGTGCATAGGTCTTCATGCTTTCCTTTCACCCCAAGTGATTATCAACTT	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+BLAT;BOWTIE+STAR	intronic/UTR	0	44	12	37	19	1423703	+	19	44174830	+	16.1436	3.0671	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000071626	ENSG00000167380	DAZAP1	ZNF226	CACGGAGGTAGTCATGATCTATGACGCCGAGAAGCAGAGGCCCCGAG*GAGAGAAAAATCAAAGTAAGTTAATTACTGTTCAAGACAGAGAATCA	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE	in-frame	0	44	6	22	19	1422396	+	19	44175498	+	16.1436	3.0671	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000135525	ENSG00000237499	MAP7	AL357060.2	CGGCGACGGCCACAGGGGCGGCGACGGCGCAGTGCGAAGCGAAACAG*GGCAAGAATCTTCTGTTCCATATGCAACATCTTCTGGCAGCCTTGTC	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	44	16	30	6	136550342	-	6	137824577	-	41.3361	4.0201	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000135525	ENSG00000237499	MAP7	AL357060.2	TGGCGGCGACGGCCACAGGGGCGGCGACGGCGCAGTGCGAAGCGAAACAG*TTCCCCTCAGCCTTTTGAGTGTTGGTCGCTGATCGTGGTTATGGAGGAGG	antisense	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	44	2	19	6	136550342	-	6	137825938	-	41.3361	4.0201	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000142453	ENSG00000105499	CARM1	PLA2G4C	CGAGGTGCGCGCCGGCCCGGACTCGGCGGGCATCGCCCTCTACAGCC*ACCATCCGGGCTACCACTGACTACTGCCGCCGCCACAAGATCCCCTT	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	41	23	30	19	10871922	+	19	48055049	-	18.5146	3.5367	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000142453	ENSG00000105499	CARM1	PLA2G4C	CGAGGTGCGCGCCGGCCCGGACTCGGCGGGCATCGCCCTCTACAGCC*GCTCTACTACCCGAAGGATAGTGCCCGAAGTTGCTGCTTGGCATAGA	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE	in-frame	0	41	6	29	19	10871922	+	19	48048388	-	18.5146	3.5367	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000142453	ENSG00000105499	CARM1	PLA2G4C	TACCATTTGGACAACGGCTTCTACAGCTACCAGCTACTCCCCCGCCCCAG*ACCATCCGGGCTACCACTGACTACTGCCGCCGCCACAAGATCCCCTTTCC	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	intronic/CDS(truncated)	0	41	3	31	19	10894576	+	19	48055049	-	18.5146	3.5367	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000142453	ENSG00000105499	CARM1	PLA2G4C	CGAGGTGCGCGCCGGCCCGGACTCGGCGGGCATCGCCCTCTACAGCC*GTGATATTGAGGCATGGAGTGACACATACGACACATTCAAGCTTGCT	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE	in-frame	0	41	2	26	19	10871922	+	19	48053147	-	18.5146	3.5367	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000142453	ENSG00000105499	CARM1	PLA2G4C	TGCCTGCTAGCCCTGCAGCCTGTCCCCCACCTCTCCAGGCCATGTGCACA*TCACTCCCTTCAGCCACACGCTTCATGGCCTTGAGTTCACCTTGGCTGTC	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/UTR	0	41	1	14	19	10898448	+	19	48048266	-	18.5146	3.5367	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000105499	ENSG00000142453	PLA2G4C	CARM1	TCTTTAAAAGTCCTGTCTCCAGATACAACCCCATGGGGGATGAGGGCTTC*CACAACGGACGTGACATGCTGCTTTTTTTAATTTTATTTTTTTATGAAAA	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/UTR	0	41	1	14	19	48067963	-	19	10922174	+	3.5367	18.5146	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000105287	ENSG00000167487	PRKD2	KLHL26	CTCCACGCCAGTGAGGAGGAGGAAGGCGAGGGAGGCAAGGCCCAGAG*GGCCATGTTCACCGGCGGCATGCGGGAGGCAAGCCAGGACGTCATCG	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	40	27	30	19	46700799	-	19	18667664	+	11.5657	10.691	TRUE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000163328	ENSG00000138430	GPR155	OLA1	TACGGAGACAGGCTGGTACAAGGGGGAGTCATCCAACATATTACCAACGA*CAAAATTCCTGCCTTTCTAAATGTGGTGGATATTGCTGGCCTTGTGAAAG	chimerdb3seq,oesophagus,100K<gap<200K	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	in-frame	0	29	5	37	2	174436267	-	2	174223160	-	10.2578	38.6967	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000163328	ENSG00000138430	GPR155	OLA1	GGAGGCGCAGGTTGCAGTGAACCAAGATCACATCACTGCACTTCAACCTG*GGAGACAGGGTCTCGCTCTGTCACCCAGGCTGGAGTGCATGGCGTGATCG	chimerdb3seq,oesophagus,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	29	2	29	2	174434648	-	2	174128400	-	10.2578	38.6967	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000163328	ENSG00000138430	GPR155	OLA1	CCTTATATAAAATGGTGTAGGCCGGGCATGGTGGCTCACGCCTGTAATCC*CAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCACCCACCTCGGCCTC	chimerdb3seq,oesophagus,100K<gap<200K	BOWTIE+BLAT	UTR/intronic	0	29	1	37	2	174435743	-	2	174214859	-	10.2578	38.6967	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000163328	ENSG00000138430	GPR155	OLA1	ACGCCTGTAATCCCAGTACTTTGGGAGGCCGAGTCAGGTGGATCACCTGA*CTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGC	chimerdb3seq,oesophagus,100K<gap<200K	BOWTIE+BLAT	UTR/intronic	0	29	1	37	2	174435706	-	2	174225963	-	10.2578	38.6967	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000163328	ENSG00000138430	GPR155	OLA1	TACTCAGGAGGCTGAGGCAGGAGAATCGCTTGAATCTGGGAGGCAGAGGT*TGCAGTGGCACGATCTCGGCTCACCGCAACCTCTGCCTCCCGGGTTCAAG	chimerdb3seq,oesophagus,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	UTR/intronic	0	29	1	24	2	174435552	-	2	174147392	-	10.2578	38.6967	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000163328	ENSG00000138430	GPR155	OLA1	TTTCTTTTTTCCATTTCCTTGACAAATAGTACTCATTTAAAAACTAGAGG*GCTGAGATTACAGGCGTGAGCCACTGCACCCGGACGAGGCAGCTTTAACT	chimerdb3seq,oesophagus,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	29	1	23	2	174434928	-	2	174225303	-	10.2578	38.6967	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000163328	ENSG00000138430	GPR155	OLA1	TTTCTTTTTTCCATTTCCTTGACAAATAGTACTCATTTAAAAACTAGAGG*GCTGAGATTACAGGCGTGAGCCACCACTCCCAACCAAGACCTGATTTTTC	chimerdb3seq,oesophagus,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	29	1	23	2	174434928	-	2	174096910	-	10.2578	38.6967	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000163328	ENSG00000138430	GPR155	OLA1	GAGGAAATAAAAATGACCTGTCAACAATTTATCCATTATCACCGTGACCT*TCTTTCCTTGTCAATATTGATACTTTATTTTTTAGCAGCTATACAGATTT	chimerdb3seq,oesophagus,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/intronic	0	29	1	15	2	174439928	-	2	174210009	-	10.2578	38.6967	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000163328	ENSG00000138430	GPR155	OLA1	GAGGCGCAGGTTGCAGTGAACCAAGATCACATCACTGCACTTCAACCTGG*GAGTCAGGGTCTTGCTATGTTATCCGGGCTGGTCTTGAACTCCTGGACTC	chimerdb3seq,oesophagus,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	29	1	15	2	174434647	-	2	174219275	-	10.2578	38.6967	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000163328	ENSG00000138430	GPR155	OLA1	AAAATAAAAATTGTGGGACTCGGACTCCTGCGTGTATTACAGAACCCAAT*GAAGACAATAAATTTATATGTTAACTTACTTACATGTTTTGAATCTTCCC	chimerdb3seq,oesophagus,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/intronic	0	29	1	14	2	174473169	-	2	174186196	-	10.2578	38.6967	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000138430	ENSG00000163328	OLA1	GPR155	TTTTTTATCTCATATTAGTGCCTGTGATGGCATCTTTCATCTAACAC*GCCTTCTAGCAATTTCTTTGTTTCTTTTGAAAAAGCGAGAGAGGGTA	chimerdb3seq,oesophagus,100K<gap<200K,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	29	17	29	2	174223033	-	2	174461672	-	38.6967	10.2578	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000138430	ENSG00000163328	OLA1	GPR155	TTTTTTATCTCATATTAGTGCCTGTGATGGCATCTTTCATCTAACAC*AATTCCTGCTCTCCTTGTTGGTGTTCTTTTGATAACTGGAAAACACA	chimerdb3seq,oesophagus,100K<gap<200K,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	29	7	29	2	174223033	-	2	174461492	-	38.6967	10.2578	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000138430	ENSG00000163328	OLA1	GPR155	TTTTTTATCTCATATTAGTGCCTGTGATGGCATCTTTCATCTAACAC*ATGATCACCACAGCAGTCACCCTGTTCTGCAGCATCCTGATAGCTGG	chimerdb3seq,oesophagus,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	29	2	24	2	174223033	-	2	174460088	-	38.6967	10.2578	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000196235	ENSG00000131848	SUPT5H	ZSCAN5A	CTTTTAGTTTTCCATCTTTTCCCTCCCTGGTGCTCATTGGAATCTGAG*GGTGACCCGTGTGGTATATACTCCCAGAATTGAATACTAACTCCTGTGTC	m21,oesophagus	BOWTIE+STAR	UTR/intronic	0	22	33	37	19	39476572	+	19	56227653	-	27.7153	4.6931	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000196235	ENSG00000131848	SUPT5H	ZSCAN5A	GATCCTGGGCGAGGATCGGGAAGCCACGGGCGTCCTACTGAGCATTGATG*ATATGGCTGCAAATTGCACATCCTCATGGAGTCTAGGAGAATCCTGCAAC	m21,oesophagus	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/UTR	0	22	27	37	19	39476313	+	19	56225048	-	27.7153	4.6931	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000196235	ENSG00000131848	SUPT5H	ZSCAN5A	TTCCTTTTAGTTTTCCATCTTTTCCCTCCCTGGTGCTCATTGGAATCTGA*ATATGGCTGCAAATTGCACATCCTCATGGAGTCTAGGAGAATCCTGCAAC	m21,oesophagus	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	UTR/UTR	0	22	2	29	19	39476571	+	19	56225048	-	27.7153	4.6931	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000196235	ENSG00000131848	SUPT5H	ZSCAN5A	TCAAGATCCTCAACCTCCGCTTCCTGGGGAAGCTCCTGGAAGCCTGAAGC*AGATATGGCTGCAAATTGCACATCCTCATGGAGTCTAGGAGAATCCTGCA	m21,oesophagus	BOWTIE+STAR	UTR/UTR	0	22	1	29	19	39476402	+	19	56225050	-	27.7153	4.6931	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A891-01A	ENSG00000131848	ENSG00000196235	ZSCAN5A	SUPT5H	AGGAAGGCTAAGGCAGGAGAATTGCTTGAACCCTGGAAGCGGAGGTTGCA*GATCGGGAAGCCACGGGCGTCCTACTGAGCATTGATGGTGAGGATGGCAT	m21,oesophagus	BOWTIE+STAR	intronic/CDS(truncated)	0	22	1	16	19	56260291	-	19	39476277	+	4.6931	27.7153	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000010310	ENSG00000126254	GIPR	RBM42	CCGCAGGGAGTGCCAGGAGACCTTGGCAGCCGCGGAACCGCCTTCAG*ATGACTTCCGGATCTTCTGTGGGGATCTGGGCAATGAGGTGAACGAT	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	20	18	29	19	45670734	+	19	35637158	+	0.346	23.1386	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000010310	ENSG00000126254	GIPR	RBM42	TGCTGCTGCGGCTCTCACTGTGCGGGCTGCTGCTCCAGAGGGCGGAG*GCCAAGGTGATCCGTGACAAGCGCACAGGCAAGACCAAGGGCTACGG	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	20	2	17	19	45669592	+	19	35637250	+	0.346	23.1386	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000132002	ENSG00000130529	DNAJB1	TRPM4	CCTTAAAGGTAGATCACTGATTCACAGGGGAGCAGGCGGAGGCAAGG*GCTGACCCCGGGTTTGTACCACCTGGGCCGCACTGTCCTCTGCATCG	oesophagus,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	18	19	30	19	14527687	-	19	49200300	+	17.3676	12.7207	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000132002	ENSG00000130529	DNAJB1	TRPM4	TTTTATATTTTTAGCAGAGATGGGGTTTCACCATGTTGGCCAGGCTGGTC*CTGCGGGGGGCGCCGGTGCCTACGCCGCTGGTTCCACTTCTGGGGCGCGC	oesophagus	BOWTIE+STAR	intronic/CDS(truncated)	0	18	5	34	19	14519168	-	19	49196515	+	17.3676	12.7207	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000132002	ENSG00000130529	DNAJB1	TRPM4	GCCAAACGCGATCGTGTTGCCTACAATTGAGGAAACAGAGGCCTTGAAAG*GCTGACCCCGGGTTTGTACCACCTGGGCCGCACTGTCCTCTGCATCGACT	oesophagus	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	18	3	37	19	14519795	-	19	49200300	+	17.3676	12.7207	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000132002	ENSG00000130529	DNAJB1	TRPM4	GGAATTCACAGGCCTGTCATGAGAGACACGATGAGAAGTCCTTAAAG*GCTGACCCCGGGTTTGTACCACCTGGGCCGCACTGTCCTCTGCATCG	oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	UTR/CDS(truncated)	0	18	2	16	19	14527726	-	19	49200300	+	17.3676	12.7207	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000132002	ENSG00000130529	DNAJB1	TRPM4	TTTTGCATTTTTAATAGAGATGGGGTTTCACCATGTTGGCCAGGCTGGTC*CTGCGGGGGGCGCCGGTGCCTACGCCGCTGGTTCCACTTCTGGGGCGCGC	oesophagus	BOWTIE+STAR	intronic/CDS(truncated)	0	18	1	34	19	14524646	-	19	49196515	+	17.3676	12.7207	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000132002	ENSG00000130529	DNAJB1	TRPM4	GGACCTTGGGAGATGCGCTTCCGTCCAGATCCTCACCTTGCTTTAGGAGG*CTGACCCCGGGTTTGTACCACCTGGGCCGCACTGTCCTCTGCATCGACTT	oesophagus	BOWTIE+BOWTIE2	intronic/CDS(truncated)	0	18	1	25	19	14519480	-	19	49200301	+	17.3676	12.7207	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000132002	ENSG00000130529	DNAJB1	TRPM4	CAGTCTTCCGTCCCAAAATCCTTCTCCCCACGGTTGGGAGAATAGCGCTG*GCTGACCCCGGGTTTGTACCACCTGGGCCGCACTGTCCTCTGCATCGACT	oesophagus	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	18	1	20	19	14519418	-	19	49200300	+	17.3676	12.7207	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000198858	ENSG00000105639	R3HDM4	JAK3	TGCGGCCCGGAGGCGGCGGAGGGCACCCCGGGCGGGCGGCGGCTGCT*CACCGCAGTGACCTGGTGAGTGGGCGCCTCCCCGTGGGCCTCAGTCT	chimerdb3seq,cancer,tcga-cancer,oesophagus,exon-exon	BOWTIE	out-of-frame	0	13	9	26	19	913087	-	19	17843172	-	30.8816	16.3715	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000198858	ENSG00000105639	R3HDM4	JAK3	CGACTCCCCCCACTCCCGGGTCCGCGCCCCCCCACTGCCCTGATCCACGC*CAGCTTTTACTTCCCCAATTGGTTTGGGCTGGAGAAGTGCCACCGCTTCG	chimerdb3seq,cancer,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/intronic	0	13	8	36	19	912559	-	19	17843494	-	30.8816	16.3715	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000119139	ENSG00000107242	TJP2	PIP5K1B	CCTCGCCCAGCGCCCGACACCGCCGGCCGCGGCGGCGGCCGCCACCGGCT*CTAGCCCTGGGATCCCGACACAGGCCAGACCTGGTCCCTAGCACTCCATC	cancer,oesophagus,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	UTR/intronic	0	12	11	31	9	69121721	+	9	68940642	+	0.4683	6.184	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000119139	ENSG00000107242	TJP2	PIP5K1B	TCGCCCAGCGCCCGACACCGCCGGCCGCGGCGGCGGCCGCCACCGGCTCT*AGCAAAGGGTTACCTTCCAGTTCAACATTTACCTTGGAAGAGGGGACCAT	cancer,oesophagus,100K<gap<200K	BOWTIE+BOWTIE2;BOWTIE+STAR	UTR/intronic	0	12	7	35	9	69121723	+	9	68991138	+	0.4683	6.184	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000119139	ENSG00000107242	TJP2	PIP5K1B	TCACCCAAGGGATCCGTTTGCACATTAACGTCTGAGAAGTACTGGCCTAG*CCCTGGGATCCCGACACAGGCCAGACCTGGTCCCTAGCACTCCATCACTG	cancer,oesophagus,100K<gap<200K	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	intronic/CDS(truncated)	0	12	1	31	9	69123113	+	9	68940646	+	0.4683	6.184	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000101109	ENSG00000225106	STK4	AL162457.2	AAAATTCTTCAGATTGGAAAATACCACAGGATGGAGACTACGAGTTT*TCTTCAGGAGAGAATTAACATCCAATGGATTCCCAGAAAACTTTTCC	antisense,cancer,exon-exon	BOWTIE;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	11	21	30	20	45025130	+	20	61739090	-	18.7078	3.7481	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000107242	ENSG00000154330	PIP5K1B	PGM5	TCCGATATTTCAGAGAACTTTTTGGTATCAAGCCTGATGATTACTTG*GCTCTGACCACCTCCGAGAGAAGGATGGCCTGTGGGCTGTCTTGGTC	known,tcga,chimerdb3seq,tcga-cancer,oesophagus,100K<gap<200K,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	10	16	30	9	68876794	+	9	68479418	+	6.184	0.7846	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000105426	ENSG00000267059	PTPRS	AC005943.1	GGTGTGGAGGGCTCTGACTACATCAACGCCAGCTTCATTGATGGCTACAG*CTCTTCTGGGAGAAGAAGCTGAGCGGCCTGAACGCCTTCGACATTGCTGA	exon-exon	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	10	3	22	19	5211590	-	19	1582712	-	1.8518	0	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000105426	ENSG00000071655	PTPRS	MBD3	GTGGAGGGCTCTGACTACATCAACGCCAGCTTCATTGATGGCTACAG*CTCTTCTGGGAGAAGAAGCTGAGCGGCCTGAACGCCTTCGACATTGC	chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	10	11	29	19	5211590	-	19	1582712	-	1.8518	4.6113	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000105483	ENSG00000105357	CARD8	MYH14	TCCTACCCTAAAGTCACCACCTGCTGCTTTTCTGGAGCGCTTACCAG*GCTGACTTCGCGCTGGAGGCCCTGGCCAAGGCCACCTACGAGCGCCT	chimerdb3seq,cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	UTR/CDS(truncated)	0	9	6	28	19	48255792	-	19	50248987	+	0.5729	46.9662	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000105357	ENSG00000105483	MYH14	CARD8	GATGGTCTCAGCAGTTCTCCAGTTTGGCAACATTGCCTTGAAGAGAGAAC*TCCTGAGACCATCCCCTCCCTCTCCAGTCCGTGGAAAAAATTGTCTTCCA	chimerdb3seq,cancer,oesophagus	BOWTIE+STAR	CDS(truncated)/intronic	0	9	1	14	19	50244301	+	19	48216833	-	46.9662	0.5729	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000104881	ENSG00000125505	PPP1R13L	MBOAT7	CCGCGCTGCACGGCCAGGAGGGCTACGTGCCGCGGAACTACTTCGGG*GAGCGCCTGGACCATGCTGCTGAGCGCCTACTGGCACGGCCTCCACC	oncogene,chimerdb3seq,cancer,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	9	3	18	19	45382527	-	19	54174431	-	18.0197	26.3234	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000197124	ENSG00000266958	ZNF682	AC005779.1	GGAGCCCTGGAATGTGAAGAGACATGAGACCATAGCCAAACCCCCAG*GAGTCTCTCTCTGTGGCCACCACTGCTCCAGGCCCATGGCAGGTACT	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	9	8	24	19	20023004	-	19	45202406	+	0.9311	NA	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000197124	ENSG00000266958	ZNF682	AC005779.1	CAGGAGCCCTGGAATGTGAAGAGACATGAGACCATAGCCAAACCCCCAGG*CGAGACGGGATTTCACCATGTTGCCCAGACTGGTCTGTAACTCCTGGCCT	antisense	BOWTIE+BOWTIE2	intronic/intronic	0	9	1	33	19	20023003	-	19	45198890	+	0.9311	NA	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000186567	ENSG00000267751	CEACAM19	AC009005.1	GGGAGACCTCACTCAAGAAGTGACCTTAGAGGAGAGACCAGAAGAAG*GAGAGGCTGGCGGTTACCTTTCTTGGGGAGACGCGTCCGACTGCTTC	antisense,exon-exon	BOWTIE;BOWTIE+STAR	UTR/exonic(no-known-CDS)	0	8	6	30	19	44673845	+	19	571596	-	4.6144	1.2918	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000186567	ENSG00000267751	CEACAM19	AC009005.1	GGGAGACCTCACTCAAGAAGTGACCTTAGAGGAGAGACCAGAAGAAGGTG*GCGCGTTTACCCTATTTTAAAAAAGTTTTAAGTTTTAGCCAACCGGGATC	antisense	BOWTIE+BOWTIE2	intronic/intronic	0	8	4	37	19	44673848	+	19	571868	-	4.6144	1.2918	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000186567	ENSG00000267751	CEACAM19	AC009005.1	CAACTCTGAATGGACTATGAAGGCCAAGACTGAGGTCCAGGTAGCTG*GAGAGGCTGGCGGTTACCTTTCTTGGGGAGACGCGTCCGACTGCTTC	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	8	3	29	19	44672964	+	19	571596	-	4.6144	1.2918	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000118156	ENSG00000185453	ZNF541	C19ORF68	CGGCAGATCCCTCCAAGTCCAAGCTGACAATATTCAGCAGAATCCAG*GTGAAGCTGGTGTTCGTGGAGGACCAGGCTGTGGTGGAGACGGTGTT	tcga-cancer,oesophagus,exon-exon	BOWTIE	in-frame	0	8	9	29	19	47544126	-	19	48194653	+	1.5703	1.992	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000118156	ENSG00000185453	ZNF541	C19ORF68	AGAATCCAGGTACCAGCTCTCTCTCACGTGGCCTGACCAGAGTGGAGTGA*AGCTGGTGTTCGTGGAGGACCAGGCTGTGGTGGAGACGGTGTTCTTCCTG	tcga-cancer,oesophagus	BOWTIE+BOWTIE2	intronic/CDS(truncated)	0	8	1	34	19	47544085	-	19	48194657	+	1.5703	1.992	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000118156	ENSG00000185453	ZNF541	C19ORF68	CCCTGCGGATGCCTCGCCGCTCTTCCGCCAGCTCTTCCTCAAGTCGCAGG*GTGGATTCTGAGGGCTTCCCTCTGGAGAGGAAGCATGTGATGAGAGGTGT	tcga-cancer,oesophagus	BOWTIE+BOWTIE2	CDS(truncated)/UTR	0	8	1	28	19	47544890	-	19	48197054	+	1.5703	1.992	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A891-01A	ENSG00000002822	ENSG00000106266	MAD1L1	SNX8	GCAAGCCATGCTCTCTGTTCCTGCCTGGGGCAGGACAACTCCAGGTCACA*CAGAAAGAGGCCTGCTAGGCAGGGGTGGCGGAGGCCACCTTCCTTCTCAC	cell_lines,chimerdb3seq,cancer,10K<gap<100K	BOWTIE+STAR	intronic/UTR	0	7	1	15	7	2152060	-	7	2252470	-	0.0537	6.1376	TRUE	TRUE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000106266	ENSG00000002822	SNX8	MAD1L1	GGCAGCTGAGGCGGAGGCTGACGAGGAGGCGGATCCCCCGGCGTCAG*GAGCGGGACGGTATGCGGGCCATCCTGGGGTCCTACGACAGCGAGCT	cell_lines,chimerdb3seq,cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	7	7	30	7	2314328	-	7	2014642	-	6.1376	0.0537	TRUE	TRUE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000254901	ENSG00000069399	BORCS8	BCL3	CAGAGACTGAAGACTGAACGAGTGTGGCCAGCATTCCTCCTGCACCTGCC*CACGCCCCTGGCTACGAACTTGTCCCATTCCTCCTCTGCCACCTCAACGG	oncogene,chimerdb3seq,cancer,tumor	BOWTIE+BLAT	UTR/intronic	0	6	2	36	19	19178288	-	19	44757888	+	1.2336	22.9633	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000254901	ENSG00000069399	BORCS8	BCL3	CAGGCCATCAGCATCCGGGACCATATGAATGCCAGTGCCCAGGGCCACAG*GTCATCGACATCCTGAGGGGGAAGGCCACCCGGCCTGCTTCCACCTCCCA	oncogene,chimerdb3seq,cancer,tumor,exon-exon	BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	6	1	18	19	19182573	-	19	44758724	+	1.2336	22.9633	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000181666	ENSG00000007306	HKR1	CEACAM7	AGCGCCCTGGAGAGAGGAGAGAAAATGTCCACTGGACCTCTGTCCAG*CCTCGCTTTTAACCTTCTGGAACCTGCCAAACAGTGCCCAGACCAAT	chimerdb3seq,cancer,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	6	9	27	19	37347872	+	19	41687221	-	5.6244	10.8572	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000181666	ENSG00000007306	HKR1	CEACAM7	GGAAGCGCCCTGGAGAGAGGAGAGAAAATGTCCACTGGACCTCTGTCCAG*AGGACAAGCAGGCAGCAGAGACCATGGGGTCCCCTTCAGCCTGTCCATAC	chimerdb3seq,cancer,tcga-cancer,oesophagus	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/UTR	0	6	2	36	19	37347872	+	19	41688188	-	5.6244	10.8572	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000181666	ENSG00000007306	HKR1	CEACAM7	AGCGCCCTGGAGAGAGGAGAGAAAATGTCCACTGGACCTCTGTCCAG*CGGAGCCACCCAAGCCCTCCATCACCAGCAACAACTTCAATCCGGTG	chimerdb3seq,cancer,tcga-cancer,oesophagus,exon-exon	BOWTIE	in-frame	0	6	2	27	19	37347872	+	19	41684063	-	5.6244	10.8572	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000181666	ENSG00000007306	HKR1	CEACAM7	CTGCTGTGGTTGTGATACCATGATTATGTTGAATCTGCAGATAAATTTTG*AGGACAAGCAGGCAGCAGAGACCATGGGGTCCCCTTCAGCCTGTCCATAC	chimerdb3seq,cancer,tcga-cancer,oesophagus	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	intronic/UTR	0	6	1	35	19	37360523	+	19	41688188	-	5.6244	10.8572	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000171456	ENSG00000088325	ASXL1	TPX2	GGTTGTTTTATAAACTGCCTGGCCGAATCAGCCTTTTCACGCTCAAG*TTCTAACAACAAAAAGAAGCCAGAGGAAGAAGGCAGTGCTCATCAAG	chimerdb3seq,cancer,tcga-cancer,oesophagus,exon-exon	BOWTIE	out-of-frame	0	5	10	27	20	32369123	+	20	31771560	+	8.9468	56.3439	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000171456	ENSG00000088325	ASXL1	TPX2	AGTGATCTTCCCACCACAGCTTCACAAAGCACTGGGATGGATTACAG*TTCTAACAACAAAAAGAAGCCAGAGGAAGAAGGCAGTGCTCATCAAG	chimerdb3seq,cancer,tcga-cancer,oesophagus,exon-exon	BOWTIE	UTR/CDS(truncated)	0	5	2	30	20	32371874	+	20	31771560	+	8.9468	56.3439	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000171456	ENSG00000088325	ASXL1	TPX2	TTTTACCTCGTTGGGTGCTGGGGATATTTGTATTTCTACATATGTTCTTT*CCTTTCAACCTGTCCCAAGGAAAGAAAAGAACATTTGATGAAACAGTTTC	chimerdb3seq,cancer,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/CDS(truncated)	0	5	1	17	20	32400348	+	20	31778846	+	8.9468	56.3439	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000064489	ENSG00000069399	BORCS8-MEF2B	BCL3	CCTGATCCTGGAAGAGACTCGGGGCCCCCCAGCCTCCGCCAACCCAG*CACGGCGCCAACGTGAACGCGCAAATGTACTCCGGCAGCTCCGCCCT	oncogene,cancer,tumor,exon-exon	BOWTIE	UTR/CDS(truncated)	0	5	2	25	19	19180686	-	19	44758246	+	0.008	22.9633	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000064489	ENSG00000069399	BORCS8-MEF2B	BCL3	GCCATCAGCATCCGGGACCATATGAATGCCAGTGCCCAGGGCCACAG*GTCATCGACATCCTGAGGGGGAAGGCCACCCGGCCTGCTTCCACCTC	oncogene,cancer,tumor,exon-exon	BOWTIE	out-of-frame	0	5	2	23	19	19182573	-	19	44758724	+	0.008	22.9633	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000184305	ENSG00000251095	CCSER1	AC097478.1	CCCTGAGTGCCCGGGAGGAGCCTTAACAAGCGCACGGAGCCCTCAAG*ATTTTTTGTTCATTCTGAAAATCACATCGCCAGATCCAACACCTTTT	antisense,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	5	13	30	4	90127831	+	4	89587821	+	0.5142	0.3494	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000142459	ENSG00000105426	EVI5L	PTPRS	TGGCCGAGCTCGGGCTCTGCATCTATCAGTTCGAGTACATGCTGCAG*GAGATGGTCATCACAAACTTGCAGCCTGAGACCGCGTACTCCATCAC	chimerdb3seq,oesophagus,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	5	11	29	19	7850122	+	19	5225844	-	1.9561	1.8518	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000159399	ENSG00000197961	HK2	ZNF121	TTTGACCAGGAGATTGACATGGGCTCACTGAACCCGGGAAAGCAACT*GACCTATTCAAACTCAGTCTGTCTCTTGACTGGAGGAGGAGAAGGAA	chimerdb3seq,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	CDS(truncated)/UTR	0	5	8	28	2	74874449	+	19	9569082	-	11.0824	3.7524	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000159399	ENSG00000197961	HK2	ZNF121	GAGTGGGGGGCCTTCGGGGACGATGGCTCGCTCAACGACATTCGCACTGA*TAATCCTCTCAAACTTCGCCACTGCTTGATCAACTAAGTTGATGTAATAT	chimerdb3seq,oesophagus	BOWTIE+STAR	CDS(truncated)/UTR	0	5	1	14	2	74874401	+	19	9564741	-	11.0824	3.7524	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000142556	ENSG00000089327	ZNF614	FXYD5	AGGTGAAATAATTTGCCCTAGAGATCAATTTGATGAATACAGTAAATAAG*GTGGCAAGTGCAGGCAGCTGTCCCGGTTATGCCGGAATCGTTGCAGGTGA	cancer	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	5	6	35	19	52015643	-	19	35169566	+	3.6184	8.4058	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000142556	ENSG00000089327	ZNF614	FXYD5	CCAGAAGAGAAGACATGGAATAAATAACCCTGTTGAGTTTATTGGAG*GTGGCAAGTGCAGGCAGCTGTCCCGGTTATGCCGGAATCGTTGCAGG	cancer,exon-exon	BOWTIE	in-frame	0	5	4	26	19	52017117	-	19	35169566	+	3.6184	8.4058	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000142556	ENSG00000089327	ZNF614	FXYD5	AATAAATAACCCTGTTGAGTTTATTGGAGGTGAGAAAACACTTCTACATG*GTGGCAAGTGCAGGCAGCTGTCCCGGTTATGCCGGAATCGTTGCAGGTGA	cancer	BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	5	1	22	19	52017096	-	19	35169566	+	3.6184	8.4058	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000163808	ENSG00000106829	KIF15	TLE4	TTGGTGCGGTGGAGCAGGTGGTAACCTCAGCTGCTGAAGCCTATCAG*GCACCGCATCAGCCTGCTCAACCCTTTAAATTTACAATTTCCGAATC	tcga-cancer,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	4	4	27	3	44786574	+	9	79573689	+	6.8061	1.7118	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000152270	ENSG00000262655	PDE3B	SPON1	ATAAACTGCAGGTGGAGAATTCCTCCTTACCTCAAGCAGATGAGATTCAG*GTTGTAGGATGCGCCCATGGACGGCCTGGTCAGAATGCACCAAACTGTGC	oesophagus	BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	4	8	37	11	14869630	+	11	14265524	+	2.9648	2.9539	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000152270	ENSG00000262655	PDE3B	SPON1	TGCATTTGAAATGGACAGAAGGCATTGTCAATGAATTTTATGAGCAG*GTTGTAGGATGCGCCCATGGACGGCCTGGTCAGAATGCACCAAACTG	oesophagus,exon-exon	BOWTIE	out-of-frame	0	4	3	28	11	14861366	+	11	14265524	+	2.9648	2.9539	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000147471	ENSG00000162571	PLPBP	TTLL10	ACCAGGTTGAGCTGAGCATGGGCATGTCCGCGGATTTCCAGCATGCG*GGCCCTCGCCCGGGCACCCCCCGGCCAATGGACCACAGCTGCACCCG	oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	CDS(truncated)/UTR	0	4	8	27	8	37776016	+	1	1179189	+	59.8501	1.7701	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000147471	ENSG00000162571	PLPBP	TTLL10	TGGCCAGGCATGGTGACTCATGCCTGTAATCCCAGCAATTTGGGAGACAG*AGGCTGGTCTTGAACTCCTGACCTCAGGTGATCCGCCTGCCAAAGTGCTG	oesophagus	BOWTIE+STAR	UTR/intronic	0	4	2	19	8	37778724	+	1	1191039	+	59.8501	1.7701	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000147471	ENSG00000162571	PLPBP	TTLL10	TGACCAGGTTGAGCTGAGCATGGGCATGTCCGCGGATTTCCAGCATGCGG*CAGGCGCCCCACCCAGCAGGCCTGACGCTGCCCCTCCTTCCAGCCGGCAC	oesophagus	BOWTIE+BOWTIE2	intronic/intronic	0	4	1	32	8	37776017	+	1	1178863	+	59.8501	1.7701	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000147471	ENSG00000162571	PLPBP	TTLL10	GGAGTTCAAGACCAGCCTCAGCAACAGCAGGAGCCCCACCCCCCGTCTCT*CAAAGTGCTGGGATTACAGGCGTGAGCCACTGCACCCAGCCATGTATCCC	oesophagus	BOWTIE+STAR	UTR/intronic	0	4	1	26	8	37778798	+	1	1186348	+	59.8501	1.7701	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000147471	ENSG00000162571	PLPBP	TTLL10	TAATCCCAGCAATTTGGGAGACAGAGGCGGAAGGATCACCTGAGCCTAGG*CTCAGGTGATCCACCCACCTCAGCTTCCCAAAGTGCTGGGATTACAGACG	oesophagus	BOWTIE+STAR	UTR/intronic	0	4	1	16	8	37778750	+	1	1195576	+	59.8501	1.7701	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000147471	ENSG00000162571	PLPBP	TTLL10	ATGTGAGTTTGAATTACACCATCTGTGCCAATTACAAAGCAATTAAAAGA*TTTTTTTTTTTTTCTTTTTGGTCAGTTTCTCTAAGTCCTTATCAATTTTG	oesophagus	BOWTIE+STAR	UTR/intronic	0	4	1	16	8	37779754	+	1	1190248	+	59.8501	1.7701	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000105618	ENSG00000152433	PRPF31	ZNF547	CACTGGCAGCCCGTGTGGACAGTTTCCACGAGAGCACAGAAGGGAAG*GGTCCCCTGGCGATGGCAGAAATGAACCCTGCACAGGGTCATGTGGT	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE	CDS(truncated)/UTR	0	4	3	26	19	54126617	+	19	57368544	+	16.4427	1.2005	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000162571	ENSG00000147471	TTLL10	PLPBP	GCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGTGGGCG*ATCACTTGAGCCCAGGAGTTTGAGGCTGCAGTGAGCTATGATTGCACCAC	oesophagus	BOWTIE+STAR	UTR/UTR	0	4	1	23	1	1174893	+	8	37778854	+	1.7701	59.8501	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000104812	ENSG00000197487	GYS1	GALP	TGCGAATGGGGCGATCAAGTCCAGAGCCGGGGCACTTTCAGAGTTTGAAG*ACGGGCTCCCCTACTCCCACCCTCCACAGCCCTCCAAGAGGAATGTGATG	oesophagus	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	UTR/CDS(truncated)	0	3	3	29	19	48968792	-	19	56183135	+	18.4983	1.7153	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000188283	ENSG00000160321	ZNF383	ZNF208	GCATGGCCTTGAGTACTCCAGTTTTGGAGATGTTTTGGAATATAGAAGCC*ATCTGATGGTCATTTTTTACTTTATAAATTTAAATATGCACTTTTCATCA	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	3	11	34	19	37242612	+	19	21959216	-	0.7154	0.0391	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000188283	ENSG00000160321	ZNF383	ZNF208	CAGGAGAACGGCCTCAAGGAAGACTAACCATCTGCAATACTAGAAGCCAT*CTGATGGTCATTTTTTACTTTATAAATTTAAATATGCACTTTTCATCATC	NA	BOWTIE+BLAT;BOWTIE+BOWTIE2	CDS(truncated)/intronic	0	3	1	30	19	37230455	+	19	21959214	-	0.7154	0.0391	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A891-01A	ENSG00000153944	ENSG00000180198	MSI2	RCC1	AGAACAAGAAAAGCTGCAACCTTGGGGGTAGAAGAAGGTGAGAAACCTAG*AACGATCCTCCACTTGACCAAGAAAAAAGTGATTCTCCCAGAAGCACAAA	cancer	BOWTIE+STAR	intronic/UTR	0	2	1	15	17	57272674	+	1	28538579	+	3.9329	29.4424	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000099326	ENSG00000268460	MZF1	AC006262.1	TGAGGTTATTGATCTTTCTTACTGATTTATTGTAGCTCTTTACTTAGGAG*GCCACACAAATCTCATCTCACATTGTAATCCCCATGTGTCAGGGGAAGGA	NA	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	UTR/exonic(no-known-CDS)	0	2	14	35	19	58564399	-	19	46208569	+	2.2974	0.7028	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000099326	ENSG00000268460	MZF1	AC006262.1	CCAGCCTGGCTGGTGCCCTGCTCATTCACTTGCATGGCCAGAAGTACCAG*TGATTCTGGGAACTGTGGGCAAGAAGAGAGGCGGGAAAGCCAGAGCCATC	NA	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	intronic/exonic(no-known-CDS)	0	2	2	27	19	58567242	-	19	46208932	+	2.2974	0.7028	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000099326	ENSG00000268460	MZF1	AC006262.1	CTTATATGCAAGAGAGGGGCACCACAAATCTGGCTGACAGCTCTGAGCAG*TGATTCTGGGAACTGTGGGCAAGAAGAGAGGCGGGAAAGCCAGAGCCATC	NA	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	intronic/exonic(no-known-CDS)	0	2	1	35	19	58567736	-	19	46208932	+	2.2974	0.7028	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000166949	ENSG00000103599	SMAD3	IQCH	CAATGTCAACAGGAATGCAGCAGTGGAGCTGACACGGAGACACATCG*GTGTGGGCAACCGGCCTTAACCTCGCATATAGTGACCAGCTGGCCCT	cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	2	4	26	15	67181453	+	15	67465127	+	10.1468	1.6169	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000166949	ENSG00000103599	SMAD3	IQCH	CCAGCGCTATGGCTGGCACCCGGCCACCGTCTGCAAGATCCCACCAG*GTGTGGGCAACCGGCCTTAACCTCGCATATAGTGACCAGCTGGCCCT	cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	2	4	24	15	67184864	+	15	67465127	+	10.1468	1.6169	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000166949	ENSG00000103599	SMAD3	IQCH	CAATGTCAACAGGAATGCAGCAGTGGAGCTGACACGGAGACACATCG*ATGCTGGCAACCAGTCGCTATGCAGTGATGACCACCCAGCTAAGACA	cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	2	1	13	15	67181453	+	15	67475696	+	10.1468	1.6169	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000121749	ENSG00000139292	TBC1D15	LGR5	CATTGGATGATGCATTAGATTCCTCTAGTATTCTCTATGCTAGAAAG*GAATTTGGCTTGGAACAAAATTGCTATTATTCACCCCAATGCATTTT	oncogene,chimerdb3seq,oesophagus,exon-exon	BOWTIE	out-of-frame	0	2	10	28	12	71873003	+	12	71577925	+	4.2652	38.3725	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000121749	ENSG00000139292	TBC1D15	LGR5	CATTGGATGATGCATTAGATTCCTCTAGTATTCTCTATGCTAGAAAG*GGACCTATCGTCCAACCTCCTGTCGTCTTTTCCTATAACTGGGTTAC	oncogene,chimerdb3seq,oesophagus,exon-exon	BOWTIE	out-of-frame	0	2	1	14	12	71873003	+	12	71578804	+	4.2652	38.3725	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000197863	ENSG00000198723	ZNF790	TEX45	AGCATGGGGAGTCGGAAGGGGACAAATCCGCGATCCCAGTCATGCAT*GTATGACAAGGCCCAGGCCACAGCCCACATCCACTGTGTAAATATCC	chimerdb3seq,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	UTR/CDS(truncated)	0	2	7	28	19	36850002	-	19	7505324	+	1.6269	1.3327	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000197863	ENSG00000198723	ZNF790	TEX45	GATTCCCCTGGCGCGGACTCTGGCACCAACAAAACTATCTCTTTGAG*GACCACCAAGGCCGAGCACTTCTATGCCAGGGAGCCAGGTGAGAGCC	chimerdb3seq,oesophagus,exon-exon	BOWTIE	UTR/CDS(truncated)	0	2	2	27	19	36850700	-	19	7505399	+	1.6269	1.3327	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000197863	ENSG00000198723	ZNF790	TEX45	TCCGCCTAAGTTCCTGAGCCTCCTGACCCAACCAGTTTCAGAAATGGGTA*TGACAAGGCCCAGGCCACAGCCCACATCCACTGTGTAAATATCCGTCCTG	chimerdb3seq,oesophagus	BOWTIE+BOWTIE2	intronic/CDS(truncated)	0	2	1	33	19	36843284	-	19	7505327	+	1.6269	1.3327	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000197863	ENSG00000198723	ZNF790	TEX45	ATCCGCGATCCCAGTCATGCATGTGAGACTGGGCAAAGGAAGGCTCGAGT*ATGACAAGGCCCAGGCCACAGCCCACATCCACTGTGTAAATATCCGTCCT	chimerdb3seq,oesophagus	BOWTIE+BOWTIE2	intronic/CDS(truncated)	0	2	1	28	19	36849974	-	19	7505326	+	1.6269	1.3327	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A891-01A	ENSG00000137501	ENSG00000073921	SYTL2	PICALM	ACAAGAGAGACGGCGAGGCGCGCTCCCTGCCCGGCAGCGACTCGGAG*ACTTAATTCAGTGCACAAATGAGATGAATGTGAACATCCCACAGTTG	known,cell_lines,chimerdb3seq,cancer,tumor,oesophagus,100K<gap<200K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	1	11	27	11	85810954	-	11	86031611	-	1.8569	34.5066	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Esophagus	TCGA-LN-A49M-01A	ENSG00000044115	ENSG00000123213	CTNNA1	NLN	CAGCTTCCCCAGGAGCAAAAAGCGAAGATTGCGGAACAGGTGGCCAGCTT*TCTCTCTTCTTCCTGACTACCTGGTTCTTCTGACCTTTTCTCTACAAAGA	cancer,oesophagus	BOWTIE+STAR	CDS(truncated)/intronic	0	51	1	15	5	138930534	+	5	65862716	+	68.9666	3.3086	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-LN-A49M-01A	ENSG00000044115	ENSG00000123213	CTNNA1	NLN	GGAGGAGCGTCTGGAAAGCATCATTAGTGGGGCTGCCTTGATGGCCGACT*AATGATGGTTTCCAGCTTCATCCACGTCCCTGCAAAGGATATAAACTCAT	cancer,oesophagus	BOWTIE+STAR	CDS(truncated)/intronic	0	51	1	15	5	138827620	+	5	65847170	+	68.9666	3.3086	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-LN-A49M-01A	ENSG00000044115	ENSG00000123213	CTNNA1	NLN	TGGAGGAGCGTCTGGAAAGCATCATTAGTGGGGCTGCCTTGATGGCCGAC*GGTCATCACAAGTGATCACTACTTTTGTTTTTCATAGGCACCGATCCATA	cancer,oesophagus	BOWTIE+STAR	CDS(truncated)/intronic	0	51	1	14	5	138827619	+	5	65796658	+	68.9666	3.3086	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-LN-A49M-01A	ENSG00000044115	ENSG00000123213	CTNNA1	NLN	GCTTCAGCGAGGAGCGCTTTAGGCCTTCCCTGGAGGAGCGTCTGGAAAGC*CTCAAGCGATCCTCCCATCTCAGACTCCTGAGTAGCTGAGACTACAGGAA	cancer,oesophagus	BOWTIE+STAR	CDS(truncated)/intronic	0	51	1	14	5	138827589	+	5	65800787	+	68.9666	3.3086	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-LN-A49M-01A	ENSG00000044115	ENSG00000123213	CTNNA1	NLN	GGACGACAGTGGCAATGACATCATTGTGCTGGCCAAGCAGATGTGCATGA*CATCAGATGTAATTTCTTTCAAGATCTTCTTTTTGTTATTTTATTTGTTT	cancer,oesophagus	BOWTIE+STAR	CDS(truncated)/intronic	0	51	1	14	5	138930626	+	5	65798641	+	68.9666	3.3086	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49M-01A	ENSG00000123213	ENSG00000044115	NLN	CTNNA1	CCATAATTTTGCAGCAGCTACTCCCACTGCGAACCAAGGTGGCCAAACT*AGTGGCAATGACATCATTGTGCTGGCCAAGCAGATGTGCATGATTATGAT	cancer,oesophagus	BOWTIE+STAR	out-of-frame	0	51	42	37	5	65785830	+	5	138930584	+	3.3086	68.9666	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49M-01A	ENSG00000123213	ENSG00000044115	NLN	CTNNA1	CAGGAAATCAAATCAATGAAGAAAAGAATGAGTGAGCTATGTATTGATTT*AATATCAGTCACTGTTCGTCACTCAAATGAATTTGCTAAATACAACACTG	cancer,oesophagus	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/UTR	0	51	1	30	5	65780225	+	5	138934130	+	3.3086	68.9666	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49O-01A	ENSG00000185052	ENSG00000132669	SLC24A3	RIN2	TTCCGAAGATGCCGGACTCCGGAACAGCAAGAACTGCACCGAACCAG*ATGTGGTGCTGGAAAAAGCCATGCACAAGTGCATCTTGAAGCCCCTC	tumor,100K<gap<200K,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	8	22	29	20	19281087	+	20	19990006	+	0.5371	7.9482	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49O-01A	ENSG00000142453	ENSG00000127616	CARM1	SMARCA4	CCTACCAGCGCGCCATCCTGCAAAACCACACCGACTTCAAGGACAAG*GAGGCCACTGTCTGCAGCTCCCGTGAAGATGTCCACTCCAGACCCAC	known,tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	5	7	30	19	10909207	+	19	10984124	+	10.4449	5.7676	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49O-01A	ENSG00000142453	ENSG00000127616	CARM1	SMARCA4	CCTACCAGCGCGCCATCCTGCAAAACCACACCGACTTCAAGGACAAG*CAGGAGGCCACTGTCTGCAGCTCCCGTGAAGATGTCCACTCCAGACC	known,tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	5	5	25	19	10909207	+	19	10984121	+	10.4449	5.7676	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49O-01A	ENSG00000142453	ENSG00000127616	CARM1	SMARCA4	AGGCACCTACCAGCGCGCCATCCTGCAAAACCACACCGACTTCAAGGACA*ACAGAGTGTCGCTCTATTGCCCAGGCAGGAGTGCAGTGGTGCGATCCG	known,tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer,10K<gap<100K	BOWTIE+BOWTIE2	CDS(truncated)/intronic	0	5	2	37	19	10909205	+	19	10983456	+	10.4449	5.7676	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49O-01A	ENSG00000142453	ENSG00000127616	CARM1	SMARCA4	CCTACCAGCGCGCCATCCTGCAAAACCACACCGACTTCAAGGACAAG*CGTCTCGCCCTTTTGCCCAGGCTAGAGTGCAGTGGTGCGGTCATGGT	known,tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	5	2	24	19	10909207	+	19	10980777	+	10.4449	5.7676	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49O-01A	ENSG00000142453	ENSG00000127616	CARM1	SMARCA4	CTCTGATCAGTACCCTGAGGCCTTCCCACCTGACCCCAGCTTCCCCTGCA*CCGCCCTTCCCCCGCGCCCCCTGCCGTCCCACCCGCCGCCTCGCCCGTGA	known,tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer,10K<gap<100K	BOWTIE+STAR	intronic/CDS(truncated)	0	5	1	14	19	10911549	+	19	10987733	+	10.4449	5.7676	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49O-01A	ENSG00000198682	ENSG00000171862	PAPSS2	PTEN	GCCTACAACAAAGCCAAAAAAGCCATGGACTTCTATGATCCAGCAAG*GTTTTTGGATTCAAAGCATAAAAACCATTACAAGATATACAATCTTT	cancer,tumor,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	4	4	27	10	87745231	+	10	87925513	+	2.8583	2.3191	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49O-01A	ENSG00000198682	ENSG00000171862	PAPSS2	PTEN	CTGGAAAAGACCACAGAAAACAAAGAATCCAACCCTTTCATCTTACAGGT*TTTTGGATTCAAAGCATAAAAACCATTACAAGATATACAATCTGTAAGTA	cancer,tumor,100K<gap<200K	BOWTIE+BOWTIE2	UTR/CDS(truncated)	0	4	3	37	10	87746903	+	10	87925515	+	2.8583	2.3191	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49O-01A	ENSG00000198682	ENSG00000171862	PAPSS2	PTEN	GATGGCTTCATGGCCCCCAAAGCATGGAAGGTCCTGACAGATTATTACAG*GTTTTTGGATTCAAAGCATAAAAACCATTACAAGATATACAATCTGTAAG	cancer,tumor,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	4	1	24	10	87745951	+	10	87925513	+	2.8583	2.3191	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49O-01A	ENSG00000198682	ENSG00000171862	PAPSS2	PTEN	TTTCATCTTACAGGTGAACAAACTGTGATGATGCACATGTATGTGTTTTG*TAGGGTTCCGAATTTGCCACATCCTCACCATCGTGTTGTTTTGTTTATGT	cancer,tumor,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	4	1	18	10	87746938	+	10	87908168	+	2.8583	2.3191	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OJ-11A	ENSG00000085224	ENSG00000113719	ATRX	ERGIC1	GCCTGTAGTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCACTTGAAC*CCGGTGGCAGCTGGCAGGGTTTTGCTCAGCACGTGCCGGCCTTCCTCGAA	oncogene,cancer	BOWTIE+STAR	intronic/UTR	0	2	1	36	X	77664355	-	5	172915582	+	8.8725	14.8939	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OJ-11A	ENSG00000085224	ENSG00000113719	ATRX	ERGIC1	AAAGTAAAAAAATAAGAGATAAAACTTCTAAAAAGAAGGATGAATTATCT*CCTTTCCCTTTTGTCCTGAAAGGGAGGAGCAATGGTCCAGGCATTAATTC	oncogene,cancer	BOWTIE+STAR	CDS(truncated)/UTR	0	2	1	15	X	77682073	-	5	172952046	+	8.8725	14.8939	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OJ-11A	ENSG00000085224	ENSG00000113719	ATRX	ERGIC1	AGAAGAAAAAAAGACAAAGCCTAAAGAGCATAAAGAAGTCAAAGGCAGAA*TCTTCTCAATCATCATGACAGCTCTGATGTTGAGACTGTTATTGAGCCCA	oncogene,cancer	BOWTIE+STAR	CDS(truncated)/UTR	0	2	1	15	X	77663394	-	5	172933374	+	8.8725	14.8939	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OJ-11A	ENSG00000156650	ENSG00000153006	KAT6B	SREK1IP1	GATTGCGCTATTGCACTCCAGCCTGGGTGACAGAGCGAGACTCTATCTCA*AAAAAAAAAAAAAGATTTTAAGGAAGGAAATGACTTTTATTAGGGTTTGG	cancer	BOWTIE+STAR	intronic/UTR	0	2	2	28	10	74841565	+	5	64720525	-	2.5329	7.456	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-LN-A49W-01A	ENSG00000146555	ENSG00000185290	SDK1	NUPR2	GTGACTTGGTTTAGAGAAGGGCACAAGATTATTCCAAGCAACAGAAT*GATACCGAAGGACCTGTTCGAAGTATTTACTGTAACTCCAACTGTAA	exon-exon	BOWTIE;BOWTIE+STAR	CDS(truncated)/UTR	0	8	17	29	7	3642105	+	7	56114897	-	11.22	4.2127	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A49W-01A	ENSG00000174206	ENSG00000255886	C12ORF66	AC020611.2	GAGCTCGTTGGCCTTTTGGATGCCATCATGAAAAAATACAGCTCCAG*AGCTTCGCCGTTGATGTCTCTCCTCTAGTCGAATATGGAAGACTGGA	antisense,10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	6	10	29	12	64215678	-	12	64042940	-	2.9345	0.2082	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A5U5-01A	ENSG00000134001	ENSG00000171723	EIF2S1	GPHN	AGAAGTCGGCTCTGGGCTCCAGTGCGGGAATCACACACATACCTCAG*CCAACTCAGACAGTAATGCCAGGACAAGTCATGCGGGTTACAACAGG	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,oesophagus,100K<gap<200K,exon-exon	BOWTIE;BOWTIE+STAR	UTR/CDS(truncated)	0	156	32	30	14	67360456	+	14	67110140	+	20.2923	16.8721	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-LN-A5U5-01A	ENSG00000134001	ENSG00000171723	EIF2S1	GPHN	AGGAAAGTGGGCCGAGTGGATTGTACAGCCTCTACAATATGCCGAAA*CCAACTCAGACAGTAATGCCAGGACAAGTCATGCGGGTTACAACAGG	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,oesophagus,100K<gap<200K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	156	1	13	14	67360734	+	14	67110140	+	20.2923	16.8721	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-LN-A5U5-01A	ENSG00000171723	ENSG00000134001	GPHN	EIF2S1	ATCATTGTTAATCTTACCAATCTGGTAGGTGAAAAATTGTATTTTTATTG*AAAAATCTTGAATCTCCCATCAAAGCCTTTTCATTAAAAATACAATTTCA	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,oesophagus,100K<gap<200K	BOWTIE+STAR	intronic/UTR	0	156	1	17	14	66849574	+	14	67385459	+	16.8721	20.2923	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A5U5-01A	ENSG00000171723	ENSG00000134001	GPHN	EIF2S1	ATCATTTTTAATCTTACCAATCTGGTAGGTGAAAAATTGTATTTTTATTG*AAAAATCTTGAATCTCCCATCAAAGCCTTTTCATTAAAAATACAATTTCA	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,oesophagus,100K<gap<200K	BOWTIE+STAR	intronic/UTR	0	156	1	17	14	66849642	+	14	67385459	+	16.8721	20.2923	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A5U5-01A	ENSG00000171723	ENSG00000134001	GPHN	EIF2S1	TTTCTGTGCTTTCTTAGAAGCAAACCTGATTAGGTACAGAAGAAGCCTAT*AGTTAAAAGCATTTTAATACTAAGACCCTAATTCTTTTATCTTTATTTTA	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,oesophagus,100K<gap<200K	BOWTIE+STAR	intronic/UTR	0	156	1	15	14	66865612	+	14	67383887	+	16.8721	20.2923	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A5U5-01A	ENSG00000171723	ENSG00000134001	GPHN	EIF2S1	GAGTCTCGCTCTGTTGCCAGGCTGGAGTGCAGGGGCGTGATCTCAGCTCA*CTGGGCTCAAGCTATCCTCCTGCCTCTGCCTCTGTAAGAGTGTGAGCCAC	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,oesophagus,100K<gap<200K	BOWTIE+STAR	intronic/UTR	0	156	1	15	14	67049587	+	14	67385717	+	16.8721	20.2923	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A5U5-01A	ENSG00000171723	ENSG00000134001	GPHN	EIF2S1	AGATCAAGCCACTGCATTCCAGCCTGGGCAACAGAGCAAGACCCTGTCTC*AAAAAAAAAAAAAAACCAAAAATCTTGAATCTCCCATCAAAGCCTTTTCA	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,oesophagus,100K<gap<200K	BOWTIE+STAR	intronic/UTR	0	156	1	15	14	67039792	+	14	67385442	+	16.8721	20.2923	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A5U5-01A	ENSG00000197562	ENSG00000103253	RAB40C	HAGHL	GAGCCTGCAGGACGGCGCGGCAGAGTCCCCGTACGCCTACAGTAACG*CCCTTCCTAGGGTGTGGAGAGCGGGCCCCGCCCTGAAGGGGCACCGT	10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	5	1	13	16	590433	+	16	727412	+	6.3654	1.781	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A5U5-01A	ENSG00000128641	ENSG00000116117	MYO1B	PARD3B	GAGGAAGCAACGCCTGGAGGACTTGGCCACTCTCATTCAGAAGATATATC*TTGTAAATGAGAGTGGAAAGGGAACATACACCATACACCTGGTATGTGTG	chimerdb3seq,oesophagus	BOWTIE+STAR	CDS(truncated)/intronic	0	3	1	16	2	191393142	+	2	205498556	+	13.1244	0.3428	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A5U5-01A	ENSG00000116117	ENSG00000128641	PARD3B	MYO1B	TGGATCCAGATGATGTCTTGGCAGATGTTGTTGAAGATAAAGACAAG*TGTAAAAAATACAGGGACCAATTCACAGACCAGCAGAAACTTATTTA	chimerdb3seq,oesophagus,exon-exon	BOWTIE	in-frame	0	3	2	18	2	204686282	+	2	191411066	+	0.3428	13.1244	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-LN-A5U5-01A	ENSG00000116117	ENSG00000128641	PARD3B	MYO1B	TGATCATCAAACAGTTAAAGGTGGAAAATAAAATATGGTATTTATGAGAA*CCAGAATATTGTTTTCACCCAAATTTGAGTAGATATTTTAAACACCTAAC	chimerdb3seq,oesophagus	BOWTIE+STAR	intronic/UTR	0	3	1	18	2	204704565	+	2	191424791	+	0.3428	13.1244	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-LN-A5U5-01A	ENSG00000116117	ENSG00000128641	PARD3B	MYO1B	AGAGCAAATGGCAGAATCAGGTCAGATTAGCATGCTTGCCAAAGATTTAG*AAAAATGGGAGTGTCCCAACATGTAAACGAAAAAACAACCGTCTCCTTGA	chimerdb3seq,oesophagus	BOWTIE+STAR	intronic/CDS(truncated)	0	3	1	15	2	205171940	+	2	191423895	+	0.3428	13.1244	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A5U5-01A	ENSG00000197081	ENSG00000037474	IGF2R	NSUN2	GACGGCCCTCAGCGGGGTCTTCTCCCCACCCTCAGGCTGCTGGGATCATA*GGCTTCTTCTGGTCACTGGTGTCTGAAACCAAATCCAGAGCAGCCTGTGG	cancer	BOWTIE+STAR	intronic/UTR	0	2	1	16	6	160064594	+	5	6599880	-	11.5266	23.2273	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OG-01A	ENSG00000132541	ENSG00000227036	RIDA	LINC00511	CAAGTGGACAGCTTGTGTCAGGAGGGGTAGCAGAAGAAGCTAAACAA*GGGAGAAGAAGAGGATGGAGAAAAAAACTGGATCATCTCGTGACATG	lincrna,chimerdb3seq,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	6	16	27	8	98108646	-	17	72599144	-	6.0507	4.3633	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OG-01A	ENSG00000132541	ENSG00000227036	RIDA	LINC00511	TCTGCCCGCCTCAGCCTCCCAAAGTGCTGGGATTATAGGCATGAGCCACC*TGGCTCAGGCTGGACCACCTCTTGAGAGGCAGGAGCTCTGGATTTGATCA	lincrna,chimerdb3seq,oesophagus	BOWTIE+BOWTIE2	intronic/exonic(no-known-CDS)	0	6	1	35	8	98111336	-	17	72404737	-	6.0507	4.3633	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-L5-A4OG-01A	ENSG00000132541	ENSG00000227036	RIDA	LINC00511	AGTGGTCTGCCCGCCTCAGCCTCCCAAAGTGCTGGGATTATAGGCATGAG*GCAAGAGGATGGCTGGAGCCTGGGATGTTGAGGCTGCAATGAACTGTGAT	lincrna,chimerdb3seq,oesophagus	BOWTIE+BLAT	intronic/exonic(no-known-CDS)	0	6	1	25	8	98111341	-	17	72404480	-	6.0507	4.3633	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L7-A6VZ-01A	ENSG00000125676	ENSG00000235450	THOC2	AC079760.1	ATCATAAGTCCTCGGACAAGCACAGATAATGAAGACTTTCCATCAAG*AGAAAAAGTCATAAGATCAGCAAGAAGAGAAACTGTAGATTTGCCTC	lincrna,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	2	2	20	X	123610918	-	7	91380867	-	9.5244	1.2835	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-L7-A6VZ-01A	ENSG00000125676	ENSG00000235450	THOC2	AC079760.1	CATGTTTCCAAAGTCTGGGATGACATCAGCCCTCAATTCTATGCTACATT*GAGAATGACCAGAAAAGGGACAGTTGGTATTCAGTTATTTGATTCTTGTT	lincrna	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	14	X	123627799	-	7	91397522	-	9.5244	1.2835	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000085733	ENSG00000149571	CTTN	KIRREL3	GCGGCGGAATCCAGGGCCGACCCGGGCCGGACCGACCCCAGGCGGCG*TGCCGCCTGATGACCCCGTCATCCTGGGGGGCCCTGTGATCAGCCTG	oncogene,chimerdb3seq,cancer,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	UTR/CDS(truncated)	0	57	27	29	11	70398614	+	11	126473466	-	22.7397	16.6845	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000085733	ENSG00000149571	CTTN	KIRREL3	GGCGCGGCGGAATCCAGGGCCGACCCGGGCCGGACCGACCCCAGGCGGCG*GGAGCAGCAGAGGCCTGAGACTCTCAACGTGTCCCCAAGCACAAGCATGG	oncogene,chimerdb3seq,cancer,tcga-cancer,oesophagus	BOWTIE+STAR	UTR/intronic	0	57	7	37	11	70398614	+	11	126474932	-	22.7397	16.6845	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000085733	ENSG00000149571	CTTN	KIRREL3	GGCGCGGCGGAATCCAGGGCCGACCCGGGCCGGACCGACCCCAGGCGGCG*GGCCGCCTCTACGACTACGGGCAGCGGTTTGTGCTGGGCATGGGCAGCTC	oncogene,chimerdb3seq,cancer,tcga-cancer,oesophagus	BOWTIE+STAR	UTR/CDS(truncated)	0	57	1	15	11	70398614	+	11	126424861	-	22.7397	16.6845	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000149571	ENSG00000085733	KIRREL3	CTTN	CAGGCTCTGTGCCTGGTCTCCAAGGAGCAGGGGCAGCTCATCAGGAAGGA*GATCAGTTGAAGGCTAGAAGTGTGAAGTGCAGATGAGTGTGTGTTCTTCC	oncogene,chimerdb3seq,cancer,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/UTR	0	57	1	16	11	126546435	-	11	70436169	+	16.6845	22.7397	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000149571	ENSG00000085733	KIRREL3	CTTN	GGTCACACCTCGTGGCACCCACTGCCACCACCACACCTCTAGCCTTCAAG*TGTTCAATTTCAGTAGTTTGATCAGTTGAAGGCTAGAAGTGTGAAGTGCA	oncogene,chimerdb3seq,cancer,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/UTR	0	57	1	15	11	126699128	-	11	70436150	+	16.6845	22.7397	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000149571	ENSG00000085733	KIRREL3	CTTN	CAGCTGTGGTGCATTCCTTGTGTGTCTGGAATGGTGGCACAGGCCAGGGC*CCGCTGACTACCGAGAGGCCAGCAGCCAGCAGGGCCTGGCCTATGCCACA	oncogene,chimerdb3seq,cancer,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/CDS(truncated)	0	57	1	15	11	126834782	-	11	70433183	+	16.6845	22.7397	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000149571	ENSG00000085733	KIRREL3	CTTN	ACTCTCTAGTCAGAAAGACTTGGATTCAAATCTTAGCTCTGCTCTTTCCT*AGAGAGCCCAGCGGATGGCCAAGGAGCGGCAGGAGCAGGAAGAGGCCAGG	oncogene,chimerdb3seq,cancer,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/CDS(truncated)	0	57	1	14	11	126679531	-	11	70429138	+	16.6845	22.7397	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000149571	ENSG00000085733	KIRREL3	CTTN	GAGAAAACAAAGGCTCAAAAGCGTGGGAACTCATTGAAGGTCATGCAGCA*GTGAAGCCAGCTCTGCATCCTTCCTTAGAGCAGTTATGTTGTTACCTTCA	oncogene,chimerdb3seq,cancer,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/UTR	0	57	1	14	11	126763668	-	11	70422165	+	16.6845	22.7397	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000110063	ENSG00000110092	DCPS	CCND1	TGATATCTACAGCACCTATCACTTGTTCCCTCCAAGACAACTGAATG*ATGTGAAGTTCATTTCCAATCCGCCCTCCATGGTGGCAGCGGGGAGC	oncogene,chimerdb3seq,cancer,tumor,oesophagus,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	in-frame	0	52	31	30	11	126306744	+	11	69647994	+	92.4537	927.6724	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000110063	ENSG00000110092	DCPS	CCND1	CAATGATATCTACAGCACCTATCACTTGTTCCCTCCAAGACAACTGAATG*GGGAGTTTTGTTGAAGTTGCAAAGTCCTGGAGCCTCCAGAGGGCTGTCGG	oncogene,chimerdb3seq,cancer,tumor,oesophagus	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	52	15	37	11	126306744	+	11	69641119	+	92.4537	927.6724	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000110063	ENSG00000110092	DCPS	CCND1	TGATATCTACAGCACCTATCACTTGTTCCCTCCAAGACAACTGAATG*GTCTGCGAGGAACAGAAGTGCGAGGAGGAGGTCTTCCCGCTGGCCAT	oncogene,chimerdb3seq,cancer,tumor,oesophagus,exon-exon	BOWTIE	out-of-frame	0	52	9	28	11	126306744	+	11	69643031	+	92.4537	927.6724	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000110063	ENSG00000110092	DCPS	CCND1	TGATATCTACAGCACCTATCACTTGTTCCCTCCAAGACAACTGAATG*CAAATGGAGCTGCTCCTGGTGAACAAGCTCAAGTGGAACCTGGCCGC	oncogene,chimerdb3seq,cancer,tumor,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	52	3	19	11	126306744	+	11	69643832	+	92.4537	927.6724	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000110063	ENSG00000110092	DCPS	CCND1	TGGGTGGCTGGGGCAGGTCTCCCACAGGCCTCGGCAGACCAGGGCATGCT*GGACCCTCTCATGTAACCACGAACACCTATCGATTTTGCTAAAAATCAGA	oncogene,chimerdb3seq,cancer,tumor,oesophagus	BOWTIE+BLAT;BOWTIE+STAR	intronic/intergenic	0	52	2	33	11	126328602	+	11	69639940	+	92.4537	927.6724	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000110063	ENSG00000110092	DCPS	CCND1	CCAATGATATCTACAGCACCTATCACTTGTTCCCTCCAAGACAACTGAAT*GTAACGTCACACGGACTACAGGGGAGTTTTGTTGAAGTTGCAAAGTCCTG	oncogene,chimerdb3seq,cancer,tumor,oesophagus	BOWTIE+BOWTIE2	CDS(truncated)/UTR	0	52	1	37	11	126306743	+	11	69641098	+	92.4537	927.6724	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000110063	ENSG00000110092	DCPS	CCND1	ATGAGGCCTCTGGGGATGGGGATGGAGAGGATGCCGTTGTGATCCTGGAG*CTGAGCCTCCAGTTCCAGGTGGTGGGAGGTCTTTTTGTTTCCACTTGCAG	oncogene,chimerdb3seq,cancer,tumor,oesophagus	BOWTIE+STAR	CDS(truncated)/intronic	0	52	1	16	11	126306623	+	11	69643544	+	92.4537	927.6724	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000110063	ENSG00000110092	DCPS	CCND1	GCTGCCAGTGTGGGTCCCGGCCCTGAGCACCACACGGGGCTGTGGGTCCT*AGCAGAGTCCGCACGCTCCGGCGAGGGGCAGAAGAGCGCGAGGGAGCGCG	oncogene,chimerdb3seq,cancer,tumor,oesophagus	BOWTIE+STAR	intronic/UTR	0	52	1	14	11	126326392	+	11	69641185	+	92.4537	927.6724	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000110063	ENSG00000110092	DCPS	CCND1	AGGATCCATGGAGGCAGCTCTTCCCCTGAGTCCTGTGAGCGGTGGAGGGG*GAGGAGGTGGACCTGGCTTGCACACCCACCGACGTGCGGGACGTGGACAT	oncogene,chimerdb3seq,cancer,tumor,oesophagus	BOWTIE+STAR	UTR/CDS(truncated)	0	52	1	14	11	126337941	+	11	69651229	+	92.4537	927.6724	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000110080	ENSG00000137691	ST3GAL4	C11ORF70	ACAAACTGCTGAGCCTGCCAATGCAACAGCCACGGAAGATTAAGCAG*GCTTTTTTCAAAGACCCAAATGTTATTCCCAATTTGAAGTTACTTTC	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	41	26	29	11	126409411	+	11	102058880	+	73.5912	13.117	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000110080	ENSG00000137691	ST3GAL4	C11ORF70	AGCAGACCATTCACTACTATGAGCAGATCACGCTCAAGTCCATGGCG*GCTTTTTTCAAAGACCCAAATGTTATTCCCAATTTGAAGTTACTTTC	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	41	20	28	11	126413648	+	11	102058880	+	73.5912	13.117	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000110080	ENSG00000137691	ST3GAL4	C11ORF70	ACAAACTGCTGAGCCTGCCAATGCAACAGCCACGGAAGATTAAGCAG*GTTTTGCTAGTGGAAGACTCAGAAAAATATGAAATATTCAGCCAACC	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE	in-frame	0	41	6	30	11	126409411	+	11	102075873	+	73.5912	13.117	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000110080	ENSG00000137691	ST3GAL4	C11ORF70	GGGAAGGCTCCACTTCTTCACTTAAAGGGACTGCAGATGGTGTGAAGCAG*GCTTTTTTCAAAGACCCAAATGTTATTCCCAATTTGAAGTTACTTTCAGA	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	41	2	30	11	126418615	+	11	102058880	+	73.5912	13.117	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000110080	ENSG00000137691	ST3GAL4	C11ORF70	AGCAGACCATTCACTACTATGAGCAGATCACGCTCAAGTCCATGGCG*GTTTTGCTAGTGGAAGACTCAGAAAAATATGAAATATTCAGCCAACC	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE	in-frame	0	41	2	18	11	126413648	+	11	102075873	+	73.5912	13.117	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000110080	ENSG00000137691	ST3GAL4	C11ORF70	CTGACAAACTGCTGAGCCTGCCAATGCAACAGCCACGGAAGATTAAGCAG*GCTGGAGTGCAGTGGTGCAGTCACAGTTCGCTGCAGCTTCAATCATCTTC	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	41	1	34	11	126409411	+	11	102074745	+	73.5912	13.117	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000110080	ENSG00000137691	ST3GAL4	C11ORF70	GAGCTATCAAGAACCTCACGTCCTTCTGACCTGGGCAAGAGCTGTAGCCT*GCTTTTTTCAAAGACCCAAATGTTATTCCCAATTTGAAGTTACTTTCAGA	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+STAR	UTR/CDS(truncated)	0	41	1	17	11	126414068	+	11	102058880	+	73.5912	13.117	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000110080	ENSG00000137691	ST3GAL4	C11ORF70	GATCCAGTCAGGGTGGGGGCGCTGGAGCCGTGGGAGCCCGGCCAGGGCAG*CATCCTCTACTGGCCTGTAAGGTTTCTTCTGAGAAATCCATTGTGAGTCT	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+STAR	UTR/intronic	0	41	1	16	11	126414279	+	11	102071784	+	73.5912	13.117	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000110080	ENSG00000137691	ST3GAL4	C11ORF70	GACCTGGGCAAGAGCTGTAGCCTGTCGGTTGCCTACTCTGCTGTCTGGGT*CATACTGGAACCAGTTTAGGAGAGCCTGATTGCTAGACTTTCAGGAATCT	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+STAR	UTR/intronic	0	41	1	15	11	126414095	+	11	102053986	+	73.5912	13.117	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000110080	ENSG00000137691	ST3GAL4	C11ORF70	CTGGCTATGAGGGTGACGTGGGCTCCAAGACCACCATGCGTCTCTTCTAC*TTTGGGGTCCTAGTGGTTACATGTTATAGACTCAATGACTGAACTATGCC	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+STAR	CDS(truncated)/intronic	0	41	1	15	11	126408376	+	11	102063894	+	73.5912	13.117	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000110080	ENSG00000137691	ST3GAL4	C11ORF70	GAGCTGCGCGCGGAACCGTGCTGCCCCGCCCCGCTCCACCCGTGAGG*GCTTTTTTCAAAGACCCAAATGTTATTCCCAATTTGAAGTTACTTTC	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE	UTR/CDS(truncated)	0	41	1	14	11	126355842	+	11	102058880	+	73.5912	13.117	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000110080	ENSG00000137691	ST3GAL4	C11ORF70	AAACAACCCAGACACACTCCTCGTCCTGGTAGCTTTCAAGGCAATGGACT*CAATCCAGTGGAAAAAATATATGTTATATCTTACATTGGTCACCTTTTTA	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+STAR	CDS(truncated)/intronic	0	41	1	14	11	126408458	+	11	102075140	+	73.5912	13.117	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000110080	ENSG00000162344	ST3GAL4	FGF19	GAGCTGCGCGCGGAACCGTGCTGCCCCGCCCCGCTCCACCCGTGAGG*GTTTGCTGGAGATCAAGGCAGTCGCTCTGCGGACCGTGGCCATCAAG	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE	UTR/CDS(truncated)	0	20	16	30	11	126355842	+	11	69703364	-	73.5912	166.2609	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000110080	ENSG00000162344	ST3GAL4	FGF19	GAGCTGCGCGCGGAACCGTGCTGCCCCGCCCCGCTCCACCCGTGAGG*CTTCAGTACTCGGAGGAAGACTGTGCTTTCGAGGAGGAGATCCGCCC	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	UTR/CDS(truncated)	0	20	16	29	11	126355842	+	11	69699576	-	73.5912	166.2609	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000110080	ENSG00000162344	ST3GAL4	FGF19	GTCCGCCTGTGTGCAGGAGTCGCAAGGTCGCTGAGCAGGACCCAAAG*CTTCAGTACTCGGAGGAAGACTGTGCTTTCGAGGAGGAGATCCGCCC	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE	UTR/CDS(truncated)	0	20	1	14	11	126356302	+	11	69699576	-	73.5912	166.2609	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000110080	ENSG00000162344	ST3GAL4	FGF19	TTGCCTATACTGAAGCCCTGGGTGCCACTGCTGGCCCAGCAGGGAGGAGG*CGTGCTTCTACAAGAACAGTCCTGAGTCCACGTTCTGTTTAGCTTTAGGA	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/UTR	0	20	1	14	11	126358884	+	11	69699199	-	73.5912	166.2609	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000110080	ENSG00000162344	ST3GAL4	FGF19	CTTTGTTCTGCCTTAGGGACCAGCTGGTCCCCTGCTGTGGTTCCACACAG*CAAGTCTTGTCAATAACTTGCTGTGTGGAAGCAGCGGGGGAAGACCTAGA	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+STAR	intronic/UTR	0	20	1	14	11	126364004	+	11	69698443	-	73.5912	166.2609	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000110063	ENSG00000137693	DCPS	YAP1	TGATATCTACAGCACCTATCACTTGTTCCCTCCAAGACAACTGAATG*TCACATCGATCAGACAACAACATGGCAGGACCCCAGGAAGGCCATGC	oncogene,chimerdb3seq,cancer,tumor,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	14	18	28	11	126306744	+	11	102162456	+	92.4537	419.9844	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000110063	ENSG00000137693	DCPS	YAP1	TGATATCTACAGCACCTATCACTTGTTCCCTCCAAGACAACTGAATG*GTCCTCTTCCTGATGGATGGGAACAAGCCATGACTCAGGATGGAGAA	oncogene,chimerdb3seq,cancer,tumor,oesophagus,exon-exon	BOWTIE	in-frame	0	14	1	14	11	126306744	+	11	102186018	+	92.4537	419.9844	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000064309	ENSG00000137693	CDON	YAP1	ATTACGGCAGTATGCAGAAAAGGAACCAAGGCCAGAGAGACAAATAATGC*GCCAGGCGTGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAG	oncogene,chimerdb3seq,cancer,tumor,oesophagus	BOWTIE+BLAT	UTR/intronic	0	7	1	26	11	125959952	-	11	102180402	+	38.2835	419.9844	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000064309	ENSG00000137693	CDON	YAP1	GAATACCAGGACCAAAAGGAAAGATTTGGTGCCACTTTAATTTAGAAACA*ACTATAAGGTTTTGAGTTAGCTGGAAAAGTGATCAGATTAATAAATGTAT	oncogene,chimerdb3seq,cancer,tumor,oesophagus	BOWTIE+STAR	intronic/UTR	0	7	1	21	11	126011226	-	11	102231443	+	38.2835	419.9844	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000064309	ENSG00000137693	CDON	YAP1	GGACCACTGCAGCGTCAGTGATGTTCGTAAGCTATGGTTGAGCAAAGGAA*CATCTCTTGTATCAGTGAGACCTGGAGTCACAGGAGATCATTTTGGAGCT	oncogene,chimerdb3seq,cancer,tumor,oesophagus	BOWTIE+BLAT;BOWTIE+STAR	UTR/intronic	0	7	1	19	11	125956415	-	11	102127847	+	38.2835	419.9844	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000064309	ENSG00000137693	CDON	YAP1	TACTTCGTCCTGTCCCAAGCTGGTGCAAGCTCTCTCCATATTCAGGCTGT*GTTGTGAAGATTTAGGGGGACCTTGATAGAGAACTTTATAAACTTCTTTC	oncogene,chimerdb3seq,cancer,tumor,oesophagus	BOWTIE+STAR	CDS(truncated)/UTR	0	7	1	18	11	126010424	-	11	102232288	+	38.2835	419.9844	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000064309	ENSG00000137693	CDON	YAP1	ACCTACCTTCAGCTCTAGAAAATTTGAATTATTAAATTTAAAGATTTTAA*AATTGTGGGTGTGCCTATCATAACAATTGTTTTCTGTATCTTGAAAAAGT	oncogene,chimerdb3seq,cancer,tumor,oesophagus	BOWTIE+STAR	intronic/UTR	0	7	1	17	11	125976202	-	11	102233157	+	38.2835	419.9844	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000064309	ENSG00000137693	CDON	YAP1	GGCATTTCCATGAAGAAGTAATCTTATTAATCAAGCTCATTAAAAAAAGT*ACTTTGTCATGGAAATGTGAAAGTTTATGTGAAAGTTTCAAGGTCAAAAG	oncogene,chimerdb3seq,cancer,tumor,oesophagus	BOWTIE+STAR	UTR/intronic	0	7	1	16	11	126015037	-	11	102177424	+	38.2835	419.9844	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000064309	ENSG00000137693	CDON	YAP1	TACCTACCTTCAGCTCTAGAAAATTTGAATTATTAAATTTAAAGATTTTA*AAATTTATCAACTTTTTACATTTGTGTTATTTTCAGTCAGGGCTTCTTAG	oncogene,chimerdb3seq,cancer,tumor,oesophagus	BOWTIE+STAR	intronic/UTR	0	7	1	14	11	125976203	-	11	102232737	+	38.2835	419.9844	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000064309	ENSG00000137693	CDON	YAP1	AATAATGCCTCATGTCCCACTGCTTTAAAATTACATTAATTTATAAAATG*GTTATCTTTCTCTTCGAAGTTCTGATATTAAATAAATCATAGATTTATTT	oncogene,chimerdb3seq,cancer,tumor,oesophagus	BOWTIE+STAR	UTR/intronic	0	7	1	14	11	125959910	-	11	102214593	+	38.2835	419.9844	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000064309	ENSG00000137693	CDON	YAP1	AGCCTGTTTACATGGAAGATCTCATGTGTACTTCAACCTTTAAAAAATGA*TCTTCAATATAAGCTATGAAGTAATAGTTGGTTGTGAATTAAAGTGGCAC	oncogene,chimerdb3seq,cancer,tumor,oesophagus	BOWTIE+STAR	intronic/UTR	0	7	1	14	11	125987436	-	11	102231646	+	38.2835	419.9844	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000064309	ENSG00000137693	CDON	YAP1	CAGAGAATACCAGGACCAAAAGGAAAGATTTGGTGCCACTTTAATTTAGA*ACCAGCTAGCACCTCTGTGTTTTAAGGGTCTTTCAATGTTTCTAGAATAA	oncogene,chimerdb3seq,cancer,tumor,oesophagus	BOWTIE+STAR	intronic/UTR	0	7	1	14	11	126011230	-	11	102231694	+	38.2835	419.9844	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000137693	ENSG00000064309	YAP1	CDON	AGACCTGGAGTCACAGGAGATCATTTTGGAGCTTTAAAATGTGACTGTCC*CACACACAAACAGACACACACACTTGGAGCTAGTGAGTCATGCTGGCAGC	oncogene,chimerdb3seq,cancer,tumor,oesophagus	BOWTIE+STAR	intronic/UTR	0	7	6	30	11	102127913	+	11	125956634	-	419.9844	38.2835	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000170677	ENSG00000060069	SOCS6	CTDP1	CAGTCGCGCCGGCGCTGGGCGAGGAAGCGGAGCCGGGCCGCCTCCGG*AGCGGTTCTGGTGAGGTTGGAAGGATGCAGCCACCCGGTTGTCATGA	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	UTR/CDS(truncated)	0	5	12	29	18	70289090	+	18	79695225	+	7.4538	7.893	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-IG-A3I8-01A	ENSG00000100412	ENSG00000284665	ACO2	AC002472.4	GGCATTGTCCTGGCCAATGCTTGTGGCCCCTGCATTGGCCAGTGGGACAG*AAGGGACCGAGTCATTACTGAGGGGAAGAGAGGAAGCTCAGATGGTGCCA	pseudogene	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/intronic	0	4	4	37	22	41523278	+	22	21074394	-	10.1481	2.6817	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	unprocessed_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A4-01A	ENSG00000157014	ENSG00000237838	TATDN2	AC092422.1	CTTTGGAAGAAATGGCTTCTCTAGAGGAGGAAGCCTGCAGCCTTAAG*AATCCTGAACATCATCATAAAAAGACAGTCACCAGTCCTGCTCATCT	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	30	33	30	3	10249614	+	3	24858674	+	3.9508	7.6322	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A4-01A	ENSG00000157014	ENSG00000237838	TATDN2	AC092422.1	TCTGAAACCTTGAGAACTGTGATGGGCAGTGGAAAGAAGAGGGAAAG*AATCCTGAACATCATCATAAAAAGACAGTCACCAGTCCTGCTCATCT	lincrna,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	30	3	23	3	10249067	+	3	24858674	+	3.9508	7.6322	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A4-01A	ENSG00000157014	ENSG00000237838	TATDN2	AC092422.1	AAGTGAAGGCTTCCTGATCTCAGAAGCACGTTGTGGGCTTGGAAACCGAC*CAAGTGCTTCTGAGCATCAGCAGGAGCAAAACTCAATGCAGGCCCCACAG	lincrna	BOWTIE+STAR	UTR/intronic	0	30	1	14	3	10248965	+	3	24958982	+	3.9508	7.6322	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A4-01A	ENSG00000272410	ENSG00000237838	AC022384.1	AC092422.1	CCTCTTTGGAAGAAATGGCTTCTCTAGAGGAGGAAGCCTGCAGCCTTAAG*AATCCTGAACATCATCATAAAAAGACAGTCACCAGTCCTGCTCATCTGGA	lincrna,exon-exon	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	28	7	22	3	10249614	+	3	24858674	+	0	7.6322	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A4-01A	ENSG00000124198	ENSG00000022840	ARFGEF2	RNF10	CAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTA*AAAAAAAAAAAAATCCAAAAATTAGCCAGGCGGGTGCCTGTAATCCCAGC	NA	BOWTIE+STAR	intronic/intronic	0	2	1	28	20	49006132	+	12	120575077	+	12.3776	40.74	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Esophagus	TCGA-IG-A51D-01A	ENSG00000089280	ENSG00000124334	FUS	IL9R	AGGCTATGGCCAGAGCAGCTATTCTTCTTATGGCCAGAGCCAGAACA*GCTGGACCTTGGAGAGTGAGGCCCTGAGGCGAGACATGGGCACCTGG	oncogene,chimerdb3seq,cancer,tumor,oesophagus,exon-exon	BOWTIE	in-frame	0	18	14	29	16	31182664	+	X	156002906	+	37.386	1.8962	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Esophagus	TCGA-IG-A51D-01A	ENSG00000089280	ENSG00000124334	FUS	IL9R	AGGCTATGGCCAGAGCAGCTATTCTTCTTATGGCCAGAGCCAGAACA*TTAAGCTGGACCCGCCCTCTGACTTGCAGAGCAACATCAGTTCTGGC	oncogene,chimerdb3seq,cancer,tumor,oesophagus,exon-exon	BOWTIE	in-frame	0	18	8	28	16	31182664	+	X	156004420	+	37.386	1.8962	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Esophagus	TCGA-IG-A51D-01A	ENSG00000089280	ENSG00000124334	FUS	IL9R	AGGCTATGGCCAGAGCAGCTATTCTTCTTATGGCCAGAGCCAGAACA*GTCCTGGTGGTGACTCCAACCCTGCCCTCACATATCCCAAGAGCAGG	oncogene,chimerdb3seq,cancer,tumor,oesophagus,exon-exon	BOWTIE;BOWTIE+STAR	CDS(truncated)/UTR	0	18	4	26	16	31182664	+	X	156001330	+	37.386	1.8962	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Esophagus	TCGA-IG-A51D-01A	ENSG00000089280	ENSG00000124334	FUS	IL9R	TTGCCTATGAGTTGCAACATCACTAACAGCTTCTGAGAGGCTGGCTTTAT*GGAGAGGGTTTGTTTTGGAAAGAACATCACCCTCTCAGTTTCCTGGGGTC	oncogene,chimerdb3seq,cancer,tumor,oesophagus	BOWTIE+STAR	UTR/intronic	0	18	2	36	16	31183768	+	X	155998356	+	37.386	1.8962	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000078369	ENSG00000160075	GNB1	SSU72	AAATTTACATGTATTGGAGACCAGACCAGAAGCCCTTCTGAATTAAG*CAAACGGGGATTCAGCGTCCGATCCTTTGGAACAGGGACTCACGTGA	chimerdb3seq,exon-exon	BOWTIE;BOWTIE+STAR	UTR/CDS(truncated)	0	83	34	30	1	1839190	-	1	1564916	-	66.0232	20.4588	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000078369	ENSG00000160075	GNB1	SSU72	GCCGAGGCGGCGGTGTGGGCGCGTCAGGCCGCGACGAGGGCGCTGAG*CAAACGGGGATTCAGCGTCCGATCCTTTGGAACAGGGACTCACGTGA	chimerdb3seq,exon-exon	BOWTIE;BOWTIE+STAR	UTR/CDS(truncated)	0	83	23	29	1	1890820	-	1	1564916	-	66.0232	20.4588	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000078369	ENSG00000160075	GNB1	SSU72	CAGACAAATTTACATGTATTGGAGACCAGACCAGAAGCCCTTCTGAATTA*TGATTTCAAAACCACATATGACCAGATGTACAATGATCTTCTTAGGAAAG	chimerdb3seq	BOWTIE+BOWTIE2	UTR/CDS(truncated)	0	83	1	29	1	1839192	-	1	1564832	-	66.0232	20.4588	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000078369	ENSG00000160075	GNB1	SSU72	GCCGAGGCGGCGGTGTGGGCGCGTCAGGCCGCGACGAGGGCGCTGAG*CTATACACAGAATGGGATTTTACATATGCTGGACAGAAATAAGAGAA	chimerdb3seq,exon-exon	BOWTIE	UTR/CDS(truncated)	0	83	1	14	1	1890820	-	1	1545002	-	66.0232	20.4588	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000078369	ENSG00000160075	GNB1	SSU72	TGCAATACAAATACAGCCTTTTCTGTTTGTTTCAGACAAATTTACATGTA*TTGGAACAGGGACTCACGTGAAGCTTCCAGGACCAGCTCCCGACAAGCCC	chimerdb3seq	BOWTIE+STAR	UTR/CDS(truncated)	0	83	1	14	1	1839224	-	1	1564890	-	66.0232	20.4588	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000139263	ENSG00000258231	LRIG3	AC020637.1	ATTCCAAATCTGGGACCAGTCTCGGCAAATATTACACTTCTCTCCTT*TTCTCAAACAGTAGCTGCCACTTCTAGCTGGGAGAGAAATGAGAGCT	lincrna,exon-exon	BOWTIE;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	39	31	30	12	58913982	-	12	58812414	+	7.7501	7.008	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000139263	ENSG00000258231	LRIG3	AC020637.1	ATTCCAAATCTGGGACCAGTCTCGGCAAATATTACACTTCTCTCCTT*AATAGAATGCAACTGAAGAAATGGCTGGTGCAATTCAGCAAGGTAAA	lincrna,exon-exon	BOWTIE;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	39	27	30	12	58913982	-	12	58805941	+	7.7501	7.008	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000139263	ENSG00000258231	LRIG3	AC020637.1	ACCATTCCAAATCTGGGACCAGTCTCGGCAAATATTACACTTCTCTCCTT*ATGCTTAAGAAACAAATCTGGCTGAGTTAACAAGTCCTGCCTTGTGACAA	lincrna	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/intronic	0	39	7	35	12	58913982	-	12	58685646	+	7.7501	7.008	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000139263	ENSG00000258231	LRIG3	AC020637.1	ACCATTCCAAATCTGGGACCAGTCTCGGCAAATATTACACTTCTCTCCTT*TTTGTTCCTGATTCTGTCCTGTAGTAAATCATAGAACATATCAACTTTGT	lincrna	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/intronic	0	39	4	30	12	58913982	-	12	58606365	+	7.7501	7.008	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000139263	ENSG00000258231	LRIG3	AC020637.1	ATTCCAAATCTGGGACCAGTCTCGGCAAATATTACACTTCTCTCCTT*GGCCTGAATTTTCTGCTCCTGAATTCAAACATTAAAATGTGTGGTAT	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	39	4	27	12	58913982	-	12	58801260	+	7.7501	7.008	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000139263	ENSG00000258231	LRIG3	AC020637.1	ACCATTCCAAATCTGGGACCAGTCTCGGCAAATATTACACTTCTCTCCTT*GTCTGGGCCAAGCCTTGGATGGATTGAACCCCTCGGTAAACTTTAACAAT	lincrna	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	39	3	36	12	58913982	-	12	58606766	+	7.7501	7.008	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000139263	ENSG00000258231	LRIG3	AC020637.1	CCATTCCAAATCTGGGACCAGTCTCGGCAAATATTACACTTCTCTCCTTG*CTCACCTCATTCACCGGAAAATGCTGCAGAATGAAGACATAAGAGTGGAA	lincrna	BOWTIE+BOWTIE2	UTR/intronic	0	39	3	32	12	58913981	-	12	58722881	+	7.7501	7.008	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000139263	ENSG00000258231	LRIG3	AC020637.1	ATTCCAAATCTGGGACCAGTCTCGGCAAATATTACACTTCTCTCCTT*GTTCTGTTGATGTGATGGAATACGTTTACTGATTTGTGTATGTTGAA	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	39	3	26	12	58913982	-	12	58800375	+	7.7501	7.008	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000139263	ENSG00000258231	LRIG3	AC020637.1	CCATTCCAAATCTGGGACCAGTCTCGGCAAATATTACACTTCTCTCCTTG*ATTTGTGCTTACTACTGGGAATAAAATGAAGAACAAGACACAATCTCTAA	lincrna	BOWTIE+BOWTIE2	UTR/intronic	0	39	2	37	12	58913981	-	12	58712098	+	7.7501	7.008	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000139263	ENSG00000258231	LRIG3	AC020637.1	ATTCCAAATCTGGGACCAGTCTCGGCAAATATTACACTTCTCTCCTT*GTTTTGGTATCAGGATGATGCTGGCCTCATAAAATGAGTCAGGGAAG	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	39	2	28	12	58913982	-	12	58800583	+	7.7501	7.008	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000139263	ENSG00000258231	LRIG3	AC020637.1	CAACAATGAATTGGAGACCATTCCAAATCTGGGACCAGTCTCGGCAAATA*ATGGTGATCCAGTATCTCCAGAATCCATCACCACTGCTGACCTCCCACTC	lincrna	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	39	1	26	12	58913998	-	12	58812467	+	7.7501	7.008	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000139263	ENSG00000258231	LRIG3	AC020637.1	ACCATTCCAAATCTGGGACCAGTCTCGGCAAATATTACACTTCTCTCCTT*ACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCTCGG	lincrna	BOWTIE+BLAT	CDS(truncated)/intronic	0	39	1	26	12	58913982	-	12	58664499	+	7.7501	7.008	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000139263	ENSG00000258231	LRIG3	AC020637.1	CAAATATTACACTTCTCTCCTTGTAAGTGAATATCAGCAGAATTCCTCAT*AATAGAATGCAACTGAAGAAATGGCTGGTGCAATTCAGCAAGGTAAAAGA	lincrna	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	UTR/exonic(no-known-CDS)	0	39	1	25	12	58913954	-	12	58805941	+	7.7501	7.008	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000139263	ENSG00000258231	LRIG3	AC020637.1	ACCATTCCAAATCTGGGACCAGTCTCGGCAAATATTACACTTCTCTCCTT*CCTCTGGTAATGAACATTCTACTCACTACCTCTGTGAGATCGTGTATTTT	lincrna	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/intronic	0	39	1	25	12	58913982	-	12	58698083	+	7.7501	7.008	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000139263	ENSG00000258231	LRIG3	AC020637.1	ACCATTCCAAATCTGGGACCAGTCTCGGCAAATATTACACTTCTCTCCTT*TGTGAGGAATCCTACCAAACCTCTTGGGGACCTCATCTGTTGTGCTTGTG	lincrna	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/intronic	0	39	1	23	12	58913982	-	12	58720763	+	7.7501	7.008	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000139263	ENSG00000258231	LRIG3	AC020637.1	ACCATTCCAAATCTGGGACCAGTCTCGGCAAATATTACACTTCTCTCCTT*ACAGAGTCTCGCTCTGTCACCAAGGCTGGAGTGCAGTGGCACAATCTCGG	lincrna	BOWTIE+STAR	CDS(truncated)/intronic	0	39	1	19	12	58913982	-	12	58674717	+	7.7501	7.008	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000139263	ENSG00000258231	LRIG3	AC020637.1	ATTCCAAATCTGGGACCAGTCTCGGCAAATATTACACTTCTCTCCTT*CATTAAAATGTGTGGTATATCAGTACTGGGATTTATGAGGACAATGT	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	39	1	14	12	58913982	-	12	58802826	+	7.7501	7.008	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000139263	ENSG00000258231	LRIG3	AC020637.1	GGAGACCATTCCAAATCTGGGACCAGTCTCGGCAAATATTACACTTCTCT*AAGGCTTTGCAGATAATAAAGAATTGGGCAAGCATGACACCACCAAGGGA	lincrna	BOWTIE+STAR	CDS(truncated)/intronic	0	39	1	14	12	58913986	-	12	58632900	+	7.7501	7.008	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000257084	ENSG00000153179	MIR200CHG	RASSF3	CGTCTCCCCAGCACCCACTCTCTGGGGGCAGGTGGGCCCGGTGACAG*GATGTTGAGAAAGAGAAGGAAACCCACAGTTACCTCAGCAAAGAGGA	lincrna,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	exonic(no-known-CDS)/CDS(truncated)	0	15	14	29	12	6963348	+	12	64684787	+	4.2891	10.6286	TRUE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000185420	ENSG00000135747	SMYD3	ZNF670-ZNF695	GTGTGCAAGGGGAGTCGTGGCGTCGTCTGCGACCGCTGCCTTCTCGG*CCATGTGAAGATGTGCTTGCTTCCCCTTTGCCTTCTGCCATGATTCT	cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	7	15	30	1	246507054	-	1	246967792	-	2.5614	0.0629	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000185420	ENSG00000135747	SMYD3	ZNF670-ZNF695	GTGTGCAAGGGGAGTCGTGGCGTCGTCTGCGACCGCTGCCTTCTCGG*GGTCCAGTCGTCGACCATCGAGCTGCTTTGAAGACCCTGCGGAGGTT	cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	7	2	25	1	246507054	-	1	246945827	-	2.5614	0.0629	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000185420	ENSG00000197472	SMYD3	ZNF695	ACGGTGTGCAAGGGGAGTCGTGGCGTCGTCTGCGACCGCTGCCTTCTCGG*CCATGTGAAGATGTGCTTGCTTCCCCTTTGCCTTCTGCCATGATTCTAAG	known,tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE+STAR	out-of-frame	0	7	2	15	1	246507054	-	1	246967792	-	2.5614	0.2213	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	FALSE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000197472	ENSG00000185420	ZNF695	SMYD3	TGATCTCCCTTGGTGAGGATAGCTTCAATATGCAATTCCTATTTCACAGT*CTTTCATTGCTTCCAGCTCGACTCTGCTTCCACTGAACATAGAACTCAAT	known,tcga,chimerdb3seq,cancer,tcga-cancer	BOWTIE+STAR	intronic/intronic	0	7	1	16	1	246999910	-	1	246141864	-	0.2213	2.5614	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000163104	ENSG00000152208	SMARCAD1	GRID2	CTCAGAAGATAACAGAACTCCGGCCCTTTAATAGTTGGGAGGCTCTG*GTTGTGGAGACTAATTTGGTTGCTTTTGACTGTCACTGGATCATTAT	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE	in-frame	0	4	11	27	4	94253007	+	4	93207404	+	7.3865	2.1891	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000163104	ENSG00000152208	SMARCAD1	GRID2	GGAAGCCTATAATTCAAGCGTTAGGTGAAGGGAAGGCATAAGCACTG*GTTGTGGAGACTAATTTGGTTGCTTTTGACTGTCACTGGATCATTAT	chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE	UTR/CDS(truncated)	0	4	7	25	4	94253671	+	4	93207404	+	7.3865	2.1891	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000163104	ENSG00000152208	SMARCAD1	GRID2	AGGCTCAGAAGATAACAGAACTCCGGCCCTTTAATAGTTGGGAGGCTCTG*CAGGAAGACCCTGGAGAAGTTTTTCAGTTTCTCTGAAGGCTGCATTCTCA	chimerdb3seq,tcga-cancer,oesophagus	BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/intronic	0	4	1	34	4	94253007	+	4	93164993	+	7.3865	2.1891	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000157510	ENSG00000183111	AFAP1L1	ARHGEF37	CGGCCCGCTCCCCGGGGACCGGGCCGGCGCCATGGACCGAGGCCAGG*AACCTGCTGACATGGCCAAGCATGGAGCCGACGAGCCATCCTCCAGG	exon-exon	BOWTIE;BOWTIE+STAR	CDS(truncated)/UTR	0	2	4	30	5	149271984	+	5	149597759	+	2.2958	8.0967	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000104731	ENSG00000103257	KLHDC4	SLC7A5	AAGGATCTCTGGGTCCTGCATTTGGCCACCAAGACCTGGGAACAAGTCAA*GCGGGTGCGGGCCCGAAGCGGCGCGCGCTAGCGGCGCCGGCGGCCGAGGA	tcga-cancer,oesophagus,10K<gap<100K	BOWTIE+STAR	out-of-frame	0	2	4	35	16	87748673	-	16	87869419	-	2.5087	243.4515	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000104731	ENSG00000103257	KLHDC4	SLC7A5	GTCCAGGTTTGTAGCCTATAAGCATTGGGCTCTCCCGTCAGTGCAGGCGT*GTGCGGGCCCGAAGCGGCGCGCGCTAGCGGCGCCGGCGGCCGAGGAGAAG	tcga-cancer,oesophagus,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	2	3	37	16	87736165	-	16	87869415	-	2.5087	243.4515	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000104731	ENSG00000103257	KLHDC4	SLC7A5	GATCTCTGGGTCCTGCATTTGGCCACCAAGACCTGGGAACAAGTCAA*TGCTGCTCACGGCCGTGAACTGCTACAGCGTGAAGGCCGCCACCCGG	tcga-cancer,oesophagus,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	2	2	29	16	87748673	-	16	87851849	-	2.5087	243.4515	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000104731	ENSG00000103257	KLHDC4	SLC7A5	TGAGGTGCTGGTGTGTGGATGGATGAGGTGCTGGTGTGTGGATGGATGAG*GTGCTGACTGAGGCCTGCTTCCCCCTCCCCCTCCTGCTGTGCTGGAATTC	tcga-cancer,oesophagus,10K<gap<100K	BOWTIE+BLAT	intronic/UTR	0	2	1	31	16	87738771	-	16	87830563	-	2.5087	243.4515	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000104731	ENSG00000103257	KLHDC4	SLC7A5	ATCCGTGCCTCGTTGGAGGGCTGCGTGTGGCCAGCGCTAGCAGCTATTTT*CCACGCACGACGTCAGCCTCTTACCTTCCCGCCTCGGCTAGGGGTCCTCG	tcga-cancer,oesophagus,10K<gap<100K	BOWTIE+STAR	UTR/UTR	0	2	1	14	16	87740956	-	16	87830953	-	2.5087	243.4515	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000104731	ENSG00000103257	KLHDC4	SLC7A5	ATCCGTGCCTCGTTGGAGGGCTGCGTGTGGCCAGCGCTAGCAGCTATTTT*CCACAACAAGCAAGTGCATTTTCAGTCGTTGTGCTTTTTTGTTTTGTGCT	tcga-cancer,oesophagus,10K<gap<100K	BOWTIE+STAR	UTR/UTR	0	2	1	14	16	87740956	-	16	87830379	-	2.5087	243.4515	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000104731	ENSG00000103257	KLHDC4	SLC7A5	AGCTGTATTGCAGTGAGCCTTGTCAGGGTGTTGAGTCCTGTTCGCTGGCT*CAGGGTTGGGGGGTGCCGGCATCTCCCCTAGCTCACCAGGCCTGGCCTCT	tcga-cancer,oesophagus,10K<gap<100K	BOWTIE+STAR	intronic/UTR	0	2	1	14	16	87747724	-	16	87832282	-	2.5087	243.4515	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000104731	ENSG00000103257	KLHDC4	SLC7A5	CTATGGAACTACTGGGCTTTTAGAATGATAGGAAACCTGGCCTGTCCCTT*GGCCGAGGACCACCAGCAGGCAGGTGGACTGACTGTGTTGGGCAAGACCT	tcga-cancer,oesophagus,10K<gap<100K	BOWTIE+STAR	UTR/UTR	0	2	1	14	16	87750880	-	16	87831183	-	2.5087	243.4515	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000104731	ENSG00000103257	KLHDC4	SLC7A5	CACCAAGACCTGGGAACAAGTCAAGTAAGAAGCCAGATGAGAAGCTGAGC*TGTGGCATCGGCTTCACCATCATCCTCAGCGGGCTGCCCGTCTACTTCTT	tcga-cancer,oesophagus,10K<gap<100K	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	14	16	87748647	-	16	87834510	-	2.5087	243.4515	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-LN-A4A1-01A	ENSG00000104731	ENSG00000103257	KLHDC4	SLC7A5	GCACACCATCTCTCTGCCATTAAAGCAGCAGAGCGGAAGTGCCCTTGCTT*GTTGTGCTTTTTTGTTTTGTGCTAACGTCTTACTAATTTAAAGATGCTGT	tcga-cancer,oesophagus,10K<gap<100K	BOWTIE+STAR	intronic/UTR	0	2	1	14	16	87747910	-	16	87830352	-	2.5087	243.4515	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Esophagus	TCGA-L5-A43C-11A	ENSG00000139083	ENSG00000152102	ETV6	FAM168B	TTAAAATGTTTTATCTTTTCTTGGCTTTGTAAACAAAACCTTGTAAAAAA*CGGTACTTTTTTTAAGCTAAGTCAGCATTGTCTTCCAGTGTTAAAGGCAT	oncogene,cancer,tumor	BOWTIE+STAR	intronic/UTR	0	2	1	14	12	11814356	+	2	131048138	-	3.7729	15.7268	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-D8-A27F-01A	ENSG00000130702	ENSG00000118900	LAMA5	UBN1	GTACAACGAGGTCAACGTCACCCTGGACCTGGGCCAG*GCTGCCAGAGCTGCTGAGGGGGAGAGCAGACAGAAGT	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	72	18	25	20	62362400	-	16	4868833	+	10.6839	22.0091	TRUE	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-D8-A27F-01A	ENSG00000156030	ENSG00000187097	ELMSAN1	ENTPD5	AGACGGATCAACGTGGGCTCCCGGTTCCAGGCAGAAATCCCCTTGATGAG*GCCTGACGTACTCAGCAGCATGTCCCAACCCAAGAGGAAACAGAACTCGG	oncogene,18cancers,tumor,100K<gap<200K	BOWTIE+BLAT	CDS(truncated)/UTR	0	52	15	25	14	73726925	-	14	73961356	-	4.8355	2.0961	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-D8-A27F-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	CCGCCTGCCTCAGCCTCCAAAGTAGCTGAGACTACAG*CAGTTTAAGTATAGTGTGCCTGGGTTGGGTGCGGTGG	antisense,m2,exon-exon	BOWTIE	exonic(no-known-CDS)/UTR	0	15	4	24	10	87246115	-	10	46593287	+	0.5824	0.1352	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-D8-A27F-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	CCGCCTGCCTCAGCCTCCAAAGTAGCTGAGACTACAG*GTGTGTTTGTCAAAGTGTCTCTGATGAACCACAACAA	antisense,m2,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	15	3	25	10	87246115	-	10	46585598	+	0.5824	0.1352	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-D8-A27F-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	CCGGAGCTTCTCAGAAGACAGAGGGTTTTCTTTTGAG*ATTCCAGTTCTTTGATGAAAGTCTCTATTCCACCCAT	antisense,m2,exon-exon	BOWTIE	exonic(no-known-CDS)/UTR	0	15	2	18	10	87288442	-	10	46593989	+	0.5824	0.1352	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-D8-A27F-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	CCGCCTGCCTCAGCCTCCAAAGTAGCTGAGACTACAG*ATTCCAGTTCTTTGATGAAAGTCTCTATTCCACCCAT	antisense,m2,exon-exon	BOWTIE	exonic(no-known-CDS)/UTR	0	15	2	17	10	87246115	-	10	46593989	+	0.5824	0.1352	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-D8-A27F-01A	ENSG00000157933	ENSG00000162687	SKI	KCNT2	CGACTATGGCAACAAGTACAAGCGGCGGGTGCCCCGG*GGTACAAGTTGAATTCTATATGAATGAAAATACATTT	oncogene,tcga,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	11	3	19	1	2229735	+	1	196492341	-	4.8461	4.7908	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-D8-A27F-01A	ENSG00000071242	ENSG00000267413	RPS6KA2	LINC01901	TACGCCATGAAGGTCCTTAAGAAAGCCACCCTAAAAG*AAGTTCCATTGAGGTGAAGCAATGATGCAAGGCTTTT	lincrna,ribosomal,tumor,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	8	3	23	6	166531232	-	18	39862249	-	6.7522	0.5503	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-D8-A27F-01A	ENSG00000178764	ENSG00000247081	ZHX2	BAALC-AS1	CCCAGCCCGGGTCCCCGCGTTCACAGCCCCAGCGCAG*GGGAGATGGAACCCTGAGCAGCCCATGTACATGGAAG	antisense,18cancers,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	8	5	23	8	122781946	+	8	103285902	-	19.9731	1.0539	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-GI-A2C9-01A	ENSG00000182551	ENSG00000131773	ADI1	KHDRBS3	TATGCAAAGATAAACTACCAAATTATGAAGAAAAG*GACTATGATGATGGATATGGCACTGCTTATGATGA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	85	5	20	2	3513857	-	8	135606955	+	19.7157	12.8179	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-GI-A2C9-01A	ENSG00000131773	ENSG00000182551	KHDRBS3	ADI1	CGCCACCCCCGACACAAGAGACTTATGGAGAATAT*ATTAAGATGTTCTACGAGGAGCATTTGCACTTGGA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	85	14	24	8	135582073	+	2	3500993	-	12.8179	19.7157	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-GI-A2C9-01A	ENSG00000171634	ENSG00000154217	BPTF	PITPNC1	CACTCCTGGACAAGGATCTGCAAATTGAAGTGCAG*GATCCTAAGCACTTCAAGTCAGAGAAGACAGGACG	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	41	4	18	17	67948306	+	17	67669508	+	7.5756	2.7744	FALSE	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-GI-A2C9-01A	ENSG00000173065	ENSG00000109118	FAM222B	PHF12	GCTGCGGAGCGAACCTCACCTTTCCAGGGCGCAAG*TAACCCTCCACTGAGTGAAGAAATGTTGCCTCCTG	tcga,chimerdb3seq,tcga-cancer,oesophagus,10K<gap<100K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	37	3	22	17	28812209	-	17	28927063	-	11.9222	6.6596	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-GI-A2C9-01A	ENSG00000173065	ENSG00000109118	FAM222B	PHF12	GTGATGCTGTGTTCTTCACTGCATGATTTCAAAAG*TAACCCTCCACTGAGTGAAGAAATGTTGCCTCCTG	tcga,chimerdb3seq,tcga-cancer,oesophagus,10K<gap<100K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	37	3	22	17	28790378	-	17	28927063	-	11.9222	6.6596	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-GI-A2C9-01A	ENSG00000173065	ENSG00000109118	FAM222B	PHF12	GGAGCAGCCATGAGGGCCGGGCCCAGTCACCGACC*TAACCCTCCACTGAGTGAAGAAATGTTGCCTCCTG	tcga,chimerdb3seq,tcga-cancer,oesophagus,10K<gap<100K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	37	3	20	17	28842682	-	17	28927063	-	11.9222	6.6596	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-GI-A2C9-01A	ENSG00000244625	ENSG00000089063	MIATNB	TMEM230	CTCTCTGGAGCCGAGAGAGGCCGGTTTCCCCCACC*CTGTGTCAGCGTGTTATGATGCCGTCCCGTACCAA	lincrna,m26,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	29	7	24	22	26672987	+	20	5109445	-	0.2892	62.661	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-GI-A2C9-01A	ENSG00000134602	ENSG00000126970	STK26	ZC4H2	AAAATGGTGAAGAAACTAATTGAAAAATTTCAAAA*GAACAAGACCCTGCAGATGGAGAAGATCAAGGCTC	cell_lines,exon-exon	BOWTIE	in-frame	0	12	3	22	X	132073093	+	X	64921988	-	18.5356	1.7667	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-GI-A2C9-01A	ENSG00000134602	ENSG00000126970	STK26	ZC4H2	CCCGGCATCACAGATAAAATGGTGAAGAAACTAATTGAAAAATTTCAAAA*GGCCAAACATTCCACAGATTTCATCTCATTGAAGCATCCAACAATTCCAT	cell_lines	BOWTIE+STAR	CDS(truncated)/intronic	0	12	1	14	X	132073093	+	X	64968567	-	18.5356	1.7667	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-GI-A2C9-01A	ENSG00000075151	ENSG00000244038	EIF4G3	DDOST	TCAAAACTTAAATTCAAGAAGGAGCCCTGTCCCAG*ATTTTGGAGGCAACATCAACGTGGAGACCATCAGT	cell_lines,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	11	5	23	1	20941491	-	1	20656187	-	10.1943	91.5951	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-GI-A2C9-01A	ENSG00000100393	ENSG00000065150	EP300	IPO5	TCCGGCCCTCTCGGCGTCCGCCAGCGATGGCACAG*GAAACCTATGAGAATATCCCAGGCCAGTCAAAGAT	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	5	4	22	22	41093098	+	13	97982503	+	11.6613	23.6438	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AC-A2BK-01A	ENSG00000196365	ENSG00000128000	LONP1	ZNF780B	AACTGAGCAAGCTGCAGCAGCGCCTGGGGCGGGAG*ATTTGGAGTCAAAATATGGACCTGAGAAAATATCT	oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	54	14	23	19	5707060	-	19	40036626	-	21.0001	7.6969	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AC-A2BK-01A	ENSG00000145555	ENSG00000215196	MYO10	AC026790.1	AAGGCATCGTCGTCTTCCGGACAGACTATGGTCAG*CCATGTGAAGACGTGCCTGCCTCCCTGTTACCTTC	antisense,100K<gap<200K,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	10	2	21	5	16877609	-	5	17162565	-	43.7134	0.1157	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AC-A2BK-01A	ENSG00000118200	ENSG00000137936	CAMSAP2	BCAR3	AACAAAAACTGAAAGAACATCACACAGTTGAAGCTCCAGGAGGTCAAAAG*ATCCATTATTTGGGCAGGATTCTGTAGGGAAAACTCATCACCACTTCATA	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	6	6	24	1	200815644	+	1	93784191	-	32.8528	7.3226	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AC-A2BK-01A	ENSG00000197182	ENSG00000187498	MIRLET7BHG	COL4A1	GCAGGACCCGAGGCCAGGAGCCAGGGGCCCAGAAG*GGTGGCTGTGCTGGCTCTGGCTGTGGCAAATGTGA	lincrna,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	5	5	21	22	46053920	+	13	110242734	-	0.0221	17.7812	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AC-A2BK-01A	ENSG00000197182	ENSG00000187498	MIRLET7BHG	COL4A1	GACCTGTGCGCCCCAGGTCACGATCGGGTTCACGGCGACTCCTGAGGACG*GGTGGCTGTGCTGGCTCTGGCTGTGGCAAATGTGACTGCCATGGAGTGAA	lincrna,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	5	1	16	22	46072648	+	13	110242734	-	0.0221	17.7812	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AC-A2BK-01A	ENSG00000221914	ENSG00000142192	PPP2R2A	APP	GGTGAAAGGAGCAGTAGATGATGATGTAGCAGAAG*GTACCCACTGATGGTAATGCTGGCCTGCTGGCTGA	18cancers,chimerdb3seq,exon-exon	BOWTIE	out-of-frame	0	5	2	23	8	26293740	+	21	26112146	-	11.9263	137.8383	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-AR-A1AY-01A	ENSG00000134046	ENSG00000134516	MBD2	DOCK2	ATCAGACCCACAACGAATGAATGAACAGCCACGTCAG*ATCCCCTTCTTGGGAGCTGGGATTAAGATCCATGAGA	tcga,cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	157	18	25	18	54188874	-	5	170075947	+	20.378	3.9884	FALSE	TRUE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AR-A1AY-01A	ENSG00000134046	ENSG00000134516	MBD2	DOCK2	TTTACTGTTGGTCCCCAAGAGATTCAACAGGGGCCAT*ATCCCCTTCTTGGGAGCTGGGATTAAGATCCATGAGA	tcga,cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	157	7	23	18	54187714	-	5	170075947	+	20.378	3.9884	FALSE	TRUE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AR-A1AY-01A	ENSG00000173120	ENSG00000175634	KDM2A	RPS6KB2	ACCCGAAGAAGAAAGGATTCGTTACAGCCAGAGATTG*CCGCCCTTCACCGCAGAGAACCGGAAGAAAACCATGG	known,ribosomal,oncogene,cell_lines,18cancers,chimerdb3seq,m143,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	144	18	25	11	67121358	+	11	67433340	+	18.9808	5.8377	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-AR-A1AY-01A	ENSG00000173120	ENSG00000175634	KDM2A	RPS6KB2	GCTGGAGTGCGATGATACGATCTCGGCTCACTGCAACCTCGGCCTCCCAG*CCGCCCTTCACCGCAGAGAACCGGAAGAAAACCATGGATAAGATCATCAG	known,ribosomal,oncogene,cell_lines,18cancers,chimerdb3seq,m143,100K<gap<200K	BOWTIE+STAR	intronic/CDS(truncated)	0	144	18	24	11	67149815	+	11	67433340	+	18.9808	5.8377	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-AR-A1AY-01A	ENSG00000173120	ENSG00000175634	KDM2A	RPS6KB2	GCAACCTCGGCCTCCCAGGTTCAAGTGATTCTCCTGCCTCAGCCACCCAA*CCGCCCTTCACCGCAGAGAACCGGAAGAAAACCATGGATAAGATCATCAG	known,ribosomal,oncogene,cell_lines,18cancers,chimerdb3seq,m143,100K<gap<200K	BOWTIE+STAR	intronic/CDS(truncated)	0	144	1	20	11	67149847	+	11	67433340	+	18.9808	5.8377	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-AR-A1AY-01A	ENSG00000198563	ENSG00000112619	DDX39B	PRPH2	ATATGAGCGCTTCTCTAAATACATGCCCAATGTCAAG*TCGAATCAAGAGCAACGTGGATGGGCGGTACCTGGTG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	34	13	23	6	31538763	-	6	42704611	-	10.7199	7.8524	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AR-A1AY-01A	ENSG00000160957	ENSG00000071894	RECQL4	CPSF1	GCCTCACAGCCACAGCCACACGCCGCACTGCCAGTGACGTGGCACAGCAC*CTGGGCATCCGCCTGCTGGAAGGAGGTAGGTGGGTGGGGACGGTGGTGGG	18cancers,chimerdb3seq,cancer,100K<gap<200K	BOWTIE+BLAT	CDS(truncated)/intronic	0	15	3	23	8	144514021	-	8	144398213	-	13.9098	16.7238	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-AR-A1AY-01A	ENSG00000162236	ENSG00000197901	STX5	SLC22A6	CACACATGGTTAAGGAACAGGAGGAAACCATTCAGAG*GTGGAAAGAGAAACTGGGGCAGCAGCAACAGGAACAG	100K<gap<200K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	8	1	14	11	62824166	-	11	62936486	-	20.8305	0.0079	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Breast	TCGA-A7-A26F-01B	ENSG00000268362	ENSG00000233836	AC092279.1	AC139769.1	GAAAGGATTGTGACATATCGTTGGACCCAGAATTGAG*GGACTCTTGACGTTTAGGTATGTGGCCATAGAATTCT	pseudogene,lincrna,exon-exon	BOWTIE	exonic(no-known-CDS)/exonic(no-known-CDS)	0	2	2	16	19	24049548	+	19	23807826	+	16.8668	9.6406	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	lincRNA	transcribed_unprocessed_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0H7-01A	ENSG00000215012	ENSG00000101457	RTL10	DNTTIP1	CCAGGACCCTCTTCGCGGGCGATTCGCGTAGCCTCAG*TATGCAGCTGACCCCCAGGATAAGCACTGGCTGGCTG	chimerdb3seq,exon-exon	BOWTIE	UTR/CDS(truncated)	0	74	16	24	22	19854443	-	20	45809114	+	5.1254	13.3229	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0H7-01A	ENSG00000215012	ENSG00000101457	RTL10	DNTTIP1	CCCTGCCCCTGGCCTCCAGCCAGCTGCCAGTGGCCCCTCAGCTGCCTGTG*TATGCAGCTGACCCCCAGGATAAGCACTGGCTGGCTGAGCAGCATCACAT	chimerdb3seq	BOWTIE+STAR	in-frame	0	74	1	16	22	19851629	-	20	45809114	+	5.1254	13.3229	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-BH-A0H7-01A	ENSG00000022277	ENSG00000182463	RTFDC1	TSHZ2	AGCCTTGAAAGAGATAAAAGCGGAAGTTTGCCACACG*GACGAATGCCTTAGTTTCCACTTTCCAGCCTGGATCC	chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	69	12	24	20	56484189	+	20	53487144	+	35.3717	3.2511	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-BH-A0H7-01A	ENSG00000022277	ENSG00000182463	RTFDC1	TSHZ2	TGTTTTCTGAGCGAGCCTTGAAAGAGATAAAAGCGGAAGTTTGCCACACG*CATATTCTGGAAACTCTCAAGAAACAAAAGTTGCTGCCAGACAATGCTCT	chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	69	4	24	20	56484189	+	20	53444251	+	35.3717	3.2511	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-BH-A0H7-01A	ENSG00000022277	ENSG00000182463	RTFDC1	TSHZ2	TGTTTTCTGAGCGAGCCTTGAAAGAGATAAAAGCGGAAGTTTGCCACACG*GGTGGCTGAGCTGCAGGAGAGAAGGTGAGGGCATCAGGAAGAGAAAGTAC	chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	69	1	20	20	56484189	+	20	53336189	+	35.3717	3.2511	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-BH-A0H7-01A	ENSG00000022277	ENSG00000182463	RTFDC1	TSHZ2	TGTTTTCTGAGCGAGCCTTGAAAGAGATAAAAGCGGAAGTTTGCCACACG*GGAAGATTTTCCTGCATGCTTGGTCTGTGACCTGGGTTTATGAAGAATGA	chimerdb3seq,tcga-cancer	BOWTIE+BLAT	CDS(truncated)/intronic	0	69	1	20	20	56484189	+	20	53283860	+	35.3717	3.2511	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-BH-A0H7-01A	ENSG00000022277	ENSG00000182463	RTFDC1	TSHZ2	TGTTTTCTGAGCGAGCCTTGAAAGAGATAAAAGCGGAAGTTTGCCACACG*TGAGTAAAAGCTTCCTGAGGGCTGGCCAGAAGCAGATGCCAGCACTATGC	chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	69	1	19	20	56484189	+	20	53437900	+	35.3717	3.2511	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0H7-01A	ENSG00000100014	ENSG00000101158	SPECC1L	NELFCD	ACCAGGAGATTGCGAGGGAGCGATGCGGTGCAGCGCG*CAGGAGGATGATTCTGGAGAAGGAGAGGATGATGCGG	chimerdb3seq,cancer,m26,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	34	11	25	22	24270983	+	20	58986093	+	4.7502	38.2285	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0H7-01A	ENSG00000100014	ENSG00000101158	SPECC1L	NELFCD	CAGTCCGATGGGGCTACTTTATTCCAGAACAATCACA*CAGGAGGATGATTCTGGAGAAGGAGAGGATGATGCGG	chimerdb3seq,cancer,m26,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	34	4	24	22	24276803	+	20	58986093	+	4.7502	38.2285	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0H7-01A	ENSG00000101166	ENSG00000196090	PRELID3B	PTPRT	GCACCATGAAGATCTGGACTTCGGAGCACGTCTTTGA*GTGGCTGTTCCTTTGATGAGCACTACAGCAACTGTGG	chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	30	5	25	20	59042699	-	20	42885932	-	59.5013	4.6568	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-BH-A0H7-01A	ENSG00000101199	ENSG00000101019	ARFGAP1	UQCC1	GGTTCTTAAAGAAGTCAGGGTGCAGGATGAGAACAAC*AGGAACCAGACTAGCATTTCTCAGTGGGTTCCAGTAT	cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	24	3	20	20	63275640	+	20	35394196	-	21.3625	7.4329	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Breast	TCGA-BH-A0H7-01A	ENSG00000101199	ENSG00000101019	ARFGAP1	UQCC1	GCCTGACCCCGGCGGCCCTGCCCGCCCCTCCCTCCAG*AGGAACCAGACTAGCATTTCTCAGTGGGTTCCAGTAT	cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	24	2	22	20	63272920	+	20	35394196	-	21.3625	7.4329	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Breast	TCGA-BH-A0H7-01A	ENSG00000101199	ENSG00000101019	ARFGAP1	UQCC1	GGTTCTTAAAGAAGTCAGGGTGCAGGATGAGAACAAC*CTTTCTACTACCAAAGATTCCCCACAGCCTGTTGAGG	cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	24	1	13	20	63275640	+	20	35382025	-	21.3625	7.4329	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0H7-01A	ENSG00000100422	ENSG00000100372	CERK	SLC25A17	TGGCTGCAGACCCTGCGGGAGATGCTGGAGAAGCTGA*GGAAGCGTGACAGCAATGACAGTGTTTTTTCCCCTGG	tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	23	5	24	22	46720086	-	22	40799083	-	12.5312	13.3883	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0H7-01A	ENSG00000100422	ENSG00000100372	CERK	SLC25A17	TGGCTGCAGACCCTGCGGGAGATGCTGGAGAAGCTGA*GAGTGGTTAATGTGTTGCTAACAACTCCACTCTGGGT	tcga-cancer,exon-exon	BOWTIE	in-frame	0	23	2	23	22	46720086	-	22	40779125	-	12.5312	13.3883	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0H7-01A	ENSG00000100422	ENSG00000100372	CERK	SLC25A17	TGGCTGCAGACCCTGCGGGAGATGCTGGAGAAGCTGA*TTGATGAGAAAAGAAAATCCAAAACTACACACATGGT	tcga-cancer,exon-exon	BOWTIE	in-frame	0	23	1	14	22	46720086	-	22	40794580	-	12.5312	13.3883	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0H7-01A	ENSG00000088298	ENSG00000101134	EDEM2	DOK5	GATGTGAACGCCTCTGTGTTTGAAACAAACATTCGAG*GTTACAGAACTCAATAATGTGAAGAACGTAGCTCGAT	tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	21	2	19	20	35142373	-	20	54588483	+	15.4786	1.7055	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0H7-01A	ENSG00000184708	ENSG00000251322	EIF4ENIF1	SHANK3	GATACAGACCGGCCTTCCCTGGTGCGCAGGATAGTAG*AGAAGCTGGACGAGATGCTGGCAGCCGCCGCAGAGCC	cell_lines,tcga-cancer,exon-exon	BOWTIE	in-frame	0	17	5	21	22	31468175	-	22	50714917	+	2.6409	2.5414	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0H7-01A	ENSG00000130699	ENSG00000133424	TAF4	LARGE1	GGTACCAGGGGCGACCACCACTTCCTCAGCTGCCACG*AACCTACATTAAGAAACGCATTCAGATGCATCAGCCG	chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	14	4	23	20	62010046	-	22	33856802	-	4.2158	3.7846	TRUE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0H7-01A	ENSG00000167323	ENSG00000215271	STIM1	HOMEZ	GTGGAGGACCTGTGGAAGGCATGGAAGTCATCAGAAG*CTATCTCTGAAGGGCACAAATCAGAAGGCACCATGCC	tcga-cancer,exon-exon	BOWTIE	in-frame	0	13	4	24	11	4023987	+	14	23277187	-	7.5325	4.8367000000000004	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0H7-01A	ENSG00000173402	ENSG00000164048	DAG1	ZNF589	GAGCGAACACCTGCCGCGGTCCTCCCGCCGGCGCTGG*GGACCAGTGACTTTCGAGGATGTGGCTGTGCTTTTCA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	7	3	16	3	49470433	+	3	48260813	+	28.8565	7.0374	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0H7-01A	ENSG00000141519	ENSG00000141552	CCDC40	ANAPC11	TGAGGGAGAGAAGGAAGGGAATAATGAAAGCCACATG*GCAAGGTGCCCGGCGACGACTGCCCGCTGGTGTGGGG	exon-exon	BOWTIE	in-frame	0	5	6	24	17	80038186	+	17	81899920	+	0.3123	13.0839	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Breast	TCGA-BH-A0H7-01A	ENSG00000100084	ENSG00000272259	HIRA	LINC01749	CACCCTGACGGGACCAAGTTCGCAACTGGAGGACAAG*GGAGACAAGAGACACACAGCCACAGAGGACAAGGCCA	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	5	3	19	22	19410716	-	20	63079992	+	1.0205	1.5517	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0H7-01A	ENSG00000101447	ENSG00000100014	FAM83D	SPECC1L	GGACGCTCTGCGCCAGCAGCTCCGCTCGGCGCGAGAG*ACCAAGAGCAGTGATGACCTTTTAGCTGGAATGGCCG	oncogene,tcga,chimerdb3seq,tumor,m2,tcga-cancer,exon-exon	BOWTIE	in-frame	0	4	2	21	20	38926925	+	22	24313313	+	5.3004	4.7502	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0H7-01A	ENSG00000100426	ENSG00000061656	ZBED4	SPAG4	GCAGCCGGCCGGGAGCCGCCCCAGAGGCCGGGCCGAG*GAGCCTCCATCGACCTGCAGAAGACATCCCACGATTA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	4	11	23	22	49853989	+	20	35619195	+	5.6284	8.115	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Breast	TCGA-BH-A0H7-01A	ENSG00000052795	ENSG00000198589	FNIP2	LRBA	CCCAGGGCAGGGCTCCTAAGGAAGGACCCGCCTTTAG*TATCTCCTCCTGCAGAGTCCATTGATGTTCACAGACA	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	3	3	22	4	158769319	+	4	150321383	-	3.8947	16.1475	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-BH-A0H7-01A	ENSG00000052795	ENSG00000198589	FNIP2	LRBA	CCCAGGGCAGGGCTCCTAAGGAAGGACCCGCCTTTAG*AGTCCATTGATGTTCACAGACAAAGCCCAGCAGGATG	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	3	3	17	4	158769319	+	4	150321368	-	3.8947	16.1475	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01B	ENSG00000123130	ENSG00000184831	ACOT9	APOO	TGGCAGGATTCTTGAGGATCTTGACAGCTTGGGAG*TTATAGGTAAACATTGGAAACTCCATAGAATAAAT	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	125	13	23	X	23730527	-	X	23833612	-	26.1328	93.0139	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01B	ENSG00000123130	ENSG00000184831	ACOT9	APOO	TGGCAGGATTCTTGAGGATCTTGACAGCTTGGGAG*GAAAAACTAGACCAGACCTCTGTTATCTTCTGTGA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	125	10	24	X	23730527	-	X	23833510	-	26.1328	93.0139	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01B	ENSG00000123130	ENSG00000184831	ACOT9	APOO	AGACATCCATGGAAGTGAAGATGCAAATGTTCCAG*GTAATTCAGAGGTCCGTGGGGCCAGCCAGCCTGAG	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	125	10	22	X	23721881	-	X	23880952	-	26.1328	93.0139	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01B	ENSG00000123130	ENSG00000184831	ACOT9	APOO	TTTGTAATGGTGGCTCGTGATTCTGAAAATAAAGG*GTAATTCAGAGGTCCGTGGGGCCAGCCAGCCTGAG	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	125	6	23	X	23713135	-	X	23880952	-	26.1328	93.0139	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01B	ENSG00000123130	ENSG00000184831	ACOT9	APOO	CGGCAGCCTAGCGCAATGAGGCGGGCAGCACTGCG*TTATAGGTAAACATTGGAAACTCCATAGAATAAAT	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	125	5	24	X	23743125	-	X	23833612	-	26.1328	93.0139	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01B	ENSG00000123130	ENSG00000184831	ACOT9	APOO	CGGCAGCCTAGCGCAATGAGGCGGGCAGCACTGCG*GAAAAACTAGACCAGACCTCTGTTATCTTCTGTGA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	125	5	18	X	23743125	-	X	23833510	-	26.1328	93.0139	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01B	ENSG00000123130	ENSG00000184831	ACOT9	APOO	ATGTTGTATATCTCGTATTTCATATTGCATCGTATCAGGAGGTACAGGTT*GTCTTTCTGTAGAACTGCCTAAGAGCCGGGAGAATTCATGCTTTTGAAAC	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K	BOWTIE+BLAT	intronic/UTR	0	125	2	22	X	23711801	-	X	23883962	-	26.1328	93.0139	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01B	ENSG00000123130	ENSG00000184831	ACOT9	APOO	TCTTTCCTTTGTTCTTCAGTTACATGGTGATGAATTTTGTCCTGTTTTGG*CAAAAATAAAGAAGCTAGTGTATCCGCCTGGTTTCATGGGATTAGCTGCC	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K	BOWTIE+BLAT	in-frame	0	125	1	20	X	23713178	-	X	23858730	-	26.1328	93.0139	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01B	ENSG00000092929	ENSG00000167881	UNC13D	SRP68	GTGGAGCTTTGCTACATGAACACCAACTTGGTGCAGGAGAACTTCAGCAG*TACCATGGATTTGAAATGAACTCATCCTTGCTGTGAGCATCCAGGAGCCC	18cancers,chimerdb3seq,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	30	5	24	17	75832966	-	17	76039342	-	28.7487	13.7396	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-A7-A13D-01B	ENSG00000181617	ENSG00000234124	FDCSP	CSN1S2AP	CAGTCTCTCAAGACCAGGAACGAGAAAAAAGAAGT*AAGAACATGTAAGATTCTTGAATTAACTGCTGCAA	pseudogene,18cancers,100K<gap<200K,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	17	5	22	4	70233026	+	4	70082681	+	25709.4132	24.7803	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	transcribed_unitary_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A13D-01B	ENSG00000177479	ENSG00000132153	ARIH2	DHX30	AAACAGCCAACTACATTAGTGCTCACACTAAAGAC*AGCCTGGGCCTGGTGGACAGGAACAACGAACCGCT	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	13	6	18	3	48973816	+	3	47845700	+	12.0778	8.6224	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01B	ENSG00000171456	ENSG00000101337	ASXL1	TM9SF4	AACTGCCTGGCCGAATCAGCCTTTTCACGCTCAAG*GATTGGTTGCCGTGGTCTTTACTGCTTTTCTCCCT	tcga,cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	13	3	24	20	32369123	+	20	32133013	+	17.0787	26.0154	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01B	ENSG00000078114	ENSG00000138081	NEBL	FBXO11	AACATGCCATGGAGGTCAATAAACACCAGAGTAAT*ATGATGATGTGCCTGCAGATATGGTTGCAGAAGAA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	12	7	24	10	20880794	-	2	47839769	-	48.2001	23.3395	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01B	ENSG00000185630	ENSG00000162946	PBX1	DISC1	GTTTAATGTGTTGTGTGAAATCAAAGAAAAAACAG*AAACAAGTGTGAAGGAAAATACTATGAAGTACATG	oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	9	5	23	1	164563311	+	1	231958828	+	18.0741	8.3699	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01B	ENSG00000140694	ENSG00000085721	PARN	RRN3	CCAGGGATTTGATTTTAATAAAGTTTTTCGAAATG*ATCTTCCTGCAAATTTTGACACATGTCACAGAGCC	tcga,chimerdb3seq,m3,tcga-cancer,exon-exon	BOWTIE	in-frame	0	8	4	20	16	14617590	-	16	15084705	-	13.7874	29.3035	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01B	ENSG00000152558	ENSG00000137675	TMEM123	MMP27	TGGGCTTCCACACAACTCCAGTGCTAACTCAACAG*GTTTGATGAAATGACCCAAACCATGGACAAAGGGT	known,tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	5	4	23	11	102448812	-	11	102693041	-	262.7894	16.0494	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01B	ENSG00000084463	ENSG00000070019	WBP11	GUCY2C	GATAATCCGAGACATGGAGAAATTGGATGAAATGG*AAAATATAGAAAAGATTATGAACTTCGTCAGAAAA	10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	5	2	19	12	14799635	-	12	14656617	-	28.6617	6.4848	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A13D-01B	ENSG00000089597	ENSG00000065029	GANAB	ZNF76	CCTGGGTTGATATATCTTCCAACACTGCCGGGAAG*ATTTGTGACCCAGAAGGAAATCTCTGACCTCAGCT	18cancers,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	4	4	22	11	62632565	-	6	35281056	+	40.4387	4.5888	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01B	ENSG00000172830	ENSG00000173120	SSH3	KDM2A	AACGCAGCAAACCTGGAGGAGCTGCAGAGGAACAG*GTCTTCTGGCTCATCCCCCCTACAGCCCACAACCT	oncogene,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	3	2	22	11	67308458	+	11	67217731	+	4.0583	18.0695	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01B	ENSG00000187531	ENSG00000176155	SIRT7	CCDC57	CAGACACCATCCTGTGTCTAGGGTCCAGCCTGAAG*AAATGGGGTCTCACTATGTCACCCAGGCTGGTCTC	tcga,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	2	1	14	17	81914294	-	17	82113765	-	9.4868	10.860900000000001	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A1J5-01A	ENSG00000121274	ENSG00000162105	PAPD5	SHANK2	AGATGAGGATTCGGTGAAAGTTTTAGACAAAGCAACT*ACACAGGCAGCCATGCCGCGCAGCCCAACATCCAGCG	18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	475	23	25	16	50216195	+	11	71147338	-	7.0501	51.9961	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-EW-A1J5-01A	ENSG00000121274	ENSG00000162105	PAPD5	SHANK2	AGATGAGGATTCGGTGAAAGTTTTAGACAAAGCAACT*GATCACACTCTGTTGCCCAAGCTGAGAGCAGTGGTGC	18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	475	8	24	16	50216195	+	11	71174844	-	7.0501	51.9961	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-EW-A1J5-01A	ENSG00000121274	ENSG00000162105	PAPD5	SHANK2	AACACAAAGTCGCAGATGAGGATTCGGTGAAAGTTTTAGACAAAGCAACT*GTTGGCTCTGAAGACATGTGGCCATTTCCTCAGTCCCTTCACACCCGCAT	18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	475	4	22	16	50216195	+	11	71194652	-	7.0501	51.9961	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-EW-A1J5-01A	ENSG00000132749	ENSG00000131626	TESMIN	PPFIA1	CAACTCTTCCAGGACCACCAAAAATAACTTTGGCTGG*GCATGAATTGCTGGAGGAAGCCCGGAGACAAGGTTTA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	28	11	25	11	68738700	-	11	70362095	+	17.6608	31.7727	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AR-A24Z-01A	ENSG00000100266	ENSG00000197933	PACSIN2	ZNF823	CGTTGGAGTAGAAGTGTCCAGCGACAGCTTCTGGGAG*GACTCAGTGGCCTTTGAAGATGTGGCTGTGAACTTCA	tcga,cell_lines,18cancers,chimerdb3seq,cancer,m13,tcga-cancer,exon-exon	BOWTIE	in-frame	0	17	10	24	22	42912021	-	19	11725327	-	11.6557	7.4319	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AR-A24Z-01A	ENSG00000100266	ENSG00000197933	PACSIN2	ZNF823	CGTTGGAGTAGAAGTGTCCAGCGACAGCTTCTGGGAG*AAGTCATACATGTGAAATTAAAGATGACAGTCAATGT	tcga,cell_lines,18cancers,chimerdb3seq,cancer,m13,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	17	2	15	22	42912021	-	19	11723342	-	11.6557	7.4319	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AR-A24Z-01A	ENSG00000100266	ENSG00000197933	PACSIN2	ZNF823	CTGCAGTCAGCTCACTTTATAGAGGAAGAACTCGGCTGCTTCAGCTCAAT*GACTCAGTGGCCTTTGAAGATGTGGCTGTGAACTTCACACAAGAGGAGTG	tcga,cell_lines,18cancers,chimerdb3seq,cancer,m13,tcga-cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	17	1	24	22	42995149	-	19	11725327	-	11.6557	7.4319	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AR-A24Z-01A	ENSG00000134709	ENSG00000175582	HOOK1	RAB6A	GCCTAAGCTGCCCCTGTGCGACAGCCTCATGATCTGG*CTCTTTCGACGTGTAGCAGCAGCTTTGCCGGGAATGG	known,18cancers,chimerdb3seq,m10,exon-exon	BOWTIE	in-frame	0	15	16	24	1	59815180	+	11	73679720	-	61.9099	86.3117	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-AR-A24Z-01A	ENSG00000034693	ENSG00000112419	PEX3	PHACTR2	TGAATTCCGAGAGCCTCACAGCTCTGCTAAAAAACAG*CTGGCTCCTCTCATTCAAAAAAAACAACTGGCTCTAA	10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	11	1	14	6	143462997	+	6	143765261	+	6.7453	3.5611	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-AR-A24Z-01A	ENSG00000135862	ENSG00000143502	LAMC1	SUSD4	TGAACGATAACAAGACGGCCGCAGAGGAGGCACTAAGGAAGATTCCTGCC*TTAAATGTGTCCCGGAGATTCTGGTATGTTGTGTCTTTGTTCTCATTGGT	18cancers	BOWTIE+BLAT	CDS(truncated)/intronic	0	9	4	25	1	183136450	+	1	223281083	-	16.7095	4.2326	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-AR-A24Z-01A	ENSG00000137968	ENSG00000122420	SLC44A5	PTGFR	GTTCTTCAGCGTCTATGCAATGTGTGTTGAAACAATTTTCATCTGCTTCT*CTTTGCTGCCCATCCTTGGACATCGAGACTATAAAATTCAGGCGTCGAGG	18cancers	BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	5	2	21	1	75211468	-	1	78493243	+	5.9983	0.7851	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-AR-A24Z-01A	ENSG00000110395	ENSG00000074201	CBL	CLNS1A	TACTCTCTTCATGATGAAGGAATTGGCTGGTGCCAAG*GAAAAAGGAGGAAAAAAATGTACTGGGGAACAAGACA	oncogene,18cancers,cancer,tumor,exon-exon	BOWTIE	CDS(truncated)/UTR	0	4	2	23	11	119278713	+	11	77530014	-	3.2631	11.0868	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-AR-A24Z-01A	ENSG00000152104	ENSG00000224260	PTPN14	AL023754.1	TGCCAAATGTGTCATGGCTTCAGCAAGAGGCCACAAG*ATCCACTGACTCACACCTGCCTCTCTGCTTGTCCAGA	lincrna,cancer,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	3	3	23	1	214451805	-	1	209542918	-	1.7481	0.5767	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AR-A24Z-01A	ENSG00000152104	ENSG00000224260	PTPN14	AL023754.1	TGCCAAATGTGTCATGGCTTCAGCAAGAGGCCACAAG*GGGTAACCACCACAGGCCCACAGGCTAAAATTGAGCT	lincrna,cancer,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	3	2	17	1	214451805	-	1	209546139	-	1.7481	0.5767	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AR-A24Z-01A	ENSG00000152104	ENSG00000224260	PTPN14	AL023754.1	TGCCAAATGTGTCATGGCTTCAGCAAGAGGCCACAAG*GCCCTTGTAGGACATGTGAATGCCAGTGCTCATGGAG	lincrna,cancer,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	3	1	14	1	214451805	-	1	209541429	-	1.7481	0.5767	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AR-A24Z-01A	ENSG00000151693	ENSG00000224184	ASAP2	MIR3681HG	GGCGCAGTGCCGGAACACTGTGGCGGCCATCGAGGAG*GAGCCTTCATCTACCACATAAGAATTGCAGCAAACCC	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	2	1	14	2	9207230	+	2	12558206	+	3.549	0.5015	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AR-A24Z-01A	ENSG00000105576	ENSG00000173406	TNPO2	DAB1	CCCTGCCCTTGCCAGAATTTCCTGCGCTGTTCCACCTCATTCAACTTCAG*GAAATTGTGGGTTTCTTGGAAGGCTCTGGATATCTGTGACAGACCTCAGG	NA	BOWTIE+STAR	UTR/intronic	0	2	1	22	19	12723249	-	1	57970865	-	22.0093	0.1232	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04Q-01A	ENSG00000171208	ENSG00000177200	NETO2	CHD9	TTGCATCTGGACCATTAAAGCCACTCCAAAAGCTAAG*ATGCAACTTCTCCAGGAGTGCTTATGTTACCCAAAGA	18cancers,cancer,m14,exon-exon	BOWTIE	CDS(truncated)/UTR	0	18	3	19	16	47122657	-	16	53121300	+	6.4378	3.9496000000000002	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04Q-01A	ENSG00000171208	ENSG00000177200	NETO2	CHD9	GCCAAGCCGTTGATTGCATCTGGACCATTAAAGCCACTCCAAAAGCTAAG*ATCTCTCCAAACTTGATTTAGATGCAACTTCTCCAGGAGTGCTTATGTTA	18cancers,cancer,m14	BOWTIE+BLAT	CDS(truncated)/intronic	0	18	1	21	16	47122657	-	16	53121279	+	6.4378	3.9496000000000002	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04Q-01A	ENSG00000171208	ENSG00000177200	NETO2	CHD9	GCCAAGCCGTTGATTGCATCTGGACCATTAAAGCCACTCCAAAAGCTAAG*CACATCCTTCAGATCCCAGGTTAGACTCCCTTCTTCCAGGATACGTTCCC	18cancers,cancer,m14	BOWTIE+STAR	CDS(truncated)/intronic	0	18	1	17	16	47122657	-	16	53082798	+	6.4378	3.9496000000000002	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04Q-01A	ENSG00000099810	ENSG00000147889	MTAP	CDKN2A	CCGGCGATATTGTCATTATTGATCAGTTCATTGACAG*AGACGCTGCGGATCCCAGAGGCTTAACTGGCAGCTGG	tcga,cell_lines,chimerdb3pub,chimerdb3seq,cancer,tumor,m12,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	17	6	24	9	21818202	+	9	21989955	-	1.5075	6.6309	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04Q-01A	ENSG00000099810	ENSG00000147889	MTAP	CDKN2A	CCGGCGATATTGTCATTATTGATCAGTTCATTGACAG*GTCATGATGATGGGCAGCGCCCGAGTGGCGGAGCTGC	tcga,cell_lines,chimerdb3pub,chimerdb3seq,cancer,tumor,m12,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	17	3	20	9	21818202	+	9	21971208	-	1.5075	6.6309	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04Q-01A	ENSG00000099810	ENSG00000147889	MTAP	CDKN2A	GAGGAGATTCAGCCCGGCGATATTGTCATTATTGATCAGTTCATTGACAG*GTATAAATCAATTTTCAGGACGTATGTGAAAAGCGCAATCTTCAGGAAGT	tcga,cell_lines,chimerdb3pub,chimerdb3seq,cancer,tumor,m12,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	17	2	17	9	21818202	+	9	21992480	-	1.5075	6.6309	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04Q-01A	ENSG00000099810	ENSG00000147889	MTAP	CDKN2A	GAGGAGATTCAGCCCGGCGATATTGTCATTATTGATCAGTTCATTGACAG*TTATAATGGTTTCCGCAGGATGAGAGGGGTTGGGAAAAAGTTTGGTGATA	tcga,cell_lines,chimerdb3pub,chimerdb3seq,cancer,tumor,m12,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	17	1	15	9	21818202	+	9	21990601	-	1.5075	6.6309	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A0CE-01A	ENSG00000137522	ENSG00000152207	RNF121	CYSLTR2	GGTGCAGTGGAAGCAGAGGCACCCACGCTCCTACAAT*CATGGAGAGAAAATTTATGTCCTTGCAACCATCCATC	18cancers,chimerdb3seq,exon-exon	BOWTIE	CDS(complete)/UTR	0	31	9	25	11	71960891	+	13	48706817	+	4.4655	9.8242	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A0CE-01A	ENSG00000137522	ENSG00000152207	RNF121	CYSLTR2	CGCGCCCGGCAGATTTTTACAACCTATTCTGAAGAAA*CATGGAGAGAAAATTTATGTCCTTGCAACCATCCATC	18cancers,chimerdb3seq,exon-exon	BOWTIE	UTR/UTR	0	31	2	21	11	71962289	+	13	48706817	+	4.4655	9.8242	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A0CE-01A	ENSG00000153395	ENSG00000049656	LPCAT1	CLPTM1L	GCACGAGCTGCGCCTCAGCGCCCTGCAGAAGGCCCAG*CTTCTCTTTGATTTCCTGGCCTTTAAAAATGACATCA	cell_lines,18cancers,chimerdb3seq,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	24	10	24	5	1523710	-	5	1331883	-	10.8727	16.9684	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A0CE-01A	ENSG00000153395	ENSG00000049656	LPCAT1	CLPTM1L	GCACGAGCTGCGCCTCAGCGCCCTGCAGAAGGCCCAG*CTGTGGAAAGTGAAGAAGGCATTGAAGATGACTATTT	cell_lines,18cancers,chimerdb3seq,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	24	2	21	5	1523710	-	5	1325816	-	10.8727	16.9684	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A0CE-01A	ENSG00000153395	ENSG00000049656	LPCAT1	CLPTM1L	GCAGAAACCCAGCTAAGTTCCCAGTTGAGATAAACCA*CTTCTCTTTGATTTCCTGGCCTTTAAAAATGACATCA	cell_lines,18cancers,chimerdb3seq,100K<gap<200K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	24	1	13	5	1521347	-	5	1331883	-	10.8727	16.9684	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A0CE-01A	ENSG00000122042	ENSG00000122033	UBL3	MTIF3	AAACGGCAAGATGTCCAGTAATGTCCCGGCGGATATG*CTGTCATTCTTCTCTACAGAAGAGCTTCTCCTCATCA	18cancers,chimerdb3seq,cancer,m22,exon-exon	BOWTIE	CDS(truncated)/UTR	0	24	10	25	13	29849512	-	13	27445156	-	7.0783	24.6273	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A0CE-01A	ENSG00000169398	ENSG00000022567	PTK2	SLC45A4	CTGGGACTCCGGAGGGTCTGATGAAGCACCGCCCAAG*ATCATCCAGTCACTCGATGGGGATTACCAGCGGACCA	tcga,18cancers,chimerdb3seq,tcga-cancer,oesophagus,exon-exon	BOWTIE	CDS(truncated)/UTR	0	18	6	21	8	140717598	-	8	141254629	-	12.8439	25.9121	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A15E-01A	ENSG00000163909	ENSG00000049089	HEYL	COL9A2	ACGGACCCATCGACGTGGGCCAAGAGGGCCAGCTGAG*GGGGACCCTGGACCAGATGGACCATCGGGGCCCCCAG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	21	2	16	1	39639546	-	1	40311715	-	3.5125	12.3552	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A15E-01A	ENSG00000107882	ENSG00000107862	SUFU	GBF1	TTAATGCAGGGCTTGGCACGATACGTGTTCCAGTCAG*ATCCCACCCATGAGGGCACAGCAGAGGGCATGGAGAA	tcga,cell_lines,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	7	7	24	10	102550106	+	10	102351256	+	7.6446	6.9973	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A0D0-01A	ENSG00000063176	ENSG00000267335	SPHK2	AC008687.1	AGGACCAGCAGATGAATGGACACCTTGAAGCAGAGGAGCAGCAGGACCAG*GCAATCACTGGCATGAGAAGGGGTCAGACCAGTGTGAGCTGTGGAAGGAG	m2	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	23	5	24	19	48620553	+	19	49023914	-	1.3293	0	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A0D0-01A	ENSG00000063176	ENSG00000267335	SPHK2	AC008687.1	GAATGGACACCTTGAAGCAGAGGAGCAGCAGGACCAG*GGGCTGCTGCTGTTGCTGCTGCTGAGCATGGGCGGGA	m2,exon-exon	BOWTIE	CDS(truncated)/CDS(no-known-start-or-end)	0	23	3	18	19	48620553	+	19	49023603	-	1.3293	0	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A0D0-01A	ENSG00000149633	ENSG00000171004	KIAA1755	HS6ST2	GGAATTCGAGAAGGCCGACCCCCCTGGGGGGATGCAG*GAACTTCCACTACATCACCATCCTCCGAGACCCAGTG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	9	5	24	20	38223538	-	X	132629093	-	3.972	6.0835	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A0D0-01A	ENSG00000124333	ENSG00000092969	VAMP7	TGFB2	GTGGATGAACTGAAAGGAATCATGGTCAGAAACATAG*ATGCCATCCCGCCCACTTTCTACAGACCCTACTTCAG	18cancers,cancer,exon-exon	BOWTIE	in-frame	0	9	8	25	X	155900587	+	1	218405169	+	48.4818	4.6161	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A0D0-01A	ENSG00000171517	ENSG00000184005	LPAR3	ST6GALNAC3	CCCATGAAGCTAATGAAGACGGTGATGACTGTCTTAG*AGTCCAGTCTGGCTCATATCTCAGCACAGGGTGGTTT	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	7	2	22	1	84865385	-	1	76627452	+	3.3094	1.8121	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A0D0-01A	ENSG00000198373	ENSG00000259700	WWP2	AC012379.2	CCGGGCAGGAGTGGCCCTGCCTTTTGAGAAGTCTCAGCTCACTTTGAAAG*GAGCACTCGCATCCTTCAATCGCCGACTAGAAGCTCGCCCGGTGGGCGGA	NA	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	6	2	25	16	69787080	+	15	48811100	+	4.4581	2.1173	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A0D0-01A	ENSG00000183495	ENSG00000061936	EP400	SFSWAP	AGAGGAGGAAGAAAAATCTGAGGTTATCAATGACGAG*CGACCGTGGCAGCCATGTATTACAGCTACTACATGCT	tcga,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	4	2	25	12	131961954	+	12	131753123	+	4.1799	7.1641	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A0D0-01A	ENSG00000243944	ENSG00000104131	AC117386.2	EIF3J	GGGGAGGGAAACTCTTTACTTGTTTTTATCTGCCTGATTTAAGTGTCTGA*GAAACTTATTTTTATTTGCCTGATTTAAGTGTCTGAGAAACAAATCTTTG	antisense	BOWTIE+BLAT	intronic/UTR	0	2	2	20	3	150052404	+	15	44561852	+	0	24.8112	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A0D0-01A	ENSG00000104131	ENSG00000243944	EIF3J	AC117386.2	ATTTCATAGCAGCAGTCACTAAATTGGAAACAAAAGGTTGCAACGTGACA*AAAAAAAATTGTGTAGTATTTACCAGCACCATTCAGTAATACAGTCTTAA	antisense	BOWTIE+STAR	UTR/intronic	0	2	17	24	15	44561462	+	3	150051943	+	24.8112	0	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-BH-A0GY-01A	ENSG00000130881	ENSG00000161277	LRP3	THAP8	ACATCCAGGGCGACCGTGGTGACATGATTACCATCAG*GTTCCCACTGAAGGATGGTCCCCGGCTGCAGGCCTGG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	14	2	23	19	33202986	+	19	36040136	-	3.5125	8.0229	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0GY-01A	ENSG00000196090	ENSG00000184672	PTPRT	RALYL	TGCTGGGTCTTAACAAGCATAAAAAGGAAAAAAAGGAAACTCAGGCAAAG*GGCGGATCACCTGAGGTCACGAGTTCAAGACCAGCCTGACCAACATGGAG	cancer	BOWTIE+BLAT	UTR/intronic	0	3	1	21	20	42078785	-	8	84510583	+	0.6022	0.0247	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0IQ-01A	ENSG00000185630	ENSG00000183230	PBX1	CTNNA3	AGCCAAGCTAACTCGCCCTCAACTCCCAACTCGGCTG*GCTGGAAAAAAAGAAAGGAGTAATACCCTGAATATTG	oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	38	10	24	1	164812149	+	10	66775524	-	9.6892	1.6514	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-B6-A0IQ-01A	ENSG00000185630	ENSG00000183230	PBX1	CTNNA3	GTCAGCCCATGGAAGCCAAGCTAACTCGCCCTCAACTCCCAACTCGGCTG*TTTGTTTACAGATGAAGAATGTGACTGCTTTCCCTATACAGTGCTGACCT	oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	38	1	25	1	164812149	+	10	66778658	-	9.6892	1.6514	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-B6-A0IQ-01A	ENSG00000152818	ENSG00000203734	UTRN	ECT2L	TAGTATCTTGGCCAGGGAACTCAAACAGCAGATGCAG*GCTCTATGAACACATCCATGATCTCAGCCTTTTCCTC	18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	20	8	25	6	144577288	+	6	138900948	+	5.1943	0.368	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-B6-A0IQ-01A	ENSG00000215252	ENSG00000250007	GOLGA8B	AC087457.1	CCCAAGCAGGGCTCCATGGGTCGGGCGGCGGGCATTG*GAGGAAAGAGCTCAATGCGGAATCACATAGGCAAAGG	antisense,m14,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	15	3	20	15	34582750	-	15	34777271	+	5.3985	0.2723	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0IQ-01A	ENSG00000215252	ENSG00000250007	GOLGA8B	AC087457.1	ACGGCGGCGGACCGGGGCAGCCCCGCGCCCTGGCCAG*GAGGAAAGAGCTCAATGCGGAATCACATAGGCAAAGG	antisense,m14,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	15	2	22	15	34583516	-	15	34777271	+	5.3985	0.2723	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0IQ-01A	ENSG00000105135	ENSG00000105137	ILVBL	SYDE1	GTACAGCCCCGCGGCCCCCTGCGCTGGCTCGATCCTG*GCCACCCAGCCCAGCGCCCAGAGCCCAGCCCTCCAGA	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	5	3	24	19	15116152	-	19	15109056	+	37.1257	4.858	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0IQ-01A	ENSG00000116991	ENSG00000196922	SIPA1L2	ZNF252P	AAGTGCATAATCCATGTACCGAAAATGTGTGTTATAG*GCTGTGATTCTAGGATTGAAAAAGAGGAAATGATTCC	pseudogene,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	5	4	24	1	232471371	-	8	144978553	-	8.8883	2.3503	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	transcribed_unitary_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0IQ-01A	ENSG00000135525	ENSG00000118520	MAP7	ARG1	CACAGGGGCGGCGACGGCGCAGTGCGAAGCGAAACAG*CTACATTTTGAAAACTCTAGGCATTAAATACTTTTCA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	4	2	23	6	136550342	-	6	131583060	+	6.6796	1.1698	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-B6-A0IQ-01A	ENSG00000197933	ENSG00000141968	ZNF823	VAV1	TAAGGAGGACACCCGGACACCTGGAAGCTGGGAAATG*TTCCTGTGCCTTAAGAACATTAGAACCTTCCTGTCCA	oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	4	2	25	19	11738817	-	19	6820702	+	2.7653	2.8536	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A08S-01A	ENSG00000137497	ENSG00000275700	NUMA1	AATF	TCACCCTGTTCTAGTGTGTGGAGGCTTCCACCAGGAG*GTCACAAGGCACTTAAAGCATTGTTGAGGTCATTGGT	tcga,18cancers,chimerdb3seq,cancer,m220,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	221	23	25	11	72069842	-	17	36986617	+	15.6386	28.7292	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A08S-01A	ENSG00000137497	ENSG00000275700	NUMA1	AATF	CGGAGAATCGCGAGGCAGAGCGGGAGCGCGCAGCCAG*GTCACAAGGCACTTAAAGCATTGTTGAGGTCATTGGT	tcga,18cancers,chimerdb3seq,cancer,m220,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	221	4	22	11	72080458	-	17	36986617	+	15.6386	28.7292	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A08S-01A	ENSG00000137497	ENSG00000275700	NUMA1	AATF	TCTCCTGCCTCAGCCTCCCTAGTAGCTATGATTACAG*GTCACAAGGCACTTAAAGCATTGTTGAGGTCATTGGT	tcga,18cancers,chimerdb3seq,cancer,m220,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	221	3	24	11	72068496	-	17	36986617	+	15.6386	28.7292	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A08S-01A	ENSG00000137497	ENSG00000275700	NUMA1	AATF	TCACCCTGTTCTAGTGTGTGGAGGCTTCCACCAGGAG*TGAGGAGATTTCTAGTGAAGATGATGAGCTGGTAGAA	tcga,18cancers,chimerdb3seq,cancer,m220,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	221	2	19	11	72069842	-	17	36988519	+	15.6386	28.7292	TRUE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A08S-01A	ENSG00000167258	ENSG00000264458	CDK12	AC025211.1	ATTTTGGACTTGCTCGGCTCTATAACTCTGAAGAGAG*AGGCAGTGGAAAATATGACAACAGAAGAGAAGGCACT	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	13	9	25	17	39509761	+	17	32686253	+	21.4574	1.0605	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A8-A08S-01A	ENSG00000167258	ENSG00000264458	CDK12	AC025211.1	ATCAAACTAGCAGATTTTGGACTTGCTCGGCTCTATAACTCTGAAGAGAG*GACAAGAGCTTAGGACCAGATATTCAGAAAGGCTGTAACACTGACCCTCT	antisense	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	13	1	23	17	39509761	+	17	32670916	+	21.4574	1.0605	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A8-A08S-01A	ENSG00000108306	ENSG00000176658	FBXL20	MYO1D	GCGAATTGACCTATTTGATTTCCAGAGGGATATTGAG*ATTTGAAAAAGGGCGCATCTATACGTTCATTGGAGAA	known,18cancers,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	13	6	25	17	39301001	-	17	32780784	-	22.9908	56.0112	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A08S-01A	ENSG00000108306	ENSG00000176658	FBXL20	MYO1D	GCAGTAACTGGCAGCGAATTGACCTATTTGATTTCCAGAGGGATATTGAG*GCTGGAGTGAAGTGGCGCGATCTCAGCTCACTGCAACCTCTGCCCCCTGG	known,18cancers,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	13	2	18	17	39301001	-	17	32786792	-	22.9908	56.0112	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A08S-01A	ENSG00000108306	ENSG00000176658	FBXL20	MYO1D	TGTTGTTACCCTGTGCCGCTGTGCTCAGGTCTCCAGG*ATTTGAAAAAGGGCGCATCTATACGTTCATTGGAGAA	known,18cancers,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	13	1	13	17	39303585	-	17	32780784	-	22.9908	56.0112	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A08S-01A	ENSG00000108671	ENSG00000167258	PSMD11	CDK12	CTGGGATCTCTCCTGGCAAAGACTGGACAAGCTGCAG*ATGTGAAAAACAAGACCCAGAGAGGGGAAATCATTTG	18cancers,exon-exon	BOWTIE	CDS(truncated)/UTR	0	10	5	23	17	32447046	+	17	39551038	+	90.6444	21.4574	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A08S-01A	ENSG00000184154	ENSG00000198382	LRTOMT	UVRAG	CAGTGGGACGCCAAGACTGGAGAGGAAGCGACTGCGG*AGAACTCTTCTTGAAGACTAATGCTCAGTTGACAATT	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	6	7	24	11	72080885	+	11	76007534	+	1.8648	4.6933	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A08S-01A	ENSG00000184154	ENSG00000198382	LRTOMT	UVRAG	CACTTAGAGGCCCAGTGGCAGGTGCAGGGAACTTATG*AGAACTCTTCTTGAAGACTAATGCTCAGTTGACAATT	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	6	1	13	11	72083848	+	11	76007534	+	1.8648	4.6933	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A07I-01A	ENSG00000108375	ENSG00000250107	RNF43	CACNA1G-AS1	ACGGGCCCCCCGCCCCTGCCTGTCACTGGCTAGCAAG*AATCCCATCATCGCGTGCACATCTCATCCCAGGAGGG	antisense,oncogene,18cancers,cancer,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	71	13	23	17	58370911	-	17	50557458	-	0.9754	16.1752	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A8-A07I-01A	ENSG00000166750	ENSG00000275066	SLFN5	SYNRG	CCCGGAGGGAGACGCGCTGCCGAGGAGAACCCAGCGG*GAGAAAGCTTTGCAGAATTCAGATCTGCAGGAACTGA	18cancers,chimerdb3seq,exon-exon	BOWTIE	UTR/CDS(truncated)	0	20	5	23	17	35243143	+	17	37554059	-	6.7365	12.6959	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A8-A07I-01A	ENSG00000167107	ENSG00000008294	ACSF2	SPAG9	GGCAGGAAGCCAGGTTGCAGGGTGTCCGCTTCCTCAG*CACTCCCACCAAAGGCATAGAGAACAAAGCTTTTGAT	oncogene,tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	19	6	21	17	50426389	+	17	51014353	-	27.5374	19.2589	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A07I-01A	ENSG00000132964	ENSG00000161405	CDK8	IKZF3	CTTATGGTCACGTCTACAAAGCCAAGAGGAAAGATGG*ATATACAAACAAATGCGGAACTGAAAAGCACTCAGGA	known,oncogene,tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	15	5	23	13	26254769	+	17	39832151	-	3.7108	10.5153	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A07I-01A	ENSG00000132964	ENSG00000161405	CDK8	IKZF3	AAAGGCAAGAGCAAGCTCGGTAGTTGGCTGAATCGAAATGGAAGGCCAAG*ATATACAAACAAATGCGGAACTGAAAAGCACTCAGGAGCAGTCTGTGCCC	known,oncogene,tcga,18cancers,chimerdb3seq,cancer,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	15	1	23	13	26262629	+	17	39832151	-	3.7108	10.5153	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A07I-01A	ENSG00000133597	ENSG00000130226	ADCK2	DPP6	TCTCTCTAGTGTCTTTAAGTTGCTGATGACTCACAAG*ATATATCAACACTCGTATACTGGATATTACGTCCTGA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	9	3	25	7	140690813	+	7	154637821	+	4.9135	0.5628	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A07I-01A	ENSG00000133597	ENSG00000130226	ADCK2	DPP6	TCTCTCTAGTGTCTTTAAGTTGCTGATGACTCACAAG*ATGAAGAAAGTGAAGTCCAGGAAGTTGACATTGCCTC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	9	1	14	7	140690813	+	7	154587650	+	4.9135	0.5628	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A07I-01A	ENSG00000121057	ENSG00000153930	AKAP1	ANKFN1	CTCCGCATCCCGCACCCCGATGGTAGCCGAGGAGCTG*GAATTGTCGTGTGAAAATGACGCAACAAATGCAAAAT	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	3	5	23	17	57085398	+	17	56350766	+	5.2551	5.2227	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A07I-01A	ENSG00000118200	ENSG00000133056	CAMSAP2	PIK3C2B	TTTTTTTTTTTTTGGTATACTTTATACGTGGTGTATAGTTCTACCACAAG*AAGCCACATCCCTAGAGCTCAGGGATTTTTAAAGGCCCTGCTCTGAGAGG	NA	BOWTIE+BLAT	intronic/intronic	0	2	2	24	1	200748810	+	1	204467351	-	21.541	23.406	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A8-A07I-01A	ENSG00000278540	ENSG00000141736	ACACA	ERBB2	CCTCCCACCTCAGCCACCCAAGTAGCTGGGACTACAG*GGACCCAGCCTCCAACACTGCCCCGCTCCAGCCAGAG	known,oncogene,chimerdb3seq,cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	1	6	21	17	37369370	-	17	39715286	+	49.7947	592.5404	FALSE	TRUE	TRUE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A8-A07I-01A	ENSG00000278540	ENSG00000141736	ACACA	ERBB2	ACGAGGTCAGGAGTTCGAGGCCAGCCTGGCCAATATG*GTTGGATGATTGACTCTGAATGTCGGCCAAGATTCCG	known,oncogene,chimerdb3seq,cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	1	1	14	17	37345253	-	17	39726562	+	49.7947	592.5404	FALSE	TRUE	TRUE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0BW-11A	ENSG00000100345	ENSG00000166862	MYH9	CACNG2	GAAGCAGCGCCTGTTCCCGGGGCAGATCCAGGTTCAG*GGGCCGTGAGGGCCTCCAGCATTTTCCCAATCCTGAG	cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	92	15	25	22	36387807	-	22	36566493	-	224.6085	8.7813	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0BW-11A	ENSG00000074755	ENSG00000132382	ZZEF1	MYBBP1A	ATCATCAGACAACTACAGGCCTGCTCTCTGGTTCCAG*CTCCCAAAGCAGTTCAAGTTTGCCCCAGAGATGGACG	cancer,exon-exon	BOWTIE	in-frame	0	7	2	25	17	4123907	-	17	4550353	-	7.4659	15.8203	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-A2-A0D4-01A	ENSG00000100528	ENSG00000255468	CNIH1	AP001107.9	GCTCACTGCCGCGCTCATCTTCTTCGCCATTTGGCAC*ATTGAAGGTGGCGGGTTCCTGTAGTCCCAGCTACTCA	antisense,m3,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	9	4	21	14	54441247	-	11	66353455	+	17.1928	1.8461	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-A2-A0D4-01A	ENSG00000100528	ENSG00000255468	CNIH1	AP001107.9	CAAGAATCCTATAGACCAGTGTAATACCCTGAATCCC*ATTGAAGGTGGCGGGTTCCTGTAGTCCCAGCTACTCA	antisense,m3,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	9	1	13	14	54436369	-	11	66353455	+	17.1928	1.8461	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A0D4-01A	ENSG00000139687	ENSG00000102543	RB1	CDADC1	AACAGCATACAAGGATCTTCCTCATGCTGTTCAGGAG*AGGATCATAAAACAGGAGTTGGGGCAGTCATTTGGGC	cancer,tumor,exon-exon	BOWTIE	out-of-frame	0	5	3	18	13	48463835	+	13	49274291	+	1.6979	1.0401	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A0D4-01A	ENSG00000139687	ENSG00000102543	RB1	CDADC1	TCAAAATCATTGTAACAGCATACAAGGATCTTCCTCATGCTGTTCAGGAG*AATTCAGCAGAACCCTGCCTGTGTTCCAGAGTAAGAGGGCGATGTGAATC	cancer,tumor	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	5	1	20	13	48463835	+	13	49269698	+	1.6979	1.0401	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Breast	TCGA-A2-A0D4-01A	ENSG00000153002	ENSG00000142599	CPB1	RERE	CATTAACATAATCCGCGAGTTGGCCAGCACGACCCAG*GGAGGCAAAGCTGACATGAACCTTTTGTCGTGGGACT	oncogene,cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	4	1	13	3	148828077	+	1	8353178	-	6339.1625	11.8683	FALSE	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A26J-01A	ENSG00000124935	ENSG00000006534	SCGB1D2	ALDH3B1	CTCCTGCTGGTCACGCTGGCCCTCTGCTGCTACCAGG*TCAGCCTTCGAGTCGGAGGTGTCTGAGGTTGCCATCA	exon-exon	BOWTIE	out-of-frame	0	42	10	24	11	62242362	+	11	68018527	+	300.9955	6.72	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A26J-01A	ENSG00000054118	ENSG00000133216	THRAP3	EPHB2	TGGGATCCAGTACGAGTTGAATCATTGTTCAAATAAG*AAACGCTAATGGACTCCACTACAGCGACTGCTGAGCT	cancer,tumor,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	27	7	24	1	36259484	+	1	22781421	+	51.7509	2.9539	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A26J-01A	ENSG00000054118	ENSG00000133216	THRAP3	EPHB2	TTGGGGTAGTGTCTGGGATCCAGTACGAGTTGAATCATTGTTCAAATAAG*ACCCAGTTCTGCTTCTTTCCATCCCACCTGCTTTGTTGTGCTTCATGAAA	cancer,tumor,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	UTR/intronic	0	27	2	25	1	36259484	+	1	22714895	+	51.7509	2.9539	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A26J-01A	ENSG00000010803	ENSG00000126070	SCMH1	AGO3	TCCCAATATCAAGAAGCTGCTGACATCCTGGATCTAG*GGGTTTCACAGACCAGCTGCGTAAGATTTCTAAGGAT	tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	5	2	18	1	41160875	-	1	36027114	+	10.3712	2.0936	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-GM-A3XL-01A	ENSG00000140105	ENSG00000116062	WARS	MSH6	TCGAGGACGACGACAAGCTCGAGCAGATCAGGAAG*GTAGGCACAACTTACGTAACAGATAAGAGTGAAGA	18cancers,cancer,exon-exon	BOWTIE	in-frame	0	28	3	21	14	100337062	-	2	47798611	+	164.137	13.8271	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-GM-A3XL-01A	ENSG00000167522	ENSG00000169783	ANKRD11	LINGO1	GTCCTCGTCAGCACTGACTTTCAGCTATGGAATCG*GTGAGCAAGAGGATGCTGGCGGGGGGCGTGAGGAG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	27	9	22	16	89418284	-	15	77615900	-	4.6459	21.4578	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-GM-A3XL-01A	ENSG00000165929	ENSG00000066427	TC2N	ATXN3	CATTCAACCCAGGACACAAGAAACTCCTTCACATCTGGAAGAACTTGAAG*GTTTGGAATTTCAGCTGGGCAGCTTCGATCCCACCACCTGTAGCCACTGA	18cancers,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	21	12	24	14	91812312	-	14	92050536	-	3.9415	1.6803	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Breast	TCGA-GM-A3XL-01A	ENSG00000143774	ENSG00000059588	GUK1	TARBP1	GGCTGCGGCCGCCCTGGGCCGGGCCCCACCGGACG*GATGTTGGCTCTTTCACCCATCCTGGCATATGTGT	18cancers,exon-exon	BOWTIE	in-frame	0	5	3	21	1	228140363	+	1	234467650	-	126.38	13.391	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-GM-A3XL-01A	ENSG00000265728	ENSG00000267247	AP001099.1	AP005264.3	ACTCATGCATGCCTGTGAATTACCTCAAAAGCACT*CGGCAGGCTTGAGTGGACTGCTCCCGGGAAGCCAC	lincrna,m2,exon-exon	BOWTIE	exonic(no-known-CDS)/exonic(no-known-CDS)	0	3	1	13	18	10599121	+	18	12230853	-	0.5142	0.2789	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	lincRNA	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0RG-01A	ENSG00000186260	ENSG00000070404	MKL2	FSTL3	CTCCTTGCAGTCCAGTCAAAACTTACCCCCTCTGAACGAAAGGAAAAATG*ACGGGCAGCGCCCACTGCGTGGTGTGTCGAGCGGCGCCCTGCCCTGTGCC	oncogene,tcga,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+STAR	out-of-frame	0	14	1	14	16	14140760	+	19	681386	+	7.7657	5.4752	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0RG-01A	ENSG00000172575	ENSG00000148948	RASGRP1	LRRC4C	CTGGACGATCTCATTGACAGCTGCATTCAATCTTTTG*ATTGGCAAACGCACTGCCTACTTACAGCATAGAGACC	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	10	6	17	15	38559821	-	11	40140853	-	1.9401	3.0452	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-B6-A0RG-01A	ENSG00000172575	ENSG00000148948	RASGRP1	LRRC4C	CTGGACGATCTCATTGACAGCTGCATTCAATCTTTTG*ACTGTTTGAATTCCAGAAGGACCAACACCAGATAAAT	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	10	2	19	15	38559821	-	11	40116334	-	1.9401	3.0452	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-B6-A0RI-01A	ENSG00000138398	ENSG00000150938	PPIG	CRIM1	ACCGGACCCAGAGAAGAGGAAAACTCTACCGGTGCAG*AACCAACCATCATCACAGTTGATCCACCTGCATGTGG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(no-known-start-or-end)/CDS(truncated)	0	49	7	25	2	169584490	+	2	36499219	+	5.9525	19.0311	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-B6-A0RI-01A	ENSG00000138398	ENSG00000150938	PPIG	CRIM1	AAAGCTTCAAAATCCTAAGACTCAGCACTGTTGCGGG*AACCAACCATCATCACAGTTGATCCACCTGCATGTGG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	49	5	24	2	169584899	+	2	36499219	+	5.9525	19.0311	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-B6-A0RI-01A	ENSG00000189067	ENSG00000238098	LITAF	ABCA17P	CTCAGACCTCCCGGCTCGACAGGCGGCGCGGGCGGCG*TGATGAGCCCTCCTCTTCAGCTAGGAAAATGACGGTG	pseudogene,tumor,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	17	14	24	16	11586886	-	16	2361116	+	28.5981	1.4985	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	transcribed_unitary_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0RI-01A	ENSG00000189067	ENSG00000238098	LITAF	ABCA17P	TGGGGGAGACACCAGGTCCGCGCCAGGCGTCTCGGGG*TGATGAGCCCTCCTCTTCAGCTAGGAAAATGACGGTG	pseudogene,tumor,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	17	6	25	16	11587151	-	16	2361116	+	28.5981	1.4985	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	transcribed_unitary_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A3Y0-01A	ENSG00000186777	ENSG00000173406	ZNF732	DAB1	AGTGAAGATACATGAGACAGTAGCCAAACACCCAG*GTCAGGATCGCAGTGAAGCCACTTTGATAAAGAGG	tcga,18cancers,chimerdb3seq,m30,tcga-cancer,exon-exon	BOWTIE	in-frame	0	59	7	24	4	295438	-	1	57145429	-	1.3675	2.3686	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A3Y0-01A	ENSG00000186777	ENSG00000173406	ZNF732	DAB1	GATGTTGGAGAACTACAGGAACCTGATCTCCCTGG*GTCAGGATCGCAGTGAAGCCACTTTGATAAAGAGG	tcga,18cancers,chimerdb3seq,m30,tcga-cancer,exon-exon	BOWTIE	in-frame	0	59	3	16	4	296029	-	1	57145429	-	1.3675	2.3686	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A3Y0-01A	ENSG00000173898	ENSG00000162344	SPTBN2	FGF19	ATGGAAAAGAATATTTATTCCAGGCCAAGGATGAG*CTTCAGTACTCGGAGGAAGACTGTGCTTTCGAGGA	known,tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	38	8	23	11	66686398	-	11	69699576	-	11.5723	14.0586	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AR-A0TX-01A	ENSG00000124225	ENSG00000124212	PMEPA1	PTGIS	AACTGCAAACGCTCTTTGTTCCAGAGCATGGAGATCA*GGGAATATGGGTCCCGCTGCCTTCTGGCTCCTGCTCT	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	45	8	24	20	57709474	-	20	49514395	-	209.2205	24.0354	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AR-A0TX-01A	ENSG00000124225	ENSG00000124212	PMEPA1	PTGIS	CTGAAGGCGGACAGTCTCCTGCGAAACCAGGCAATGG*GGGAATATGGGTCCCGCTGCCTTCTGGCTCCTGCTCT	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	45	2	24	20	57710460	-	20	49514395	-	209.2205	24.0354	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AR-A0TX-01A	ENSG00000124225	ENSG00000124212	PMEPA1	PTGIS	AATTTGCCTGAGTGTCAGTGGTTAAGAATACAAAAAG*GGGAATATGGGTCCCGCTGCCTTCTGGCTCCTGCTCT	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	45	1	14	20	57700016	-	20	49514395	-	209.2205	24.0354	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AR-A0TX-01A	ENSG00000124198	ENSG00000219438	ARFGEF2	FAM19A5	CACTCCCAGCTGCGCAGGGCCTGCCAGGTGGCGCTCG*GTCAGCTGGCCGCCGGCACCTGTGAGATTGTGACCTT	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	38	4	25	20	48922010	+	22	48646597	+	18.4849	8.7402	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AR-A0TX-01A	ENSG00000127334	ENSG00000226332	DYRK2	AL354836.1	TCTCCGGGCCAGCAACGCTGCCGCCGCAGCCCACACG*TGGAAGGCAGCGAACTGGCCCGCTCAGCACACCGCGG	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	25	3	24	12	67649945	+	20	62305826	-	22.2624	25.9423	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AR-A0TX-01A	ENSG00000067191	ENSG00000275023	CACNB1	MLLT6	CCCCATCATTGTTTACATCAAGATCACCTCTCCCAAG*CCTTACAGAGCAGCAGAGACATCTCCTTCAGCAGCAA	tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	10	6	25	17	39183713	-	17	38722678	+	0.8045	51.9698	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AR-A0TX-01A	ENSG00000038532	ENSG00000184617	CLEC16A	ZNF840P	GAGAAGACATTTTTTTGGACATGTTTGAAGATGAGTATAGGAGCATGACA*CATGTCAACCAGCATTGGCAACGTTTCGTGCCCTCAATGAATCTGGGAAT	pseudogene	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	9	2	22	16	11047342	+	20	46490830	+	4.7083	3.3318	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	unprocessed_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AR-A0TX-01A	ENSG00000126351	ENSG00000067191	THRA	CACNB1	AAAGCGAAAAAGAAAGAACGGCCAATGTTCCCTGAAAACCAGCATGTCAG*GACCGGGAAGCCTTAAGGAAGGAAGCAGAGCGCCAGGCATTAGCGCAGCT	oncogene,18cancers,cancer	BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	9	2	22	17	40076938	+	17	39191536	-	16.4179	0.8045	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-AR-A0TX-01A	ENSG00000126351	ENSG00000067191	THRA	CACNB1	CAGCCAGGGCTCCTCTGGACCTGGATGTGGAACAGTAATTCATGTGTTCC*GAGGAGGACCGGGAAGCCTTAAGGAAGGAAGCAGAGCGCCAGGCATTAGC	oncogene,18cancers,cancer	BOWTIE+BLAT	intronic/CDS(truncated)	0	9	1	23	17	40077039	+	17	39191542	-	16.4179	0.8045	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-AR-A0TX-01A	ENSG00000256248	ENSG00000111110	AC134511.1	PPM1H	ACTGTATCGCCCCTTTCAGATCTGCAGCTAAATGATTACTGTACAGTGTG*GGTTATCAATGCCGGGAAGAGCACACACAATGAAGACCAAGCCAGCTGTG	lincrna	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	8	1	19	12	66934447	-	12	62832279	-	NA	27.8531	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AR-A0TX-01A	ENSG00000167186	ENSG00000130703	COQ7	OSBPL2	GGAGGAGGACCCTGAAAAATACGAGGAACTTCTTCAG*ATCTTCAGTGTCTATTGGATTTTTCCAAGAGAAAGTT	exon-exon	BOWTIE	CDS(truncated)/UTR	0	6	2	23	16	19075860	+	20	62256057	+	11.2911	23.2794	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-AR-A0TX-01A	ENSG00000093000	ENSG00000100320	NUP50	RBFOX2	CCAAGACCCAGCGAGTGCAGCGGCGGCCGCCGAGGAG*GGTAACCAGGAGCCGACAACAACTCCTGACGCAATGG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	6	2	17	22	45164296	+	22	35810004	-	10.2543	15.2275	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AR-A0TX-01A	ENSG00000124222	ENSG00000124160	STX16	NCOA5	TAATTCCATCCAAAACCGGCAGCTGTTAGCCGAGCAA*ATATTAATAAGGCAGCGGAAAGAAGAAATATGAATAC	exon-exon	BOWTIE	CDS(truncated)/UTR	0	3	2	21	20	58652087	+	20	46079453	-	49.0991	26.3153	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-AR-A0TX-01A	ENSG00000067191	ENSG00000171475	CACNB1	WIPF2	CAGATGGGAGCACGTCCTCGGATACCACATCCAACAGCTTTGTCCGCCAG*GATGTTGCTGTCATCCAGGCTGGAGTGCAGTGGTGTGATCATAGCTCACC	NA	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	2	2	20	17	39194884	-	17	40283272	+	0.8045	49.6587	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A15E-06A	ENSG00000163909	ENSG00000049089	HEYL	COL9A2	ACGGACCCATCGACGTGGGCCAAGAGGGCCAGCTGAG*GGGGACCCTGGACCAGATGGACCATCGGGGCCCCCAG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	54	8	25	1	39639546	-	1	40311715	-	1.5199	16.8588	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A15E-06A	ENSG00000205593	ENSG00000185386	DENND6B	MAPK11	TGGTTCTTGCTAGCGTCCACGAGCTGGACCTGTTCAG*GACCTGAAGCCCAGCAACGTGGCTGTGAACGAGGACT	18cancers,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	23	7	24	22	50315714	-	22	50267174	-	0.366	4.2913	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A15E-06A	ENSG00000205593	ENSG00000185386	DENND6B	MAPK11	CCAGGCCCAGCACAGGTGGATTGTCACAGCTTGGGGTCGTCATGATTACC*CGACCGCAGGGTGAGGGTCGGGTCCAGCAGGGCTCCGTCCCAGCCTCCTG	18cancers,10K<gap<100K	BOWTIE+BLAT	intronic/UTR	0	23	1	22	22	50315077	-	22	50267249	-	0.366	4.2913	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A15E-06A	ENSG00000164323	ENSG00000168491	CFAP97	CCDC110	ACAGAAGGAACAACAAAGGATTGAGAGAGAAAACTTG*GTCCTTCAGCAGCAGTTGGAATCATTTCAGGCTTTGC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	17	7	24	4	185175786	-	4	185462708	-	14.1698	5.1145	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A15E-06A	ENSG00000164323	ENSG00000168491	CFAP97	CCDC110	ACAGAAGGAACAACAAAGGATTGAGAGAGAAAACTTG*AATATGGCTGCATAGCAGAATCAGAAAATCAAATCCA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	17	2	23	4	185175786	-	4	185463049	-	14.1698	5.1145	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A15E-06A	ENSG00000127022	ENSG00000176783	CANX	RUFY1	ATTCAGAAAACTTCAAGACATCACCATCAGCAGGCTCCAGTTGAACACTA*GTTGCAGCACTCGGAGCGGGCGAGGCAGGGGGCTGAGGAGCGGAGCCACA	18cancers,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	9	4	21	5	179728784	+	5	179596562	+	162.355	19.1082	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A15E-06A	ENSG00000127022	ENSG00000176783	CANX	RUFY1	TTCCAGGGTCAAAGTACAGAATAGAATACATTGATACAAAGTACAGAAAA*AGGATCACTTAAGGTCAGAAGTTCAAGAACAGGCTGGCCAACATGGTGAA	18cancers,10K<gap<100K	BOWTIE+BLAT	UTR/intronic	0	9	1	23	5	179729736	+	5	179595117	+	162.355	19.1082	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A15E-06A	ENSG00000127022	ENSG00000176783	CANX	RUFY1	TGAAAATGATTATAAGCCCTGCATAATGTTAAGCTTTATTGTGATTACGT*GTTGCAGCACTCGGAGCGGGCGAGGCAGGGGGCTGAGGAGCGGAGCCACA	18cancers,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	9	1	21	5	179729650	+	5	179596562	+	162.355	19.1082	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A15E-06A	ENSG00000107882	ENSG00000107862	SUFU	GBF1	TTAATGCAGGGCTTGGCACGATACGTGTTCCAGTCAG*ATCCCACCCATGAGGGCACAGCAGAGGGCATGGAGAA	tcga,cell_lines,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	9	8	24	10	102550106	+	10	102351256	+	6.5263	8.4995	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A15E-06A	ENSG00000158019	ENSG00000196396	BABAM2	PTPN1	GAACATGGAAATTTATGCTGGGAAAAAAAACAACTGG*TTAAAATGCGCACAATACTGGCCACAAAAAGAAGAAA	cell_lines,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	6	2	21	2	28025420	+	20	50574517	+	12.2874	21.4489	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A15E-06A	ENSG00000056586	ENSG00000148187	RC3H2	MRRF	GCTGTCAGGGCTCGAGGATGCCAGTTTTTAGGGCCAG*TGGATGTTTCCAAGGATTGTCTTCAGTCATGGCCTTG	tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	6	2	18	9	122890312	-	9	122270864	+	10.7327	4.3851	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A15E-06A	ENSG00000196396	ENSG00000124126	PTPN1	PREX1	TTATACAGTGCGACAGCTAGAATTGGAAAACCTTACA*GTCCTGTTCTCGAACATCGAAGACATCCTGGAAGTTC	cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	5	4	24	20	50574654	+	20	48745147	-	21.4489	113.9073	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0WA-01A	ENSG00000144744	ENSG00000114541	UBA3	FRMD4B	TAGATGTTTCCAATCTAAATAGGCAGTTTTTATTTAG*TGTCTTCTACAAATGCTTCTGGGAACTGGAGGACCCA	tcga,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	10	3	23	3	69071535	-	3	69176656	-	17.4515	3.1084	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0WA-01A	ENSG00000144744	ENSG00000114541	UBA3	FRMD4B	CTGAAGTTGCTGCAGAATTTCTAAATGACAGAGTTCCTAATTGCAATGTA*TGTCTTCTACAAATGCTTCTGGGAACTGGAGGACCCAGTTAACCATAGGG	tcga,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K	BOWTIE+BLAT	out-of-frame	0	10	1	20	3	69067933	-	3	69176656	-	17.4515	3.1084	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0WA-01A	ENSG00000144744	ENSG00000114541	UBA3	FRMD4B	AGCTGGCGGCTTAGGATGTGAGCTCCTGAAAAATCTG*TGTCTTCTACAAATGCTTCTGGGAACTGGAGGACCCA	tcga,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	10	1	13	3	69075430	-	3	69176656	-	17.4515	3.1084	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0WA-01A	ENSG00000114790	ENSG00000243629	ARHGEF26	LINC00880	TAAGCCATTGAGATCCACATGGAGCCAACTCTCTGCG*GGCTCAGGGAGGACTGACAGGACTAGAGTTGACAACC	lincrna,18cancers,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	4	4	22	3	154129719	+	3	157083275	-	12.0062	0.0313	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0I2-01A	ENSG00000174547	ENSG00000111728	MRPL11	ST8SIA1	GGTCTGCCCGTTCTCTGGGCATTCGCGTGGTGAAGGA*ATGCAATCTCCCTCCTTTGTCAAGTGAATACACTAAG	ribosomal,tcga,18cancers,chimerdb3seq,m19,tcga-cancer,exon-exon	BOWTIE	in-frame	0	21	4	24	11	66437104	-	12	22249098	-	20.7217	0.9585	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-B6-A0I2-01A	ENSG00000174547	ENSG00000111728	MRPL11	ST8SIA1	TCCTGGCATGTGCAGTGTGACGAGAGGGCCCAGAAAGCTCTGGACTCGGG*ATTTGCACTTAGAGAAAAAGTTTACCCAGAAGAACTTACACCAAAATGTA	ribosomal,tcga,18cancers,chimerdb3seq,m19,tcga-cancer	BOWTIE+BLAT	intronic/intronic	0	21	1	25	11	66437047	-	12	22251527	-	20.7217	0.9585	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-B6-A0I2-01A	ENSG00000077157	ENSG00000144567	PPP1R12B	RETREG2	CACGGTCAACGTGGACGGCTTGACAGCCCTGCACCAG*ATTTGGACCAGCAGAGCCTGCCAAGTGAACCAGAGGA	exon-exon	BOWTIE	out-of-frame	0	7	1	13	1	202349142	+	2	219182013	+	1.3883	12.7152	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0I2-01A	ENSG00000255345	ENSG00000150687	AP002957.1	PRSS23	AGCTGGCTGCTAGCCCTGGATCCCTTGTTTCCTGAG*ACACAGCTGGATCCTCCCTGTTTACCCCAGTGGATGC	lincrna,exon-exon	BOWTIE	exonic(no-known-CDS)/UTR	0	2	7	22	11	79092883	+	11	86932695	+	0.8039	4.0163	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0I2-01A	ENSG00000255345	ENSG00000150687	AP002957.1	PRSS23	TCCTAGGGCCCCACTCAAGGCACCATCCTCTCCTGGGTGGAGGCTACAGC*GGAGGCCGAGGTGGGTGGATCACCTGAGATCAGGAGTTCGAAACCAGCCT	lincrna	BOWTIE+BLAT	exonic(no-known-CDS)/intronic	0	2	2	23	11	79093508	+	11	86926122	+	0.8039	4.0163	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A3KC-01A	ENSG00000149273	ENSG00000182704	RPS3	TSKU	CGTTACAAACTCCTAGGAGGGCTTGCTGTGCGGAG*CCCCCACCATGCCGTGGCCCCTGCTGCTGCTGCTG	ribosomal,18cancers,chimerdb3seq,m6,exon-exon	BOWTIE	CDS(truncated)/UTR	0	57	13	24	11	75402446	+	11	76795609	+	408.2155	51.1329	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A3KC-01A	ENSG00000149273	ENSG00000182704	RPS3	TSKU	CAGGCAGAGTCTCTGCGTTACAAACTCCTAGGAGGGCTTGCTGTGCGGAG*GCCATCAGCAAACTTAGAGTCACTGTGGACCTGGCCCTGTGGGCCCAACA	ribosomal,18cancers,chimerdb3seq,m6	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	57	5	24	11	75402446	+	11	76789506	+	408.2155	51.1329	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A3KC-01A	ENSG00000145050	ENSG00000181555	MANF	SETD2	TCTGCCGGGAAGCAAGAGGCAAAGAGAATCGGTTG*GAGGTATATCGAATTCCAAAGAAAAGTCAAACTGA	tcga,cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	40	10	24	3	51386335	+	3	47067118	-	16.6597	12.6473	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A3KC-01A	ENSG00000114648	ENSG00000164081	KLHL18	TEX264	GGCGGCAGGGCAAGCTGTGCGACGTGACCCTCAAG*CTGCCTTGAGGTGCAGTGTTGGGGATCCAGAGCCA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	18	4	22	3	47283094	+	3	51674271	+	2.6219	8.7355	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A3KC-01A	ENSG00000114648	ENSG00000164081	KLHL18	TEX264	GGCGGCAGGGCAAGCTGTGCGACGTGACCCTCAAG*GTGCCCCCTGATAAGTGCCGATGTGCCGTGGGCAG	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	18	2	21	3	47283094	+	3	51684413	+	2.6219	8.7355	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A3KC-01A	ENSG00000137522	ENSG00000196482	RNF121	ESRRG	GAGGTGGTGCTGCTGGGGAACGGGAGCTGGATGAG*AGCTGACAATTTACTGGTTCATCAATGAAACAATA	tcga,18cancers,chimerdb3seq,cancer,m11,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	12	2	22	11	71929124	+	1	216939673	-	14.5513	4.0059	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A3KC-01A	ENSG00000137522	ENSG00000196482	RNF121	ESRRG	GAGGTGGTGCTGCTGGGGAACGGGAGCTGGATGAG*CTTTAAAAAGTTGAAGTCTATTGGAAACCTTCTTA	tcga,18cancers,chimerdb3seq,cancer,m11,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	12	2	20	11	71929124	+	1	216865178	-	14.5513	4.0059	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A3KC-01A	ENSG00000047849	ENSG00000227398	MAP4	KIF9-AS1	GAAGAAACCGTGCTCAGAAACTAGCCAGATTGAAG*GGACCATGCCTGGCCGGATGCTGCCGCCTGGCTTC	antisense,18cancers,chimerdb3seq,cancer,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	9	5	23	3	47998638	-	3	47236057	+	22.2401	1.3635	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A3KC-01A	ENSG00000197345	ENSG00000054965	MRPL21	FAM168A	GCCAGACCCAGTTGAGGAGACCAGACACCATGCAG*GATATACTGCGGGGACACCATACAAGGTCCCACCG	ribosomal,tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	8	5	23	11	68897927	-	11	73411536	-	21.2368	20.8455	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A3KC-01A	ENSG00000254469	ENSG00000162105	AP002495.1	SHANK2	CGTTCTGACCCCGGGCTGTGTTCCGACCCCTGTTGGATAGTAAATCCCAG*GGAGGCTGTGCCTGGGCTGCTGTGCAAGAGAACTTTCTGTAGTTAGAGCC	m2	BOWTIE+STAR	intronic/intronic	0	3	1	18	11	71910677	-	11	70909737	-	1.6875	7.4288	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A3KC-01A	ENSG00000254469	ENSG00000162105	AP002495.1	SHANK2	ATGACTCTGTGGTGGGTCCCTCAGCCCTTCTGAGCTCTGTGCTGAACAAG*GGAGGCTGTGCCTGGGCTGCTGTGCAAGAGAACTTTCTGTAGTTAGAGCC	m2	BOWTIE+STAR	CDS(truncated)/intronic	0	3	1	15	11	71916074	-	11	70909737	-	1.6875	7.4288	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04P-01A	ENSG00000133704	ENSG00000140945	IPO8	CDH13	CGGATCATTGATCTTGTTCTGCAGAAACATGTAATTG*AGAACCCACAATCCTATTAACAGCGAACTTCTCTTGA	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	55	8	22	12	30656684	-	16	83180870	+	8.942	0.3927	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A04P-01A	ENSG00000133704	ENSG00000140945	IPO8	CDH13	CGGATCATTGATCTTGTTCTGCAGAAACATGTAATTG*ATGAAGATTTGGCAAGTTCTGTGCCTAGCACGATGGC	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	55	2	19	12	30656684	-	16	83171522	+	8.942	0.3927	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A04P-01A	ENSG00000205268	ENSG00000147573	PDE7A	TRIM55	TCTCTTCGGCTGCCCCAATCCCCGGCAGCTCTCTCAG*GAATGTTGCAGAAAACAGAAACAAGAGCTTTGTGAGA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	51	15	25	8	65841371	-	8	66149645	+	5.916	24.8875	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A04P-01A	ENSG00000205268	ENSG00000147573	PDE7A	TRIM55	TCTCTTCGGCTGCCCCAATCCCCGGCAGCTCTCTCAG*AATGCCAAAACCCTGCTAAAAAAAATCTCGGAAGCAT	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	51	2	25	8	65841371	-	8	66150217	+	5.916	24.8875	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A04P-01A	ENSG00000205268	ENSG00000147573	PDE7A	TRIM55	CCGAGGAGCCATCAGCTTCAGCTCCAGCTCCGCTCTCTTCGGCTGCCCCA*ATGATGAAAGGGACCTCTGAACAGGATTTCTGCAAAAATAGCCCCAAACT	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT	CDS(truncated)/UTR	0	51	1	23	8	65841391	-	8	66174680	+	5.916	24.8875	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A04P-01A	ENSG00000231574	ENSG00000237978	LINC02015	KCNMB2-AS1	ATTAGAGCGTCATCCATTAATGCTTTGGCTAGGAGGG*GCATTCTAATATATGCATTCTTCATAACAACTGTGTG	lincrna,antisense,exon-exon	BOWTIE	exonic(no-known-CDS)/exonic(no-known-CDS)	0	42	17	25	3	177827830	+	3	178749236	-	10.4864	8.5392	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04P-01A	ENSG00000231574	ENSG00000237978	LINC02015	KCNMB2-AS1	AAAATTGTAGGAAAAGAGAGCACTTTGGCACGGAAGG*GCATTCTAATATATGCATTCTTCATAACAACTGTGTG	lincrna,antisense,exon-exon	BOWTIE	exonic(no-known-CDS)/exonic(no-known-CDS)	0	42	13	25	3	177816996	+	3	178749236	-	10.4864	8.5392	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04P-01A	ENSG00000231574	ENSG00000237978	LINC02015	KCNMB2-AS1	AGTGCTGGGAAGTCATGCAGGGATTGGAAACCACAAAGATTCTACAGAAA*GCATTCTAATATATGCATTCTTCATAACAACTGTGTGAAACATATTAATA	lincrna,antisense	BOWTIE+BLAT;BOWTIE+STAR	intronic/exonic(no-known-CDS)	0	42	12	25	3	177820889	+	3	178749236	-	10.4864	8.5392	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04P-01A	ENSG00000231574	ENSG00000237978	LINC02015	KCNMB2-AS1	ATTAGAGCGTCATCCATTAATGCTTTGGCTAGGAGGG*AAGGAAATAAACTTAAGGAGAAAGAAGAAACAAAGAT	lincrna,antisense,exon-exon	BOWTIE	exonic(no-known-CDS)/exonic(no-known-CDS)	0	42	2	19	3	177827830	+	3	178757136	-	10.4864	8.5392	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04P-01A	ENSG00000231574	ENSG00000237978	LINC02015	KCNMB2-AS1	AGAGCATGATCATGTAATTCACAGCAACCAGGGCAAGCCTCACAGATGGG*GCATTCTAATATATGCATTCTTCATAACAACTGTGTGAAACATATTAATA	lincrna,antisense	BOWTIE+BLAT;BOWTIE+STAR	intronic/exonic(no-known-CDS)	0	42	2	19	3	177830776	+	3	178749236	-	10.4864	8.5392	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04P-01A	ENSG00000231574	ENSG00000237978	LINC02015	KCNMB2-AS1	ATTAGAGCGTCATCCATTAATGCTTTGGCTAGGAGGG*GAAATAAACTTAAGGAGAAAGAAGAAACAAAGATGGG	lincrna,antisense,exon-exon	BOWTIE	exonic(no-known-CDS)/exonic(no-known-CDS)	0	42	2	13	3	177827830	+	3	178757133	-	10.4864	8.5392	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04P-01A	ENSG00000231574	ENSG00000237978	LINC02015	KCNMB2-AS1	ATTCTGAAGTATTTTGGCTGCTAACTGGGACTTCCATTGTGTGGTCTAAG*GCATTCTAATATATGCATTCTTCATAACAACTGTGTGAAACATATTAATA	lincrna,antisense	BOWTIE+BLAT;BOWTIE+STAR	intronic/exonic(no-known-CDS)	0	42	1	24	3	177834886	+	3	178749236	-	10.4864	8.5392	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04P-01A	ENSG00000231574	ENSG00000237978	LINC02015	KCNMB2-AS1	AGTGCTGGGAAGTCATGCAGGGATTGGAAACCACAAAGATTCTACAGAAA*CTAAATTTTCTTTTACAAGAAGGAAATAAACTTAAGGAGAAAGAAGAAAC	lincrna,antisense	BOWTIE+BLAT;BOWTIE+STAR	intronic/intronic	0	42	1	23	3	177820889	+	3	178757155	-	10.4864	8.5392	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04P-01A	ENSG00000231574	ENSG00000237978	LINC02015	KCNMB2-AS1	CCACAAAGTTTATATTAGAGCGTCATCCATTAATGCTTTGGCTAGGAGGG*GACTGCCAGGGTGAAAAGTTTTCCCTCTTATTACCTAATGAGGCTCTGCC	lincrna,antisense	BOWTIE+BLAT;BOWTIE+STAR	exonic(no-known-CDS)/intronic	0	42	1	22	3	177827830	+	3	178750806	-	10.4864	8.5392	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04P-01A	ENSG00000172667	ENSG00000223941	ZMAT3	LINC01014	GCGGCGCGGAGACTGCCGGCGCGTCCCGGGGGTTCCG*GTGGGAAACTACATGTGCGTGCTTGACACAACTTGAA	18cancers,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	14	11	24	3	179071595	-	3	178456614	+	55.0978	53.6908	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	sense_intronic	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04P-01A	ENSG00000172667	ENSG00000223941	ZMAT3	LINC01014	ATTCCATCCTTCGTGATGGCATCCATACCGGGTTGAG*GTGGGAAACTACATGTGCGTGCTTGACACAACTTGAA	18cancers,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	14	3	23	3	179071327	-	3	178456614	+	55.0978	53.6908	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	sense_intronic	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04P-01A	ENSG00000159216	ENSG00000236532	RUNX1	LINC01695	ATCAAAATCACAGTGGATGGGCCCCGAGAACCTCGAA*TAGGCCCACAGCCAAGCCATTGAGAGACAAGTCCATG	lincrna,oncogene,cancer,tumor,m11,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	12	4	24	21	34859474	-	21	28212351	-	6.5516	1.0581	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-A2-A04P-01A	ENSG00000260484	ENSG00000274295	AC131902.2	AC131902.3	AAAAGAGAATCTCCAGAAAAACAAGGGATGAGGCTGTACAGCAAGTTAAA*GTGGAATCAGAACCCAACCAGCATGAATTCTTGGTTCCTCCAGTGGTTAA	pseudogene,lincrna	BOWTIE+BLAT	exonic(no-known-CDS)/exonic(no-known-CDS)	0	8	1	22	8	53388906	-	8	53394215	+	1.4315	0	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	lincRNA	processed_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04P-01A	ENSG00000275163	ENSG00000172667	AC117457.1	ZMAT3	GGAATGAGAGCACAAAGATTATAGAATACTGCAAGCAAATGGGGTGGAGG*GGTGGTTTTGGAACCTAACCTACTTTGTGTCTTCATTGTCAGAACTAAGG	NA	BOWTIE+BLAT	intronic/UTR	0	4	1	22	3	178493257	+	3	179020713	-	0.0849	55.0978	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04P-01A	ENSG00000008283	ENSG00000251095	CYB561	AC097478.1	GGCGCGGGGAGGCTGAAGGGACGCTCGGGTAGGCAAG*GTAGTCGTACAGTGTCCAGAAGGCAAAAGGACAAGTA	antisense,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	3	8	25	17	63446245	-	4	89719826	+	17.9657	0.8352	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04P-01A	ENSG00000008283	ENSG00000251095	CYB561	AC097478.1	GGCGCGGGGAGGCTGAAGGGACGCTCGGGTAGGCAAG*GTGGGTGTCATTGTGACTGGCTGCTACCTCCCCATGA	antisense,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	3	4	23	17	63446245	-	4	89691285	+	17.9657	0.8352	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04P-01A	ENSG00000008283	ENSG00000251095	CYB561	AC097478.1	TTTGGATCTTTGCTCCTGCGCCGCGTTCTAGAGCAAG*GTAGTCGTACAGTGTCCAGAAGGCAAAAGGACAAGTA	antisense,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	3	3	25	17	63445898	-	4	89719826	+	17.9657	0.8352	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04P-01A	ENSG00000008283	ENSG00000251095	CYB561	AC097478.1	GGCGCGGGGAGGCTGAAGGGACGCTCGGGTAGGCAAG*ATTGTGGTCTACTCTATAGAAGGGATCATGCTTTGAA	antisense,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	3	1	14	17	63446245	-	4	89642417	+	17.9657	0.8352	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04P-01A	ENSG00000228221	ENSG00000237978	LINC00578	KCNMB2-AS1	CTCATTCCTAGTAAGATCATGTGCAAATTTCTCTCAGGACTCAGTGCCAG*GCATTCTAATATATGCATTCTTCATAACAACTGTGTGAAACATATTAATA	lincrna,antisense	BOWTIE+BLAT	intronic/exonic(no-known-CDS)	0	3	1	23	3	177631939	+	3	178749236	-	13.8371	8.5392	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	lincRNA	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04P-01A	ENSG00000135999	ENSG00000144229	EPC2	THSD7B	GAGTTTAAACAGCCAAAACAGTTCATTCATATTCAGC*GTCCGTGGGGAAGGTGTACAGGAGACTGTGGTCCCGG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	2	1	14	2	148690373	+	2	137056420	+	3.1365	0.8905	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04P-01A	ENSG00000169733	ENSG00000081377	RFNG	CDC14B	ACCGACGGGGACGACCCTGAGCTCGAGCTCCAGGGCG*TCTCTCCATTTCAAGGACTAAAACAGTCTTGCGTTAA	exon-exon	BOWTIE	out-of-frame	0	2	3	21	17	82051294	-	9	96503789	-	14.4141	1.6438	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04P-01A	ENSG00000172667	ENSG00000197584	ZMAT3	KCNMB2	TGGGAGTCGGGGGATTCCATCCTTCGTGATGGCATCCATACCGGGTTGAG*GAGTATCCCAGAAAGAAGAAGAAAGAAGGAAGCTGGACTGCAGGAATTGG	NA	BOWTIE+BLAT;BOWTIE+STAR	UTR/intronic	0	2	3	22	3	179071327	-	3	178378010	+	55.0978	16.1841	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AO-A124-01A	ENSG00000198887	ENSG00000184903	SMC5	IMMP2L	AGAGAGGATGTTCTAGAGGCATGGTTGAAATTGAATT*GTCTCCTAAAAACCCAGAACAGAAGATCATTAAGAGA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	423	20	25	9	70267975	+	7	110963565	-	16.2706	10.6224	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AO-A124-01A	ENSG00000198887	ENSG00000184903	SMC5	IMMP2L	GGGTTTTTTGTGAAGAGAGGATGTTCTAGAGGCATGGTTGAAATTGAATT*CAGCAGCACAGCAAGTGGATAAAAGCACAGACTCTGGAGCCAGCCTGTCT	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	423	7	25	9	70267975	+	7	111149053	-	16.2706	10.6224	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AO-A124-01A	ENSG00000198887	ENSG00000184903	SMC5	IMMP2L	GGGTTTTTTGTGAAGAGAGGATGTTCTAGAGGCATGGTTGAAATTGAATT*AGATTTATCAGAGGAGGATAAAGCTCACCTAATGCAAAGGTTGGTTTCTG	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	423	2	25	9	70267975	+	7	111124820	-	16.2706	10.6224	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AO-A124-01A	ENSG00000198887	ENSG00000184903	SMC5	IMMP2L	GGGTTTTTTGTGAAGAGAGGATGTTCTAGAGGCATGGTTGAAATTGAATT*GGTAGGTCCAGGTAAAGCCAAAGGCCTTATCCTTATCTACACTGCTGGGG	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	423	1	20	9	70267975	+	7	111210936	-	16.2706	10.6224	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AO-A124-01A	ENSG00000198887	ENSG00000184903	SMC5	IMMP2L	GGGTTTTTTGTGAAGAGAGGATGTTCTAGAGGCATGGTTGAAATTGAATT*GGCAGTAAAGAGCAGCTGATAATAGACACAAGCCAACATTTAATGAAGTC	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	423	1	15	9	70267975	+	7	111140293	-	16.2706	10.6224	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AO-A124-01A	ENSG00000223959	ENSG00000198211	AFG3L1P	AC092143.1	GAAGCACTTTGTACAGTATTACCTGGCCAGAGGTCTG*TTCTGGGAAGTCATCAGTGATGAGCATGGCATCGACC	pseudogene,10K<gap<100K,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	19	8	24	16	89981923	+	16	89932571	+	1.0639	0	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	transcribed_unitary_pseudogene	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AO-A124-01A	ENSG00000223959	ENSG00000198211	AFG3L1P	AC092143.1	ACGTGGAAGCACTTTGTACAGTATTACCTGGCCAGAG*TTCTGGGAAGTCATCAGTGATGAGCATGGCATCGACC	pseudogene,10K<gap<100K,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	19	2	24	16	89981918	+	16	89932571	+	1.0639	0	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	transcribed_unitary_pseudogene	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AO-A124-01A	ENSG00000055609	ENSG00000183166	KMT2C	CALN1	GTGCTACCCTGGAAGGGGTTTCGGACTACTATTCTCAGTTGATCTACAAG*GATGAATTCCTACAATGGAATTGCTGGGTCCAGGGTGTGCACACTTAAGA	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	17	4	25	7	152157761	-	7	72128133	-	7.8781	0.5481	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AO-A124-01A	ENSG00000055609	ENSG00000183166	KMT2C	CALN1	AGAAACAAGCTATGTACTCTAGCACTGACACGTTTACCCACTTGAAACAG*GTAAAAGGAACAAAATGGTCTATTGTGTCTGGCCTCTTAGCTCAACATTA	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	17	1	17	7	152158863	-	7	72208804	-	7.8781	0.5481	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AO-A124-01A	ENSG00000055609	ENSG00000183166	KMT2C	CALN1	GTACAAAGGATAATAAACTAGTTGAGAAGCAGAACCCAGCTGAAGGACTG*GATGAATTCCTACAATGGAATTGCTGGGTCCAGGGTGTGCACACTTAAGA	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	17	1	16	7	152162117	-	7	72128133	-	7.8781	0.5481	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AO-A124-01A	ENSG00000055609	ENSG00000183166	KMT2C	CALN1	TAAACTAGTTGAGAAGCAGAACCCAGCTGAAGGACTG*AAATCCGAGAGGCCTTTCGGGTTCTGGACCGGGATGG	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	17	1	14	7	152162117	-	7	72106294	-	7.8781	0.5481	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AO-A124-01A	ENSG00000161526	ENSG00000180901	SAP30BP	KCTD2	TTATGAAGAAGAAGAAGATGAGAACAGTAGACAGTCG*ACCCAGAAACGCCTCCCAATCCCTCCACACCGCGGCT	cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	13	6	25	17	75668625	+	17	75035232	+	4.5721	8.7969	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AO-A124-01A	ENSG00000168758	ENSG00000111186	SEMA4C	WNT5B	AGCTGTTTGACCAGGAGCCCATGAGAAGCCTGGTGCTATCTCAGAGCAAG*GAGTGGTGACTCTTTCTGATCCATGGCCTGTGCTTACAAGATAGCCGGAT	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	11	14	25	2	96863682	-	12	1614402	+	33.7512	3.6442	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AO-A124-01A	ENSG00000168758	ENSG00000111186	SEMA4C	WNT5B	GGAGCCCATGAGAAGCCTGGTGCTATCTCAGAGCAAG*GGAACCCTACTCTGGAAACTGTCAGTCCCAGGGCACT	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	11	8	24	2	96863682	-	12	1631298	+	33.7512	3.6442	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AO-A124-01A	ENSG00000168758	ENSG00000111186	SEMA4C	WNT5B	AGCTGTTTGACCAGGAGCCCATGAGAAGCCTGGTGCTATCTCAGAGCAAG*TGTTTCTACTGAATCAGACCTCCCAGCTGGGCTCCCACCTTCCAGATGCT	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	11	8	24	2	96863682	-	12	1614725	+	33.7512	3.6442	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AO-A124-01A	ENSG00000168758	ENSG00000111186	SEMA4C	WNT5B	AGCTGTTTGACCAGGAGCCCATGAGAAGCCTGGTGCTATCTCAGAGCAAG*GCTGGATGGACATGGCCCCTTAAGGAAATGAAAGTGAGTGACTGAGTCCT	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	11	2	18	2	96863682	-	12	1627554	+	33.7512	3.6442	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AO-A124-01A	ENSG00000168758	ENSG00000111186	SEMA4C	WNT5B	AGCTGTTTGACCAGGAGCCCATGAGAAGCCTGGTGCTATCTCAGAGCAAG*AGAGGAAGCGAAATGCTGAGTCGGCTCCTGGCGTAGCGGCTGCCATTCAT	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	11	1	25	2	96863682	-	12	1619712	+	33.7512	3.6442	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-AO-A124-01A	ENSG00000072958	ENSG00000141977	AP1M1	CIB3	GTCGCTGGTCTTTTCTTTCCTCTATAAGGTGGTGCAG*GACAACCCCTTCCGCCAGAGGATTGCCCAGGTATTCT	18cancers,exon-exon	BOWTIE	in-frame	0	5	2	22	19	16206408	+	19	16168284	-	2.8752	0.1783	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AO-A124-01A	ENSG00000101639	ENSG00000260372	CEP192	AQP4-AS1	TAGAAATCAAACAACTTGGAAATCGATCACAACCAGGCATTAAGTTCACA*AGGAACCAGGGGATGACTTGAGGTGGTGAAAGGTGGCAGAACTGCCAAAT	antisense,18cancers	BOWTIE+STAR	CDS(truncated)/intronic	0	5	5	23	18	13073185	+	18	27170280	+	8.5569	0.0497	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-AO-A124-01A	ENSG00000112367	ENSG00000112290	FIG4	WASF1	GTTTGGCTCTCCCATCATCATCTTGAATTTAGTGAAG*GTAAATATGCTGAAGATATATTTGGAGAATTATTCAA	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	5	3	24	6	109743772	+	6	110113460	-	2.8507	19.7494	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-AO-A124-01A	ENSG00000133794	ENSG00000187079	ARNTL	TEAD1	TCTACGCTAGAGGGCTTCCTGTGTGCCGGGCACTGTG*GTAGGAATGAATTGATAGCCAGATACATCAAACTCAG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	4	2	18	11	13326467	+	11	12862250	+	1.5458	6.9122	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AO-A124-01A	ENSG00000131149	ENSG00000064270	GSE1	ATP2C2	GGCAGTGCTCATGGACCAGAAGAGCCCCAAGTGGAAAGTGCTCCTGCCGG*CCTAAGAGAAGGAAAACTCCAGCACCTGCTTGCTCGAGAACTGGTTCCTG	cancer	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	2	3	25	16	85371278	+	16	84415483	+	4.5954	1.0384	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AO-A124-01A	ENSG00000131149	ENSG00000064270	GSE1	ATP2C2	AGCCGGGAGGAGGACGGACCAGACCTTACTGGTGCAG*CCTAAGAGAAGGAAAACTCCAGCACCTGCTTGCTCGA	cancer,exon-exon	BOWTIE	CDS(no-known-start-or-end)/CDS(truncated)	0	2	3	22	16	85357643	+	16	84415483	+	4.5954	1.0384	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AO-A03L-01A	ENSG00000173226	ENSG00000075461	IQCB1	CACNG4	ATCAAGGCTGGGCCGGACCCGGTGGCCTGGCAACAGG*GGATCTATAAAGGGCACTGCTTCCGGATCAATCACTT	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	127	15	25	3	121834391	-	17	67018189	+	14.3015	45.7682	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AO-A03L-01A	ENSG00000268750	ENSG00000180532	AC010522.1	ZSCAN4	TCCGATGGCTGCGGCTGCGCCGAGGCGCCCTACTCAG*GACCAGTGATGGTATAGAACACTGTATTAGAGACATG	100K<gap<200K,exon-exon	BOWTIE	CDS(no-known-start-or-end)/UTR	0	38	4	20	19	57819945	+	19	57670245	+	0	6.1021	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AO-A03L-01A	ENSG00000268750	ENSG00000180532	AC010522.1	ZSCAN4	TCCGATGGCTGCGGCTGCGCCGAGGCGCCCTACTCAG*CTTGCAGTTTTAAAGAATCCACCAACTGTTGAAACAA	100K<gap<200K,exon-exon	BOWTIE	CDS(no-known-start-or-end)/UTR	0	38	2	20	19	57819945	+	19	57676041	+	0	6.1021	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AO-A03L-01A	ENSG00000082781	ENSG00000173193	ITGB5	PARP14	TGCAGGGATGAGGTGATCACATGGGTGGACACCATCG*GCATTTTCAGATGAATTTGCCAGAAGGGCTAATGGAA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	14	3	24	3	124769013	-	3	122708190	+	44.8303	23.1362	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AO-A03L-01A	ENSG00000101019	ENSG00000151062	UQCC1	CACNA2D4	TCAATTCATGGTTTCTTATAACCCTACTCCACGTCTG*TGCAGCACTGTGGATGGGCCGTGCACACAGAGCTGCG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	8	2	24	20	35366557	-	12	1810587	-	17.1095	1.7774	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AO-A03L-01A	ENSG00000197457	ENSG00000058866	STMN3	DGKG	TCCTTCTTTCCCTTGGACGCCCAGTGCTGGCCTTGGAGGACGGTCAGCTG*GTGCTATCACATCTCCCCTAAAATCTTCTCCAAGCTAAAATTTCTCTATT	NA	BOWTIE+BLAT	UTR/intronic	0	5	5	24	20	63640230	-	3	186282068	-	8.4279	0.3621	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-AO-A03L-01A	ENSG00000058866	ENSG00000188001	DGKG	TPRG1	GTGAGAAGTCTGATGGCTGCGTGTCCGCCAAGGGCGAACTTGTCATGCAG*GTACCAGGAAGCCCAGCTGTGCTGTAGTTCCTGCTCTTAGATTTCTGTGG	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	3	2	17	3	186265247	-	3	189229738	+	0.3621	11.0246	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AO-A03L-01A	ENSG00000188001	ENSG00000058866	TPRG1	DGKG	CTGGAGAGACCATTCAAGGCTTCTGGCTCTTGACAAA*GACAGGCCAGGTGAGAAGTCTGATGGCTGCGTGTCCG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	3	4	24	3	189215383	+	3	186265306	-	11.0246	0.3621	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AN-A0G0-01A	ENSG00000078124	ENSG00000137513	ACER3	NARS2	GAGAACTACTCCGTGACCTGGTACATCGCCGAGTTCT*CATTTCTTATACTGAAGCAGTGGAGATCTTAAAGCAA	18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	240	20	25	11	76861079	+	11	78469313	-	6.9715	28.9612	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AN-A0G0-01A	ENSG00000078124	ENSG00000137513	ACER3	NARS2	GAGAACTACTCCGTGACCTGGTACATCGCCGAGTTCT*TGGGGTGCTGACCTACGGACTGAACATGAAAAGTACC	18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	240	13	25	11	76861079	+	11	78466013	-	6.9715	28.9612	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AN-A0G0-01A	ENSG00000078124	ENSG00000137513	ACER3	NARS2	CGCTGGACTGGTGCGAGGAGAACTACTCCGTGACCTG*CATTTCTTATACTGAAGCAGTGGAGATCTTAAAGCAA	18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	240	5	22	11	76861062	+	11	78469313	-	6.9715	28.9612	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AN-A0G0-01A	ENSG00000078124	ENSG00000137513	ACER3	NARS2	GAGAACTACTCCGTGACCTGGTACATCGCCGAGTTCT*GTTGCTGCTGTTGATCTTCTGGTTCCTGGAGTTGGGG	18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	240	4	20	11	76861079	+	11	78443758	-	6.9715	28.9612	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AN-A0G0-01A	ENSG00000008441	ENSG00000266975	NFIX	FARSA-AS1	AGCCAGTCCAGCGGGTGGCCCAACGATGTGGATGCAG*AGAACAGACTCAGCCGTCACCTGCACCAGGCCGCTCT	antisense,18cancers,cancer,10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	124	18	24	19	13075671	+	19	12933149	+	26.4741	13.0427	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AN-A0G0-01A	ENSG00000077522	ENSG00000133019	ACTN2	CHRM3	GCTCCTGGACCCAGCCTGGGAGAAGCAGCAGAGGAAG*GTTTTGCTGTGGCGTGGCACCTGGTCTCTTTCTAGAA	18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	82	15	25	1	236686799	+	1	239678186	+	0.1506	12.0871	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AN-A0G0-01A	ENSG00000077522	ENSG00000133019	ACTN2	CHRM3	GCTCCTGGACCCAGCCTGGGAGAAGCAGCAGAGGAAG*CACTTGTGTTCTGATTAGTGGCCAAATAAATGACAGT	18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	82	13	25	1	236686799	+	1	239632224	+	0.1506	12.0871	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AN-A0G0-01A	ENSG00000008441	ENSG00000179218	NFIX	CALR	CACCACCCGCTGCCTGTGCTTGCTGGAGTCAGACCAG*CTCCCCTCCAACCTGGGGGGCAGTGGTGTGGAGAAGC	cell_lines,18cancers,cancer,m60,10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	62	15	25	19	13078735	+	19	12944212	+	26.4741	875.5441	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-AN-A0G0-01A	ENSG00000130762	ENSG00000234396	ARHGEF16	AL590822.1	CAGGCGGACGTGGTCCTGGTTCTGCAGCAGGAGGATG*GAAGGGGACCCTGCACCATCTTGGCTGGGGTTGTAGC	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	10	6	24	1	3479913	+	1	2220535	+	72.2356	3.3769	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AN-A0G0-01A	ENSG00000008441	ENSG00000179262	NFIX	RAD23A	CACCACCCGCTGCCTGTGCTTGCTGGAGTCAGACCAG*GTGAAGGTGCTAAAGGAGAAGATAGAAGCTGAGAAGG	cell_lines,cancer,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	10	2	22	19	13078735	+	19	12947848	+	26.4741	96.0164	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-A2-A259-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	CCGCCTGCCTCAGCCTCCAAAGTAGCTGAGACTACAG*CAGTTTAAGTATAGTGTGCCTGGGTTGGGTGCGGTGG	antisense,m2,exon-exon	BOWTIE	exonic(no-known-CDS)/UTR	0	5	3	20	10	87246115	-	10	46593287	+	0.6185	0.0523	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A1LK-01A	ENSG00000049618	ENSG00000188580	ARID1B	NKAIN2	GAACTTAATACAGCAAGAAAGACCATCAAGTTTACCA*GAAACAGACCTTATCCTGACTTTTAATATATCAATGC	cell_lines,18cancers,cancer,exon-exon	BOWTIE	in-frame	0	43	10	22	6	156935576	+	6	124658186	+	1.1902	7.3886	FALSE	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A1LK-01A	ENSG00000143379	ENSG00000144283	SETDB1	PKP4	TGGCACAAAGGCACCCTTATTGCCATCCAGACAGTTG*ACGTGCCAAATACTGGTGTAAGCAAACCTAGAGTTTC	oncogene,tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	8	2	24	1	150942688	+	2	158620990	+	4.1755	8.5462	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A1LK-01A	ENSG00000005483	ENSG00000187416	KMT2E	LHFPL3	TAACGGGGTTCGGGTGTCTCGTGTGTGAACATCACAG*TTCTGCTAAGCCAATATTCTCTAGAATGAGCACAAAA	tcga,18cancers,chimerdb3seq,tcga-cancer,oesophagus,100K<gap<200K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	7	6	23	7	105014535	+	7	104906187	+	4.7036	3.3586	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A1LK-01A	ENSG00000143776	ENSG00000136628	CDC42BPA	EPRS	TGGAGATGGAATACAGATCCTGAAAGATCTGCCCATG*AATCCTGAGGTTGGCTTGAAGCCTGTGTGGTATAGTC	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	6	5	24	1	227016080	-	1	220007338	-	2.8672	30.8215	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-E2-A1LK-01A	ENSG00000270024	ENSG00000147065	C8ORF44-SGK3	MSN	TAGATTGGTGGTGCCTTGGGGCTGTTCTGTATGAAATGCTGTATGGATTG*GCTCCTTTTTTATTCTGTCTTTATGGCTCCTACTCTCCCTTTTCCTCTCT	cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	14	8	66843547	+	X	65635011	+	NA	130.5342	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A1LK-01A	ENSG00000101337	ENSG00000088325	TM9SF4	TPX2	TCCTGCCGAAGTGCTGGGATTGCAGGTGTGAGCCTCCATGCCTGGCCTGG*TTGACAACACTTACTACAAAGAGGCAGAAAAAGAAAATCTTGTGGAACAA	tcga,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	25	20	32124160	+	20	31766556	+	23.1393	32.6589	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-D8-A27H-01A	ENSG00000140497	ENSG00000221955	SCAMP2	SLC12A8	CCCCTTCGCGGACCCAGTGGATGTAAACCCCTTCCAG*ATTTCTTCCTGAAGTCCAGGCTCCAAGAACAAGATGT	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	68	12	25	15	74873199	-	3	125092198	-	54.9878	4.5596	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-D8-A27H-01A	ENSG00000140497	ENSG00000221955	SCAMP2	SLC12A8	CCCCTTCGCGGACCCAGTGGATGTAAACCCCTTCCAG*GCTGTTGGGTCCCTTCTCATCATGTTTGTGATACAGT	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	68	2	15	15	74873199	-	3	125091556	-	54.9878	4.5596	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-D8-A27H-01A	ENSG00000059588	ENSG00000054267	TARBP1	ARID4B	AACACATGCAGGTTGAAAGGTTCCAGTGCCCAAGATG*AATACAGATTCTGTTCATCTTGCTCTGAAATTAAATA	known,18cancers,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	65	10	23	1	234446803	-	1	235131997	-	7.1465	8.3319	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-D8-A27H-01A	ENSG00000059588	ENSG00000054267	TARBP1	ARID4B	ATTGTTCAAGAGTATGTTAAGTCATCTGCTTGGGAAA*AATACAGATTCTGTTCATCTTGCTCTGAAATTAAATA	known,18cancers,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	65	1	13	1	234450428	-	1	235131997	-	7.1465	8.3319	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-D8-A27H-01A	ENSG00000185811	ENSG00000198589	IKZF1	LRBA	GGAGGACAGCAAAGCTCCAAGAGTGACAGAGTCGTGG*GTGAGACTGCTGCTCCTCGGGCCATTTTGACCGGCCA	oncogene,tcga,cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	32	5	22	7	50327757	+	4	150286034	-	0.8794	3.0517	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-D8-A27H-01A	ENSG00000185811	ENSG00000198589	IKZF1	LRBA	AGGGATTTCCATGCAATAATTCCCAAATCTTTCTCTC*GTGAGACTGCTGCTCCTCGGGCCATTTTGACCGGCCA	oncogene,tcga,cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	32	2	14	7	50368065	+	4	150286034	-	0.8794	3.0517	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-D8-A27H-01A	ENSG00000161203	ENSG00000197724	AP2M1	PHF2	AAGAACAATTTTGTGCTCATATATGAGCTGCTGGATG*CTGTGTTGGGGTGGAAGAGGAGGAGGCGCCCGACATC	18cancers,exon-exon	BOWTIE	out-of-frame	0	6	2	24	3	184179122	+	9	93629970	+	66.7557	15.3602	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-D8-A27H-01A	ENSG00000161203	ENSG00000197724	AP2M1	PHF2	GAAAACCTTCATCACGCAGCAGGGCATCAAGAGTCAG*CTGTGTTGGGGTGGAAGAGGAGGAGGCGCCCGACATC	18cancers,exon-exon	BOWTIE	out-of-frame	0	6	1	13	3	184180251	+	9	93629970	+	66.7557	15.3602	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-D8-A27H-01A	ENSG00000184384	ENSG00000149972	MAML2	CNTN5	AGGAATGGGATACCAAGTCTCCCAACAACAGAGACAG*AAAGTGTGGACTATGGGCCAGTTTTTGTGCAAGAACC	oncogene,tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	5	7	23	11	96091892	-	11	99844852	+	16.6089	1.5018	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-D8-A27H-01A	ENSG00000112078	ENSG00000008083	KCTD20	JARID2	CATAATCTTACTTATCCTCTAGGTCCCAGGAATGAAG*GATGACAGTGATGGGATTCCGTGGTCAGAAGAACGGG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	3	3	23	6	36470257	+	6	15374117	+	24.1969	5.2108	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-D8-A27H-01A	ENSG00000196586	ENSG00000038945	MYO6	MSR1	GCCCCGCCGCCGCGCACCTGCCTTCGCTCCCGCACCG*AAGTATGGAGCAGTGGGATCACTTTCACAATCAACAG	exon-exon	BOWTIE	UTR/CDS(truncated)	0	2	2	22	6	75749423	+	8	16177992	-	36.5432	5.3379	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A109-01A	ENSG00000141084	ENSG00000067533	RANBP10	RRP15	ACTTTGAAGTGAAGATTGTCAGCAAAGGAAGAGATGG*ACTGAAGTGAAATCAGAAGAAGGCCCAGGTTGGACGA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	206	21	25	16	67805428	-	1	218330948	+	4.2996	8.3451	FALSE	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A109-01A	ENSG00000167880	ENSG00000108984	EVPL	MAP2K6	AGGGGTCCCCCAAAGGCTCCCCCAGCAGGCACAGCCG*GCAAGAAGCGAAACCCTGGCCTTAAAATTCCAAAAGA	tcga,18cancers,chimerdb3seq,m42,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	61	15	24	17	76027101	-	17	69505780	+	4.0754	3.257	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A109-01A	ENSG00000167880	ENSG00000108984	EVPL	MAP2K6	GGCTCCCCCGCCAAGGGGTCCCCCAAAGGCTCCCCCAGCAGGCACAGCCG*GTTTTAGGATGAGCAACTTTGGAACGGAGGAGGCCTTTAGAAGAAAGAAG	tcga,18cancers,chimerdb3seq,m42,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	61	6	22	17	76027101	-	17	69485316	+	4.0754	3.257	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A109-01A	ENSG00000156469	ENSG00000254300	MTERF3	LINC01111	TGCACAATGTGATGAGCATTCCCCACCACATCATTGTCAAGTTCCCACAG*AAGGAGCCTCTCCCCATGGCCATCACCACCCCAGGCCTGCAGCAAGTATT	lincrna,18cancers	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	41	12	25	8	96243919	-	8	76500559	+	47.4709	11.0794	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A109-01A	ENSG00000156469	ENSG00000254300	MTERF3	LINC01111	GAGCATTCCCCACCACATCATTGTCAAGTTCCCACAG*GATACTGTTTACTGAAAACCCACCAATCTGATCTTTT	lincrna,18cancers,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	41	7	24	8	96243919	-	8	76518800	+	47.4709	11.0794	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A109-01A	ENSG00000156469	ENSG00000254300	MTERF3	LINC01111	GAGCATTCCCCACCACATCATTGTCAAGTTCCCACAG*GTCAAAAACTTGAAGCACAGAGTGGGATGTCAGATGC	lincrna,18cancers,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	41	2	20	8	96243919	-	8	76523195	+	47.4709	11.0794	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A109-01A	ENSG00000156469	ENSG00000254300	MTERF3	LINC01111	GAGCATTCCCCACCACATCATTGTCAAGTTCCCACAG*TCCTGGGATACATGTGCAGAATGTGCAGAATGTGTAC	lincrna,18cancers,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	41	2	20	8	96243919	-	8	76510391	+	47.4709	11.0794	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A109-01A	ENSG00000156469	ENSG00000254300	MTERF3	LINC01111	TGCACAATGTGATGAGCATTCCCCACCACATCATTGTCAAGTTCCCACAG*GTAATGTGGAGCCAGGAAGACTCATAAAACAAGAAAGTGACACCATCAGG	lincrna,18cancers	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	41	1	20	8	96243919	-	8	76517101	+	47.4709	11.0794	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A109-01A	ENSG00000132661	ENSG00000215305	NXT1	VPS16	GCCGCGGCCCGCGCTGACCCTGGACGTCGCCGCGCAG*GAAATATGAGCTGTACAGCATGGACTGGGACCTGAAG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	33	14	25	20	23351061	+	20	2859719	+	11.4702	17.632	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A109-01A	ENSG00000198382	ENSG00000149269	UVRAG	PAK1	TGAAAAACTTCATGGAGCATGGACTAATGGTCAGGTG*CATCAATTCCTGAAGATTGCCAAGCCCCTCTCCAGCC	oncogene,tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	24	9	24	11	76116015	+	11	77323360	-	27.1648	5.9679	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A109-01A	ENSG00000198382	ENSG00000149269	UVRAG	PAK1	TGAAAAACTTCATGGAGCATGGACTAATGGTCAGGTG*GTGAGAAAACTGAGGTTTCAAGTGTTTAGTAACTTTT	oncogene,tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	24	2	14	11	76116015	+	11	77325376	-	27.1648	5.9679	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A109-01A	ENSG00000078124	ENSG00000198382	ACER3	UVRAG	AAGAACACTTTACCTGAGATATAGGCCAAAAGTGAAG*CTAAGATATCAACATGGACTAGGGACTCCAGACTTGC	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	21	8	24	11	77019776	+	11	76115924	+	2.1749	27.1648	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A109-01A	ENSG00000078124	ENSG00000198382	ACER3	UVRAG	TCAGTTTGTATACAAGAACACTTTACCTGAGATATAGGCCAAAAGTGAAG*CTCCAGGAAAGCAGCCCTCTGACAGTCTCTGGCCCATGACTCACCTTTCC	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	21	1	14	11	77019776	+	11	76067243	+	2.1749	27.1648	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A109-01A	ENSG00000186470	ENSG00000180573	BTN3A2	HIST1H2AC	TGATGCTCTAATGGAAAAATGGCCCTCTTCAAGCCTG*GTTGCAAAAGCTTCTCATTTCAGAGAGATGCCAGGAT	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/UTR	0	19	2	25	6	26374798	+	6	26138054	+	8.8433	50.1852	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A109-01A	ENSG00000168014	ENSG00000171631	C2CD3	P2RY6	ATAAGCTGAAGAAGAGGTCAGCAGGCAAGAGAAATAG*CCTCCCTGAACATAGGAAACCCACCTGGGCAGCCATG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	14	4	25	11	74118228	-	11	73296485	+	4.2499	3.5797	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A109-01A	ENSG00000168014	ENSG00000171631	C2CD3	P2RY6	GAGTCAAGTGATCATAAGCTGAAGAAGAGGTCAGCAGGCAAGAGAAATAG*GCTGTCTGCTCTACAGATATCCTCGAAAAGATCATCTGGAACAAAGGCAG	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	14	1	18	11	74118228	-	11	73277836	+	4.2499	3.5797	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A109-01A	ENSG00000166582	ENSG00000101311	CENPV	FERMT1	AGCTTCTATACTCCACGATCAAACCCCGGAGGCTTCG*ATATATCCCAAGACTGGTCAGACTTTGCTCTTTGGTG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	14	6	25	17	16344597	-	20	6116044	-	2.4843	1.4647	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A109-01A	ENSG00000101311	ENSG00000239704	FERMT1	CDRT4	GTTTTTAAAGCTGTCAGTGATATCTGCAAAATCCTGA*GACTCACAGAAAACACTGGACTTCCCCGGAAGCTACT	cell_lines,18cancers,exon-exon	BOWTIE	in-frame	0	13	6	25	20	6115811	-	17	15438200	-	1.4647	0.1088	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A109-01A	ENSG00000101311	ENSG00000239704	FERMT1	CDRT4	GTTTTTAAAGCTGTCAGTGATATCTGCAAAATCCTGA*GAATCTGAACCTGTGATGTTAAGAAATCAGTAAATAT	cell_lines,18cancers,exon-exon	BOWTIE	CDS(truncated)/UTR	0	13	4	23	20	6115811	-	17	15440285	-	1.4647	0.1088	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A109-01A	ENSG00000154914	ENSG00000173818	USP43	ENDOV	AACCACCATGGCAACCTGCAAGGTGGGCATTACACAG*ATCCGACTCCTGCAGACTCGAGGAGACTCATTCCCTC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	13	7	23	17	9701700	+	17	80425032	+	3.1557	4.2953	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A109-01A	ENSG00000172831	ENSG00000092978	CES2	GPATCH2	GGAGTGGTGTGAGGGATGGAACCACCCATCCGGCCAT*GCAAACAAGCATGCATTTAGGATCCTTATGCACGGGA	18cancers,chimerdb3seq,exon-exon	BOWTIE	in-frame	0	7	5	24	16	66938241	+	1	217449337	-	4.0658	2.59	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A109-01A	ENSG00000172831	ENSG00000092978	CES2	GPATCH2	GCCTGTGGGCTTCTGCTGCTTCTTGTCCGGGGCCAGG*GCAAACAAGCATGCATTTAGGATCCTTATGCACGGGA	18cancers,chimerdb3seq,exon-exon	BOWTIE	out-of-frame	0	7	1	13	16	66935711	+	1	217449337	-	4.0658	2.59	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A109-01A	ENSG00000175155	ENSG00000132622	YPEL2	HSPA12B	AGCCCCACGCTGGCCGGACAGGGCCGCCTGTCGCCGG*GGGGCCCTTATGGCGCGGTGGGCGTGGACCTGGCCTT	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	5	4	21	17	59331824	+	20	3749969	+	1.6774	5.4752	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A109-01A	ENSG00000198740	ENSG00000250310	ZNF652	AC006487.2	GGATTTCAACATGAAGCAGTACTTCGACGAACACATGAAAACACACACTG*GCCCCCTCCTGGGTGTGGATAATTTGGAATCAGTTAAAAGGGAGTCTTGA	antisense,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/intronic	0	4	3	18	17	49311312	-	17	49545802	-	35.4104	2.2345	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A109-01A	ENSG00000198740	ENSG00000250310	ZNF652	AC006487.2	GGATTTCAACATGAAGCAGTACTTCGACGAACACATGAAAACACACACTG*GAACCCCCACTGAGAAGCTCCTCTCTGTGGGGCACCTCTGGGCGCCAGTG	antisense,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	4	1	21	17	49311312	-	17	49567985	-	35.4104	2.2345	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A109-01A	ENSG00000198740	ENSG00000250310	ZNF652	AC006487.2	GGATTTCAACATGAAGCAGTACTTCGACGAACACATGAAAACACACACTG*ATCTATATAACGCGTACGGCGAGAAGTTCCCGCTTCCTTTACACTCAAGC	antisense,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/intronic	0	4	1	17	17	49311312	-	17	49568357	-	35.4104	2.2345	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A109-01A	ENSG00000198740	ENSG00000249906	ZNF652	AC006487.1	GGATTTCAACATGAAGCAGTACTTCGACGAACACATGAAAACACACACTG*TGCTCTATGCCTAGTGATTTTTGATGCCACTATTGTTTTGGGGAGCCATG	antisense,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/intronic	0	3	1	14	17	49311312	-	17	49539308	-	35.4104	0.2372	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A109-01A	ENSG00000053918	ENSG00000104755	KCNQ1	ADAM2	ATCGCGGCAGCAACACGATCGGCGCCCGCCTGAACCGAGTAGAAGACAAG*GAGTTGTTCCCTTTCCAAAGGCCCTTTATTAGAACCTGCTTATAGTGGAG	NA	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	2	2	23	11	2778037	+	8	39790841	-	1.0012	4.3982	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-C8-A12Q-01A	ENSG00000127527	ENSG00000074201	EPS15L1	CLNS1A	AAAGAAGTCTGGCCTCTCGGACATTATCCTTGGGAAG*ATGGGATGGAGGTGGATACCACACCAACAGTTGCTGG	tcga,18cancers,chimerdb3seq,cancer,m37,tcga-cancer,exon-exon	BOWTIE	in-frame	0	69	18	25	19	16441892	-	11	77619695	-	7.8333	30.7772	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-C8-A12Q-01A	ENSG00000163125	ENSG00000160691	RPRD2	SHC1	ACTATCGTCTATCATTGGATGAAGTGGCTCCGGAGAT*GATGGCTGGCTTTGATGGCTCAGCATGGGATGAGGAG	known,tcga,18cancers,chimerdb3seq,cancer,m44,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	49	12	25	1	150364919	+	1	154966517	-	26.433	45.566	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-C8-A12Q-01A	ENSG00000160691	ENSG00000163125	SHC1	RPRD2	GGCCCGCGGTGCGGTGCGGAGACTCCATGAGGCCCTG*CTGCATATCCCCACCGTTTGAATCTCTTTTACCTTGC	known,tcga,18cancers,chimerdb3seq,cancer,m44,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	49	2	20	1	154974248	-	1	150417596	+	45.566	26.433	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-C8-A12Q-01A	ENSG00000172613	ENSG00000173120	RAD9A	KDM2A	GCCGTCTTCGACCCAGCCTCGTGCCCCCACATGCTCCGCGCCCCAGCACG*ACACGGCCTTGCCAGGAGAGCCTGCCCTCAGACTGCAGGACCAGAACCCC	oncogene,18cancers,cancer,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	35	10	24	11	67393790	+	11	67257484	+	9.4399	59.826	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-C8-A12Q-01A	ENSG00000172613	ENSG00000173120	RAD9A	KDM2A	GGGAAATGGGGACTCCAGTTGAAGCAAACGTCCCTGGCGAGGACCAGCTC*ATCTCCCAAACCTCACGTCCTTAACTGTGCTCTCCCTCCTTTCCTCTCCC	oncogene,18cancers,cancer,10K<gap<100K	BOWTIE+BLAT	intronic/UTR	0	35	2	22	11	67394416	+	11	67255596	+	9.4399	59.826	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-C8-A12Q-01A	ENSG00000173227	ENSG00000173715	SYT12	C11ORF80	GAAGTACGGCGAGAGCTGCGCAGAGGCCAGGGAGAAG*CTAACCCTAGAAAAAAAGGACTCAGCCCAGGGCACTG	cell_lines,18cancers,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	33	7	25	11	67034838	+	11	66838370	+	5.718	3.0782	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-C8-A12Q-01A	ENSG00000173227	ENSG00000173715	SYT12	C11ORF80	GAAGTACGGCGAGAGCTGCGCAGAGGCCAGGGAGAAG*CAGCTAACCCTAGAAAAAAAGGACTCAGCCCAGGGCA	cell_lines,18cancers,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	33	3	22	11	67034838	+	11	66838367	+	5.718	3.0782	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-C8-A12Q-01A	ENSG00000166439	ENSG00000108468	RNF169	CBX1	CCAAGAACAACTCCTACTCCTTAGCTTTCCTGGCAGG*CAGCGTCACCCTTTACACCAGAAAGCTGGCGGGCACT	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	24	6	25	11	74817714	+	17	48077041	-	3.4725	44.6422	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-C8-A12Q-01A	ENSG00000166439	ENSG00000108468	RNF169	CBX1	CCAAGAACAACTCCTACTCCTTAGCTTTCCTGGCAGG*TGAGGACAACACATGGGAGCCAGAAGAGAACCTGGAT	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	24	2	21	11	74817714	+	17	48076178	-	3.4725	44.6422	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-C8-A12Q-01A	ENSG00000130822	ENSG00000172534	PNCK	HCFC1	GCTGGACCACAGGCAAACCCCATTGCCTTTGAGAGAAAGAAGAGGACCCG*CAACCAACCAGTGGTTCATCCCAGCCGTGAGGGGGGACATTCCCCCTGGG	tcga,18cancers,chimerdb3seq,m8,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	20	2	25	X	153686506	-	X	153964726	-	1.5283	18.5755	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-C8-A12Q-01A	ENSG00000130822	ENSG00000172534	PNCK	HCFC1	CTACCCTGGAAGCTGGAGGCCGGGACCAGCTCTTCAG*CAACCAACCAGTGGTTCATCCCAGCCGTGAGGGGGGA	tcga,18cancers,chimerdb3seq,m8,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	20	2	23	X	153687431	-	X	153964726	-	1.5283	18.5755	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-C8-A12Q-01A	ENSG00000269038	ENSG00000171954	AP001462.1	CYP4F22	CCTTGGGTCCAGCAAGGAAGCCCTAAGTGACGTCAACCTTTGTTCCCATG*GAGCTGGCCCTAAAGCAAGGACCTGAGTGCAAGTAATTTTTTTGGGAAGT	lincrna	BOWTIE+BLAT;BOWTIE+STAR	exonic(no-known-CDS)/UTR	0	16	5	24	11	64779143	+	19	15523693	+	0.6503	3.3195	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-C8-A12Q-01A	ENSG00000097021	ENSG00000162413	ACOT7	KLHL21	CCTTCAGACTGCACCCTGCACGGCTTTGTGCACGGAG*GGATGACTCCGCTGAGGTGGACGTGTACAACCCGACG	tcga,chimerdb3seq,m2,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	7	3	17	1	6318492	-	1	6595557	-	9.9385	6.5801	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-C8-A12Q-01A	ENSG00000182149	ENSG00000260664	IST1	AC004158.1	GTCGGTGTCTGCTGCGTTCACGGCAGGATTCGGTTAG*GTGGACAAAACAAATCTTTTTTGGAAACCAACGAAAC	lincrna,oncogene,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	7	8	24	16	71895589	+	16	72532959	+	13.1896	0.9092	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-C8-A12Q-01A	ENSG00000182149	ENSG00000260664	IST1	AC004158.1	GGTGAACCCTGAAGTCGGTGTCTGCTGCGTTCACGGCAGGATTCGGTTAG*GCTTTGGTATCAGGATGATGCTGGCCTCATAAAATGAGTTAGGGAGGATT	lincrna,oncogene	BOWTIE+STAR	UTR/intronic	0	7	2	25	16	71895589	+	16	72527780	+	13.1896	0.9092	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-C8-A12Q-01A	ENSG00000172725	ENSG00000141736	CORO1B	ERBB2	AGCGGGGCCTGGAGGTCAGCAAGTGCGAGATCGCCCG*ACAACTACCTTTCTACGGACGTGGGATCCTGCACCCT	oncogene,18cancers,cancer,exon-exon	BOWTIE	out-of-frame	0	6	4	23	11	67440118	-	17	39711928	+	93.1148	779.4494	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-C8-A12Q-01A	ENSG00000154198	ENSG00000269113	CYP4Z2P	TRABD2B	GACCCAGACTATGTCAAGATTCTCCTGAAAAGACAAG*GTGCTGTTTGCCCTGAACCAAACCCTGCTGCAGCAGG	pseudogene,18cancers,m4,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	5	4	23	1	46898843	-	1	47801619	-	23.3218	0.6524	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	transcribed_unprocessed_pseudogene	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-C8-A12Q-01A	ENSG00000154198	ENSG00000269113	CYP4Z2P	TRABD2B	CTTCAATATCCATGACCCAGACTATGTCAAGATTCTCCTGAAAAGACAAG*AATCCAGTGCAGGGTTCAGCCCGAATACGTGCTCAGAACTGTGTATCTAA	pseudogene,18cancers,m4	BOWTIE+BLAT;BOWTIE+STAR	exonic(no-known-CDS)/intronic	0	5	2	23	1	46898843	-	1	47819805	-	23.3218	0.6524	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	transcribed_unprocessed_pseudogene	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-C8-A12Q-01A	ENSG00000154198	ENSG00000269113	CYP4Z2P	TRABD2B	CTTCAATATCCATGACCCAGACTATGTCAAGATTCTCCTGAAAAGACAAG*GGCAACCACAAGTCCTAACTCATGTTGGAGCCTCAGTTTCCTCATCTATT	pseudogene,18cancers,m4	BOWTIE+BLAT;BOWTIE+STAR	exonic(no-known-CDS)/intronic	0	5	1	20	1	46898843	-	1	47907536	-	23.3218	0.6524	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	transcribed_unprocessed_pseudogene	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-C8-A12Q-01A	ENSG00000231028	ENSG00000112339	LINC00271	HBS1L	GCCACGCGAGCGGGAACAGTCTCCTCCACTCGGAGCG*ATTTTGAAGATGATGATCTCTACGGCCAGTCTGTAGA	lincrna,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	4	4	24	6	135498000	+	6	135050647	-	0.2146	18.8969	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-C8-A12Q-01A	ENSG00000231028	ENSG00000112339	LINC00271	HBS1L	GAATACAGGCCATTTCCTGTACCTACAGCCACCCGCT*ATTTTGAAGATGATGATCTCTACGGCCAGTCTGTAGA	lincrna,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	4	2	18	6	135498517	+	6	135050647	-	0.2146	18.8969	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-C8-A12Q-01A	ENSG00000135541	ENSG00000231028	AHI1	LINC00271	AACTGTCACAGAGGTGATACGTTCCTGTGCTGCAAAA*CCACTCATCATGCCTTACCTGGATGATGCAGAAGTCC	lincrna,oncogene,cancer,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	3	3	24	6	135404951	-	6	135518593	+	5.9516	0.2146	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-C8-A12Q-01A	ENSG00000135541	ENSG00000231028	AHI1	LINC00271	TTATTTTATTGTATTTCTTTTAGGAGGTGATACGTTCCTGTGCTGCAAAA*ACATACTGAAGACCACCCATTCTGTGTGTTTGCCTGGAAATGCAATTCTC	lincrna,oncogene,cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	3	2	18	6	135404951	-	6	135504051	+	5.9516	0.2146	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-C8-A12Q-01A	ENSG00000087460	ENSG00000022277	GNAS	RTFDC1	AGATGAGGATCCTGCATGTTAATGGGTTTAATGGAGA*GTTCTGCTTCCTTCGGTGCTGCGGCTGTGTGTTTTCT	oncogene,18cancers,cancer,tumor,exon-exon	BOWTIE	in-frame	0	3	2	21	20	58895684	+	20	56484111	+	106.0529	24.6531	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-C8-A12Q-01A	ENSG00000143850	ENSG00000170382	PLEKHA6	LRRN2	TGGATTCCACCCAGGAAGGAGCTGTGTATTTCATCAA*GGCTGCCCCTGATGGGGCCTGGCAATGACTGAGCAGG	18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(no-known-start-or-end)/UTR	0	3	2	24	1	204367799	-	1	204620218	-	18.9616	1.9255	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-C8-A12Q-01A	ENSG00000143850	ENSG00000170382	PLEKHA6	LRRN2	AAGGGCTGGGAAGTGGATTCCACCCAGGAAGGAGCTGTGTATTTCATCAA*GGGTGATGTCTAATCTCCTGAAGAAAGGAACTCTGGAGTCACAGAGATTG	18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(no-known-start-or-end)/UTR	0	3	1	14	1	204367799	-	1	204621645	-	18.9616	1.9255	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-C8-A12Q-01A	ENSG00000168883	ENSG00000115423	USP39	DNAH6	CTTTGCAGTAAGAAGACTTTTCAGATCACCAAACAAG*TGATGTGGTGCGACTTGAAAAACCCAGGTTGGAAGAA	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	3	7	23	2	85630946	+	2	84718204	+	15.8332	0.2555	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-C8-A12Q-01A	ENSG00000103319	ENSG00000175267	EEF2K	VWA3A	GAGCTTTTGACTCTGGCCAGAACCTCAGCCCGGACAG*TGGGTGGCAAAATATGGGCTCAAAAAATTGAAGCTGG	tcga,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	2	3	20	16	22273750	+	16	22144247	+	7.1483	0.5164	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-C8-A12Q-01A	ENSG00000182149	ENSG00000260185	IST1	AC009097.1	GTCGGTGTCTGCTGCGTTCACGGCAGGATTCGGTTAG*GAAAGGTCTGTAACTGATTGTTTGCAAGGTGCAAGAT	antisense,oncogene,100K<gap<200K,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	2	4	21	16	71895589	+	16	71663906	+	13.1896	0.5791	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-C8-A12Q-01A	ENSG00000182149	ENSG00000260185	IST1	AC009097.1	GAGTCGGTAATCGTGCCACTGCATTTCAGTCTGGAGGACAGAGTGAGACC*CTTGCAGGAAAGGTCTGTAACTGATTGTTTGCAAGGTGCAAGATTCGCAG	antisense,oncogene,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	intronic/intronic	0	2	1	24	16	71896961	+	16	71663899	+	13.1896	0.5791	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-C8-A12Q-01A	ENSG00000182149	ENSG00000260185	IST1	AC009097.1	CCTCTTGGAACTCAACAGCATAAACTTTGAGGAGGGTCGGGACCCAGGAG*CTTGCAGGAAAGGTCTGTAACTGATTGTTTGCAAGGTGCAAGATTCGCAG	antisense,oncogene,100K<gap<200K	BOWTIE+STAR	intronic/intronic	0	2	1	15	16	71896309	+	16	71663899	+	13.1896	0.5791	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-C8-A12Q-01A	ENSG00000197702	ENSG00000077514	PARVA	POLD3	GGAGGGACCCTGGCCCGGAGGAAGAAAGCCAAGGAGG*GTGACATACAAATGGCTGAGCTATACACTAGGGGTTC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	2	2	21	11	12377783	+	11	74594061	+	14.5719	9.9244	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-C8-A12Q-01A	ENSG00000170525	ENSG00000108021	PFKFB3	FAM208B	GAGAAGGCCTGGGAGCGGCTGTAAATAATACCCGAGAGGAAATAGGCCCG*GTAACTGGGGAAGAAGCTAAACAAGAATCATTGGAGACTTCTAATCTTGT	tcga,chimerdb3seq,tcga-cancer	BOWTIE+BLAT	UTR/CDS(truncated)	0	2	1	24	10	6164007	+	10	5746179	+	31.2012	16.4589	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-BH-A0HX-01A	ENSG00000168172	ENSG00000066855	HOOK3	MTFR1	AAAATCTTTACAGGATCAAGGCTCAAAAGCAGAAGAT*AAAAGACTCGTTAAAGTCAGAACCTGCTGGACAAGAA	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/CDS(no-known-start-or-end)	0	10	5	22	8	42997637	+	8	65770947	+	4.2062	17.8824	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-BH-A0HX-01A	ENSG00000168172	ENSG00000066855	HOOK3	MTFR1	TTGAAGAATTACAAAAATCTTTACAGGATCAAGGCTCAAAAGCAGAAGAT*ACGGAGTCTCGCCCTGTGGCGTAGGCTAGAGTGCAGTGGCGCAATCTCAG	tcga,chimerdb3seq,cancer,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	10	1	18	8	42997637	+	8	65761081	+	4.2062	17.8824	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-BH-A0HX-01A	ENSG00000185619	ENSG00000174227	PCGF3	PIGG	CCCGGCAGAGGGACGGACACGCGGACGTCTAGCGGAG*TGGTTCAGCACTGAGTCATGCTTGCTTCTGCTACGCA	tcga,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	7	2	24	4	731110	+	4	539153	+	5.5768	4.6629	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-BH-A0HX-01A	ENSG00000105287	ENSG00000104879	PRKD2	CKM	CTCAAGGGCCTCTTCCGGCAGGGCCTGCAATGCAAAG*CTCTCAACAGCCTGACGGGCGAGTTCAAAGGGAAGTA	known,tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	5	4	24	19	46704169	-	19	45311920	-	10.1147	0.8091	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AR-A2LK-01A	ENSG00000104365	ENSG00000168040	IKBKB	FADD	TCCGGCCCTTCCTCCCCAACTGGCAGCCCGTGCAGTG*ACCTGTGTGCAGCATTTAACGTCATATGTGATAATGT	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	42	11	23	8	42309025	+	11	70206133	+	23.6824	23.3219	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A094-01A	ENSG00000183579	ENSG00000100325	ZNRF3	ASCC2	CGGGGCCACGCTCAGCGCCGAGGGCGAGATCGTGCAG*GTGATCTTTGACGAGACTCTACAGAAGTGCCTGGACT	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	175	18	24	22	28884066	+	22	29825257	-	3.4829	150.7906	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A094-01A	ENSG00000183579	ENSG00000100325	ZNRF3	ASCC2	CGGGGCCACGCTCAGCGCCGAGGGCGAGATCGTGCAG*CACCCCGAGCAGAAGGCAGACCGGTATTTTGTGTTAT	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	175	15	25	22	28884066	+	22	29825780	-	3.4829	150.7906	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A094-01A	ENSG00000183579	ENSG00000100325	ZNRF3	ASCC2	CGGGGCCACGCTCAGCGCCGAGGGCGAGATCGTGCAG*GAGGGTCACGCAGCACAATGCCAGCTCTGCCCCTGGA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	175	6	23	22	28884066	+	22	29832342	-	3.4829	150.7906	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A094-01A	ENSG00000198586	ENSG00000138385	TLK1	SSB	TGGAAGCTTGGGATCTTTAAGTGACAAAGAATCAGAG*TATTATTTTGGCGACTTCAATTTGCCACGGGACAAGT	tcga,18cancers,chimerdb3seq,m21,tcga-cancer,exon-exon	BOWTIE	in-frame	0	46	8	25	2	171082781	-	2	169805474	+	9.8481	21.734	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A094-01A	ENSG00000198586	ENSG00000138385	TLK1	SSB	AAGTGACGGGACTTTATCTGCAGTAGGTTCCCTTGAG*TATTATTTTGGCGACTTCAATTTGCCACGGGACAAGT	tcga,18cancers,chimerdb3seq,m21,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	46	3	20	2	171081640	-	2	169805474	+	9.8481	21.734	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A094-01A	ENSG00000187164	ENSG00000229847	SHTN1	EMX2OS	AAGCAGCTGCAGCTCATTACCAGTCTGAAGGAGCAAG*ATACAAGCAAGGAAACGTGTGGCATCTGGCTACCATG	antisense,18cancers,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	40	5	22	10	117005022	-	10	117473422	-	7.5942	1.8521	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A8-A094-01A	ENSG00000187164	ENSG00000229847	SHTN1	EMX2OS	AAGCAGCTGCAGCTCATTACCAGTCTGAAGGAGCAAG*GGTCATCTCAGGCTGGCTGCATGCCTCAGCTGAAGAT	antisense,18cancers,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	40	5	20	10	117005022	-	10	117492109	-	7.5942	1.8521	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A8-A094-01A	ENSG00000254093	ENSG00000253695	PINX1	AC011008.1	GCCGAACTGAACACTTGCCATGGGCAGGAAACCACAG*TTTCTGTATGTTATAGAAGTTCAAAGAAGACAAACTC	antisense,tumor,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	15	2	24	8	10831665	-	8	10846218	+	0.9379	4.3834	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A8-A094-01A	ENSG00000148396	ENSG00000165661	SEC16A	QSOX2	CCTGGGTGCCGAGACCTGCCCCCTGCCTAGTTTCCAG*GCTTTGAAGACGACCCCCAGGCTGTGCTGCAGACAAT	18cancers,chimerdb3seq,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	13	7	23	9	136459134	-	9	136211452	-	25.3193	8.3936	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A8-A094-01A	ENSG00000072121	ENSG00000182185	ZFYVE26	RAD51B	GCGCTGAGAGCTCTATTGCTTTGGGCGCCGGGAGCAG*GCACTTCTGGATCCAGCTGTGTGATAGCCGCACTAGG	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	2	7	22	14	67816534	-	14	68411424	+	1.692	0.9222	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A1PC-01B	ENSG00000187098	ENSG00000156469	MITF	MTERF3	TATTACGAACTCAAAAGTCAACCGCTGAAGAGCAG*AACTGGATGAATTGCCTCCATTGTCTCCAATGCAG	oncogene,tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	20	4	21	3	69739701	+	8	96257114	-	0.8023	26.7906	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A1PC-01B	ENSG00000187098	ENSG00000156469	MITF	MTERF3	GAAGAGCCCAAAACCTATTACGAACTCAAAAGTCAACCGCTGAAGAGCAG*CCAATTTCAGAGGAAGAGGCTATTCAGATTATTGCAGACCCTCCATTGCC	oncogene,tcga,18cancers,chimerdb3seq,cancer,tcga-cancer	BOWTIE+STAR	out-of-frame	0	20	1	14	3	69739701	+	8	96257079	-	0.8023	26.7906	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A1PC-01B	ENSG00000187098	ENSG00000156469	MITF	MTERF3	TATTACGAACTCAAAAGTCAACCGCTGAAGAGCAG*ACTAAGAAAAATGGCTTTGTCAGCCCAACAGATAC	oncogene,tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	20	1	13	3	69739701	+	8	96258700	-	0.8023	26.7906	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A1PC-01B	ENSG00000143590	ENSG00000139144	EFNA3	PIK3C2G	CGAGTTCCACGCCGGCCACGAGTACTACTACATCT*GCTTGATAGAGAAGGTAACAACTGAACTATCCACA	known,tcga,cell_lines,18cancers,chimerdb3seq,exon-exon	BOWTIE	in-frame	0	16	13	24	1	155085404	+	12	18346641	+	8.0535	2.7036	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-EW-A1PC-01B	ENSG00000251474	ENSG00000163913	RPL32P3	IFT122	GTTGAGCAGCGGGTTGTTGGTGGAGCAGCGGTAGCACAAGGGCACCAACT*CCTGACCATCCGCGCCAAGCCCTTCCACGACAGTGAGGTGAGGATGCAGC	pseudogene,ribosomal	BOWTIE+BLAT	intronic/CDS(truncated)	0	2	1	22	3	129394042	-	3	129514518	+	4.9322	15.6752	FALSE	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	transcribed_unprocessed_pseudogene	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AR-A256-01A	ENSG00000167986	ENSG00000134825	DDB1	TMEM258	ATTTAACGGGAAGCTGTTAGCCAGCATCAATAGCACG*GTAACAACCAGATGGCTTCACTGAAACCTGCTTTTGT	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	131	22	25	11	61308983	-	11	61789235	-	46.8818	23.367	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AR-A256-01A	ENSG00000131558	ENSG00000004864	EXOC4	SLC25A13	GGCAGATGTATGGGTGAAGATCCAAGATGTTCTACAG*GCTGGAGGCTCCCAGGTGATTTTCACAAATCCTTTAG	tcga,cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	46	7	24	7	133375002	+	7	96146696	-	13.4743	26.048	TRUE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AR-A256-01A	ENSG00000116001	ENSG00000163235	TIA1	TGFA	GGCGCCGCCGCGACAGCAGCAGCCATGGAGGACGAGATGCCCAAGACTCT*GGTCTCCGTGAGAATGAAATGAGAGAATATACGTAAAGCACTTAGAACAG	tcga,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/intronic	0	45	1	16	2	70248405	-	2	70502911	-	22.3544	20.6281	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AR-A256-01A	ENSG00000115998	ENSG00000163235	C2ORF42	TGFA	CAGCAGCAGCCATGGAGGACGAGATGCCCAAGACTCT*ACCCGCCCGTGGCTGCAGCAGTGGTGTCCCATTTTAA	18cancers,cancer,100K<gap<200K,exon-exon	BOWTIE	UTR/CDS(complete)	0	41	10	24	2	70248405	-	2	70465733	-	3.9962	20.6281	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AR-A256-01A	ENSG00000115998	ENSG00000163235	C2ORF42	TGFA	CAGCAGCAGCCATGGAGGACGAGATGCCCAAGACTCT*CAGACCCGCCCGTGGCTGCAGCAGTGGTGTCCCATTT	18cancers,cancer,100K<gap<200K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	41	6	24	2	70248405	-	2	70465736	-	3.9962	20.6281	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AR-A256-01A	ENSG00000108100	ENSG00000119522	CCNY	DENND1A	AACCTGCAGCACATCAGCGACCGGGAGAACATAGACG*CCTCACAGTTAGCCAAGTTGGCCAGAACTTCACATTC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	33	9	23	10	35337207	+	9	123757822	-	23.1817	6.7468	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AR-A256-01A	ENSG00000108100	ENSG00000119522	CCNY	DENND1A	AACCTGCAGCACATCAGCGACCGGGAGAACATAGACG*CTATCTCCCCTGGTTCGAGGTATTTTATAAGCTGCTT	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	33	2	25	10	35337207	+	9	123676789	-	23.1817	6.7468	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AR-A256-01A	ENSG00000101421	ENSG00000078699	CHMP4B	CBFA2T2	ACGGCCGCCAAGAAGCACGGCACCAAAAACAAGCGCG*AACTGCTGGAACTGTGGCCGCAAAGCCAGCGAGACAT	known,tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	30	16	25	20	33811658	+	20	33644347	+	107.0301	11.2349	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AR-A256-01A	ENSG00000198373	ENSG00000182173	WWP2	TSEN54	GCCCTGCCTTTTGAGAAGTCTCAGCTCACTTTGAAAG*CTCTGTCCTGTCCCCGTATGAGAGGCAGCTTAACCTG	tcga,18cancers,chimerdb3seq,m25,tcga-cancer,exon-exon	BOWTIE	in-frame	0	26	7	22	16	69787080	+	17	75521409	+	15.8653	13.3228	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AR-A256-01A	ENSG00000198373	ENSG00000182173	WWP2	TSEN54	GCCCTGCCTTTTGAGAAGTCTCAGCTCACTTTGAAAG*ATCCCCAGGCTGAGGAGGTGGGTCAGTGGCCCACCCG	tcga,18cancers,chimerdb3seq,m25,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	26	2	22	16	69787080	+	17	75521355	+	15.8653	13.3228	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AR-A256-01A	ENSG00000103197	ENSG00000131634	TSC2	TMEM204	ACAGACGGAGTTTATCATCACCGCGGAAATACTGAGA*GTTTTGTCCTGGTCATCGGGCTCGTGACTTTCTACAG	tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	13	5	24	16	2048753	+	16	1554782	+	10.0948	6.0113	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AR-A256-01A	ENSG00000103197	ENSG00000131634	TSC2	TMEM204	CGTCGGGGCGGCCCGGAGCGCGGTGGCGCGGCGCGGG*GTTTTGTCCTGGTCATCGGGCTCGTGACTTTCTACAG	tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	13	3	25	16	2048065	+	16	1554782	+	10.0948	6.0113	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AR-A256-01A	ENSG00000255027	ENSG00000149571	AP000842.2	KIRREL3	GCCAGAAACCTTGTTCCAGCAGTGCAGAGCAGCTCAG*AGCTGGGCCTCCAGAAGAGAGGATGCTGTCTGGTGCT	antisense,m7,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	8	3	24	11	125931305	-	11	126562912	-	0.9892	0.5297	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AR-A256-01A	ENSG00000255027	ENSG00000149571	AP000842.2	KIRREL3	TGAAAACCTCCCAGCCAGAAACCTTGTTCCAGCAGTGCAGAGCAGCTCAG*ACTTGGAAACTGAAACACAGAAAGACTACATAAATTCTCCAGAGTGACAC	antisense,m7	BOWTIE+BLAT;BOWTIE+STAR	exonic(no-known-CDS)/intronic	0	8	2	20	11	125931305	-	11	126606367	-	0.9892	0.5297	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AR-A256-01A	ENSG00000204120	ENSG00000135902	GIGYF2	CHRND	ACCATTGGCTCTGGTACCCTTTACAGAAGAAGAACAG*CTCTTCCTGGAGACCCTGCCGGAGCTCCTGCACATGT	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	8	3	24	2	232749082	+	2	232533931	+	9.8678	5.7034	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AR-A256-01A	ENSG00000204120	ENSG00000135902	GIGYF2	CHRND	TTTCTCTTTTTTTTTTTTTTTTTTTTGGCAGAGAAACTTTTCCATGTCTG*TTAGTGAATGGGTTCTGCTCCGCACCATGGGTGATGTGGGAGAGCTGGAA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K	BOWTIE+BLAT	CDS(truncated)/intronic	0	8	1	22	2	232756241	+	2	232533411	+	9.8678	5.7034	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AR-A256-01A	ENSG00000164219	ENSG00000185261	PGGT1B	KIAA0825	TGGATTTATTCCCTGCAGGTCCTTCCCACAGAAGACA*GTGGGAAATGAAGAAGGATGAAACACTAGAAGAGGAA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	8	5	16	5	115253137	-	5	94154124	-	2.624	0.1936	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AR-A256-01A	ENSG00000164219	ENSG00000185261	PGGT1B	KIAA0825	TTTATTCCCTGCAGGTCCTTCCCACAGAAGACAGTGA*GTGGGAAATGAAGAAGGATGAAACACTAGAAGAGGAA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	8	2	23	5	115253133	-	5	94154124	-	2.624	0.1936	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AR-A256-01A	ENSG00000141499	ENSG00000129353	WRAP53	SLC44A2	GCACCCAACCTGAGAACTTCTTGAAAGGCTGTAAGTG*ACCTTCCCCTCCTCCAATGAGTCCCGCCAATGCCCCA	18cancers,cancer,exon-exon	BOWTIE	out-of-frame	0	8	2	22	17	7689322	+	19	10636323	+	1.7393	197.7899	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AR-A256-01A	ENSG00000249859	ENSG00000188897	PVT1	AC099489.1	CTGTGACCTGTGGAGACACGGCCAGATCTGCCCTCCA*GTCTCTGTGGACATTCACAATGGCAGCTCCGGCTTCG	lincrna,oncogene,cancer,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	6	4	24	8	127794734	+	16	11417839	-	1.2335	0.9931	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AR-A256-01A	ENSG00000249859	ENSG00000188897	PVT1	AC099489.1	CTTCGGCACAAGGGCCCAACTGGAATTCCACTTACGG*GCACCCTCAGTGTCACTGCTGACTCAGCTGTGCTGGG	lincrna,oncogene,cancer,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	6	3	18	8	127796071	+	16	11425433	-	1.2335	0.9931	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AR-A256-01A	ENSG00000156515	ENSG00000156502	HK1	SUPV3L1	TTGCCAACATTCGTAAGGTCCATTCCTGATGGCTCTG*TTTGCCAGGCAGTATAGCAGGAATGAGCCCCTGACCT	18cancers,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	3	2	23	10	69343989	+	10	69207793	+	37.653	18.508	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-AR-A256-01A	ENSG00000143341	ENSG00000121481	HMCN1	RNF2	CTTTTCAACTTTGCGTTGGTGCCTTTCCATGATCCAG*GAGGCAATAACAGATGGCTTAGAAATTGTGGTTTCAC	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	3	4	22	1	185735047	+	1	185091579	+	2.522	12.3451	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AR-A256-01A	ENSG00000159200	ENSG00000159216	RCAN1	RUNX1	CCTGGACCCGCGCGTGTTCGTGGACGGCCTGTGCCGG*ATACAAGGCAGATCCAACCATCCCCACCGTGGTCCTA	known,oncogene,tcga,cell_lines,chimerdb3seq,cancer,tumor,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	1	2	22	21	34614760	-	21	34799462	-	75.2043	12.7011	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0H0-01A	ENSG00000105429	ENSG00000188368	MEGF8	PRR19	GCTGGTGTGGCAATGAGGACAACCCCACACTGGGACG*GGGCCAAGCCTGGGGTCTCTGAGAGAAAGATGACACC	18cancers,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	44	5	21	19	42351761	+	19	42310271	+	6.8328	2.9239	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0H0-01A	ENSG00000105429	ENSG00000188368	MEGF8	PRR19	AGCCACGAGTGTGGCTGGTGTGGCAATGAGGACAACCCCACACTGGGACG*GCCTTCCCCCGGAGGAACCTGATTCAGGATGCCAGGGATGCCATCGTGCA	18cancers,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	44	4	23	19	42351761	+	19	42310062	+	6.8328	2.9239	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0H0-01A	ENSG00000105429	ENSG00000188368	MEGF8	PRR19	CTGCCCGCTGGGCATACGCCCGCTGTCCTGACGTGGATGAGTGTCGCCTG*GGAGCACCGGGGTCTCTTCAACCACGAGGTGAAATCCCTAGATGTTGCAA	18cancers,10K<gap<100K	BOWTIE+BLAT	out-of-frame	0	44	1	19	19	42352346	+	19	42309797	+	6.8328	2.9239	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0H0-01A	ENSG00000197323	ENSG00000009307	TRIM33	CSDE1	TGGCAGCAGCACAGCACTACTATACAGCAAGCGACTG*ATGATGTTGAATTTGAAGTATCATCGGACCGACGGAC	tcga,cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	24	8	24	1	114427748	-	1	114738072	-	11.6809	217.102	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0H0-01A	ENSG00000009307	ENSG00000266903	CSDE1	AC243964.2	TCCTAAAACCACTAGCCCAAATAAAGGCAAAGAGAAG*GTGCTGTTCTAGGCGCTGAGGATGCAGCCGTGCACAA	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	17	3	23	1	114730258	-	19	44699177	-	217.102	1.1476	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0H0-01A	ENSG00000188368	ENSG00000104866	PRR19	PPP1R37	CGCCTCCTCTCCAGGGACGGAAGCCTTCACTTAGGAG*CCCAGAATGTGACCGTGGACGAGGTCATCGGCGCCTA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	14	8	24	19	42302503	+	19	45138514	+	2.9239	8.6778	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0H6-01A	ENSG00000124198	ENSG00000174871	ARFGEF2	CNIH2	CCCAAGGGTAGTCAGCACATCCCTTGACTGCTTGCAG*ATCATAGCCTTTGATGAGCTGCGGACCGACTTCAAGA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	40	13	25	20	48941987	+	11	66282259	+	14.0584	8.8054	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0AV-01A	ENSG00000156642	ENSG00000103351	NPTN	CLUAP1	AGCGCTCCTAAAGCAAACGCCACCATTGAAGTGAAAG*GTAACGATGACTCGGACATAGACATCCAGGAGGACGA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	348	25	25	15	73587524	-	16	3530568	+	44.7307	10.8869	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0AV-01A	ENSG00000156642	ENSG00000103351	NPTN	CLUAP1	GGCTCCCTCCTCCCAGGGCCAGGCGCCGCTCAGAACG*GTAACGATGACTCGGACATAGACATCCAGGAGGACGA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	348	2	18	15	73633125	-	16	3530568	+	44.7307	10.8869	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-BH-A0AV-01A	ENSG00000159842	ENSG00000174238	ABR	PITPNA	TCCTACTGTGTGCCAAGCTGAAGAAGACCTCTGCAGG*TTATTACAAATGAGTACATGAAAGAAGACTTTCTGAT	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	9	1	14	17	1069969	-	17	1543027	-	7.4302	18.1317	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0AV-01A	ENSG00000185015	ENSG00000171174	CA13	RBKS	TGTTTTAAAGCAACCTATAAACATCAGCTCTCAACAG*TGAAAACCTTGTTCAATCCAGCCCCTGCCATTGCTGA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	7	3	15	8	85268627	+	2	27832777	-	0.8249	0.7992	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0AV-01A	ENSG00000138031	ENSG00000255191	ADCY3	AP003555.3	GCTGGGCTTTCCGGGACTGTGGAGGGAGCACAGGCGGGGAAGCTCCACTT*CCTGAAAACCTCTCAGGAAGGCCATCTTGGAGACCCATCTCTAACACAGA	lincrna	BOWTIE+BLAT	UTR/intronic	0	2	4	22	2	24819551	-	11	69996780	+	5.2977	0.1397	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0AV-01A	ENSG00000138031	ENSG00000255191	ADCY3	AP003555.3	CTCCACGAAAGGGGCAAAGGGACAGAAGAGCAGGCAGTGGCAGTTTCCAG*ACGTCTGCTCCCCCTTTGCCTTCCGCCGTGAGTAAAAGCTCCCTGAGGCC	lincrna	BOWTIE+BLAT;BOWTIE+STAR	CDS(no-known-start-or-end)/intronic	0	2	1	25	2	24820384	-	11	69997827	+	5.2977	0.1397	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0AV-01A	ENSG00000140575	ENSG00000213471	IQGAP1	TTLL13P	CTTATGAGTACCTTTGTCATTTGGAAGAAGCGAAGAG*GAAAGAAAAAACTGAGTCATCCCATGTGGCAATGCTG	tcga,cell_lines,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	2	3	20	15	90390873	+	15	90262006	+	98.0373	0.0077	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A8-A09I-01A	ENSG00000136478	ENSG00000261040	TEX2	WFDC21P	GCCGGCATAGTACAATGAGGCAGCCAGCGGATCTTGG*GTACCTGCGTCGAGCTCTGCACAGGTGACTGGGACTG	18cancers,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	332	22	25	17	64263168	-	17	60085203	-	18.3293	40.2181	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A8-A09I-01A	ENSG00000136478	ENSG00000261040	TEX2	WFDC21P	AAAGGATACCATTGAATAGTGACATCTGAGTTTTAAG*GTACCTGCGTCGAGCTCTGCACAGGTGACTGGGACTG	18cancers,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	332	6	24	17	64242261	-	17	60085203	-	18.3293	40.2181	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A8-A09I-01A	ENSG00000136478	ENSG00000261040	TEX2	WFDC21P	GCCGGCATAGTACAATGAGGCAGCCAGCGGATCTTGG*ATGAAGAGTTATCTTAAGGATCATCTTTCCCTAAGAT	18cancers,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	332	3	25	17	64263168	-	17	60083766	-	18.3293	40.2181	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A8-A09I-01A	ENSG00000136478	ENSG00000261040	TEX2	WFDC21P	AAATGGCAGCTTCGTCCCTTTCCTGTCTTGGGCATTG*ATGAAGAGTTATCTTAAGGATCATCTTTCCCTAAGAT	18cancers,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	332	2	23	17	64239157	-	17	60083766	-	18.3293	40.2181	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A8-A09I-01A	ENSG00000136478	ENSG00000261040	TEX2	WFDC21P	AAATGGCAGCTTCGTCCCTTTCCTGTCTTGGGCATTG*GTACCTGCGTCGAGCTCTGCACAGGTGACTGGGACTG	18cancers,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	332	2	22	17	64239157	-	17	60085203	-	18.3293	40.2181	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A8-A09I-01A	ENSG00000136478	ENSG00000261040	TEX2	WFDC21P	AATGCTTGAAAGTCGAGAACCGCAGTTACTTTTACTCGAATCTGTCAGAG*GTACCTGCGTCGAGCTCTGCACAGGTGACTGGGACTGCAACCCCGGAGAC	18cancers	BOWTIE+BLAT;BOWTIE+STAR	intronic/exonic(no-known-CDS)	0	332	1	18	17	64262727	-	17	60085203	-	18.3293	40.2181	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A8-A09I-01A	ENSG00000131759	ENSG00000176658	RARA	MYO1D	CTTCCAGTTAGTGGATATAGCACACCATCCCCAGCCA*ATTTGAAAAAGGGCGCATCTATACGTTCATTGGAGAA	known,oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	102	16	24	17	40331396	+	17	32780784	-	73.8266	128.6296	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A09I-01A	ENSG00000131759	ENSG00000176658	RARA	MYO1D	TCTCCAGCACCAGCTTCCAGTTAGTGGATATAGCACACCATCCCCAGCCA*GCTGGAGTGAAGTGGCGCGATCTCAGCTCACTGCAACCTCTGCCCCCTGG	known,oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	102	5	23	17	40331396	+	17	32786792	-	73.8266	128.6296	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A09I-01A	ENSG00000131759	ENSG00000176658	RARA	MYO1D	CCGCTCCGGACTCCGCTTTGGAATGGCTCAAACCACT*ATTTGAAAAAGGGCGCATCTATACGTTCATTGGAGAA	known,oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	102	4	22	17	40342867	+	17	32780784	-	73.8266	128.6296	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A09I-01A	ENSG00000131759	ENSG00000176658	RARA	MYO1D	TCCGTACTCCACCCCGCTCCGGACTCCGCTTTGGAATGGCTCAAACCACT*GCTGGAGTGAAGTGGCGCGATCTCAGCTCACTGCAACCTCTGCCCCCTGG	known,oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	102	1	25	17	40342867	+	17	32786792	-	73.8266	128.6296	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A09I-01A	ENSG00000276023	ENSG00000154920	DUSP14	EME1	GCCCTAACCGCAACCCGCTCCGCGCCGCGCCGCGCCG*GGAATTATTTGATAGCACATACTGATGGCTCTAAAGA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/UTR	0	45	5	19	17	37489958	+	17	50375185	+	15.5809	26.2729	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A09I-01A	ENSG00000108666	ENSG00000131747	C17ORF75	TOP2A	TCTCTTTCAGGAAAAGCTTACCTTTCTGCTACATGCT*GGAAAACAATTTAATTAGTATATGGAATAATGGAAAA	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	39	7	24	17	32335323	-	17	40413625	-	9.037	196.3937	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A09I-01A	ENSG00000166263	ENSG00000153944	STXBP4	MSI2	AAAGGCTCAGCTTGCTGATTATTCTGACCAAAATAAA*GTAGAATGTAAGAAAGCTCAGCCGAAAGAAGTCATGT	tcga,cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	27	5	21	17	55073076	+	17	57615970	+	1.5581	14.95	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A09I-01A	ENSG00000108306	ENSG00000265542	FBXL20	AC015845.2	CAGGGACCGCCTGCTGCACTTTGGGTTCAAGGCGACA*GAACATTGCCCTGAGACAGACATCCATGAAGAAGCCT	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	25	6	25	17	39402173	-	17	57772196	-	38.2729	5.2481	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A8-A09I-01A	ENSG00000108306	ENSG00000265542	FBXL20	AC015845.2	GAGGGACGTGAACGGAGTGACCAAGAGCAGGTTTGAG*GAACATTGCCCTGAGACAGACATCCATGAAGAAGCCT	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	25	6	22	17	39401361	-	17	57772196	-	38.2729	5.2481	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A8-A09I-01A	ENSG00000167258	ENSG00000175175	CDK12	PPM1E	TCCCACCCTTATTACCTGGAGATGATGACATGGATAG*GACCAGGAAGAACAAGCTTACTTTGCAGTGTTTGATG	known,18cancers,cancer,exon-exon	BOWTIE	out-of-frame	0	23	6	20	17	39471763	+	17	58969539	+	153.3499	1.367	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A09I-01A	ENSG00000011258	ENSG00000172421	MBTD1	EFCAB3	AAAGCAGCCGTCCCCTCTGCAGCCTCTCTGACAAGTG*GAAATGGAAAGATTAATGTTAATTCAATAATGGAGGG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	21	5	24	17	51259143	-	17	62373814	+	12.1546	2.1706	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A09I-01A	ENSG00000108395	ENSG00000108406	TRIM37	DHX40	CTTACGATTCAGCTACTTTTGTTTTAGAGAATTTCAG*TTGATCCAGAGTACCAGAAGGAAGCAGAACAGAGACA	cancer,tumor,exon-exon	BOWTIE	out-of-frame	0	9	2	15	17	59064355	-	17	59598737	+	67.8879	62.9243	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A8-A09I-01A	ENSG00000171475	ENSG00000108799	WIPF2	EZH1	CCTCCCCCAGCCCGAGACCCTCCCAGTCGGGGAGCAG*CTGGACACCTGTTCTGCTGTTGTGTCCTGCCATTCTC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	9	6	25	17	40265146	+	17	42730918	-	51.488	4.5625	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-A8-A09I-01A	ENSG00000141376	ENSG00000108349	BCAS3	CASC3	ATTCGAGCGGCTAGAATCTTGCCTGCTCCACAGTTTG*GGTGAAGAAGGTGAATACAGTGAAGAGGAAAACTCCA	18cancers,cancer,tumor,exon-exon	BOWTIE	out-of-frame	0	8	2	23	17	60747279	+	17	40161753	+	3.2146	86.7891	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-A8-A09I-01A	ENSG00000141736	ENSG00000176658	ERBB2	MYO1D	TCTCCTGCCTCAGTCTCCTGAGTAGCTGGGACTACAG*ATTTGAAAAAGGGCGCATCTATACGTTCATTGGAGAA	oncogene,cancer,exon-exon	BOWTIE	CDS(no-known-start-or-end)/CDS(truncated)	0	8	2	15	17	39713269	+	17	32780784	-	946.9721	128.6296	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A8-A09I-01A	ENSG00000141736	ENSG00000170832	ERBB2	USP32	TCTCCTGCCTCAGTCTCCTGAGTAGCTGGGACTACAG*ATGGGTCATCTTACTCTGGAAGACTATCAGATCTGGA	oncogene,cancer,m4,exon-exon	BOWTIE	CDS(no-known-start-or-end)/CDS(complete)	0	5	2	14	17	39713269	+	17	60255258	-	946.9721	180.8743	TRUE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A8-A09I-01A	ENSG00000141736	ENSG00000170832	ERBB2	USP32	TCTCCTGCCTCAGTCTCCTGAGTAGCTGGGACTACAG*GATGCCAACCCTGTGGTAATTGAGCCATCATCTGTTT	oncogene,cancer,m4,exon-exon	BOWTIE	CDS(no-known-start-or-end)/CDS(complete)	0	5	1	13	17	39713269	+	17	60226231	-	946.9721	180.8743	TRUE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A8-A09I-01A	ENSG00000162337	ENSG00000150672	LRP5	DLG2	GCTCTACTGGGGAGACGCCAAGACAGACAAGATCGAG*GTAAACAACTACAGTTTAGAAGAAGTAACACACGAAG	tcga,chimerdb3seq,cancer,m2,tcga-cancer,exon-exon	BOWTIE	in-frame	0	4	2	21	11	68390052	+	11	83965468	-	7.5342	0.3686	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A09I-01A	ENSG00000162337	ENSG00000150672	LRP5	DLG2	GGACATGTTTGATCCAGGAGGCCAGGCCCAGCCACCCCCTGCAGCCAGAT*GTAAACAACTACAGTTTAGAAGAAGTAACACACGAAGAGGCAGTAGCAAT	tcga,chimerdb3seq,cancer,m2,tcga-cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	4	1	16	11	68390115	+	11	83965468	-	7.5342	0.3686	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-A8-A09I-01A	ENSG00000125686	ENSG00000175175	MED1	PPM1E	CCCCATACCTTTGAATCACAACATGAGATTTTATGCT*GACCAGGAAGAACAAGCTTACTTTGCAGTGTTTGATG	cancer,exon-exon	BOWTIE	in-frame	0	3	1	14	17	39423327	-	17	58969539	+	231.657	1.367	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A8-A09I-01A	ENSG00000245832	ENSG00000171533	MIR4300HG	MAP6	CAACAACACGCTTGGGCACTGTATTAACTCCATAATC*GAATGAATTCAGGGCATGGACGGACATCAAGCCTGTG	lincrna,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	3	2	21	11	82099974	-	11	75608322	-	0.1287	0.4871	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A8-A09I-01A	ENSG00000071051	ENSG00000144040	NCK2	SFXN5	AAGGGCTCCCTCGTGAAGAACCTGAAGGACACACTAG*CCAGTGCCAATATCTGCAATGTGGTCCTGATGCGGTA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	3	2	23	2	105855289	+	2	72971685	-	7.1182	2.2804	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-A8-A09I-01A	ENSG00000143799	ENSG00000141367	PARP1	CLTC	AAAAGACAAGGATAGTAAGCTTGAAAAAGCCCTAAAG*GATGCAATGCAGTATGCTTCTGAATCTAAAGATACTG	cancer,exon-exon	BOWTIE	in-frame	0	3	1	13	1	226388656	-	17	59685587	+	33.9443	639.2199	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-A8-A09I-01A	ENSG00000175175	ENSG00000125686	PPM1E	MED1	CTACTTGGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCAGAAGGCGGAG*AGTTTCAGGGCAAGCGTGAGAAAAGTGATAAAGACAAATCAAAGGTTTCC	cancer	BOWTIE+BLAT	intronic/CDS(truncated)	0	3	1	17	17	58904959	+	17	39408172	-	1.367	231.657	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A15K-01A	ENSG00000079459	ENSG00000104299	FDFT1	INTS9	CGGGGGCAAGCGGAAGGTGATGCCCAAGATGGACCAG*TCCCAGGCTGTCCAATCTTCCTGGCTGGTCCCTGAAG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	13	4	22	8	11802931	+	8	28850273	-	11.4436	4.4974	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A15K-01A	ENSG00000104299	ENSG00000168490	INTS9	PHYHIP	GTGCCAAAGGCTCAGTCTGCCTCCTTGTGGAAGAATAAGGACATTCAGAG*GGGCAGCAGCGACGCGCTGCACAGCCAGACAGGAGCTGGCTGCGGGGCAT	18cancers	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	8	3	22	8	28835292	-	8	22232003	-	4.4974	2.7039	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A15K-06A	ENSG00000079459	ENSG00000104299	FDFT1	INTS9	CGGGGGCAAGCGGAAGGTGATGCCCAAGATGGACCAG*TCCCAGGCTGTCCAATCTTCCTGGCTGGTCCCTGAAG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	11	3	24	8	11802931	+	8	28850273	-	11.5497	3.4524	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A15K-06A	ENSG00000104299	ENSG00000168490	INTS9	PHYHIP	GTGCCAAAGGCTCAGTCTGCCTCCTTGTGGAAGAATAAGGACATTCAGAG*CTGGGAACATCGTCTCACCAGGGGCAGCAGCGACGCGCTGCACAGCCAGA	18cancers	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	10	1	24	8	28835292	-	8	22232024	-	3.4524	2.9454	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A15K-06A	ENSG00000104299	ENSG00000168490	INTS9	PHYHIP	GTGCCAAAGGCTCAGTCTGCCTCCTTGTGGAAGAATAAGGACATTCAGAG*GGGCAGCAGCGACGCGCTGCACAGCCAGACAGGAGCTGGCTGCGGGGCAT	18cancers	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	10	1	21	8	28835292	-	8	22232003	-	3.4524	2.9454	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A0D1-01A	ENSG00000267374	ENSG00000163320	AC016205.1	CGGBP1	AACATTTTTGGCGCGCAATGTGGGGGCACCAGAAGCG*TAAAGGCATGACTTCCTGGCACCACAGGGAAAATCGG	lincrna,exon-exon	BOWTIE	exonic(no-known-CDS)/UTR	0	7	4	18	18	39800069	-	3	88058223	-	0.1821	8.5791	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A0D1-01A	ENSG00000260019	ENSG00000161395	LINC01992	PGAP3	CTGGAAGCTAAAAATACCAGCTCCCTGGTCATCTCAG*GCTGGACCTGTCGGGACGACTGTAAGTATGAGTGTAT	lincrna,cancer,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	6	3	25	17	27930607	-	17	39686019	-	5.4921	122.2336	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A0D1-01A	ENSG00000265666	ENSG00000004142	RARA-AS1	POLDIP2	CGCAGGGAACCGAGAGGGAGAGGCGGCATGTGGACAG*CTTTTCCTTCATAGCATTTTTGGCTACCGAGGTGTCG	antisense,18cancers,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	6	4	24	17	40341996	-	17	28354585	-	7.3705	51.8527	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A0D1-01A	ENSG00000265666	ENSG00000004142	RARA-AS1	POLDIP2	CCTAGAAGCCCTCGGGATGCACGTTTCACTGGAAGAAAGGCCTAGCTTGG*CTTTTCCTTCATAGCATTTTTGGCTACCGAGGTGTCGTCCTGTTTCCCTG	antisense,18cancers	BOWTIE+BLAT;BOWTIE+STAR	exonic(no-known-CDS)/CDS(truncated)	0	6	1	24	17	40341122	-	17	28354585	-	7.3705	51.8527	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A0D1-01A	ENSG00000106346	ENSG00000283549	USP42	AC007161.3	TTCTGTCCAAAACTGGTCAGTTAATAGGTCCTCAGTGATCCCAGAACATC*CCATTAGTGAATTGTGTTCTCTGGACCATCAGAAGCCTGGGTACATTCCT	NA	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	22	7	6149745	+	7	7993581	+	2.9988	0	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0DG-01A	ENSG00000167881	ENSG00000167419	SRP68	LPO	AACAGAGACCTCCTCCTCCCAAGTCAAGGACAATAAG*GCCCGGGAGGTATCTAACAAGATTGTTGGCTATCTGA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	67	10	25	17	76040419	-	17	58250415	+	34.6799	3.2594	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0DG-01A	ENSG00000189067	ENSG00000262117	LITAF	BCAR4	CTCAGACCTCCCGGCTCGACAGGCGGCGCGGGCGGCG*CAAAAAATCACCATGTACCAACCTATCCAAACTTATC	lincrna,oncogene,18cancers,chimerdb3seq,tumor,100K<gap<200K,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	17	7	24	16	11586886	-	16	11820297	-	92.4485	7.8945	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0DG-01A	ENSG00000189067	ENSG00000262117	LITAF	BCAR4	TAAGCTATTTAGCTCATGGAGCCTTAGATTTAATTGACAGTGTGCCTCAG*CAAAAAATCACCATGTACCAACCTATCCAAACTTATCCATGGATGAATCT	lincrna,oncogene,18cancers,chimerdb3seq,tumor,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	intronic/exonic(no-known-CDS)	0	17	2	23	16	11583714	-	16	11820297	-	92.4485	7.8945	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0DG-01A	ENSG00000189067	ENSG00000262117	LITAF	BCAR4	CTGGCCCCGCACTACTCACCTGCCCCACGGGACACAG*CAAAAAATCACCATGTACCAACCTATCCAAACTTATC	lincrna,oncogene,18cancers,chimerdb3seq,tumor,100K<gap<200K,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	17	2	18	16	11575406	-	16	11820297	-	92.4485	7.8945	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0DG-01A	ENSG00000189067	ENSG00000262117	LITAF	BCAR4	CTCAGACCTCCCGGCTCGACAGGCGGCGCGGGCGGCG*GGTCTTGTCCTGTCACTCTGGCTGGAATACAATGGCG	lincrna,oncogene,18cancers,chimerdb3seq,tumor,100K<gap<200K,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	17	1	14	16	11586886	-	16	11821755	-	92.4485	7.8945	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0DG-01A	ENSG00000170832	ENSG00000087157	USP32	PGS1	GACCAGCTACTCCGGAAGAAGAAGGACAAATTATTAG*GAGCAAGAGCAGCTCTACCTGAGGTCAGGTGTGGTGT	18cancers,cancer,exon-exon	BOWTIE	out-of-frame	0	15	4	22	17	60252381	-	17	78419546	+	58.7685	6.4758	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0DG-01A	ENSG00000185947	ENSG00000260158	ZNF267	AC137761.1	AATGTGAAGAGTGAGGAGACAGTAGCCATCCAGCCAG*ATGCTGTCATCTATATGATCTCAGTATTTTAAAAATC	lincrna,m5,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	6	2	25	16	31885256	+	16	32824418	+	2.788	0	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-BH-A0DG-01A	ENSG00000153404	ENSG00000119950	PLEKHG4B	MXI1	CAAGAGGGCCCTGCAGCACCTGCAGCAGGAAGCCTGT*AAACTTGAAGAAGCTGAAAGAAAAAGCCAGCACCAGC	cancer,tumor,exon-exon	BOWTIE	in-frame	0	3	4	23	5	113448	+	10	110279914	+	1.4902	6.6106	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0DG-01A	ENSG00000108395	ENSG00000141367	TRIM37	CLTC	GACTAGTTATATCCAACAAATAAACAACCTTAAAGAG*CTCCAGAACCTGGGTATCAACCCAGCAAACATTGGCT	cell_lines,cancer,tumor,exon-exon	BOWTIE	in-frame	0	2	4	20	17	59051214	-	17	59644276	+	25.2563	97.9062	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A8-A08L-01A	ENSG00000175029	ENSG00000148848	CTBP2	ADAM12	CGTGTGAACTATAGAGTTTGTGGACAGATTTATATTG*GGGTGAGCTTATGGAACCAAGGAAGAGCTGATGAAGT	oncogene,tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	29	12	25	10	125110990	-	10	126330509	-	17.5496	31.0613	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A08L-01A	ENSG00000175029	ENSG00000148848	CTBP2	ADAM12	GCGCCTTTCGCCGTGGACGCCGACCGTCCGGGACGAG*GGGTGAGCTTATGGAACCAAGGAAGAGCTGATGAAGT	oncogene,tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	29	3	19	10	125160319	-	10	126330509	-	17.5496	31.0613	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A08L-01A	ENSG00000086200	ENSG00000145779	IPO11	TNFAIP8	GGAATATTTGAACGTCTAAAACAGTTTCTGGAATGCA*TGGCCACAGATGTCTTTAATTCCAAAAACCTGGCCGT	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	21	8	24	5	62474464	+	5	119392816	+	4.0758	3.8332	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A08L-01A	ENSG00000086200	ENSG00000145779	IPO11	TNFAIP8	GGGTTTTTTACATGGAATATTTGAACGTCTAAAACAGTTTCTGGAATGCA*CAAATGTTGCTGAAATGGCCAAGGGAGGAGATACAGAGACAGAGAGGGAG	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	21	1	22	5	62474464	+	5	119387739	+	4.0758	3.8332	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-A8-A08L-01A	ENSG00000197183	ENSG00000149600	NOL4L	COMMD7	GGGCCAAGTGGTGTATGTGCCGGTCAAGACGGGCTCG*GTGCTTTGAAGAAGAGTCTCACAGCCAAGCAGGTCCA	tcga,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	13	9	22	20	32584570	-	20	32706760	-	5.211	37.3448	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-A8-A08L-01A	ENSG00000197183	ENSG00000149600	NOL4L	COMMD7	GGGCGGCGGCGGGACTGGCGCGGGCAGCGGCCCCGCAGCCGGCGAGAAAG*GTGCTTTGAAGAAGAGTCTCACAGCCAAGCAGGTCCAGGCGGATTTCATA	tcga,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K	BOWTIE+BLAT	in-frame	0	13	2	20	20	32584671	-	20	32706760	-	5.211	37.3448	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-A8-A08L-01A	ENSG00000197183	ENSG00000149600	NOL4L	COMMD7	GGGGAGGGGCGGCCGGAGCCGCAGCCTGGCGCAGGAGCAGCCTCCCGCGG*GTGCTTTGAAGAAGAGTCTCACAGCCAAGCAGGTCCAGGCGGATTTCATA	tcga,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	13	1	25	20	32583940	-	20	32706760	-	5.211	37.3448	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A08L-01A	ENSG00000132676	ENSG00000162772	DAP3	ATF3	GAAAGGAATAACAAGGCTTATCTCTAGGATCCATAAG*CAAAATGATGCTTCAACACCCAGGCCAGGTCTCTGCC	oncogene,cancer,exon-exon	BOWTIE	CDS(truncated)/CDS(no-known-start-or-end)	0	9	2	21	1	155709824	+	1	212615018	+	22.6458	7.2372	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A08L-01A	ENSG00000132676	ENSG00000162772	DAP3	ATF3	TCCGAGAGCTATTTCCCGCACCAATGAGAATGACCCG*CAAAATGATGCTTCAACACCCAGGCCAGGTCTCTGCC	oncogene,cancer,exon-exon	BOWTIE	CDS(truncated)/CDS(no-known-start-or-end)	0	9	2	15	1	155717128	+	1	212615018	+	22.6458	7.2372	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A08L-01A	ENSG00000177963	ENSG00000233836	RIC8A	AC139769.1	CCATGAAGCTGGTGACCATGTTTGACAAGCTCTCCAG*GTATATGCCCTCATTTTGCTTAAGACCTCTGGCCAGA	pseudogene,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	4	6	25	11	213418	+	19	23831597	+	6.0748	3.047	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	transcribed_unprocessed_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A8-A08L-01A	ENSG00000177963	ENSG00000233836	RIC8A	AC139769.1	AGAGCTGACCCACATCCTGTCTTGTGAGCCCCAGGAG*GTATATGCCCTCATTTTGCTTAAGACCTCTGGCCAGA	pseudogene,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	4	2	20	11	213497	+	19	23831597	+	6.0748	3.047	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	transcribed_unprocessed_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-A8-A08L-01A	ENSG00000262583	ENSG00000166822	AC009163.5	TMEM170A	CCCAGGGATTTTCCTGGACGGGATTGTGAAGTAGCGG*AGATGTGGTATGGTGTATTCCTGTGGGCACTGGTGTC	pseudogene,10K<gap<100K,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	2	2	17	16	75516203	-	16	75451839	-	0.4975	7.0288	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	transcribed_unprocessed_pseudogene	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AO-A0J4-01A	ENSG00000136754	ENSG00000216937	ABI1	CCDC7	CATAGTCCAGGCAGGACAGCATCTTTAAATCAGAGACCAAGGACACACAG*GGCCTTGCTTTGTTGCCTAGTCTAGAGTGTCATGGTGTGATCACAGTTCA	cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	12	1	24	10	26768852	-	10	32738500	+	13.4904	0.3529	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-AO-A0J4-01A	ENSG00000189376	ENSG00000185942	C8ORF76	NKAIN3	CAGCTTCAAAGAAGACACTTTGCTGTTGATAGCTGAG*GTCTCAGCATTAGAGAGGCAGATCTTTGACTTCCTTG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	6	4	25	8	123226500	-	8	62579539	+	1.3121	0.1218	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-AO-A0J4-01A	ENSG00000129353	ENSG00000163453	SLC44A2	IGFBP7	CCTCGGCCCGCAGGTACCACACAGGCTCCCTGGCCTTTGGCGCGCTCATC*CTGGCCATTCAGACCCGGGGTGGCCCAGAAAAGCATGAAGTAACTGGCTG	cancer	BOWTIE+BLAT	in-frame	0	2	1	19	19	10636698	+	4	57033251	-	204.8301	249.6189	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04T-01A	ENSG00000148143	ENSG00000136770	ZNF462	DNAJC1	AACCCGAAGCACCTCCCGGCGCCGGGACGCTTCTTCT*GCACCTGAATGGACAGAAGAGGACCTCAGCCAACTGA	tcga,18cancers,chimerdb3seq,m14,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	27	15	24	9	106863355	+	10	21806099	-	6.9402	11.434	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A04T-01A	ENSG00000148143	ENSG00000136770	ZNF462	DNAJC1	AGAAGAAATATAGAAAGGTACCAGCTTCAACAGAAATAAGGAACACATTG*GCACCTGAATGGACAGAAGAGGACCTCAGCCAACTGACAAGAAGTATGGT	tcga,18cancers,chimerdb3seq,m14,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	27	1	24	9	106866191	+	10	21806099	-	6.9402	11.434	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A04T-01A	ENSG00000166828	ENSG00000196739	SCNN1G	COL27A1	TGAGACAGCAATGGTCACCTCTATAGGAATGCACCTG*GGGGTTTCTCTTCTCCTGGATCTTAGTCTCGTTTGCC	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	13	2	15	16	23197427	+	9	114162715	+	1.5677	19.1312	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A04T-01A	ENSG00000140262	ENSG00000151575	TCF12	TEX9	CCAACTACACTGGGAAGCAGTCAATTCAGTGGATCAG*GCGTTTAAATGCAGAATTGCAGGCAAAAACAGCTGAC	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	13	8	24	15	56921098	+	15	56373441	+	9.42	0.7554	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A04T-01A	ENSG00000186260	ENSG00000048471	MKL2	SNX29	ACTACAACTACCAGACCATCCTGCCTGCACCATTCAA*GGTCACCTGTCTGTGTGCCCAGTTTGAAGCCGTCCTG	oncogene,tcga,cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	12	7	24	16	14240484	+	16	12027320	+	2.36	4.5959	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04T-01A	ENSG00000111647	ENSG00000119522	UHRF1BP1L	DENND1A	GTAGAGAGAAGTGACGATGGCTCTTTTCATATCAGAG*ATCCTGAGGTGCAGAGGCAATTCCCGGAGGACTACAG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	5	1	14	12	100047530	-	9	123792630	-	3.0927	5.2578	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	FALSE	Breast	TCGA-A2-A04T-01A	ENSG00000262583	ENSG00000166822	AC009163.5	TMEM170A	CCCAGGGATTTTCCTGGACGGGATTGTGAAGTAGCGG*AGATGTGGTATGGTGTATTCCTGTGGGCACTGGTGTC	pseudogene,10K<gap<100K,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	4	4	19	16	75516203	-	16	75451839	-	0.0782	7.596	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	transcribed_unprocessed_pseudogene	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04T-01A	ENSG00000112701	ENSG00000164414	SENP6	SLC35A1	AGCGGCGGTAGCGCAGGGGAGATTACTTTTCTGGAAG*AGAAACTGGTAGTCTGGGTAGATTCAAAGCATCTTTA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	3	2	21	6	75602576	+	6	87500508	+	5.4563	10.2022	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AO-A0JM-01A	ENSG00000243678	ENSG00000154240	NME2	CEP112	CAGCGCAGCGCCGCCGCCCGGCCCCTCCAGCTTCCCG*ATAACTTACATACGACAAGAATATGAAACAAAATTGA	chimerdb3seq,exon-exon	BOWTIE	UTR/CDS(truncated)	0	88	7	22	17	51166497	+	17	65641065	-	1.2491	0.8169	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-AO-A0JM-01A	ENSG00000243678	ENSG00000154240	NME2	CEP112	GGGTGAACTGGAAAACTCGACCGCACTTTAGTGCCAG*ATAACTTACATACGACAAGAATATGAAACAAAATTGA	chimerdb3seq,exon-exon	BOWTIE	UTR/CDS(truncated)	0	88	2	23	17	51165681	+	17	65641065	-	1.2491	0.8169	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-AO-A0JM-01A	ENSG00000173890	ENSG00000163558	GPR160	PRKCI	GCTCTCGCTTCGTCCTACACTTGCGCAAATGTCTCCG*GAGACCCGTGTACAGTATCATCTCAGTTGGAGTTAGA	known,oncogene,tcga,tumor,m8,100K<gap<200K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	15	2	20	3	170039043	+	3	170259969	+	12.2223	18.0183	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AO-A0JM-01A	ENSG00000173890	ENSG00000163558	GPR160	PRKCI	GCTCTCGCTTCGTCCTACACTTGCGCAAATGTCTCCG*GGATATCATGATAACACATTTTGAACCTTCCATCTCC	known,oncogene,tcga,tumor,m8,100K<gap<200K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	15	1	14	3	170039043	+	3	170235230	+	12.2223	18.0183	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AO-A0JM-01A	ENSG00000121060	ENSG00000121075	TRIM25	TBX4	AGGGGATCCACTACTGGGAGGTGGAGCTGCAGAAGAACAACTTCTGTGGG*ACGGTACCCGCCACCTGGACTTACCTTGCAAGCGATCCTATCTGGAAGCC	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	14	7	24	17	56892018	-	17	61482900	+	3.8324	3.1549	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AO-A0JM-01A	ENSG00000241484	ENSG00000227036	ARHGAP8	LINC00511	TACGACGTGGCCAGACATGGCATTCTGCAGGTGGCAG*GTATTTTTCCCTCTCCACCCTGGTCTTCTCCTGTAAC	lincrna,18cancers,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	13	3	24	22	44786606	+	17	72431224	-	0.3803	0.8167	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AO-A0JM-01A	ENSG00000241484	ENSG00000227036	ARHGAP8	LINC00511	TACGACGTGGCCAGACATGGCATTCTGCAGGTGGCAG*GTGGAATCAGAGGTTTCTGGCTGACTCGGTGGGTGCT	lincrna,18cancers,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	13	2	21	22	44786606	+	17	72428298	-	0.3803	0.8167	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AO-A0JM-01A	ENSG00000177694	ENSG00000114757	NAALADL2	PEX5L	TGTAGCATCACCATCTCTTCAGCAACTGGTAGTAGAG*TCAGATACAGAGTTTTGGGATAAGATGCAAGCAGAAT	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	13	4	24	3	175471758	+	3	179819976	-	11.1922	2.4606	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AO-A0JM-01A	ENSG00000073350	ENSG00000154975	LLGL2	CA10	CACAGGCTTCGTCCGGACCCTGTACTTTGCTGACACCTACCTGAAGGACA*GGATACACATGTTCCCCACAAGAAGTGTTCACCAGTGAGATTATCCTTGG	cell_lines,18cancers,chimerdb3seq	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	11	4	22	17	75571100	+	17	51870805	-	54.2717	1.4298	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AO-A0JM-01A	ENSG00000073350	ENSG00000154975	LLGL2	CA10	CAGCGGCTACCTGGCTGTGGCAGGCACGGCAGGGCAG*GTCAGTGGGACCATGTACAACACTGGAAGACACGTAT	cell_lines,18cancers,chimerdb3seq,exon-exon	BOWTIE	in-frame	0	11	3	19	17	75569325	+	17	51747818	-	54.2717	1.4298	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AO-A0JM-01A	ENSG00000170832	ENSG00000100266	USP32	PACSIN2	TGATTGTTCCATGTACTGTGCATACCCGGAAGAAAGACCTATATGATGCG*GTTTGTCTACAGATTTTGAGCGTTCGAAGTTGACCCCTGACTAAGTATAC	cancer,m2	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	5	1	19	17	60198331	-	22	42912157	-	23.3706	27.7841	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-AO-A0JM-01A	ENSG00000170832	ENSG00000100266	USP32	PACSIN2	TGATTGTTCCATGTACTGTGCATACCCGGAAGAAAGACCTATATGATGCG*GTCGGGAACTACAAGCGGACTGTGAAGCGGATCGACGATGGCCACCGCCT	cancer,m2	BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	5	1	18	17	60198331	-	22	42893613	-	23.3706	27.7841	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-AO-A0JM-01A	ENSG00000145012	ENSG00000237978	LPP	KCNMB2-AS1	AGTTGCTCCAAAACCTAAGTACAACCCATACAAACAACCTGGAGGTGAGG*ACAGTGTAACGTCATTTCAGAAGAAGAGGAATCCCAAAATGTAAACTTAG	antisense,cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	22	3	188406313	+	3	178565410	-	5.3873	0.0114	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AQ-A04J-01A	ENSG00000134644	ENSG00000181031	PUM1	RPH3AL	ATGGCCTACTGGGGATAACATTCATGCAGAACATCAG*GCGGCTGGTGGAGCGGCTGGAGACCATGAGGCGGAAT	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	30	4	25	1	31059204	-	17	319549	-	8.0881	2.0427	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AQ-A04J-01A	ENSG00000124789	ENSG00000121481	NUP153	RNF2	AATTAAGCCTTACCAGCAGGGGCGACAACAGCATCAG*CAATGTCTCAGGCTGTGCAGACAAACGGAACTCAACC	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	19	8	21	6	17706277	-	1	185087552	+	15.9179	10.869	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AQ-A04J-01A	ENSG00000070476	ENSG00000230524	ZXDC	COL6A4P1	CCACAGCATAACCCACCTAGGCACAAAGCCGTTCGAGTGTCCTGTGGAAG*GTCCACATCTAGAATGGAGACTTGGAAGATATTTTGGGGGATCATCCTCC	pseudogene	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	4	3	20	3	126470895	-	3	15180974	-	3.9132	0.8079	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	transcribed_unprocessed_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AQ-A04J-01A	ENSG00000205133	ENSG00000197275	TRIQK	RAD54B	AAAAGCAGAAGCAAAGAAAACAGCAATAGGCATAAAG*TTCATTCGGCTCCTAAAGAAGTAGCAGTGTCCAAGGA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	3	2	18	8	92891989	-	8	94411315	-	3.03	0.5985	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0HB-01A	ENSG00000137266	ENSG00000224846	SLC22A23	AL133351.1	CATCCGCGCCGGCCTCGTCCAGAACGTGGTCAGCAAG*GAAAAAGAATGCCTGTGTTTCGAAGTTCCTTCTTAGG	antisense,cancer,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	45	11	24	6	3455906	-	6	2990011	-	1.7638	0	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0HB-01A	ENSG00000108821	ENSG00000255713	COL1A1	OR4D2	CTCTTCGTCCCCTAGAGTCACCCACCGACCAAGAAACCACCGGCGTCGAG*GTTTCTTCTCTTTGGCTTTGTTTTCCCTTTGTGAAGTGGAGAGGGAGCTA	cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	39	5	24	17	50199556	-	17	58170595	+	611.1203	0.1171	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-BH-A0HB-01A	ENSG00000058673	ENSG00000230623	ZC3H11A	AC104461.1	AAGACACAGATGTTCCTGTTCAGAGCAACCAGCTAAT*AGTGGAGGAAGAAGAGAATCACCACATATCGTATTTA	lincrna,m4,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	35	5	23	1	203803016	+	1	200473909	+	0.0017	2.2321	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0HB-01A	ENSG00000112739	ENSG00000153046	PRPF4B	CDYL	CCGCCGCGGAGACCCAGTCGCTACGGGAGCAGCCAGA*GCAAACGAGATGCTGCTCAGTGGACGGAAGCTGACAG	chimerdb3seq,cancer,exon-exon	BOWTIE	out-of-frame	0	23	9	25	6	4021466	+	6	4952266	+	14.6922	16.3266	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0HB-01A	ENSG00000112739	ENSG00000153046	PRPF4B	CDYL	CCGCCGCGGAGACCCAGTCGCTACGGGAGCAGCCAGA*GTGCTTGAGGAATCCAAAGCCCTCGTGCGCTGCAACA	chimerdb3seq,cancer,exon-exon	BOWTIE	out-of-frame	0	23	3	19	6	4021466	+	6	4953898	+	14.6922	16.3266	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-BH-A0HB-01A	ENSG00000257315	ENSG00000230623	ZBED6	AC104461.1	CCTGTATATCTTTTTATTGTGAATGGTCTCTTCCTGTATATCTTTTTACT*AGTGGAGGAAGAAGAGAATCACCACATATCGTATTTAGAGGTCCTGCAGA	lincrna,m4	BOWTIE+BLAT;BOWTIE+STAR	intronic/exonic(no-known-CDS)	0	23	1	23	1	203804504	+	1	200473909	+	0.0089	2.2321	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-BH-A0HB-01A	ENSG00000257315	ENSG00000230623	ZBED6	AC104461.1	TTGGAACTCAGTGAAGACACAGATGTTCCTGTTCAGAGCAACCAGCTAAT*TCTCTCTCTGCTGCTGTTCTCCCTCCTCCAGATATTTTCATTTCTTCTGC	lincrna,m4	BOWTIE+STAR	UTR/intronic	0	23	1	17	1	203803016	+	1	200472041	+	0.0089	2.2321	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0HB-01A	ENSG00000108395	ENSG00000108423	TRIM37	TUBD1	TCATTGCTCCAAACTGTGTTGTTTCAGCTGTATTAGG*AGCCTACATTCATCAGTACACAAAATTTGGAATCGAA	tcga,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	10	5	24	17	59104293	-	17	59860424	-	14.2985	7.7771	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A14P-01A	ENSG00000065135	ENSG00000031698	GNAI3	SARS	GAAAAAGCGGCCAAAGAAGTGAAGCTGCTGCTACTCG*GTAGATTTCGGGCAGACAACTTGAACAAGCTGAAGAA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	211	21	25	1	109548838	+	1	109223978	+	9.7407	53.8279	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-E2-A14P-01A	ENSG00000267023	ENSG00000267131	LRRC37A16P	AC005746.2	AGAACATTCTCAGGATGACTGTTGAATTGGAAAAACT*TTGGAGCTCAGAGAAGTTATGGCCCAAGATGGAAGAG	pseudogene,antisense,m41,exon-exon	BOWTIE	exonic(no-known-CDS)/exonic(no-known-CDS)	0	48	14	24	17	68140620	-	17	61367704	-	5.2681	10.2291	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	transcribed_unprocessed_pseudogene	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-E2-A14P-01A	ENSG00000267023	ENSG00000267131	LRRC37A16P	AC005746.2	CTTACAACAATTAAGAACATTCTCAGGATGACTGTTGAATTGGAAAAACT*CTAGGAAGTTGAGGAGCGAAGATGGGAGATATCAGAAGTGTTCAGCAAAG	pseudogene,antisense,m41	BOWTIE+BLAT;BOWTIE+STAR	exonic(no-known-CDS)/intronic	0	48	1	23	17	68140620	-	17	61364216	-	5.2681	10.2291	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	transcribed_unprocessed_pseudogene	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A14P-01A	ENSG00000108474	ENSG00000214946	PIGL	TBC1D26	GGATTCCACTCTCCAGTGTAATGATTATTGACAACAG*GCAGCAGGAATTATGTGACATCCTCGTGGCCTATTCT	tcga,18cancers,chimerdb3seq,m30,tcga-cancer,exon-exon	BOWTIE	in-frame	0	38	8	24	17	16234070	+	17	15740100	+	1.359	0.1037	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A14P-01A	ENSG00000153930	ENSG00000267023	ANKFN1	LRRC37A16P	GCTGGGAAGAGGTAAAGGGAGGCTGAGGCTGCCGCAT*AAGTTACCAAGGAAACTATATTTCCTACATTGATGGA	pseudogene,m9,exon-exon	BOWTIE	CDS(no-known-start-or-end)/exonic(no-known-CDS)	0	33	10	24	17	56046325	+	17	68147523	-	0.2952	5.2681	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	transcribed_unprocessed_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A14P-01A	ENSG00000153930	ENSG00000267023	ANKFN1	LRRC37A16P	AGCCCGTGCACAGGCTGGGAAGAGGTAAAGGGAGGCTGAGGCTGCCGCAT*GATATAAACTGTGTTTCTTCACAGAAGTTACCAAGGAAACTATATTTCCT	pseudogene,m9	BOWTIE+STAR	CDS(no-known-start-or-end)/intronic	0	33	4	23	17	56046325	+	17	68147547	-	0.2952	5.2681	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	transcribed_unprocessed_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A14P-01A	ENSG00000153930	ENSG00000267023	ANKFN1	LRRC37A16P	GCAACAGCAGCAGCAGCAGCGACTGGAGCCCGTGCACAGGCTGGGAAGAG*GATATAAACTGTGTTTCTTCACAGAAGTTACCAAGGAAACTATATTTCCT	pseudogene,m9	BOWTIE+STAR	CDS(no-known-start-or-end)/intronic	0	33	1	16	17	56046299	+	17	68147547	-	0.2952	5.2681	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	transcribed_unprocessed_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A14P-01A	ENSG00000092470	ENSG00000167004	WDR76	PDIA3	AAATGATAGAGAAGAGACAGCCTCCTAAATCCAAAAG*GTGTGGACACTGCAAGAGACTTGCACCTGAGTATGAA	cell_lines,chimerdb3seq,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	13	6	24	15	43836216	+	15	43753824	+	3.3196	185.6555	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A14P-01A	ENSG00000149798	ENSG00000014216	CDC42EP2	CAPN1	CTTGCTGTCCGCCGGTCTGCCGTCTGCGCGCCTCACG*CCACCTTCTGGGTGAACCCTCAGTTCAAGATCCGGCT	18cancers,100K<gap<200K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	9	4	21	11	65314954	+	11	65204683	+	0.0273	58.9638	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A14P-01A	ENSG00000136451	ENSG00000153930	VEZF1	ANKFN1	AGCCATGGAGGCCAACTGGACCGCGTTCCTGTTCCAG*AAGCCCAGCCGGTGGAAACTAACAGCCCCAAAGCCCT	exon-exon	BOWTIE	CDS(truncated)/CDS(no-known-start-or-end)	0	8	8	25	17	57988079	-	17	56046072	+	28.5067	0.2952	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A14P-01A	ENSG00000058056	ENSG00000121879	USP13	PIK3CA	AATAGCACTACCAAATATTGAGGAGTTACCAGCCCTG*GTACAGATGAAGTTTTTAGTTGAGCAAATGAGGCGAC	known,oncogene,tcga,cell_lines,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	7	2	19	3	179701129	+	3	179224081	+	15.6952	9.2689	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A14P-01A	ENSG00000177565	ENSG00000121879	TBL1XR1	PIK3CA	GGGAGGGGGGAGCGGCGTTGGAGGCCACCGTTTCCAG*GTTTCTGCTTTGGGACAACCATACATCTAATTCCTTA	known,oncogene,tcga,prostates,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	UTR/UTR	0	3	4	25	3	177197121	-	3	179198750	+	20.9308	9.2689	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A14P-01A	ENSG00000103404	ENSG00000277855	USP31	AC097634.3	GGGCCCTCTGGACCCTGGAGTACACCCCGCAGCACAGCCGCGACTTCAAG*TAGAGACGGGGTTTCTCCATGTTGGCCAGAATGGTCTTGAACTCCAGACC	antisense	BOWTIE+STAR	CDS(truncated)/intronic	0	2	2	22	16	23148638	-	3	71627638	+	3.2235	2.0905	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AN-A0AT-01A	ENSG00000241399	ENSG00000162551	CD302	ALPL	AAAACAGCTATCCCATACAAAAGGAAATATTTATCAG*GATTGGAACATCAGTTAACATCTGACCACTGCCAGCC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	20	9	25	2	159777938	-	1	21553978	+	0.4704	13.6747	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AN-A0AT-01A	ENSG00000241399	ENSG00000162551	CD302	ALPL	AAAACAGCTATCCCATACAAAAGGAAATATTTATCAG*AGAAAGAGAAAGACCCCAAGTACTGGCGAGACCAAGC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	20	1	13	2	159777938	-	1	21560626	+	0.4704	13.6747	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-AN-A0AT-01A	ENSG00000119820	ENSG00000173163	YIPF4	COMMD1	GAATAATATGAAGTAATCAGGAAATATCTATGCCTACAGAAGCAGCAACC*GAATCTGAATTTCTGTGTTTGGAATTTGATGAGGTCAAAGTCAACCAAAT	18cancers	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	20	7	22	2	32307190	+	2	62135831	+	4.7674	12.3027	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-AN-A0AT-01A	ENSG00000156639	ENSG00000112078	ZFAND3	KCTD20	AGCAAGACTATGAATCTCTGTTCCAAATGCTTTGCTG*GATTATTACAAAACCGGTATCATCAATTGTCCTGATG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	7	2	22	6	37929999	+	6	36479591	+	36.3957	38.8959	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Breast	TCGA-AN-A0AT-01A	ENSG00000156639	ENSG00000112078	ZFAND3	KCTD20	ACAGAAGTTTATTCTCTCACAGTTCTGGAGGCCAGAAGTCTAAAACCAAG*GATGTTTGGACCAGGAAGAGAGTACAACTTCACTCGGCCCAATGAGAAGG	tcga,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	7	1	15	6	37939219	+	6	36479121	+	36.3957	38.8959	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-AN-A0AT-01A	ENSG00000171877	ENSG00000126070	FRMD5	AGO3	GCTGCTGGACGACAGCGAGTACACCTGCACCATCCAG*GACCCGCTGGGGCCCAGCCCCTACTCATGGTGCCCAG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	4	2	21	15	44194953	-	1	35945692	+	0.0169	2.5971	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-AN-A0AT-01A	ENSG00000112186	ENSG00000232598	CAP2	AL122034.1	GCATTGCCGAGGACGGGACCCCAGGGCAGCGAAGCAG*GGCTTATGTCTGGGATCCTCACAGAGACTAGAAGTGT	lincrna,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	3	3	24	6	17393746	+	6	36940363	-	10.8515	2.7804	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AN-A0AT-01A	ENSG00000107186	ENSG00000147862	MPDZ	NFIB	CCGCGGGATTAAGTTTCTCAGTCACGC*CGCCCATAACCCAGGGAACTGGAGTCAACTTCCCAATTGGAGAAATCCCA	oncogene,tcga,18cancers,chimerdb3seq,cancer,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	3	4	25	9	13279564	-	9	14150265	-	3.1541	20.4213	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AN-A0AT-01A	ENSG00000107186	ENSG00000147862	MPDZ	NFIB	AGCTGAGAAATGGCAGACATGTTTTGTACTATCACCTCCGACAGCAGTTG*CGCCCATAACCCAGGGAACTGGAGTCAACTTCCCAATTGGAGAAATCCCA	oncogene,tcga,18cancers,chimerdb3seq,cancer,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	3	3	22	9	13265664	-	9	14150265	-	3.1541	20.4213	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-A8-A09X-01A	ENSG00000082781	ENSG00000254635	ITGB5	WAC-AS1	GGGCTTTGATGCAGTACTCCAGGCAGCCGTCTGCAAG*AGTCGTCCTTGTCTACTCCACTACCAAATGTTGAAGT	antisense,18cancers,chimerdb3seq,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	29	11	24	3	124841383	-	10	28526008	-	32.5331	29.6682	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A8-A09X-01A	ENSG00000138771	ENSG00000164687	SHROOM3	FABP5	ACTTAATGAAGTTTTATCTCCTATGTAAGAATATCAAAATTGTAGTTTGG*ACAGCACGCTGCCACGCCGACGCAGACCCCTCTCTGCACGCCAGCCCGCC	18cancers,m18	BOWTIE+BLAT	UTR/UTR	0	29	3	23	4	76780646	+	8	81280536	+	5.9141	2.5643	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A8-A09X-01A	ENSG00000112977	ENSG00000130340	DAP	SNX9	AGAAAGACAAGGATGACCAGGAATGGGAAAGCCCCAG*ATTTCCTGGATTTGCGAAACCTGGCACGGAACAGTAT	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	24	5	23	5	10748175	-	6	157906128	+	73.3137	19.0993	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A09X-01A	ENSG00000112977	ENSG00000130340	DAP	SNX9	TTGAAACAGCCCAAATGCTCATCAGCCAATGAGTGGAGAAACAAAACATG*ATTTCCTGGATTTGCGAAACCTGGCACGGAACAGTATTTGTTGGCCAAAC	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	24	1	24	5	10732546	-	6	157906128	+	73.3137	19.0993	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A09X-01A	ENSG00000130340	ENSG00000112977	SNX9	DAP	GTGCTAGTTCCTCATCCATGAAAATTCCCCTTAACAA*TCCACCTAAACCCACTGTGTTCATCTCTGGGGTCATC	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	24	9	25	6	157902045	+	5	10683571	-	19.0993	73.3137	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A09X-01A	ENSG00000130340	ENSG00000112977	SNX9	DAP	TCAGGCCAGTTCGTCGGCTGCCAGCAACAATCACCAG*TCCACCTAAACCCACTGTGTTCATCTCTGGGGTCATC	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	24	1	13	6	157875176	+	5	10683571	-	19.0993	73.3137	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A09X-01A	ENSG00000152601	ENSG00000000938	MBNL1	FGR	CAGCTGCTGCAGCTGCTGCACAGAAATTAATGCGAACAGACAGACTTGAG*CTGCCCTCTTTGGCAGATTCACCATCAAGTCAGACGTGTGGTCCTTTGGG	oncogene,cancer,tumor	BOWTIE+STAR	out-of-frame	0	3	1	17	3	152432920	+	1	27613314	-	11.5724	3.6291	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A8-A07B-01A	ENSG00000186566	ENSG00000182446	GPATCH8	NPLOC4	AAAAGAAGACACAGAAGAGCTGAGACAAAAGTACAAG*ATAATTCGTGTCCAGTCCCCGGATGGAGTGAAGCGGA	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	26	2	24	17	44435065	-	17	81629805	-	5.6041	20.6666	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A07B-01A	ENSG00000099256	ENSG00000204365	PRTFDC1	C10ORF126	AATGAAGGTTGATTTCATCAGACTAAAAAGTTACAGG*GTAAGCCTAGAATTGTACGATTGGAACTCAATGACGT	exon-exon	BOWTIE	in-frame	0	8	1	13	10	24937184	-	10	28873256	+	1.5768	NA	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-EW-A1P8-01A	ENSG00000143457	ENSG00000133019	GOLPH3L	CHRM3	ACAGAAACTGTCCAAACATGGATAGAGCTACTCACTG*AAAGAAGGACTTTGCTGCTTTGGGCCAGGATCTGAAC	exon-exon	BOWTIE	CDS(truncated)/UTR	0	5	2	24	1	150661814	-	1	239492709	+	19.7833	0.4478	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A14X-01A	ENSG00000147650	ENSG00000167632	LRP12	TRAPPC9	TCTGCGTTGCTCTTGCTTTTCCTCGCTGGGGTGTACG*ACCCTGGAAGCTGTCCTGAATTTCAAATACTCTGGAG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	74	9	24	8	104588819	-	8	140024079	-	7.8465	14.9822	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A14X-01A	ENSG00000147650	ENSG00000167632	LRP12	TRAPPC9	CATTCTGAAAATGTGCATATTTCAGGAGTGTCAACTG*ACCCTGGAAGCTGTCCTGAATTTCAAATACTCTGGAG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	74	8	24	8	104531907	-	8	140024079	-	7.8465	14.9822	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A0CM-01A	ENSG00000114416	ENSG00000144560	FXR1	VGLL4	GGTGGAGGTTCGCGGCTCTAACGGGGCTTTCTACAAG*GAACAAGACTGCCAATGGAGACTGCCGCAGAGACCCC	18cancers,chimerdb3seq,m10,exon-exon	BOWTIE	out-of-frame	0	16	3	23	3	180912736	+	3	11565019	-	13.3042	14.6588	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A0CM-01A	ENSG00000144560	ENSG00000114416	VGLL4	FXR1	AGGGCAGCATCTCTGGTGCATGCTGATGACGAAAAAC*GGATTTATCAAAGATGTTCATGAAGACTCCCTTACAG	18cancers,chimerdb3seq,m10,exon-exon	BOWTIE	out-of-frame	0	16	4	23	3	11702971	-	3	180933334	+	14.6588	13.3042	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A0CM-01A	ENSG00000101311	ENSG00000125885	FERMT1	MCM8	TATCAAACAGTGGAATGTAAACTGGGAAACCCGGCAG*GTGTTAACTAAGGACCTTGAAAGGCATGCAGCTGAGT	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	5	1	14	20	6079436	-	20	5957126	+	7.7651	1.3528	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04X-01A	ENSG00000143376	ENSG00000160710	SNX27	ADAR	ATACAAACATGTGGAGCAGAATGGTGAGAAGTTTGTG*GGGTATTCCCTCAGCGGATACTACACCCATCCATTTC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	25	5	22	1	151639119	+	1	154602626	-	2.8057	102.4733	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A04X-01A	ENSG00000268750	ENSG00000180532	AC010522.1	ZSCAN4	TCCGATGGCTGCGGCTGCGCCGAGGCGCCCTACTCAG*CTTGCAGTTTTAAAGAATCCACCAACTGTTGAAACAA	m10,100K<gap<200K,exon-exon	BOWTIE	CDS(no-known-start-or-end)/UTR	0	15	9	24	19	57819945	+	19	57676041	+	0	18.2988	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04X-01A	ENSG00000268750	ENSG00000180532	AC010522.1	ZSCAN4	GTGACTCTGGAGAACCTGGCACTTATGTCCTCCCTGG*CTTGCAGTTTTAAAGAATCCACCAACTGTTGAAACAA	m10,100K<gap<200K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	15	2	19	19	57839149	+	19	57676041	+	0	18.2988	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04X-01A	ENSG00000268750	ENSG00000180532	AC010522.1	ZSCAN4	AGACTCTTGGAGCCAGAAGCTACATGACCCCTAAACG*CTTGCAGTTTTAAAGAATCCACCAACTGTTGAAACAA	m10,100K<gap<200K,exon-exon	BOWTIE	UTR/UTR	0	15	2	18	19	57820549	+	19	57676041	+	0	18.2988	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A04X-01A	ENSG00000198466	ENSG00000180532	ZNF587	ZSCAN4	TCCGATGGCAGCGGCTGTGCCGAGGCGCCCAACTCAG*CTTGCAGTTTTAAAGAATCCACCAACTGTTGAAACAA	chimerdb3seq,m2,100K<gap<200K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	13	11	24	19	57850071	+	19	57676041	+	5.147	18.2988	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A04X-01A	ENSG00000176658	ENSG00000141298	MYO1D	SSH2	ATACATGAATGTCCTCTTTTCCTGTCACGTCCGTAAG*AGCTCTCATTTGGAAGACAGTGAATCAGCAGCATTAC	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	4	4	25	17	32653843	-	17	29848929	-	16.8825	1.6407	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A04X-01A	ENSG00000176658	ENSG00000141298	MYO1D	SSH2	AACGGAAGGACAAATACATGAATGTCCTCTTTTCCTGTCACGTCCGTAAG*CTTCAAAAAGCTATACTGAGGGATATGCCAAGTCATAATGCATATTACCT	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	4	1	21	17	32653843	-	17	29827714	-	16.8825	1.6407	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0BW-01A	ENSG00000100345	ENSG00000166862	MYH9	CACNG2	GAAGCAGCGCCTGTTCCCGGGGCAGATCCAGGTTCAG*GGGCCGTGAGGGCCTCCAGCATTTTCCCAATCCTGAG	cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	115	18	25	22	36387807	-	22	36566493	-	123.9167	9.7358	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0BW-01A	ENSG00000100345	ENSG00000166862	MYH9	CACNG2	AGTCCTCTCGGGAGAAGCAGCGCCTGTTCCCGGGGCAGATCCAGGTTCAG*ACGGAGTCTCACTCTGTCGCCAGACTGGAGCGCGGTGGCATGATCTCGGC	cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	115	1	17	22	36387807	-	22	36577645	-	123.9167	9.7358	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0BW-01A	ENSG00000256248	ENSG00000128513	AC134511.1	POT1	ATCCCTATCTGCTTGCAGGCAGAGGAGCAGGAGAGAG*GTTGGAAGCTTTCTTAGAATCTATAGCCTTCATACCA	lincrna,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	13	5	22	12	67069050	-	7	124853138	-	NA	4.7539	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0BW-01A	ENSG00000143179	ENSG00000135829	UCK2	DHX9	GCTGATGTGATCATCCCTAGAGGTGCAGATAATCTGG*CGTGGGAGATGCTATCTGTACCATTGCTGCTGCTACC	18cancers,cancer,exon-exon	BOWTIE	out-of-frame	0	7	2	22	1	165905969	+	1	182881264	+	4.9754	54.4087	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0BW-01A	ENSG00000143179	ENSG00000135829	UCK2	DHX9	GCTGATGTGATCATCCCTAGAGGTGCAGATAATCTGG*ATTGTTTGTTGACACAAGTGTTTACTAACACTGGACC	18cancers,cancer,exon-exon	BOWTIE	in-frame	0	7	1	14	1	165905969	+	1	182883139	+	4.9754	54.4087	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Breast	TCGA-BH-A0BW-01A	ENSG00000112658	ENSG00000234753	SRF	FOXP4-AS1	AGCACAGACCTCACGCAGACCTCCTCCAGCGGGACAG*GTCATTCCGGACTCCTGACGCCGCCAGTCCCGCGGTG	antisense,18cancers,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	5	4	22	6	43176667	+	6	41524225	-	17.8861	0.9945	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-E2-A1LG-01A	ENSG00000123124	ENSG00000080618	WWP1	CPB2	TTGGCAAAGACACTTGGTTACCAAGAAGCCATACATG*TGGCCAAGTTCTAGCTGCTCTTCCTAGAACCTCTAGG	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	108	17	25	8	86461846	+	13	46087820	-	19.4485	7.2386	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-E2-A1LG-01A	ENSG00000123124	ENSG00000080618	WWP1	CPB2	TGCATTGAAAAAGTTGGCAAAGACACTTGGTTACCAAGAAGCCATACATG*AGAAATTTGTTGTACAGAAAATTGCTGTTGGGATGAAGCTTTGCAGCCTT	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	108	2	19	8	86461846	+	13	46105041	-	19.4485	7.2386	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-E2-A1LG-01A	ENSG00000123124	ENSG00000080618	WWP1	CPB2	GTGTATATAAGCTGTTCATTCTGTACAGTGAATTTTCCGAACCTCTCAAA*TGGCCAAGTTCTAGCTGCTCTTCCTAGAACCTCTAGGCAAGTTCAAGTTC	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	108	1	23	8	86467010	+	13	46087820	-	19.4485	7.2386	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A1LG-01A	ENSG00000160218	ENSG00000185658	TRAPPC10	BRWD1	GTGATCTACACCATGGAGAACAAGCCCATCGTCACCT*GTGATGGAGAGGTGATTGAACAAATTATAAGCCTGCA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	35	18	25	21	44012560	+	21	39258672	-	5.4263	11.6583	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A1LG-01A	ENSG00000184939	ENSG00000039068	ZFP90	CDH1	CCCAGCTAGCCATCTTCTAATTTTCATTCCTTCAAAG*TGAATTTTGAAGATTGCACCGGTCGACAAAGGACAGC	oncogene,18cancers,cancer,100K<gap<200K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	14	3	24	16	68533855	+	16	68801670	+	0.267	7.4042	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A1LG-01A	ENSG00000184939	ENSG00000039068	ZFP90	CDH1	AGGAATGGCCCCGAGGCCTCCGACCGCCGCGCCCCAG*TGAATTTTGAAGATTGCACCGGTCGACAAAGGACAGC	oncogene,18cancers,cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	14	3	21	16	68539825	+	16	68801670	+	0.267	7.4042	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-E2-A1LG-01A	ENSG00000197077	ENSG00000244752	KIAA1671	CRYBB2	GATCTCACCTAGGATGATCACCTCAACCTCCCAAGTAGCTGGGACTACAG*CTGGGTGGGCTATGAACAGGCCAACTGCAAGGGCGAGCAGTTTGTGTTTG	known,18cancers,10K<gap<100K	BOWTIE+STAR	intronic/CDS(truncated)	0	2	3	23	22	25118431	+	22	25227853	+	63.6282	1.1746	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-E2-A1LG-01A	ENSG00000197077	ENSG00000244752	KIAA1671	CRYBB2	AGACAGCACTTCAGGCTGGGAAAGGAGCCAGGCTGCCCAGAAACGTCCAT*GTCATTCCTGCACAGGACAGTCCACCATGGCCTCAGATCACCAGACCCAG	known,18cancers,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	UTR/UTR	0	2	1	24	22	25192668	+	22	25221404	+	63.6282	1.1746	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-E2-A1LG-01A	ENSG00000197077	ENSG00000244752	KIAA1671	CRYBB2	AGACAGCACTTCAGGCTGGGAAAGGAGCCAGGCTGCCCAGAAACGTCCAT*GAGCACAGCGGTCACTCATCTTGGCACCGGCACTTCTGGGGAAGGTATAA	known,18cancers,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	UTR/UTR	0	2	1	21	22	25192668	+	22	25219563	+	63.6282	1.1746	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AO-A0J2-01A	ENSG00000160305	ENSG00000275778	DIP2A	AC018630.6	CGGCCCACCGCCTCGAGGGATGAGCGCTTCCGGTCAG*ATGTGAACTATGAAGACTTTACTTTCACCATACCAGA	m310,exon-exon	BOWTIE	CDS(truncated)/UTR	0	314	22	25	21	46490719	+	12	10848407	-	2.8494	0	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AO-A0J2-01A	ENSG00000160305	ENSG00000231887	DIP2A	PRH1	CGGCCCACCGCCTCGAGGGATGAGCGCTTCCGGTCAG*GAAGTGAATAAGAAGATAACAGTGTTTCAAATGCCGT	tcga,18cancers,chimerdb3seq,m9,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	10	5	24	21	46490719	+	12	10881056	-	2.8494	0.0791	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-AO-A0J2-01A	ENSG00000188994	ENSG00000112367	ZNF292	FIG4	GGAAGCGGCCACCGACTACTGTCAGCAGCTGTGCCAG*ATGCCGATAGACAAGATTCCATTAATCTCTTCCTGGG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	9	4	25	6	87155759	+	6	109776922	+	0.7092	0.8629	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AO-A0J2-01A	ENSG00000188994	ENSG00000112367	ZNF292	FIG4	GGAAGCGGCCACCGACTACTGTCAGCAGCTGTGCCAG*AATGTGGTCCAACCCATGAAGGAGCTATATGGAATTA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	9	2	25	6	87155759	+	6	109792582	+	0.7092	0.8629	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AO-A0J2-01A	ENSG00000188994	ENSG00000112367	ZNF292	FIG4	GGAAGCGGCCACCGACTACTGTCAGCAGCTGTGCCAG*TTATACTTACTGGTGGACACCAGAGGTGATAAAGCAT	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	9	2	24	6	87155759	+	6	109784970	+	0.7092	0.8629	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AO-A0J2-01A	ENSG00000188994	ENSG00000112367	ZNF292	FIG4	CCTGCTTGGTCGCCCCGCAGCTCAAACCCCTAGGGCGAGCATGCAGACAG*ATGCCGATAGACAAGATTCCATTAATCTCTTCCTGGGAGTTTTCCATCCC	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	9	1	16	6	87180989	+	6	109776922	+	0.7092	0.8629	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AO-A0J2-01A	ENSG00000188994	ENSG00000112367	ZNF292	FIG4	GGAAGCGGCCACCGACTACTGTCAGCAGCTGTGCCAG*AACACCCATCTCGGCTTTCTCGCAAGATAACATCTAT	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	9	1	13	6	87155759	+	6	109825088	+	0.7092	0.8629	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-B6-A0I6-01A	ENSG00000145996	ENSG00000112183	CDKAL1	RBM24	CATGACAAATCCGCCCTATATTTTAGAGCATCTGGAG*GATACCTGCCCACTATGTCTATCCGCAGGCTTTTGTG	18cancers,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	26	6	25	6	20955585	+	6	17291756	+	14.5665	5.6446	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-B6-A0I6-01A	ENSG00000160972	ENSG00000173137	PPP1R16A	ADCK5	GGTGCCATCAGGCACATGAACGGTGGAGTCTTCAAAG*GTCTCTGAAGGTCGGCCTGCAGATCTCCCTGGACTAC	tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	19	4	22	8	144490212	+	8	144390671	+	6.8375	9.5204	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-B6-A0I6-01A	ENSG00000160972	ENSG00000173137	PPP1R16A	ADCK5	GGTGCCATCAGGCACATGAACGGTGGAGTCTTCAAAG*ACCTTGCCTCCCCAGGCCTTGGAGACCCACCCTCCTG	tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	19	2	23	8	144490212	+	8	144389263	+	6.8375	9.5204	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-B6-A0I6-01A	ENSG00000107829	ENSG00000198408	FBXW4	MGEA5	ACCGAGTCTGGTCCATTGCTATCAGCCCATTACTCAG*GGTGTCGTAGTCATTCTTCAGCACAATTCTTAATTGG	18cancers,cancer,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	12	4	19	10	101667886	-	10	101793998	-	8.4922	23.9744	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0I6-01A	ENSG00000107829	ENSG00000198408	FBXW4	MGEA5	ATCCAGACTGAAGACCGAGTCTGGTCCATTGCTATCAGCCCATTACTCAG*GGTTTATCTCTGCACTGAGCATTTATGGTGGTAGCTTTCCAAAATTATAT	18cancers,cancer,tcga-cancer,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	12	1	19	10	101667886	-	10	101795971	-	8.4922	23.9744	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0I6-01A	ENSG00000165804	ENSG00000092199	ZNF219	HNRNPC	CGCCGCCGCCCGCTCCGCCGCCGCCCGCCCGGGGCTC*TTTTCGGCTTTGTGAGAAACCTTACCATCAAACACGA	18cancers,chimerdb3seq,m10,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	UTR/UTR	0	12	22	25	14	21098312	-	14	21234229	-	4.0312	67.6914	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-B6-A0I6-01A	ENSG00000165804	ENSG00000092199	ZNF219	HNRNPC	TGGGGCAGAAAGAGCGGCAGAGCCAACTCCTTCCCTG*TTTTCGGCTTTGTGAGAAACCTTACCATCAAACACGA	18cancers,chimerdb3seq,m10,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	12	4	22	14	21098811	-	14	21234229	-	4.0312	67.6914	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-B6-A0I6-01A	ENSG00000165804	ENSG00000092199	ZNF219	HNRNPC	AGGCGAACAGCCATCCCGGGCACTATGTGAATTTGGG*TTTTCGGCTTTGTGAGAAACCTTACCATCAAACACGA	18cancers,chimerdb3seq,m10,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	UTR/UTR	0	12	3	23	14	21104511	-	14	21234229	-	4.0312	67.6914	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-B6-A0I6-01A	ENSG00000165804	ENSG00000092199	ZNF219	HNRNPC	CTCCCCCCTCCCGGAGGGGGGGCCCGCTCAGCGCGCCCGGCTCGGAGCAG*TTTTCGGCTTTGTGAGAAACCTTACCATCAAACACGATGGCCAGCAACGT	18cancers,chimerdb3seq,m10,tcga-cancer,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	intronic/UTR	0	12	1	21	14	21098197	-	14	21234229	-	4.0312	67.6914	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-B6-A0I6-01A	ENSG00000228144	ENSG00000100138	AC078927.1	SNU13	ACCCAAACATTGCCAAGAGAAAATGCAATGTGAGGTAAAAGATGAAAAAG*ATGTTCAAGAGATAGCAACTGTGGTGGTACCCAAACATTGCCAAGAGAAA	m5	BOWTIE+STAR	UTR/intronic	0	6	1	21	12	66128896	-	22	41676998	-	0	50.1898	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0I6-01A	ENSG00000106554	ENSG00000153157	CHCHD3	SYCP2L	TGGAGCAAGCCAAGAAAGAATCCGAAGATCAGAAACG*ATTATGACCAGCAGGTTGCTATTTCTGAAGCGCTGTG	exon-exon	BOWTIE	in-frame	0	6	1	14	7	133024546	-	6	10907542	+	22.3984	1.0567	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0I6-01A	ENSG00000170502	ENSG00000138640	NUDT9	FAM13A	AAAAAGGAAAGACTGTGGAGAATGGGCAATCCCAGGG*ATGGCAGAAATGATGTTCAGGAGAGTAGCTTAAGAGA	18cancers,exon-exon	BOWTIE	out-of-frame	0	5	4	23	4	87449253	+	4	88991150	-	3.6532	0.9124	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0I6-01A	ENSG00000105321	ENSG00000274272	CCDC9	AC069281.2	CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGCGC*GCGCGCGCGCGCGCGTCTGCTCCGCGTGTTGGTGGCTGTGGCCATGGCTC	NA	BOWTIE+BLAT	UTR/exonic(no-known-CDS)	0	3	2	24	19	47271738	+	7	100574633	-	16.1441	0.0312	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0I6-01A	ENSG00000107338	ENSG00000137449	SHB	CPEB2	AGCCGCGGAGGAGAGCGGGGCCGGCAAGAAGGACAAG*GCTATGCATTTCTTCTCTTTCAAGAAGAGAGCTCAGT	tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	3	2	17	9	38067929	-	4	15058421	+	2.4338	2.5549	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0I6-01A	ENSG00000262583	ENSG00000166822	AC009163.5	TMEM170A	CCCAGGGATTTTCCTGGACGGGATTGTGAAGTAGCGG*AGATGTGGTATGGTGTATTCCTGTGGGCACTGGTGTC	pseudogene,10K<gap<100K,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	2	1	14	16	75516203	-	16	75451839	-	0.634	6.8571	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	transcribed_unprocessed_pseudogene	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0I6-01A	ENSG00000049245	ENSG00000204624	VAMP3	DISP3	CAAGTTGAAGAGGAAATATTGGTGGAAGAATTGCAAG*ACTATGGACACGGAGGATGACCCCTTGCTGCAGGATG	exon-exon	BOWTIE	CDS(truncated)/UTR	0	2	2	24	1	7777318	+	1	11500990	+	19.3127	1.443	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0I6-01A	ENSG00000049245	ENSG00000204624	VAMP3	DISP3	AAACGAGCGCAGCCAAGTTGAAGAGGAAATATTGGTGGAAGAATTGCAAG*GTTGCTGTGAATGCTGTTAATTCATTTGTCCAGGGGAAAGTTCTATTGAA	NA	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	19	1	7777318	+	1	11497815	+	19.3127	1.443	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A1LL-01A	ENSG00000184402	ENSG00000179242	SS18L1	CDH4	AGGCAAAGGGGAGGTTACGCAGCAAACCATCCAGAAG*AAAGTTCAGCAGTACACAGTCATCGTTCAGGCCACAG	tcga,cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	95	14	25	20	62143889	+	20	61894910	+	3.768	21.3685	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A1LL-01A	ENSG00000006831	ENSG00000065970	ADIPOR2	FOXJ2	TTTAGAGGCATCTGTTCTATCTTCCCATCATAAAAAA*GGCACAGGATCTGTGGATGGTGGAGCAGTGGCAGCAG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	57	11	25	12	1754514	+	12	8044760	+	17.8435	21.1264	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A1LL-01A	ENSG00000111731	ENSG00000123104	C2CD5	ITPR2	TTTAAGACAACAGACTCAATCAGCGTTGGAACAGAGG*GAGAAGAATTTGGATTGGTTTCCTCGGATGCGAGCCA	tcga,cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	57	10	25	12	22513294	-	12	26340328	-	4.66	5.6919	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A1LL-01A	ENSG00000171723	ENSG00000258670	GPHN	AL049874.3	ATACAAGATAGTACCAGATGAAATAGAAGAAATCAAG*GGCAGGAACCAGACAGAAATGGATGGCCGCTTGTTGG	antisense,cancer,m41,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	42	6	24	14	66776521	+	14	60554235	+	4.1191	3.5056	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A1LL-01A	ENSG00000196233	ENSG00000139117	LCOR	CPNE8	AAGGGCTTAACTCATATATTTAACCCCCCTCCAAAAA*GACGCAAATCAATTTCACAGTGGCTATTGATTTTACA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	31	13	25	10	96833479	+	12	38702921	-	0.8074	8.946	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A1LL-01A	ENSG00000196233	ENSG00000139117	LCOR	CPNE8	AATTATGCAAATCCTGCTTTCTGGTGTCCATTCAGCGGCAATTTCATGCG*GACGCAAATCAATTTCACAGTGGCTATTGATTTTACAGCATCAAACGGTG	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	31	2	15	10	96833841	+	12	38702921	-	0.8074	8.946	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A1LL-01A	ENSG00000196233	ENSG00000139117	LCOR	CPNE8	GCGGCTTTCGGCAAGAACTGGATTCGTGGCGCCACAAGCTCATTCACTGT*GACGCAAATCAATTTCACAGTGGCTATTGATTTTACAGCATCAAACGGTG	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	UTR/CDS(truncated)	0	31	1	14	10	96832395	+	12	38702921	-	0.8074	8.946	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A1LL-01A	ENSG00000139921	ENSG00000258955	TMX1	LINC00519	AAAAGGCGCAGACCACAGCCGTACCCATACCCTTCAA*GGTCTTGATCAGGCTGGAGTGCAGTGACATAATCACA	lincrna,18cancers,m15,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	26	2	24	14	51249765	+	14	51304840	-	14.8637	2.7992	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A1LL-01A	ENSG00000111348	ENSG00000257599	ARHGDIB	OVCH1-AS1	AAGAAAACGCTGCTGGGAGATGGTCCTGTGGTGACAG*GTGATCAAAATGGAACACAATTGCTACCAGAAGAGAA	antisense,18cancers,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	18	3	20	12	14950532	-	12	29486886	+	41.0707	0.3089	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A1LL-01A	ENSG00000111348	ENSG00000257599	ARHGDIB	OVCH1-AS1	TCTAATTAAGTACAAGAAAACGCTGCTGGGAGATGGTCCTGTGGTGACAG*CCAGACTCCCACAACCTGACCCTGTGGAAGCATTGGGGAAATTCAAAGTG	antisense,18cancers	BOWTIE+STAR	CDS(truncated)/intronic	0	18	2	19	12	14950532	-	12	29477212	+	41.0707	0.3089	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A1LL-01A	ENSG00000143033	ENSG00000137942	MTF2	FNBP1L	TATGAAGCGGTTGGCACCACTGAAGTGACCGAATGAG*AAATCTGGTTAAGAAGTACTGCCCCAAACGTTCATCC	18cancers,exon-exon	BOWTIE	in-frame	0	17	5	23	1	93079531	+	1	93522082	+	3.1495	17.5538	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A1LL-01A	ENSG00000139132	ENSG00000069431	FGD4	ABCC9	CCAGCAAAACACTCAGCTGCAAGTCCAAAGCCACAAG*TGTTCAAAAGCTGAATGAGTTTCTCTTGAGTGATGAG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	14	7	24	12	32564289	+	12	21887934	-	0.8262	2.5254	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A1LL-01A	ENSG00000117115	ENSG00000159363	PADI2	ATP13A2	CTTCCAGTACCTAAACCGAGGCGATCGCTGGATCCAG*GTCCTGGAGGAAGAGCCGGCTGCAGACTCAGCATTTG	oncogene,18cancers,cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	13	5	25	1	17083726	-	1	16992581	-	6.0369	7.8913	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A1LL-01A	ENSG00000136866	ENSG00000233086	ZFP37	AL358975.1	GGAGATGGCTGTGTCCGAGCCCGAGGCCAGCGCCGCG*GCTTCTTCATCAGCCCTAACCCTGCCAACCACTCCTG	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	11	4	23	9	113056557	-	9	79518448	-	0.4703	0.7371	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A1LL-01A	ENSG00000166949	ENSG00000137764	SMAD3	MAP2K5	ACCCACACTCGGGCCTGTGTTGAGCAACCACGTTTGA*ATGAAGATGAAGATGGTGATCGAATTACAGTGAGAAG	prostates,18cancers,cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	10	8	24	15	67125984	+	15	67563283	+	6.2482	4.0746	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A1LL-01A	ENSG00000166949	ENSG00000137764	SMAD3	MAP2K5	CGCAGAACGTCAACACCAAGTGCATCACCATCCCCAG*ATGAAGATGAAGATGGTGATCGAATTACAGTGAGAAG	prostates,18cancers,cancer,exon-exon	BOWTIE	out-of-frame	0	10	2	21	15	67066360	+	15	67563283	+	6.2482	4.0746	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A1LL-01A	ENSG00000112308	ENSG00000137261	C6ORF62	KIAA0319	GTGGAAAGAATCTGATGAGCCTTTTAGGCCTGTTCAG*TTCTTGAGGCCAAATCTGGCTCCTAAAAAACATCAAA	18cancers,chimerdb3seq,10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	9	4	25	6	24714318	-	6	24601208	-	53.5592	4.6993	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A1LL-01A	ENSG00000112308	ENSG00000137261	C6ORF62	KIAA0319	TCCTGTTTTCTAGGTGGAAAGAATCTGATGAGCCTTTTAGGCCTGTTCAG*CTTTACGAAGGTATAATTGACAAATAAAAATTGGCTGTATTTACCAGGAA	18cancers,chimerdb3seq,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	9	2	21	6	24714318	-	6	24639086	-	53.5592	4.6993	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A1LL-01A	ENSG00000072415	ENSG00000072042	MPP5	RDH11	GCCGGGGCGGGAGGCTCCGCGGAGCCGAGGCGTGGAG*GCTCTGGCGTTACGACGTATTCTGTACACCCTGGCAC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	9	7	23	14	67241533	+	14	67685204	-	2.8988	28.7942	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A1LL-01A	ENSG00000118971	ENSG00000118307	CCND2	CASC1	CTTGTGATGCCCTGACTGAGCTGCTGGCTAAGATCACCAACACAGACGTG*GGAAAAAATGAAACTAGTGTCACTTTCTTCATCAATTATAAAGGTAAACA	18cancers,cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	7	6	24	12	4288990	+	12	25114913	-	17.1453	1.2381	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A1LL-01A	ENSG00000197905	ENSG00000111731	TEAD4	C2CD5	TAGCGCACCCATCCCACCTTCCCGCACCCTGGGACCG*ATGAACCAGAAACTCGAGATGCATGGTGGGCAGAAAT	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	7	5	25	12	2960040	+	12	22493337	-	8.823	4.66	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A1LL-01A	ENSG00000101040	ENSG00000161082	ZMYND8	CELF5	GTGGTAGAGGGCATGGATATCTCTACTCGCTCCAAAG*GCTGTGCCTTCCTCACCTACTGTGCCAGGGATTCCGC	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	6	1	14	20	47347856	-	19	3250985	+	5.629	0.8757	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-E2-A1LL-01A	ENSG00000133424	ENSG00000100612	LARGE1	DHRS7	TTCCCCTGACAAAACCATCTGCATTCCTGACTTCCCCTTTACTTTCAAAG*CCACTGGAGGGAGAAATGGAAAACATGAAAACAGCAATCTTCTTATGCTT	NA	BOWTIE+STAR	intronic/CDS(truncated)	0	4	1	16	22	33570325	-	14	60144942	-	1.3042	34.7103	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A1LL-01A	ENSG00000102908	ENSG00000262136	NFAT5	AC092115.3	TGCTGGAAGATCTCATGATGTTCAACCATTCACTTACACTCCAGACCCAG*GCAGCCAGGCGCTCCGGTGCTCACAGGCCATGGGACAGTCCAGTTCCCTG	antisense,cancer,10K<gap<100K	BOWTIE+STAR	CDS(truncated)/intronic	0	4	1	16	16	69677335	+	16	69742127	+	1.6275	0.9919	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A1LL-01A	ENSG00000136643	ENSG00000248550	RPS6KC1	OTX2-AS1	AGCTCACTCAGATTCCCTCATTGATACCTTTCCTGAGTGTAGTACGGAAG*GCATCCCAGACACAGGAAATTTTGACCGAGTTTGTGCCTTCACACAGTGC	lincrna,ribosomal,18cancers	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	3	2	24	1	213117410	+	14	57068510	+	9.4808	0.0152	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A1LL-01A	ENSG00000136643	ENSG00000248550	RPS6KC1	OTX2-AS1	AGCTCACTCAGATTCCCTCATTGATACCTTTCCTGAGTGTAGTACGGAAG*CAGGCACAAGAGCAAGAATATGGGCCAGGCGCAGCGGCTCACACCTGTAA	lincrna,ribosomal,18cancers	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	3	1	19	1	213117410	+	14	57069436	+	9.4808	0.0152	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-E2-A1LL-01A	ENSG00000151067	ENSG00000134531	CACNA1C	EMP1	GCAACATGAAGCCTAGGCGTGCCCTGAGTCACCACACTGCACATTGCAAG*GTCTGGTTGGTTTCCAATACGGTAGATGCATCAGTAGGTCTTTGGAAAAA	cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	19	12	2214619	+	12	13213479	+	0.2306	15.716	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-E2-A1LL-01A	ENSG00000127947	ENSG00000006576	PTPN12	PHTF2	ACATGATTCAGGGAGCTAGAAGACACTTTAAGTTATACTGGAAAATTCAG*TGTCTTCTTTTCATAGATTGGAGCATATGATCAACAAATATGGGAAAAAT	18cancers,chimerdb3seq,100K<gap<200K	BOWTIE+STAR	UTR/intronic	0	2	1	23	7	77639324	+	7	77893592	+	29.1028	3.7695	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A0D2-01A	ENSG00000134759	ENSG00000166974	ELP2	MAPRE2	ACTTTTTGCTCCATGGAAGAGAAAAGACCAATCACAG*GTAATTCCAGTGGAGAAGCTAGTGAAAGGACGTTTCC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	149	20	25	18	36154999	+	18	35101946	+	18.198	36.8769	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A0D2-01A	ENSG00000105983	ENSG00000155093	LMBR1	PTPRN2	CTTTCTGGAATCAGAAGGCTTTGCTGGCCTGAAAAAG*GTGCTAAAGAGATTGATATCGCAGCGACCCTGGAGCA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	113	20	25	7	156796389	-	7	157549019	-	6.3582	4.6686	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A0D2-01A	ENSG00000105983	ENSG00000155093	LMBR1	PTPRN2	CACCATAGAAACATGACAGCTTCTCCATAGAGCTTTT*GTGCTAAAGAGATTGATATCGCAGCGACCCTGGAGCA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	113	2	25	7	156779655	-	7	157549019	-	6.3582	4.6686	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A0D2-01A	ENSG00000196182	ENSG00000198625	STK40	MDM4	GCCACTCCCTGCCCCCAGCCTGGCTGGACAGCAAGGAATCCACAGCCCAC*ATGGCACCACTGCAATCCAAGGTGGGTGACAGAGACGCTGTCTCAAAGAA	known,oncogene,tcga,18cancers,cancer	BOWTIE+BLAT	UTR/UTR	0	30	2	25	1	36341099	-	1	204556648	+	15.8254	3.8082	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A0D2-01A	ENSG00000113441	ENSG00000153113	LNPEP	CAST	AGCCGCGGCGGGGGGAAAATGGAGCCCTTCACCAATG*CATGTCAGTGAAAAAACCAGTGAATCGCCTTCCAAAC	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	26	11	25	5	96936174	+	5	96675539	+	3.2906	18.0467	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A0D2-01A	ENSG00000162032	ENSG00000162039	SPSB3	MEIOB	AGGCTCCACTAACTGGGGCTACGACTCTGATGGGCAG*AAAGTTATCGGTATAGTTATTGGGAAAACAGATGTCA	tcga,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	26	4	24	16	1781358	-	16	1865835	-	0.0603	7.1172	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A0D2-01A	ENSG00000162032	ENSG00000162039	SPSB3	MEIOB	AGGCTCCACTAACTGGGGCTACGACTCTGATGGGCAG*ATATTGGATCAGAAAGGTACACTTTCAGCTTCACCAT	tcga,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	26	3	24	16	1781358	-	16	1862116	-	0.0603	7.1172	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A0D2-01A	ENSG00000162032	ENSG00000162039	SPSB3	MEIOB	CCGTGGCTCTAGCAGGCTCCACTAACTGGGGCTACGACTCTGATGGGCAG*GCACGGTGGCTCATGCCAGCACTTTGGGAGGCTGAGGCAGGCAGATCACG	tcga,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K	BOWTIE+STAR	CDS(truncated)/intronic	0	26	1	16	16	1781358	-	16	1863668	-	0.0603	7.1172	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A0D2-01A	ENSG00000228065	ENSG00000148655	LINC01515	LRMDA	CCACCAGCAATATCCACCTGTATTTGTCTTTTCATAA*GTGTCCTGGGGAAGTGTCGCTACGTTTACTATGGGAA	lincrna,18cancers,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	25	7	24	10	65585802	+	10	76557209	+	0.4428	0.3159	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A0D2-01A	ENSG00000173531	ENSG00000100104	MST1	SRRD	CACTGAGGGACTGTTGGCCCCTGTGGGGGCCTGTGAG*AAACCATCAATAGATGTCTCACAAAACATCTGGAACA	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	14	6	25	3	49684314	-	22	26488029	+	0.2132	5.4568	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	FALSE	Breast	TCGA-A2-A0D2-01A	ENSG00000100104	ENSG00000173531	SRRD	MST1	GACCTGTTTATCTCTGATTTCTGGAGTTCAGCACTAG*ATCTGTGACCCTGAACCAGCGTGTGGCCCTGATCTGC	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	14	2	18	22	26486063	+	3	49684656	-	5.4568	0.2132	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A0D2-01A	ENSG00000009413	ENSG00000010810	REV3L	FYN	GGGACAGCAATATTGAAGAACATTGTGCCAAAAAGAG*GACCAGTCCTGCCTCTGTTGTAGAAGACATGTGGTGT	oncogene,tcga,prostates,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	10	2	24	6	111379982	-	6	111780635	-	4.997	5.4851	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A0D2-01A	ENSG00000009413	ENSG00000010810	REV3L	FYN	CCTTTGACCCAAAGACTGAGTGAGTCACCTGTTTTCA*GACCAGTCCTGCCTCTGTTGTAGAAGACATGTGGTGT	oncogene,tcga,prostates,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	10	2	20	6	111381325	-	6	111780635	-	4.997	5.4851	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A0D2-01A	ENSG00000106609	ENSG00000273142	TMEM248	AC073335.2	TTTGTAAAGATTGTGGCTTCCGCCTGAACTGCTTCTTTCCTGCCTCAAAG*GCCCACCTCCTGCCTTCCAGTAGCGTCTACAAGTTTGGCTCCTGCCTCCC	lincrna,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	UTR/exonic(no-known-CDS)	0	5	7	22	7	66922246	+	7	66905658	+	35.6413	2.9873	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A0D2-01A	ENSG00000106609	ENSG00000273142	TMEM248	AC073335.2	CCCTTGCCCAGTACTGAAGAACCTTTGAAGCCATTCACACAGGATGCCAT*GCCCACCTCCTGCCTTCCAGTAGCGTCTACAAGTTTGGCTCCTGCCTCCC	lincrna,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	intronic/exonic(no-known-CDS)	0	5	4	22	7	66924334	+	7	66905658	+	35.6413	2.9873	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A0D2-01A	ENSG00000106609	ENSG00000273142	TMEM248	AC073335.2	GGTTTTGAACTCCTGACCTCGTGATCCGCCCGCCTTGGCCTCTCAAAGTG*CTCATGTTTACCTCACCAGGCCCACCTCCTGCCTTCCAGTAGCGTCTACA	lincrna,10K<gap<100K	BOWTIE+BLAT	intronic/exonic(no-known-CDS)	0	5	1	22	7	66924974	+	7	66905639	+	35.6413	2.9873	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A0D2-01A	ENSG00000162851	ENSG00000185420	TFB2M	SMYD3	CTGGCAATTAGCTTGTGAGATTAAGGTTCTGCACATG*AAAAAAGCTTGGCCAGACCACAAGCGGGAATGCAAAT	tcga,chimerdb3seq,cancer,m2,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	4	3	14	1	246551213	-	1	246335474	-	17.904	4.6772	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A0D2-01A	ENSG00000162851	ENSG00000185420	TFB2M	SMYD3	GCTCGAAAGTGACAAAACTTTTATTCCACATTTGGAG*AAAAAAGCTTGGCCAGACCACAAGCGGGAATGCAAAT	tcga,chimerdb3seq,cancer,m2,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	4	2	17	1	246564346	-	1	246335474	-	17.904	4.6772	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A0D2-01A	ENSG00000162851	ENSG00000185420	TFB2M	SMYD3	CTGGCAATTAGCTTGTGAGATTAAGGTTCTGCACATG*GAAGGAAAAGCTGATGCGATGCTCTCAGTGCCGCGTC	tcga,chimerdb3seq,cancer,m2,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	4	1	14	1	246551213	-	1	246355094	-	17.904	4.6772	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A0D2-01A	ENSG00000125247	ENSG00000102466	TMTC4	FGF14	TTAAACACAGAAGGAAATACCCAGACTGTTACTACAACCTCGGGCGTCTG*TTAGATGAGATCATGTGACTGGATCCCTCATGATGAGATGAGTGCCCCCA	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	4	8	25	13	100625535	-	13	102193363	-	13.7657	0.1542	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A0D2-01A	ENSG00000125247	ENSG00000102466	TMTC4	FGF14	GAAATACCCAGACTGTTACTACAACCTCGGGCGTCTG*ATCCCCAGCTCAAGGGTATAGTGACCAGGTTATATTG	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	4	2	20	13	100625535	-	13	101875296	-	13.7657	0.1542	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A0D2-01A	ENSG00000125247	ENSG00000102466	TMTC4	FGF14	TTAAACACAGAAGGAAATACCCAGACTGTTACTACAACCTCGGGCGTCTG*ACAGGAAGAGGAATGTCAAGGAGATTAAGTGATTTGTCCAAGATTATACC	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	4	1	21	13	100625535	-	13	102220933	-	13.7657	0.1542	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A0D2-01A	ENSG00000125247	ENSG00000102466	TMTC4	FGF14	TTAAACACAGAAGGAAATACCCAGACTGTTACTACAACCTCGGGCGTCTG*GTGCTTGCCTTTCATTGGCTAGGAACCCTTAATCTATTGTAGATGTTAAA	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	4	1	21	13	100625535	-	13	102209813	-	13.7657	0.1542	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A0D2-01A	ENSG00000125247	ENSG00000102466	TMTC4	FGF14	TTAAACACAGAAGGAAATACCCAGACTGTTACTACAACCTCGGGCGTCTG*AGAAATTTTAATAAAGTGAAGACAAGCTACATTTTGATACATTCTTGATG	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	4	1	16	13	100625535	-	13	102142809	-	13.7657	0.1542	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A15H-01A	ENSG00000086065	ENSG00000062716	CHMP5	VMP1	GGATCAGATCAAGAAGATGAGAGAGGGTCCTGCAAAG*GACTTTGCCTCCCGGGCCAAACTGGCAGTTCAAAAAC	tcga,cell_lines,18cancers,chimerdb3seq,m34,tcga-cancer,exon-exon	BOWTIE;BOWTIE+BLAT	in-frame	0	67	20	25	9	33266114	+	17	59808796	+	72.54	90.2562	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A15H-01A	ENSG00000121058	ENSG00000109089	COIL	CDR2L	AGAGCGCGCGCCTTGTGAGAGACAACGACTGCCTCAG*ACTTGCACCTAGCTGCGGAGCTGGGGAAGACTCTGCT	tcga,18cancers,chimerdb3seq,m45,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	47	12	23	17	56960775	-	17	74999504	+	12.5776	24.9869	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A15H-01A	ENSG00000109118	ENSG00000236110	PHF12	OR2AM1P	CACAATGGTCTCGTTCCCTTACCCGTCAAAGTCTGCTTCACGTGTAACAG*GACCATCCTCTTCACGCATGGGAAGCCCAAGTCGAAGGACCCACTGGGGG	pseudogene,18cancers	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	35	5	24	17	28921688	-	9	36021920	+	4.6662	4.6505	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	unprocessed_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A15H-01A	ENSG00000170832	ENSG00000227036	USP32	LINC00511	TGTAGAAGGCATACTGAATGCACATGACACCACAAAG*GTATTTTTCCCTCTCCACCCTGGTCTTCTCCTGTAAC	lincrna,18cancers,cancer,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	31	9	25	17	60265412	-	17	72431224	-	22.9281	0.7227	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A15H-01A	ENSG00000170832	ENSG00000227036	USP32	LINC00511	TGTAGAAGGCATACTGAATGCACATGACACCACAAAG*GTGGAATCAGAGGTTTCTGGCTGACTCGGTGGGTGCT	lincrna,18cancers,cancer,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	31	2	25	17	60265412	-	17	72428298	-	22.9281	0.7227	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A15H-01A	ENSG00000167632	ENSG00000169436	TRAPPC9	COL22A1	ACATACATGTACACCATCAAAGAGAAATTATTCCGACACTTGTTAAAATG*GGTGACGTGGGACCTGCGGGGCCACCTGGTGTACCAGGCTCAGTGGTGAG	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	30	6	25	8	140347757	-	8	138755829	-	5.4093	9.0542	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A15H-01A	ENSG00000167632	ENSG00000169436	TRAPPC9	COL22A1	CTTCTACAGACCATGCTGGACTTCTTGTCGGATCAGG*GGTGACGTGGGACCTGCGGGGCCACCTGGTGTACCAG	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	30	6	23	8	140360050	-	8	138755829	-	5.4093	9.0542	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A15H-01A	ENSG00000094804	ENSG00000267104	CDC6	TBC1D3P1-DHX40P1	TGATGCTCTTGATCAGGCAGTTGAAAATCAAAGAGGTCACTCTGGGGAAG*ATCCTTATATCAAATCGCCAACTGGATATCTTCACCTGTGTGTTTCCCAG	oncogene,cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	12	1	19	17	40301030	+	17	59969481	-	15.5463	0	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A15H-01A	ENSG00000121057	ENSG00000214226	AKAP1	C17ORF67	GGGGGCTGAGGATGGATGGACCATGGATGCGGAAGCAGATCATTCAGGAG*ATTCAAGCTCTGAAAGTCATATTACAGAGGAACAATTTCCTTCCTCAGGA	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	11	3	23	17	57107178	+	17	56816058	-	27.6048	4.0068	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A15H-01A	ENSG00000121057	ENSG00000214226	AKAP1	C17ORF67	GGATGGACCATGGATGCGGAAGCAGATCATTCAGGAG*GATGAAAATTTACAGGAATTCGGAGGAAAATATTTCA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	11	2	24	17	57107178	+	17	56816010	-	27.6048	4.0068	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A15H-01A	ENSG00000121057	ENSG00000214226	AKAP1	C17ORF67	GGATGGACCATGGATGCGGAAGCAGATCATTCAGGAG*GAATACATGCACCACCTGCTCGCCCTGGAGCATCGCG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	11	2	17	17	57107178	+	17	56795180	-	27.6048	4.0068	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A15H-01A	ENSG00000121057	ENSG00000214226	AKAP1	C17ORF67	CTCCGCATCCCGCACCCCGATGGTAGCCGAGGAGCTG*GAATACATGCACCACCTGCTCGCCCTGGAGCATCGCG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	11	1	14	17	57085398	+	17	56795180	-	27.6048	4.0068	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A15H-01A	ENSG00000121057	ENSG00000125447	AKAP1	GGA3	CTCCGCATCCCGCACCCCGATGGTAGCCGAGGAGCTG*ATAAAGCCACCAATCCTTCCAACCGCCAGGAGGACTG	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	8	5	23	17	57085398	+	17	75246796	-	27.6048	25.0082	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A15H-01A	ENSG00000121057	ENSG00000125447	AKAP1	GGA3	CTCCGCATCCCGCACCCCGATGGTAGCCGAGGAGCTG*CCACAACAGAAACACTGCCGGGGAGGCCGAGCCCCGA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	8	2	18	17	57085398	+	17	75249008	-	27.6048	25.0082	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A15H-01A	ENSG00000121057	ENSG00000125447	AKAP1	GGA3	CCTCGTCAGGAGAGAGAGGAGAATAAAGCCACCCTGGAAGCTGCCAAGGG*ATAAAGCCACCAATCCTTCCAACCGCCAGGAGGACTGGGAATACATAATT	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	8	1	17	17	57091451	+	17	75246796	-	27.6048	25.0082	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A15H-01A	ENSG00000121057	ENSG00000125447	AKAP1	GGA3	AATGCCTGTCATTGGGGGAAAGTGGCTCTCACTGTGGCTCCACATACCAG*ATAAAGCCACCAATCCTTCCAACCGCCAGGAGGACTGGGAATACATAATT	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	8	1	15	17	57094194	+	17	75246796	-	27.6048	25.0082	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A15H-01A	ENSG00000153944	ENSG00000171475	MSI2	WIPF2	GGAAGATGTAAAGCAATATTTCGAGCAGTTTGGCAAG*GTATATGAATGACCTAAAGGTACAAATAAAGACGGAG	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	8	6	25	17	57401471	+	17	40256391	+	3.0802	58.4798	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-E2-A15H-01A	ENSG00000137074	ENSG00000159921	APTX	GNE	TGAGTAACGTGAATTTGTCCGTCTCCGACTTCTGGAG*GAATCGGTGGTGGAATTATCCATCAGCATGAATTGAT	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	6	3	21	9	33001567	-	9	36220020	-	3.3526	8.2928	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A26G-01A	ENSG00000143164	ENSG00000197965	DCAF6	MPZL1	GTTGAGGCATCTGGACACCACACACATCATCAGTCTG*TGACAGCTGGAGTATCAGCCTTGGAAGTATATACGCC	known,tcga,cell_lines,18cancers,chimerdb3seq,m38,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	149	19	25	1	168004793	+	1	167765583	+	15.381	123.2404	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A26G-01A	ENSG00000095002	ENSG00000068724	MSH2	TTC7A	GGATATTGCAGCAGTCAGAGCCCTTAACCTTTTTCAG*GCAACTCGAGATGTGGTGCTGAGCCGGGTGCCGGAGC	tcga,cell_lines,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	36	15	24	2	47414418	+	2	47005922	+	6.026	7.0445	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A26G-01A	ENSG00000165671	ENSG00000113761	NSD1	ZNF346	AACTTCATCATCATCTACTTCACAGGAATTGCCATTT*TGGAGCACATGATCCAGAAGAACCAATGTCTCTTCAC	oncogene,tcga,cell_lines,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	34	13	25	5	177136030	+	5	177041126	+	6.3576	2.9544	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A26G-01A	ENSG00000165671	ENSG00000113761	NSD1	ZNF346	CTTCAAGGGTCTCGCCTGCTTCGCAAAACTTCTTGAACCACCACTGCACT*TGGAGCACATGATCCAGAAGAACCAATGTCTCTTCACCAACACCCAGTGT	oncogene,tcga,cell_lines,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	34	1	25	5	177169559	+	5	177041126	+	6.3576	2.9544	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-A7-A26G-01A	ENSG00000116584	ENSG00000116539	ARHGEF2	ASH1L	ACACACACACATATATATATATACACACACACACATATATATATACACAC*ATGTGGAGCTGGAAAAATCGCATGTCCAAGCCCGTTTGAGTGGTTTCTTT	oncogene,tcga,18cancers,chimerdb3seq,cancer,tcga-cancer	BOWTIE+BLAT	intronic/UTR	0	24	1	23	1	156000302	-	1	155335974	-	9.2738	15.4127	TRUE	TRUE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-A7-A26G-01A	ENSG00000116539	ENSG00000116584	ASH1L	ARHGEF2	CATTACCAGAGGAAGAAGAGCAAGAGAATAATAAAAG*CTGCAGCCAGCTGGAAGGACATTCAGGTACCCGGGTA	oncogene,tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	24	8	25	1	155438327	-	1	155983200	-	15.4127	9.2738	TRUE	TRUE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A26G-01A	ENSG00000082996	ENSG00000169903	RNF13	TM4SF4	GGCAAGACTGTTTGTGTTGCGGGGGCCGGACTTCAAG*GGATTATCTCAATGATGAGGCCTTATGGAACAAGTGC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	13	6	24	3	149813353	+	3	149498722	+	32.3226	2.9655	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A26G-01A	ENSG00000082996	ENSG00000169903	RNF13	TM4SF4	GCTCGGAGTCGGCCCTGCTGCTGAGGTCTTTGCTGCTCCTCTAGAGCTGG*GGATTATCTCAATGATGAGGCCTTATGGAACAAGTGCCGAGAGCCTCTCA	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	13	1	19	3	149813486	+	3	149498722	+	32.3226	2.9655	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A26G-01A	ENSG00000166949	ENSG00000166938	SMAD3	DIS3L	CGCAGAACGTCAACACCAAGTGCATCACCATCCCCAG*AATTACCTGGACAATTTCTGGCCTGATTTAAAAGCTG	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	13	7	23	15	67066360	+	15	66311724	+	7.0045	10.3946	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A26G-01A	ENSG00000166949	ENSG00000166938	SMAD3	DIS3L	CGCAGAACGTCAACACCAAGTGCATCACCATCCCCAG*GGAATTCTGAATGTCAACAAACACAGAGCCCAAATAG	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	13	3	21	15	67066360	+	15	66314039	+	7.0045	10.3946	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A26G-01A	ENSG00000166949	ENSG00000166938	SMAD3	DIS3L	AAGGCCATCACCACGCAGAACGTCAACACCAAGTGCATCACCATCCCCAG*TCTCGACGGGAGAGAGAGAATGAGAGTCAGGAGAGCCATGGGAAGGAGTA	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	13	1	23	15	67066360	+	15	66311790	+	7.0045	10.3946	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A26G-01A	ENSG00000113594	ENSG00000113600	LIFR	C9	GTTCCCTCAAACAGCACTGAAACTGTAATAGAATCTG*ACCAAAGGCGAGAAAAATTTCAGAACCGAACATTACG	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	9	8	22	5	38493606	-	5	39316029	-	8.4949	0.1592	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A26G-01A	ENSG00000067369	ENSG00000104093	TP53BP1	DMXL2	TGCTCCTGGGGATGATACAGAGTCGCTCCATAGCCAG*AAACTTATTGGAGAAGTGTTTAATATTGTGAGCCAAC	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	9	4	23	15	43432194	-	15	51517167	-	3.7402	3.2541	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A26G-01A	ENSG00000124942	ENSG00000255432	AHNAK	AP001458.2	AGGTCCCAAAGTGAAGGGTGACATGGATGTGTCTCTGCCAAAAGTGGAAG*TGCTCAGGAGCTGTCCCAGGAAATCAAGGCTTTTCTGACTGGCGTAGACC	10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	8	1	22	11	62525065	-	11	62649999	-	74.015	0	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A26G-01A	ENSG00000124942	ENSG00000255432	AHNAK	AP001458.2	AGGACCCAAAGTGAAGGGTGATATGGATGTGTCTCTGCCAAAAGTGGAAG*TGCTCAGGAGCTGTCCCAGGAAATCAAGGCTTTTCTGACTGGCGTAGACC	10K<gap<100K	BOWTIE+STAR	in-frame	0	8	1	22	11	62522719	-	11	62649999	-	74.015	0	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-A7-A26G-01A	ENSG00000097021	ENSG00000116237	ACOT7	ICMT	CCTGACCTCAAGTGATCCACCCGCCTCAGCCTCCCAAATTGCTGGGATTA*CAGACAGACGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCAATTTG	18cancers,m5,tcga-cancer,10K<gap<100K	BOWTIE+BLAT	intronic/UTR	0	7	1	20	1	6328404	-	1	6223415	-	6.9092	31.9011	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A26G-01A	ENSG00000070413	ENSG00000070371	DGCR2	CLTCL1	ACTTGCGAGGATGAGAGCGACGAAGCCAACTGTCCAG*CTCCAAAACCTTGGAATTAATCCAGCTAACATTGGAT	tcga,cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	7	4	23	22	19089368	-	22	19275830	-	17.1423	1.2719	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A26G-01A	ENSG00000120658	ENSG00000102531	ENOX1	FNDC3A	ATGATGTCGTATTTATAATATGTGGAGGAGAGAGAGCTCACCATGCTCAG*GTTATTCTGGTACAAGTTAACCCAGGAGAAGCATTTACAATAAGAAGAGA	18cancers	BOWTIE+STAR	UTR/CDS(truncated)	0	7	3	21	13	43667479	-	13	49075289	+	1.2778	22.7828	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A26G-01A	ENSG00000120658	ENSG00000102531	ENOX1	FNDC3A	CAAAAAGGGATAAGGCAGATATATTTAAGTGAGCCAGTTTTAAAGAAGCG*GTTATTCTGGTACAAGTTAACCCAGGAGAAGCATTTACAATAAGAAGAGA	18cancers	BOWTIE+STAR	intronic/CDS(truncated)	0	7	1	14	13	43553467	-	13	49075289	+	1.2778	22.7828	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A26G-01A	ENSG00000116237	ENSG00000097021	ICMT	ACOT7	TAAGTTTTAGCCAGTCTTCTTGGAGTCACTTTGGCTG*AGCCGAACACTGTCAGCTACAGCCAGTCCAGCTTGAT	18cancers,m5,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	7	3	23	1	6234886	-	1	6318578	-	31.9011	6.9092	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A26G-01A	ENSG00000163939	ENSG00000163931	PBRM1	TKT	CATTAGCGAACTTTTTCAGAAACTGCCTTCTAAAGTG*CCACCCCACGTCATGCTGCAGCGCCGCAGAGATCATG	tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	7	6	24	3	52658199	-	3	53242242	-	10.2639	22.9274	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A26G-01A	ENSG00000204370	ENSG00000166266	SDHD	CUL5	ATTCCCTGGCTGCAGCCCTCACTCTTCATGGTCACTG*AATTACATTTAATGTTTTCATTGATGGACAAAGTTCC	cancer,m3,exon-exon	BOWTIE	in-frame	0	7	4	24	11	112089011	+	11	108072332	+	32.6833	13.7757	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A26G-01A	ENSG00000143033	ENSG00000137948	MTF2	BRDT	TATGAAGCGGTTGGCACCACTGAAGTGACCGAATGAG*GATATAAAGATTAAGAATGCAGATTCATGGAAAAGTT	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	6	4	22	1	93079531	+	1	92004414	+	5.1031	0.2099	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A26G-01A	ENSG00000143033	ENSG00000137948	MTF2	BRDT	TATGAAGCGGTTGGCACCACTGAAGTGACCGAATGAG*GGATCTTGGGAATGGATTGACTGTAGAATCTTTTTCA	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	6	2	19	1	93079531	+	1	92005119	+	5.1031	0.2099	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A26G-01A	ENSG00000066084	ENSG00000123268	DIP2B	ATF1	TTTGTCCGCCGGACCGAGCTCACAGCGGCCACTGGAG*GTATCATCTTTATCAGAAAGTGAGGAGTCCCAGGACT	oncogene,prostates,18cancers,cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	5	3	25	12	50739586	+	12	50795909	+	8.3445	9.4418	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A26G-01A	ENSG00000146592	ENSG00000224322	CREB5	AC004009.1	TCCCCAGGTCCAGCCAATGCATTCAGAAGCCAAAATG*ATTATGAAGCAATTTCCTACCTGTTTTTTTATTTGAT	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	4	2	22	7	28724332	+	7	27408809	+	1.1571	0.0814	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A26G-01A	ENSG00000132323	ENSG00000132326	ILKAP	PER2	AGCGGATGAGGATACAGAAGGCTGGAGGAAACGTCAG*AAATTTAGAAGCGGTTTTGAAGGAGGACAGAGAGAAG	tcga,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	4	8	25	2	238182065	-	2	238249212	-	2.6771	4.2088	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A26G-01A	ENSG00000137522	ENSG00000255191	RNF121	AP003555.3	GGTGCAGTGGAAGCAGAGGCACCCACGCTCCTACAAT*GGCACTGTGCCGAGTGGTCGGAGATCACCTCCTCGGC	lincrna,exon-exon	BOWTIE	CDS(complete)/exonic(no-known-CDS)	0	4	2	19	11	71960891	+	11	70015675	+	10.8222	0.7482	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A26G-01A	ENSG00000156026	ENSG00000107736	MCU	CDH23	CGTCAGCCGCCACCGGCAGCAGCAGCACCACCGGACG*GCAACTGACAATGATGCAGGCACCTTTGGGGAAGTCA	cell_lines,18cancers,exon-exon	BOWTIE	in-frame	0	3	3	19	10	72692301	+	10	71675112	+	11.3455	0.8676	TRUE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A26G-01A	ENSG00000156026	ENSG00000107736	MCU	CDH23	TGACCTGTTCACGCAGGGGAAACTTGAACATTCGCAG*GCAACTGACAATGATGCAGGCACCTTTGGGGAAGTCA	cell_lines,18cancers,exon-exon	BOWTIE	UTR/CDS(truncated)	0	3	2	24	10	72715902	+	10	71675112	+	11.3455	0.8676	TRUE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A26G-01A	ENSG00000266714	ENSG00000125450	MYO15B	NUP85	AGCAGGCCCTGGAGGACCTCATAGCCCGGCTGGGCAG*AAAAATCAGAGATGGTGCCAAGTTGCCCCTTTATCTA	exon-exon	BOWTIE	out-of-frame	0	2	2	24	17	75602945	+	17	75209823	+	0.7991	10.9018	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A26G-01A	ENSG00000175600	ENSG00000106536	SUGCT	POU6F2	AATCAACAACATGAAGAATGTATTTGCAGAACCTCAG*CTGGTTAATAATCCACTAGCAAGTCAGGCTGCAGCGG	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	2	1	14	7	40496386	+	7	39406600	+	3.7577	0.1237	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-C8-A130-01A	ENSG00000157540	ENSG00000130584	DYRK1A	ZBTB46	ATATTCTGACCAGATTCAGCAACCTCTAACTAACCAG*AGTCTGTAGAAGAGGCGACACCAGGGCTTCCAAATGA	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	47	12	25	21	37472880	+	20	63790790	-	3.2905	5.7483	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-C8-A130-01A	ENSG00000157538	ENSG00000172264	DSCR3	MACROD2	CAAGATTAAAAGAGCGAATAAAGTTTATCACGCCGGG*CTCCAGGCGAGGACACACCTAGGATGCCTGGGAAAAG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	13	4	25	21	37267238	-	20	16041201	+	10.8536	3.7058	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-C8-A130-01A	ENSG00000106804	ENSG00000175792	C5	RUVBL1	TTAATTATGGGTAAAGAAGCCCTCCAGATAAAATACAATTTCAGTTTCAG*GCTGGAGTGCAACGGCCCAATCTCAGCTCACTGCAACCTCCGCCTCCCGG	cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	4	1	24	9	120953730	-	3	128084050	-	1.3423	11.263	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0RE-01A	ENSG00000163082	ENSG00000172339	SGPP2	ALG14	TCTCAGCAGGCTCTACACTGGGATGCATACGGTCCTG*TATACCAAATACTACATTCACCGAATTCCAAGAAGCC	tcga,cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	31	6	20	2	222525033	+	1	95027260	-	6.8222	1.3208	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-B6-A0RE-01A	ENSG00000111247	ENSG00000215039	RAD51AP1	CD27-AS1	AAAGAGAAGAAATCTAAATCCAAATGTAATGCTTTGG*GTAGACCCAGTGTAATCACAAGCATCCTTGTAAGTGG	18cancers,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	30	8	24	12	4553147	+	12	6439676	-	11.6732	5.4209	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0RE-01A	ENSG00000111642	ENSG00000110799	CHD4	VWF	GCACTTTTGAACAACAGCCTGCCCCCACCCCACCCAG*GGCCTGTGGGAGCAGTGCCAGCTTCTGAAGAGCACCT	chimerdb3seq,exon-exon	BOWTIE	out-of-frame	0	5	2	16	12	6606274	-	12	6075551	-	3.4249	6.3592	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A1FC-01A	ENSG00000117569	ENSG00000189337	PTBP2	KAZN	GGACGGAATCGTCACTGAGGTTGCAGTTGGCGTGAAG*CCATGAAAGCTGATCGGAAGCGCTTAAAGGGCGAGAA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	81	17	25	1	96723594	+	1	15034749	+	1.7482	6.3386	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A1FC-01A	ENSG00000126091	ENSG00000162367	ST3GAL3	TAL1	GCTATGCTTCAGCCTTGATGACGGCCATCTTCCCCCG*GTCCCCACACCAAAGTTGTGCGGCGTATCTTCACCAA	oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	13	5	25	1	43838311	+	1	47220174	-	0.0852	3.0893	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A1FC-01A	ENSG00000126091	ENSG00000162367	ST3GAL3	TAL1	ATGATTATTTGGACTAGGGCCGTAGCAGTGGAGAGAG*GTCCCCACACCAAAGTTGTGCGGCGTATCTTCACCAA	oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	13	2	17	1	43879507	+	1	47220174	-	0.0852	3.0893	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A1FC-01A	ENSG00000126091	ENSG00000162367	ST3GAL3	TAL1	GGCCCTCCTCCTGAGCTGTGTGAGGCTCCCAGCCAGGAGCAAGCAGCCCT*GTCCCCACACCAAAGTTGTGCGGCGTATCTTCACCAACAGCCGGGAGCGA	oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	13	1	19	1	43858636	+	1	47220174	-	0.0852	3.0893	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A1FC-01A	ENSG00000158966	ENSG00000169504	CACHD1	CLIC4	GCTGGCGGCCGAGGAGCTGGGGGTCGTCACCATGCAG*GCTGGCAGTGATGGTGAAAGCATAGGAAACTGCCCCT	tcga,cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	9	6	24	1	64470942	+	1	24797742	+	1.5413	60.7725	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A1FC-01A	ENSG00000185104	ENSG00000162599	FAF1	NFIA	CAACATGGACCGGGAGATGATCCTGGCGGATTTTCAG*CACCAATAGCTGCAGGAACTGGCCCAAATTTTTCTCT	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	9	7	25	1	50959767	-	1	61352450	+	18.7954	1.0057	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A1FC-01A	ENSG00000170471	ENSG00000101413	RALGAPB	RPRD1B	ATGCGTGGAATCAGCTGTCTGGTGGATGCATTCTTAG*ACAAAGAGGCAGCTGAACGTCTTTCAAAAACAGTAGA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	9	2	21	20	38516370	+	20	38066081	+	8.501	9.5282	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A1FC-01A	ENSG00000170471	ENSG00000101413	RALGAPB	RPRD1B	TTGCACAGACATGGTTTCGCTTTTTACACATGTTAAG*ACAAAGAGGCAGCTGAACGTCTTTCAAAAACAGTAGA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	9	2	17	20	38509208	+	20	38066081	+	8.501	9.5282	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A1FC-01A	ENSG00000129911	ENSG00000070423	KLF16	RNF126	TCCTCGCACCTAAAGTCGCACCTGCGGACGCACACAG*GATTATATCTGTCCAAGATGCGAGTCTGGTTTTATCG	exon-exon	BOWTIE	out-of-frame	0	2	3	22	19	1863041	-	19	652884	-	8.4311	8.7814	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0IJ-01A	ENSG00000188735	ENSG00000235831	TMEM120B	BHLHE40-AS1	CCATTCGGGAGAGCATTCTCATCAGCAACGGCTCAAG*GGTTGCAGAAAAGGAAGAAGAATCAGCAGAGAGCATT	antisense,18cancers,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	90	19	25	12	121761738	+	3	4900697	-	1.7763	3.6797	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0IJ-01A	ENSG00000188735	ENSG00000235831	TMEM120B	BHLHE40-AS1	TGGGTGCCGTGGCATGTCGATTTGTCCTTCACTACAG*GGTTGCAGAAAAGGAAGAAGAATCAGCAGAGAGCATT	antisense,18cancers,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	90	2	24	12	121752223	+	3	4900697	-	1.7763	3.6797	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0IJ-01A	ENSG00000188735	ENSG00000235831	TMEM120B	BHLHE40-AS1	TACTGCACCCTGACCATTCGGGAGAGCATTCTCATCAGCAACGGCTCAAG*ATGGAGTCTTGCATTGTCACCTAGGCTGGAGTGCAGTGGTGCGATCTCCA	antisense,18cancers	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	90	2	21	12	121761738	+	3	4935290	-	1.7763	3.6797	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0IJ-01A	ENSG00000100151	ENSG00000100142	PICK1	POLR2F	TTGCAGACTTGGATTATGACATCGAAGAGGATAAACT*TTTTGATGGCGACGACTTTGATGATGTGGAGGAGGAT	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	32	12	24	22	38057850	+	22	37956773	+	15.2525	19.4226	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0IJ-01A	ENSG00000100151	ENSG00000279010	PICK1	AL031587.6	CTCGGAACCATGTTTGCAGACTTGGATTATGACATCGAAGAGGATAAACT*ATCCCTCTGTCCAGGAAGCCTCTGTGGACTGCCCCTTACTTTTCATGATG	cancer,10K<gap<100K	BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	18	1	14	22	38057850	+	22	37951421	+	15.2525	NA	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	sense_overlapping	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0IJ-01A	ENSG00000259431	ENSG00000157227	THTPA	MMP14	AGCACAGTATGGCAGTAGGTAGGGCTCAGGCAGCCCCTCTATACTCAGTG*GTTCTGGCGGGTGAGGAATAACCAAGTGATGGATGGATACCCAATGCCCA	cancer	BOWTIE+BLAT	UTR/CDS(truncated)	0	18	3	24	14	23560107	+	14	22844379	+	1.1445	72.977	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0IJ-01A	ENSG00000249859	ENSG00000253929	PVT1	CASC21	ACCTAAAGCTGGAGTATTTTGAGATTGGAGAATTAAG*CTGAACCATCACATTCCTTATACAGAGTGGGACAGCA	known,lincrna,oncogene,18cancers,cancer,exon-exon	BOWTIE	exonic(no-known-CDS)/exonic(no-known-CDS)	0	15	4	23	8	127989291	+	8	127392504	+	4.3707	NA	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0IJ-01A	ENSG00000249859	ENSG00000253929	PVT1	CASC21	CTGGTCTCCATTATTTGAGATGAGTTACATCTTGGAG*CTGAACCATCACATTCCTTATACAGAGTGGGACAGCA	known,lincrna,oncogene,18cancers,cancer,exon-exon	BOWTIE	exonic(no-known-CDS)/exonic(no-known-CDS)	0	15	2	23	8	127796008	+	8	127392504	+	4.3707	NA	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0IJ-01A	ENSG00000249859	ENSG00000253929	PVT1	CASC21	CTGTCCTTACGTGACCTAAAGCTGGAGTATTTTGAGATTGGAGAATTAAG*TGTGCATGGGAGTGTGTCAGGGGAAAGGGACCGGATACGGCAGTGTACCG	known,lincrna,oncogene,18cancers,cancer	BOWTIE+STAR	exonic(no-known-CDS)/intronic	0	15	1	20	8	127989291	+	8	127391087	+	4.3707	NA	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0IJ-01A	ENSG00000249859	ENSG00000253929	PVT1	CASC21	CCCTGCGTTTCTGGAAACTCTCGAGACTTGGCCCTGAGTAGGGATGCGCT*CTGAACCATCACATTCCTTATACAGAGTGGGACAGCATTGGCTGAGTTCT	known,lincrna,oncogene,18cancers,cancer	BOWTIE+STAR	intronic/exonic(no-known-CDS)	0	15	1	17	8	127794802	+	8	127392504	+	4.3707	NA	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0IJ-01A	ENSG00000157625	ENSG00000198947	TAB3	DMD	AATTCCAGAGGGCGTGGTGTCTCAGTGCATGTTACAG*CTGACCTGAATAATGTCAGATTCTCAGCTTATAGGAC	known,tcga,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	11	4	25	X	30859487	-	X	31223121	-	1.6056	2.0255	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-B6-A0IJ-01A	ENSG00000148773	ENSG00000177453	MKI67	NIM1K	GCTCTAACCAGAAATCTTGCTGAAGTATGTCAGCACCTTTTCTCACCCTG*AGATGGGGTCTCACTGTGTTGCCTAGGCTGGTCTTGAGCTCCTGGACTCA	18cancers	BOWTIE+STAR	UTR/UTR	0	10	3	19	10	128097427	-	5	43240260	+	32.3677	2.1532	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0IJ-01A	ENSG00000148773	ENSG00000177453	MKI67	NIM1K	GCTCTAACCAGAAATCTTGCTGAAGTATGTCAGCACCTTTTCTCACCCTG*GTTGAACCAGCCAAATTTTCGAGACAGCTCACGGCTTAGAGGAAGGTTCA	18cancers	BOWTIE+BLAT;BOWTIE+STAR	UTR/UTR	0	10	1	22	10	128097427	-	5	43245082	+	32.3677	2.1532	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0IJ-01A	ENSG00000148773	ENSG00000177453	MKI67	NIM1K	CCTCCGAAATCTCCTTTGAAGCCCAGACATCTTTCTCCAGCTTCAGACTT*AGATGGGGTCTCACTGTGTTGCCTAGGCTGGTCTTGAGCTCCTGGACTCA	18cancers	BOWTIE+BLAT;BOWTIE+STAR	UTR/UTR	0	10	1	20	10	128098172	-	5	43240260	+	32.3677	2.1532	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0IJ-01A	ENSG00000163848	ENSG00000142621	ZNF148	FHAD1	GAAAAAGAAGAAGCGGAAACAACGTTCTCCCGCAAAA*CCCCAAAGGAGGAAAGGCCGCAAGACCCTCTGGTGGC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	10	2	24	3	125288103	-	1	15362642	+	6.2205	0.6343	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-B6-A0IJ-01A	ENSG00000163848	ENSG00000142621	ZNF148	FHAD1	GAAAAAGAAGAAGCGGAAACAACGTTCTCCCGCAAAA*AGATGACTTATTGGCTGCTCAGAAGGAAATTCTGTCT	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	10	2	18	3	125288103	-	1	15365827	+	6.2205	0.6343	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-B6-A0IJ-01A	ENSG00000102796	ENSG00000125871	DHRS12	MGME1	ACCATTTGATGGAACTATGGTCTATGCACAAAACAAG*GTTCAATGTGGCTTAATTGTGGTGGCCTACAAAGATG	exon-exon	BOWTIE	in-frame	0	5	1	14	13	51773930	-	20	17989939	+	0.6268	13.6078	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0IJ-01A	ENSG00000125703	ENSG00000232973	ATG4C	CYP1B1-AS1	ATTACTGCCAATCTTTTGTAGATGTCAGCATAAAGGATTTCCCTCTTGAG*GATAGCAAGATTTGACTGGACCCTGACTGACGAGATTACTATACCTAAAG	antisense	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	18	1	62834852	+	2	38177091	+	8.1992	0.2262	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-B6-A0IJ-01A	ENSG00000142949	ENSG00000147065	PTPRF	MSN	TGGATGGCCCAGCAGGCAGGCACTGTGGCCCTTCTGTCCACCAGACCCAC*CACTCTGTGCCTGACCTTGAGGAGTCTTGTGTGCATTGCTGTGAATTAGC	cancer	BOWTIE+BLAT	UTR/UTR	0	2	1	24	1	43622244	+	X	65741649	+	271.8371	254.9364	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A1-A0SM-01A	ENSG00000274211	ENSG00000132589	SOCS7	FLOT2	GGAAAGTTTCTCTATTTCTTAAGATCCAGGGTTCCAG*GGGGCTGTTGTGGTTCCGACTATAAACAGTACGTGTT	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	36	5	20	17	38377842	+	17	28889026	-	16.0406	44.0879	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A1-A0SM-01A	ENSG00000131759	ENSG00000137513	RARA	NARS2	CTTCCAGTTAGTGGATATAGCACACCATCCCCAGCCA*GGATGGATTCGTTCTGTCCGATCCCAGAAGGAAGTCT	known,oncogene,18cancers,chimerdb3seq,cancer,tumor,exon-exon	BOWTIE	out-of-frame	0	32	5	24	17	40331396	+	11	78571444	-	179.995	27.1015	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A1-A0SM-01A	ENSG00000131759	ENSG00000137513	RARA	NARS2	GCAGCCCAGTGGACTTCTCTGCTTTGCAGTCTCAGGAACTTCACTGATGC*GGATGGATTCGTTCTGTCCGATCCCAGAAGGAAGTCTTGTTCCTGCATGT	known,oncogene,18cancers,chimerdb3seq,cancer,tumor	BOWTIE+STAR	intronic/CDS(truncated)	0	32	3	18	17	40340067	+	11	78571444	-	179.995	27.1015	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A1-A0SM-01A	ENSG00000137486	ENSG00000198382	ARRB1	UVRAG	TGCGACCGTCGCGGACCATGGGCGACAAAGGGACCCG*GAAGTGCATTTTCAGCTGAGCACCTCAAACTTCAACT	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	19	5	20	11	75351588	-	11	76004005	+	16.6821	32.4374	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A1-A0SM-01A	ENSG00000198382	ENSG00000184154	UVRAG	LRTOMT	GTGTTCGCAATTCTTACGATGTCTTCTCTTTGCTACG*GGAGTATTTCCATTTTAACCGGAAACAATCCCTGAAC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	8	4	23	11	75912039	+	11	72088297	+	32.4374	1.7147	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A1-A0SM-01A	ENSG00000198382	ENSG00000184154	UVRAG	LRTOMT	GTGTTCGCAATTCTTACGATGTCTTCTCTTTGCTACG*ATCTGGTAAATGAGGAGCCAAGGACAGGACTACGACC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	8	3	25	11	75912039	+	11	72093496	+	32.4374	1.7147	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-A1-A0SM-01A	ENSG00000238045	ENSG00000141736	AC009133.1	ERBB2	TTCTGGCTCCGGGCTGAGCTTCCTGGAGAAGAGGAAG*GGCATCTGGATCCCTGATGGGGAGAATGTGAAAATTC	antisense,oncogene,cancer,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	4	1	13	16	29819540	-	17	39723912	+	0.1028	808.1614	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A1-A0SM-01A	ENSG00000048649	ENSG00000109118	RSF1	PHF12	CTGCAGGCGCCGCCGCCGGACGTCGGCAACGGAGAAG*TAACCCTCCACTGAGTGAAGAAATGTTGCCTCCTGGA	oncogene,tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	4	2	21	11	77820528	-	17	28927063	-	28.6045	5.5678	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A1-A0SM-01A	ENSG00000278053	ENSG00000175581	DDX52	MRPL48	CCTGATTATATCACCAACACGAGAACTTGCCAGCCAG*GTGGAATTCTACTAAGTATCAGTCGGCCCTACAAGAC	ribosomal,m2,exon-exon	BOWTIE	out-of-frame	0	3	2	24	17	37630030	-	11	73825708	+	4.8154	4.4194	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A1-A0SM-01A	ENSG00000278053	ENSG00000175581	DDX52	MRPL48	CCTGATTATATCACCAACACGAGAACTTGCCAGCCAG*CCCAAGAAGAAGAAGGGAAAAGTGGAAGTGAGAGCCA	ribosomal,m2,exon-exon	BOWTIE	in-frame	0	3	2	24	17	37630030	-	11	73844807	+	4.8154	4.4194	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A8-A08B-01A	ENSG00000131759	ENSG00000161395	RARA	PGAP3	GCTGGCACCCCGAACGGGTTGCTTCCCCCGCTGCGAG*GCTGGACCTGTCGGGACGACTGTAAGTATGAGTGTAT	known,oncogene,tcga,cell_lines,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	15	3	24	17	40318448	+	17	39686019	-	81.4291	125.5646	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A08B-01A	ENSG00000131759	ENSG00000161395	RARA	PGAP3	GCTGGCACCCCGAACGGGTTGCTTCCCCCGCTGCGAG*ATGAGAAAACTGAGGCACAGCAAGGCTAAATAACTTG	known,oncogene,tcga,cell_lines,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	15	1	13	17	40318448	+	17	39676755	-	81.4291	125.5646	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000134684	ENSG00000224420	YARS	ADM5	TCCCATCCCGGCTGGATATCCGTGTGGGGAAAATCATCACTGTGGAGAAG*ACTTTTGGCCTCAGTGTTCCCCGCCTGGGAAGTGGGGACTGGCCCTGGTA	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	178	6	24	1	32781048	-	19	49689688	+	12.1933	2.6514	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000134684	ENSG00000224420	YARS	ADM5	GCTGGATATCCGTGTGGGGAAAATCATCACTGTGGAGAAGGTACTCATTT*TTCCCCACGCTTTGAAGGGGGCGAGTCTCCACAGACCTCCTAGGGGGATA	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT	intronic/UTR	0	178	6	22	1	32781038	-	19	49689523	+	12.1933	2.6514	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000134684	ENSG00000224420	YARS	ADM5	TCCCATCCCGGCTGGATATCCGTGTGGGGAAAATCATCACTGTGGAGAAG*GGGACCTGGACACTGCAGCCAGGTGAGAAACCCGGGTGGCAGCAGGGACA	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	178	4	23	1	32781048	-	19	49689890	+	12.1933	2.6514	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000134684	ENSG00000224420	YARS	ADM5	ATATCCGTGTGGGGAAAATCATCACTGTGGAGAAG*GCGAGGCCAGCACCAGGTCCCCCAGCACCGCGGGC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	178	3	23	1	32781048	-	19	49690106	+	12.1933	2.6514	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000161956	ENSG00000072778	SENP3	ACADVL	GCATGCATGAGTCAACTGTGTGCATCCCATTGTGCTTTCCCCAGGCCAGT*CCGGAGTTGAGTCGGAGTGGCGAGCTGGTAAGTGGCCAGGGGTCCAGGAG	NA	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	118	3	22	17	7564590	+	17	7224367	+	4.3056	25.5456	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000090861	ENSG00000103051	AARS	COG4	CCACTTTGCTCTTTGCCAATGCAGGCATGAACCAG*AAAGTGGTGGAGAGAGAGCTGGATGCTCTTTTGGA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	112	18	24	16	70282620	-	16	70519731	-	23.2639	34.3654	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000204764	ENSG00000182132	RANBP17	KCNIP1	TTCTGGTGTAACTGTGGACATCACCATTCAGGAAG*ATAAGATTGAAGATGAGCTGGAGATGACCATGGTT	18cancers,chimerdb3seq,cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	101	8	23	5	170924550	+	5	170718758	+	1.6667	3.9155	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000204764	ENSG00000182132	RANBP17	KCNIP1	ACTTCTGCATCCATATTCTGGTGTAACTGTGGACATCACCATTCAGGAAG*ACTCAGCTTGGGACATATGAGGACAGCACAGACTTTGGAGGCAGGTAGAT	18cancers,chimerdb3seq,cancer,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/intronic	0	101	1	19	5	170924550	+	5	170678222	+	1.6667	3.9155	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000091527	ENSG00000144868	CDV3	TMEM108	TACAGCGGCCTCAGGGTTCAGGCAATGCAAATAAG*GTTTCCTGCTGATCTTGGCACTGACCGAAGCGCTG	tcga,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	100	17	24	3	133575115	+	3	133379752	+	51.544	6.044	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000130402	ENSG00000077549	ACTN4	CAPZB	CCGCCTTCATGCCCTCCGAGGGCAAGATGGTCTCG*GTCCCCAGTCTATGTGAGGATCTCCTGTCTTCTGT	oncogene,tcga,cell_lines,18cancers,chimerdb3seq,m57,tcga-cancer,exon-exon	BOWTIE	in-frame	0	96	13	24	19	38717316	+	1	19385626	-	84.839	9.7397	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000130402	ENSG00000077549	ACTN4	CAPZB	GCAGAAGGCCTCCATCCACGAGGCCTGGACTGACG*GTCCCCAGTCTATGTGAGGATCTCCTGTCTTCTGT	oncogene,tcga,cell_lines,18cancers,chimerdb3seq,m57,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	96	2	16	19	38718074	+	1	19385626	-	84.839	9.7397	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000277957	ENSG00000072778	SENP3-EIF4A1	ACADVL	GCATGCATGAGTCAACTGTGTGCATCCCATTGTGCTTTCCCCAGGCCAGT*CCGGAGTTGAGTCGGAGTGGCGAGCTGGTAAGTGGCCAGGGGTCCAGGAG	NA	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	80	8	23	17	7564590	+	17	7224367	+	0.0031	25.5456	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000090861	ENSG00000157350	AARS	ST3GAL2	GCTGATGGTGGCCGGCCTGACAACACAGGGCGTGG*GTGAACGTGTACGGGTTCGGGGCCGACAGCCGGGG	tcga,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	76	11	24	16	70269618	-	16	70381862	-	23.2639	6.5575	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000090861	ENSG00000157350	AARS	ST3GAL2	GACCACGCTCGGACCATCACTGTGGCACTGGCTGATGGTGGCCGGCCTGA*CAATCATGTGACTCAAGGAAAACTTCCGGCGCTGTGTCCAGTCTCCTCCA	tcga,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K	BOWTIE+BLAT	CDS(truncated)/UTR	0	76	1	22	16	70269633	-	16	70381489	-	23.2639	6.5575	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000249967	ENSG00000171307	AL355315.1	ZDHHC16	AGCGAGTCCTACACACAGAGCTTTCAGAGCCGGAAGCCCTTCTTTTCATG*CTATGGAAGTTGGGACCTTTTCCGGGAGGCTTATGCTGCCATTGAGGTGA	100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	49	9	23	10	97673735	+	10	97453618	+	0	25.6359	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000249967	ENSG00000171307	AL355315.1	ZDHHC16	AGCGAGTCCTACACACAGAGCTTTCAGAGCCGGAAGCCCTTCTTTTCATG*ACTTATCACCAGACCCCACCACCCACCTTCTCCTTTCGAGAAAGGATGAC	100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	49	1	24	10	97673735	+	10	97454714	+	0	25.6359	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000249967	ENSG00000171307	AL355315.1	ZDHHC16	AGCGAGTCCTACACACAGAGCTTTCAGAGCCGGAAGCCCTTCTTTTCATG*AAAATGAAACAGCTCGACAAGAACAAACTACAGGCGGTTGCCAACCAGGT	100K<gap<200K	BOWTIE+STAR	out-of-frame	0	49	1	18	10	97673735	+	10	97453799	+	0	25.6359	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000155252	ENSG00000171307	PI4K2A	ZDHHC16	TGCATGTCCTCTGCTTGCCCGGCTGCAGAGCAGAGATGTGCAGCCCTCTG*TGGTTGTTTACTGTGTACGCCAGATAGAACCGTGGGTCTCCAGCTGCTGT	known,tcga,18cancers,100K<gap<200K	BOWTIE+BLAT	UTR/intronic	0	49	1	18	10	97675278	+	10	97453182	+	10.508	25.6359	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000155252	ENSG00000171307	PI4K2A	ZDHHC16	GAGTCCTACACACAGAGCTTTCAGAGCCGGAAGCCCTTCTTTTCATG*CTATGGAAGTTGGGACCTTTTCCGGGAGGCTTATGCTGCCATTGAGGTGA	known,tcga,18cancers,100K<gap<200K	BOWTIE+STAR	in-frame	0	49	1	15	10	97673735	+	10	97453618	+	10.508	25.6359	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	GGAGCTTCTCAGAAGACAGAGGGTTTTCTTTTGAG*CAGTTTAAGTATAGTGTGCCTGGGTTGGGTGCGGT	antisense,m4,exon-exon	BOWTIE	exonic(no-known-CDS)/UTR	0	31	6	22	10	87288442	-	10	46593287	+	1.2641	0.0811	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	GCCTGCCTCAGCCTCCAAAGTAGCTGAGACTACAG*CAGTTTAAGTATAGTGTGCCTGGGTTGGGTGCGGT	antisense,m4,exon-exon	BOWTIE	exonic(no-known-CDS)/UTR	0	31	6	22	10	87246115	-	10	46593287	+	1.2641	0.0811	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	GGAGCTTCTCAGAAGACAGAGGGTTTTCTTTTGAG*ATTCCAGTTCTTTGATGAAAGTCTCTATTCCACCC	antisense,m4,exon-exon	BOWTIE	exonic(no-known-CDS)/UTR	0	31	4	20	10	87288442	-	10	46593989	+	1.2641	0.0811	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	GCCTGCCTCAGCCTCCAAAGTAGCTGAGACTACAG*ATTCCAGTTCTTTGATGAAAGTCTCTATTCCACCC	antisense,m4,exon-exon	BOWTIE	exonic(no-known-CDS)/UTR	0	31	3	22	10	87246115	-	10	46593989	+	1.2641	0.0811	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000103266	ENSG00000090565	STUB1	RAB11FIP3	ATCGCTTTTGCTGGGCCGTGATCGTCCCCCTTTGTGGGCTGGAAAAGCAG*GTTGTCTTCCTGGAAAGGCGTGTGCTGGAGCTGGAAAAGGACACGGCAGC	18cancers,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	29	5	22	16	682682	+	16	505524	+	15.9144	6.4249	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000103266	ENSG00000090565	STUB1	RAB11FIP3	GGAGCCCCCTGACCCAGGAACAGCTCATCCCCAACTTGGCTATGAAGGAG*GTTGTCTTCCTGGAAAGGCGTGTGCTGGAGCTGGAAAAGGACACGGCAGC	18cancers,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	29	2	21	16	682441	+	16	505524	+	15.9144	6.4249	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000100994	ENSG00000197586	PYGB	ENTPD6	AGGAACATCGCCTGCTCGGGCAAGTTCTCCAGTGACCGGACCATCACGGA*AGCGCTCAGGGAATCCGGGAACTACTGGATGTTGCTAAACAGGACATTCC	cell_lines,18cancers,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	23	5	24	20	25296449	+	20	25213263	+	65.9933	20.0124	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000100994	ENSG00000197586	PYGB	ENTPD6	GAACCCCAAGGAGTGGACCAAGAAGGTCATCAGGAACATCGCCTGCTCGG*AGCGCTCAGGGAATCCGGGAACTACTGGATGTTGCTAAACAGGACATTCC	cell_lines,18cancers,10K<gap<100K	BOWTIE+BLAT	out-of-frame	0	23	3	23	20	25296418	+	20	25213263	+	65.9933	20.0124	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000100994	ENSG00000197586	PYGB	ENTPD6	ACTACAGCCTTTTATTGAGTGGGGCAAGTGCTGGGCTGTGGTCGTGCCCT*GGCAACACAGTGAGACTCTGTCTCCAGAAACCAAAAAAACCCAAAAGGGT	cell_lines,18cancers,10K<gap<100K	BOWTIE+BLAT	UTR/intronic	0	23	1	21	20	25297860	+	20	25213145	+	65.9933	20.0124	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000198182	ENSG00000182472	ZNF607	CAPN12	GATTGTGAGGGAAGAAACAAGAGGAGAGTGTACAG*GTAACTGCTGGTTCCTTGCAGCTGCCGCCTCCCTT	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	23	4	23	19	37707914	-	19	38742528	-	3.7229	0.9232	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000198182	ENSG00000182472	ZNF607	CAPN12	GATGATGGAGAACTATGACAACTTAGTCTCATTGG*GTAACTGCTGGTTCCTTGCAGCTGCCGCCTCCCTT	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	23	1	14	19	37709696	-	19	38742528	-	3.7229	0.9232	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000116478	ENSG00000025800	HDAC1	KPNA6	TGAGTTCTGTCAGTTGTCTACTGGTGGTTCTGTGG*AGACCATGGCGAGCCCAGGGAAAGACAATTATCGA	oncogene,tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	19	5	24	1	32324553	+	1	32154588	+	32.1397	8.1789	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000116478	ENSG00000025800	HDAC1	KPNA6	TAACATGTCGGAGTACAGCAAGCAGATGCAGAGAT*AGACCATGGCGAGCCCAGGGAAAGACAATTATCGA	oncogene,tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	19	1	13	1	32316782	+	1	32154588	+	32.1397	8.1789	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000149182	ENSG00000149187	ARFGAP2	CELF1	CACCGCTCCCTGGGCGTCCATCTGAGCTTCATCAG*GGTGCTGTTTTGTTACATTTTACACCCGTAAAGCT	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	15	8	21	11	47176516	-	11	47487241	-	20.3749	13.595	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000125970	ENSG00000078699	RALY	CBFA2T2	AGAGAATGGGCGGGTGCTGGCCGGGCAGACCCTGG*AACTCAACAGTGACAATTGAGGAATTCCACTGTAA	18cancers,chimerdb3seq,exon-exon	BOWTIE	out-of-frame	0	14	2	19	20	34072330	+	20	33619517	+	72.2394	9.316	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000148842	ENSG00000107882	CNNM2	SUFU	CAAGTTGGACGCTATGCTGGAAGAATTTAAGAAAG*GAGCCGCAAAGACAGCCTGGAAAGTGACAGCTCCA	known,tcga,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	13	2	20	10	102920101	+	10	102615268	+	1.0518	6.8404	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000148842	ENSG00000107882	CNNM2	SUFU	CTTATACAGTACATCATTTATATTTGTTCGTTTGACCATATAATGAACAG*GAGCCGCAAAGACAGCCTGGAAAGTGACAGCTCCACGGCCATCATTCCCC	known,tcga,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	13	1	16	10	102921115	+	10	102615268	+	1.0518	6.8404	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000131149	ENSG00000103194	GSE1	USP10	TGAGCTGGAGCTCCCCGGTGGCAGCAGCGACGAAG*TATATTTTTGGAGATTTTAGCCCTGATGAATTCAA	tcga,cell_lines,chimerdb3seq,cancer,m2,tcga-cancer,exon-exon	BOWTIE	CDS(no-known-start-or-end)/CDS(truncated)	0	11	4	23	16	85171807	+	16	84733435	+	5.8211	28.4046	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0B9-01A	ENSG00000172939	ENSG00000144677	OXSR1	CTDSPL	CTGGAATATCTGCATAAAAATGGACAGATCCACAG*CCACCAGCTAAGTACCTTCTTCCAGAGGTGACGGT	tcga,cell_lines,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	2	2	15	3	38198863	+	3	37964571	+	7.3714	9.7329	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-AO-A0JL-01A	ENSG00000038532	ENSG00000189067	CLEC16A	LITAF	CAGCGCTCCGTGTTTGCATCGGTGGACAAGGTGCCAG*GTAAAATGTCGGTTCCAGGACCTTACCAGGCGGCCAC	tcga,cell_lines,chimerdb3seq,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	3	3	23	16	11126146	+	16	11556735	-	18.8135	454.1699	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A0D9-01A	ENSG00000083168	ENSG00000196115	KAT6A	ADAM5	GGTGCTATTGAGAAATTCATTGGGAAGTTGGAAGACATTTCAATCAACAG*AGAGAAGTTACATGGAGGAGGGAAGATAGGCCACTTTTCAAAAACAACGG	pseudogene,oncogene,chimerdb3seq,cancer,tumor	BOWTIE+BLAT;BOWTIE+STAR	UTR/exonic(no-known-CDS)	0	700	27	25	8	42049170	-	8	39401333	+	5.175	10.3871	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	transcribed_unitary_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A0D9-01A	ENSG00000083168	ENSG00000196115	KAT6A	ADAM5	ACCTCCAGTGTCCCTTCTTCCACATGAAAAGGATAAG*AGAGAAGTTACATGGAGGAGGGAAGATAGGCCACTTT	pseudogene,oncogene,chimerdb3seq,cancer,tumor,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	700	19	25	8	42048378	-	8	39401333	+	5.175	10.3871	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	transcribed_unitary_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A0D9-01A	ENSG00000147548	ENSG00000156675	NSD3	RAB11FIP1	ACAAGCAGATTGTTTGGGTCAAATTGGGAAATTACAG*GTGGTATAAGTTGAAATCCAAACCAGGAAAGAAGGAC	oncogene,cell_lines,chimerdb3seq,cancer,tumor,exon-exon	BOWTIE	in-frame	0	246	21	24	8	38295796	-	8	37877551	-	148.1719	252.6023	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A0D9-01A	ENSG00000147548	ENSG00000156675	NSD3	RAB11FIP1	GCTGTAAATGTAGGCTTTTGTTTCGTTTGTGCCAGAG*GTGGTATAAGTTGAAATCCAAACCAGGAAAGAAGGAC	oncogene,cell_lines,chimerdb3seq,cancer,tumor,exon-exon	BOWTIE	out-of-frame	0	246	1	13	8	38304587	-	8	37877551	-	148.1719	252.6023	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-AO-A12H-01A	ENSG00000139865	ENSG00000151338	TTC6	MIPOL1	ATCTGTCATGAAGGAAACTCTATATCCAAAATATGAG*TGCAAACGGTTAGAGCAGGAGCTTCATCATGTGAAAG	known,tcga,prostates,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	15	7	25	14	37725002	+	14	37369517	+	3.9255	0.8795	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A1PB-01A	ENSG00000139083	ENSG00000198492	ETV6	YTHDF2	ACCAAAGAGGACTTTCGCTATCGATCTCCTCATTCAG*GAACGTCAAGGTCGTGGGAAATAAAAGGCAGTTCTAC	known,oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	551	24	25	12	11839304	+	1	28768929	+	17.3078	38.8415	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A1PB-01A	ENSG00000139083	ENSG00000198492	ETV6	YTHDF2	ATGGAGGAAGACTCGATCCGCCTGCCTGCGCACCTGC*GAACGTCAAGGTCGTGGGAAATAAAAGGCAGTTCTAC	known,oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	551	4	18	12	11752579	+	1	28768929	+	17.3078	38.8415	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A1PB-01A	ENSG00000139083	ENSG00000198492	ETV6	YTHDF2	GGCATCTGTTGGGCTGCAGTCTACGAGCAATAGTTGTGACATTAACTAAG*GAACGTCAAGGTCGTGGGAAATAAAAGGCAGTTCTACACAGACTGCAGCA	known,oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	551	3	25	12	11847111	+	1	28768929	+	17.3078	38.8415	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A1PB-01A	ENSG00000178078	ENSG00000159842	STAP2	ABR	CTGGCACCCACTTCAGCCTGATTCTCCGGGATCAGGAGATCAAGTTCAAG*GCCCCAGTGTGTGACGTTCCCCTCCATGGGAACAGCAATTTTTAAGGGAT	known,tcga,18cancers,cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	13	2	22	19	4333694	-	17	1129173	-	115.0383	5.3534	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-EW-A1PB-01A	ENSG00000178078	ENSG00000159842	STAP2	ABR	CAGCCTGATTCTCCGGGATCAGGAGATCAAGTTCAAG*ACTTCAGCTACGGGACGGACGAGTACGACGGAGAGGG	known,tcga,18cancers,cancer,exon-exon	BOWTIE	out-of-frame	0	13	2	18	19	4333694	-	17	1125367	-	115.0383	5.3534	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-EW-A1PB-01A	ENSG00000118849	ENSG00000177112	RARRES1	MRVI1-AS1	ACGAGTGCTGGCCGAGGTGCAGGAGGGCCGCGCGTGG*GAGCCCTGGTATTCCTTGAACATGCATACCTTTCCCA	antisense,cancer,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	7	2	24	3	158732140	-	11	10594117	+	737.0257	0.5111	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-EW-A1PB-01A	ENSG00000143774	ENSG00000171368	GUK1	TPPP	CAGGAGCACAGCGGCATCTTTGGCTTCAGCGTGTCCC*CAACATGGCTGACAAGGCCAAGCCTGCCAAAGCTGCC	18cancers,exon-exon	BOWTIE	CDS(truncated)/UTR	0	4	3	21	1	228145624	+	5	678064	-	90.8347	9.3471	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A3U0-01A	ENSG00000080298	ENSG00000178445	RFX3	GLDC	ACCCACCAACAACACCACAATAATCCACAGCCAAG*CGGAGCCCAGGGAGAATATGCTGGACTGGCCACTA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	47	11	24	9	3525747	-	9	6565429	-	3.4754	3.8415	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A3U0-01A	ENSG00000080298	ENSG00000178445	RFX3	GLDC	TATCTCTTCTCAGTTGCTTTGGAGCATTTACTAACAAGGACAGCCTAAAC*AATTGTGAACAAGGTTGACAAAATTCTTGCCTTCAGGGAAGGCCTCTCTG	tcga,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT	intronic/intronic	0	47	1	21	9	3454555	-	9	6567629	-	3.4754	3.8415	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A3U0-01A	ENSG00000104973	ENSG00000196961	MED25	AP2A1	GCCTATGAGTTTGTCACCTGGCTCGATGGCATTAA*GTAAGAGCAAAGAGGCGGAAATTAAGAGAATCAAC	tcga,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	37	10	23	19	49819296	+	19	49781757	+	11.3508	21.7521	TRUE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A3U0-01A	ENSG00000104973	ENSG00000196961	MED25	AP2A1	GTGGTCCTCCTGCTGAGACGGACTTCGGGGGAGAC*GTAAGAGCAAAGAGGCGGAAATTAAGAGAATCAAC	tcga,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	37	2	24	19	49818616	+	19	49781757	+	11.3508	21.7521	TRUE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A3U0-01A	ENSG00000104973	ENSG00000196961	MED25	AP2A1	GAGTTTGTCACCTGGCTCGATGGCATTAAGTGAGCTTTCCCCCACTTGGG*GTAAGAGCAAAGAGGCGGAAATTAAGAGAATCAACAAGGAACTGGCCAAC	tcga,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	37	2	20	19	49819317	+	19	49781757	+	11.3508	21.7521	TRUE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A3U0-01A	ENSG00000132849	ENSG00000117069	PATJ	ST6GALNAC5	GACCCGGGCTCCCACCTGCTCCTCCAGCGCACCAG*GGATCCCAATCACCCTTCAGTACCTTATCATTATT	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	36	6	21	1	61742555	+	1	77062975	+	2.8157	6.3042	TRUE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A3U0-01A	ENSG00000119318	ENSG00000070214	RAD23B	SLC44A1	TAGTTCCCAGAGTTGGTAACCCGAGAAGATGAGCCTTAAGAAAAAAAAAA*TGTAATTTGCTAAGAATAATTCATGATCTGTTTATGCGATAACTCCTTTT	18cancers,cancer	BOWTIE+STAR	UTR/UTR	0	33	1	15	9	107284160	+	9	105390283	+	28.1342	8.5375	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-EW-A3U0-01A	ENSG00000070214	ENSG00000119318	SLC44A1	RAD23B	TCCTCATTTATGCCATTTCAGCTACAGTGTTCACA*CCCAAAGCAGTGTCCACACCAGCACCAGCTACAAC	18cancers,cancer,exon-exon	BOWTIE	in-frame	0	33	9	24	9	105361330	+	9	107306379	+	8.5375	28.1342	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-EW-A3U0-01A	ENSG00000164548	ENSG00000002746	TRA2A	HECW1	TCTGAATCCCATTCTCGATCAAGATCAAAATCCAG*GAATTGATGCGCGTACACGTGGTGGGTCATTATGC	tcga,18cancers,chimerdb3seq,m14,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	16	6	23	7	23521707	-	7	43243875	+	20.4373	0.1664	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-EW-A3U0-01A	ENSG00000164548	ENSG00000002746	TRA2A	HECW1	TCTGAATCCCATTCTCGATCAAGATCAAAATCCAG*AATCTGTACCAGAACAGGTTTTTAGGCCTGGCCGC	tcga,18cancers,chimerdb3seq,m14,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	16	5	23	7	23521707	-	7	43311763	+	20.4373	0.1664	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-EW-A3U0-01A	ENSG00000164548	ENSG00000002746	TRA2A	HECW1	AGGGTTTCCAAACACTCTGAATCCCATTCTCGATCAAGATCAAAATCCAG*CTGCGGCTGCCTTGAGTGTCAGGAGTGGAACAGCCACACCTCTTCCCAGC	tcga,18cancers,chimerdb3seq,m14,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	16	1	18	7	23521707	-	7	43283920	+	20.4373	0.1664	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A3U0-01A	ENSG00000187231	ENSG00000144331	SESTD1	ZNF385B	CGGAGCCGCCGGCCGCTAGCGTCAGCGCCAGCCAG*ATGTTCTACATTTCAACTCCATCAAATATTAAATT	tcga,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	UTR/UTR	0	15	6	21	2	179264499	-	2	179770672	-	5.943	4.926	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A3U0-01A	ENSG00000249859	ENSG00000132016	PVT1	C19ORF57	ATGCACGTTCCATCCGGCGCTCAGCTGGGCTTGAG*CTCCCCTGATGAGGAAACAGGATCTCCCTGCCGGC	known,lincrna,oncogene,18cancers,cancer,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	14	7	22	8	127890998	+	19	13893223	-	0.5302	4.2735	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-EW-A3U0-01A	ENSG00000249859	ENSG00000132016	PVT1	C19ORF57	ATGCACGTTCCATCCGGCGCTCAGCTGGGCTTGAG*AACTCATTCGGGAGGTTTGTTCCCCAGTTTGCAAA	known,lincrna,oncogene,18cancers,cancer,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	14	3	22	8	127890998	+	19	13892890	-	0.5302	4.2735	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-EW-A3U0-01A	ENSG00000100626	ENSG00000182185	GALNT16	RAD51B	CTGGATCCCCAGTCATACTGCAGATGTGCAACCCTAGAGAAGGCAAGCAG*TTCCACGTTTAACTGAAGACACACAGAAATAAATGTGTGTTGGCAGAAAG	cancer,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	9	1	18	14	69348002	+	14	68387113	+	3.1355	2.4862	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A3U0-01A	ENSG00000019485	ENSG00000110455	PRDM11	ACCS	CCCAGGACAAATCAGCTGGCTTCTTCTCCTGGCTG*ATGTTCACCCTTCCTCAAAAGGACTTCAGGGCTCC	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	9	3	23	11	45183123	+	11	44067628	+	4.184	16.2924	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-EW-A3U0-01A	ENSG00000183454	ENSG00000262151	GRIN2A	AC133065.1	TTCATGGGGGCGCATCTATGATCATGGCTGACAAG*ACTCAGGATTACCATCTCTCAGCTGGGGCCATTTG	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	7	5	22	16	10179998	-	16	10865050	-	0.1296	0.2155	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-EW-A3U0-01A	ENSG00000183454	ENSG00000262151	GRIN2A	AC133065.1	CAGTTTTACCTGATTGTTTTGTGGGAAAATGTCCATTTTTTCCTCTTATG*ACTCAGGATTACCATCTCTCAGCTGGGGCCATTTGCATTATTCATTTAAA	antisense	BOWTIE+STAR	UTR/exonic(no-known-CDS)	0	7	1	21	16	10179562	-	16	10865050	-	0.1296	0.2155	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-EW-A3U0-01A	ENSG00000185630	ENSG00000279956	PBX1	AC073082.1	GTTTAATGTGTTGTGTGAAATCAAAGAAAAAACAG*CTTGAAAATATTCAGGATATCCAGTTACTGGCCAC	oncogene,cancer,tumor,exon-exon	BOWTIE	CDS(truncated)/UTR	0	7	2	21	1	164563311	+	2	48647119	-	5.8973	0.095	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-EW-A3U0-01A	ENSG00000129595	ENSG00000171444	EPB41L4A	MCC	AGTTAACCCTTACCACCCAGCAGCAGGGCATCAAG*GGAGGAAGATGAGTACTCAGAACTGCGATCAGAAC	oncogene,18cancers,cancer,tumor,exon-exon	BOWTIE	out-of-frame	0	5	3	22	5	112418941	-	5	113122826	-	0.974	2.4364	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-EW-A3U0-01A	ENSG00000132405	ENSG00000072840	TBC1D14	EVC	AAAATATTGGGGCCATTTAGTAACTTCTTTGCAAG*AGGACACTGATGGAGGCGGCAGTGGAGAGCGTCTA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	4	4	20	4	6924111	+	4	5801950	+	4.6426	5.2572	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A3U0-01A	ENSG00000151135	ENSG00000111783	TMEM263	RFX4	AATCCCATCATACCTTAATGATGAACCACCAGAAG*ATGAGGAAAAAGAAAATAATAGAGCATCCAAGCCC	tcga,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	3	2	16	12	106967180	+	12	106639332	+	7.1392	1.5366	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A3U0-01A	ENSG00000151135	ENSG00000111783	TMEM263	RFX4	TAAAAATCAACAAGAAATCCCATCATACCTTAATGATGAACCACCAGAAG*GGGCTGGAAACGAGGCAAATGAGGGGAAATGAAACGTTTGGCAGCCCCAT	tcga,chimerdb3seq,tcga-cancer,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	3	1	23	12	106967180	+	12	106630550	+	7.1392	1.5366	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A3U0-01A	ENSG00000162402	ENSG00000260971	USP24	AC119674.1	TGTTTGTGGAGAAAATGCCTGCTCGAATATACCAG*GAGAGAAATCTAGAAGTGGAATTGCTGAGCTGTAG	lincrna,cancer,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	3	5	24	1	55093937	-	1	56183620	-	8.2875	0.3222	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-EW-A3U0-01A	ENSG00000100418	ENSG00000235760	DESI1	HCG2040054	ACAAGGATGAGTTCTTCTTCGGCAGTGGTGGTATCTCCAGCTGCCCCCCG*GCTCACTCTGTCGCCCAGGCTGGAGTGCAGTGGTGTGATCTTGGCTCACT	antisense	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	15	22	41607262	-	2	47533038	+	10.8576	0.1698	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-EW-A3U0-01A	ENSG00000128567	ENSG00000150275	PODXL	PCDH15	GTCGCCGTCGCCGTCGCCGTCGCCCTCCCAGAATG*ATTGCAAACTAGCTAGGGGAGGACCACCAGCTACC	exon-exon	BOWTIE	in-frame	0	2	1	13	7	131556260	-	10	54527877	-	34.1391	0.7132	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-AO-A0J6-01A	ENSG00000111961	ENSG00000227220	SASH1	AL133346.1	TTCTTACCCAACGTTTGATGGCTCATCAAACTGCAAT*GTATTTCCTATATCTTCCTGTCTTTTCCATGGCCAAA	antisense,tumor,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	24	8	25	6	148487715	+	6	132077208	+	2.5131	2.4551	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AO-A0J6-01A	ENSG00000111961	ENSG00000227220	SASH1	AL133346.1	ACTGGCCAGATGGTTCTTACCCAACGTTTGATGGCTCATCAAACTGCAAT*ACAGAGTCTTGCTCTGTTGCCAGATTGGAGTGAAGTGGCGCGATCTCAGC	antisense,tumor	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	24	3	23	6	148487715	+	6	132074793	+	2.5131	2.4551	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AO-A0J6-01A	ENSG00000175581	ENSG00000254631	MRPL48	AP001372.1	CATTGGAAAGTACAAGCACTTAATTAAAGCAGAAGAG*AAAAAAACAGATTCTACTTGGTTCTAGCTGAAGTATT	antisense,ribosomal,m2,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	4	3	25	11	73825796	+	11	74484177	+	6.8862	0.2278	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AO-A0J6-01A	ENSG00000111785	ENSG00000227517	RIC8B	LINC01483	TAGGTCCAACTGAAGACAAAACAGAAGAGCTACACAG*GTGCCCAAAGGAGAGAGAGAATAAACTTGAACATTCT	lincrna,18cancers,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	3	2	19	12	106825820	+	17	69845440	+	2.7475	0.0435	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AO-A0J6-01A	ENSG00000111785	ENSG00000227517	RIC8B	LINC01483	TGTTTACTAATCGTAGGTCCAACTGAAGACAAAACAGAAGAGCTACACAG*ATTGGGACCAGAGCAGCCAGCAGATGTTTTCAATTTTGGGCCCTTTGTTT	lincrna,18cancers	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	3	1	19	12	106825820	+	17	69711576	+	2.7475	0.0435	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A156-01A	ENSG00000242802	ENSG00000108823	AP5Z1	SGCA	AGCCGTGTCCGAACCGCTGTGCTGTGCCCACAGTTCCTGGCCTGGAACAG*CCTGCAGATGAGGTGCCCACCCCAGGTGATGGGATCCTGGAGCATGACCC	NA	BOWTIE+BLAT	out-of-frame	0	8	1	19	7	4787650	+	17	50170164	+	2.3987	0.5719	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0I1-01A	ENSG00000149016	ENSG00000168000	TUT1	BSCL2	GACCTGTGGCCAGTGTTGTCATGGACAAGGACAAG*GTGCTGATGTATGGACAGCCGTATCGTGTTACCTT	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	305	20	24	11	62589031	-	11	62694711	-	6.625	0.2503	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-B6-A0I1-01A	ENSG00000073060	ENSG00000150990	SCARB1	DHX37	TGGTGCCGTCGCTCATCAAGCAGCAGGTCCTTAAG*GAGGAACGGCTGAAGCTCCCAATTCTCTCCGAAGA	tcga,cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	25	6	22	12	124863595	-	12	124977490	-	35.3505	24.8716	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-B6-A0I1-01A	ENSG00000173715	ENSG00000173120	C11ORF80	KDM2A	CAGTGCATTTCCAGTCCAGCAAATGGAAATCTGGG*ATGGACGGAGAGGGGTTGCTTAACGAAGAATTGCC	oncogene,tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	15	2	20	11	66816199	+	11	67248281	+	3.615	11.9758	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0I1-01A	ENSG00000173715	ENSG00000173120	C11ORF80	KDM2A	ACAAGGTCTTGGAGCAACATCACCAGGCTGCCAAG*ATGGACGGAGAGGGGTTGCTTAACGAAGAATTGCC	oncogene,tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	15	2	19	11	66821764	+	11	67248281	+	3.615	11.9758	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0I1-01A	ENSG00000135374	ENSG00000121691	ELF5	CAT	CCTGTACTTCATCCTCCAGAACATCCGCACACAAG*GTGGTGCTCCAAATTACTACCCCAACAGCTTTGGT	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	15	7	21	11	34493479	-	11	34464105	+	134.7693	14.8448	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-B6-A0I1-01A	ENSG00000135374	ENSG00000121691	ELF5	CAT	CCTGTACTTCATCCTCCAGAACATCCGCACACAAG*GGCCGCCTTTTTGCCTATCCTGACACTCACCGCCA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	15	1	14	11	34493479	-	11	34461251	+	134.7693	14.8448	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-B6-A0I1-01A	ENSG00000249859	ENSG00000062485	PVT1	CS	ATGCACGTTCCATCCGGCGCTCAGCTGGGCTTGAG*TTGATTTATGAAGACTCTATGGATCTAATCGCAAA	lincrna,oncogene,18cancers,cancer,m5,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	6	3	23	8	127890998	+	12	56276195	-	1.6756	21.7094	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0I1-01A	ENSG00000066629	ENSG00000090061	EML1	CCNK	GTACGACACGTCCTCGCTGCTCCAGTTCTGCAACG*GATTCTAACATTTTCAGAGAACCTTTTGGAAAGAA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	4	1	14	14	99793543	+	14	99492626	+	2.0208	0.5665	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-B6-A0I1-01A	ENSG00000126460	ENSG00000161609	PRRG2	CCDC155	AGGCCAGGGAGTATTTTGAGGACAACACTCTCACG*GAACTGAGGCTGGAGATTTCACGCCTGGAGGAGCA	tcga,cell_lines,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	4	2	16	19	49583717	+	19	49408967	+	2.6403	0.6793	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-B6-A0I1-01A	ENSG00000078699	ENSG00000101421	CBFA2T2	CHMP4B	GCCTGCATTGGCCTCCCAACGTGCTGGGATTACAG*GGACATCGATAAAGTTGATGAGTTAATGCAGGACA	known,tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	3	1	14	20	33600465	+	20	33850952	+	6.8046	151.8234	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A0B3-01A	ENSG00000145685	ENSG00000182132	LHFPL2	KCNIP1	CATTAAGACTTCCCAGCATTCCTACAGATATAAATAG*ATAAGATTGAAGATGAGCTGGAGATGACCATGGTTTG	chimerdb3seq,exon-exon	BOWTIE	UTR/CDS(truncated)	0	111	15	24	5	78564813	-	5	170718758	+	12.4538	14.7031	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0B3-01A	ENSG00000145685	ENSG00000182132	LHFPL2	KCNIP1	ATTTTGCTTTGAGTCAGGAAAAGAAAACCCAGCAGTCACAAGGCACCAGA*ATAAGATTGAAGATGAGCTGGAGATGACCATGGTTTGCCATCGGCCCGAG	chimerdb3seq	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	111	2	23	5	78534529	-	5	170718758	+	12.4538	14.7031	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0B3-01A	ENSG00000185122	ENSG00000151388	HSF1	ADAMTS12	CGACCCGGACACCGACGCGCTCATCTGCTGGAGCCCG*GTATCCGCCGCCAAACTGCCCATTGCATAAAGAAGGG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	26	10	25	8	144291874	+	5	33596060	-	18.978	17.6999	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0B3-01A	ENSG00000145715	ENSG00000213585	RASA1	VDAC1	CTTTTACTTTGCAGGAGAAACTCCAGAACAAGCAGAG*CAGAAGATGGCTGTGCCACCCACGTATGCCGATCTTG	cancer,tumor,exon-exon	BOWTIE	CDS(truncated)/UTR	0	21	8	23	5	87369900	+	5	133993018	-	4.5885	73.7027	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A0B3-01A	ENSG00000204120	ENSG00000182177	GIGYF2	ASB18	AAATCTCCTGCTGTGAACCAGCAGAATTTTTGAACAG*GCCTCTGGACCCTGGAGTACAAGCGTGAGCTCACCAC	exon-exon	BOWTIE	UTR/CDS(truncated)	0	11	2	23	2	232703489	+	2	236237956	-	3.1953	1.6179	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A8-A092-01A	ENSG00000204580	ENSG00000204568	DDR1	MRPS18B	TGAGTTTGACCGGCTGAGGGCCTTCCAGGCTATGCAG*GTTCCCCTCCAGACTCTTTGCACCAAAGCTCCCTCTG	ribosomal,18cancers,cancer,exon-exon	BOWTIE	in-frame	0	15	2	20	6	30892188	+	6	30619493	+	52.5761	78.266	TRUE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-B6-A0RU-01A	ENSG00000177628	ENSG00000116521	GBA	SCAMP3	TGCCTCCGGTTGGGGCTGCTGTTTCTCTTCGCCGACG*CTCGACAGAACAATTGGCCCCCTCTACCTTCTTTTTG	tcga,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	58	7	22	1	155244506	-	1	155258954	-	26.0463	43.411	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0RU-01A	ENSG00000177628	ENSG00000116521	GBA	SCAMP3	TGCCTCCGGTTGGGGCTGCTGTTTCTCTTCGCCGACG*GCCTCAGCTGCAGCAGCCACAGCTGAGCTGCTGAAGA	tcga,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	58	5	24	1	155244506	-	1	155260450	-	26.0463	43.411	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0RU-01A	ENSG00000177628	ENSG00000116521	GBA	SCAMP3	TGGGATTTCGTTTTGCCTCCGGTTGGGGCTGCTGTTTCTCTTCGCCGACG*GAGAAAGCTCAGCCCCACAGAACCTAAGAACTATGGCTCATACAGCACTC	tcga,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K	BOWTIE+BLAT	UTR/CDS(truncated)	0	58	3	24	1	155244506	-	1	155260588	-	26.0463	43.411	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0RU-01A	ENSG00000177628	ENSG00000116521	GBA	SCAMP3	ACAGGCACCCGCCACCACGCACGGCTAATTTTTTGTATCTTTTAGTAGAG*AAAGCTCAGCCCCACAGAACCTAAGAACTATGGCTCATACAGCACTCAGG	tcga,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K	BOWTIE+BLAT	UTR/CDS(truncated)	0	58	2	22	1	155244229	-	1	155260585	-	26.0463	43.411	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0RU-01A	ENSG00000177200	ENSG00000182185	CHD9	RAD51B	TTTACATGACAGAAATCACCTATGTTTACAGCGACAG*GTTATCTTGACGAATCAGATTACAACCCATCTGAGTG	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	6	3	23	16	53157541	+	14	68291884	+	4.1486	5.1444	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-B6-A0RU-01A	ENSG00000196187	ENSG00000198121	TMEM63A	LPAR1	CAAGTGACAAAGGAAGTGAGGCAGAGGCCCACATGCCCCCACCGTTCACA*CATCTTATGCACCAGCTTTGGAGAAGACACAGGACTCAGTGTTACTATAT	cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	5	1	24	1	225848492	-	9	110997865	-	7.3008	5.9525	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Breast	TCGA-B6-A0RU-01A	ENSG00000262583	ENSG00000166822	AC009163.5	TMEM170A	CCCAGGGATTTTCCTGGACGGGATTGTGAAGTAGCGG*AGATGTGGTATGGTGTATTCCTGTGGGCACTGGTGTC	pseudogene,10K<gap<100K,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	3	2	15	16	75516203	-	16	75451839	-	0.0223	3.7799	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	transcribed_unprocessed_pseudogene	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-C8-A12L-01A	ENSG00000164941	ENSG00000258256	INTS8	AC011773.3	CTGAACACATTTCTATTTGGCCATCTTCCATTCCCAA*GAAGACTTCTTCCAAGTTGCTGGAGGAGATGGCCACT	antisense,oncogene,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	72	12	24	8	94867337	+	8	85222853	-	7.718	2.7462	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-C8-A12L-01A	ENSG00000164941	ENSG00000258256	INTS8	AC011773.3	AGATTGGAAAAGCTCTCTGTCTCATCCAGGGATTTGGAGGGTCAGAGCAG*GAAGACTTCTTCCAAGTTGCTGGAGGAGATGGCCACTAGTAGCCTTGATT	antisense,oncogene	BOWTIE+BLAT;BOWTIE+STAR	intronic/exonic(no-known-CDS)	0	72	1	24	8	94868473	+	8	85222853	-	7.718	2.7462	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-C8-A12L-01A	ENSG00000138688	ENSG00000152990	KIAA1109	ADGRA3	GGAACAAAGACTTCTGCTAGCAAAACTGGAATACCAG*GTTGGGATAATTCTTCACTATTCCACCCTTGCCACAG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	29	10	23	4	122339408	+	4	22392690	-	3.8599	2.8439	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-C8-A12L-01A	ENSG00000270647	ENSG00000198162	TAF15	MAN1A2	TTCATGAGAGGAGGTGGAAGTGGAGGTGGGCGGCGAG*ATCATACATCTGTCGGTGGCCTGGGAGACAGTTTTTA	oncogene,tcga,cell_lines,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	26	8	25	17	35842459	+	1	117493147	+	14.7592	23.353	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-C8-A12L-01A	ENSG00000196482	ENSG00000143199	ESRRG	ADCY10	TTCATGAAAATGCAGATCCACTGAGAAAGGGAATAAG*ATCATTAAGGCTTACCTAGACTATTCGCTATACCACC	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	20	3	23	1	216865061	-	1	167824855	-	0.8718	1.2142	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-C8-A12L-01A	ENSG00000196482	ENSG00000143199	ESRRG	ADCY10	TTCATGAAAATGCAGATCCACTGAGAAAGGGAATAAG*GAAGAAGAGGCTGGCACAACTTTACCGGCAAACTGTC	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	20	2	23	1	216865061	-	1	167829423	-	0.8718	1.2142	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-C8-A12L-01A	ENSG00000196482	ENSG00000143199	ESRRG	ADCY10	TGTGAAGGAAGCGCTTTGCAAAAAACCCAACTAACCAACCAAACGAACAG*ATCATTAAGGCTTACCTAGACTATTCGCTATACCACCACCTGGCTGGCTA	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	20	1	22	1	216828353	-	1	167824855	-	0.8718	1.2142	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-C8-A12L-01A	ENSG00000117174	ENSG00000107890	ZNHIT6	ANKRD26	CCAAGAGGAAGGAGAATTCAACCTTTTTTGATAAGAA*GTTGTTGTGAGACAACTTCAACAAGAACTAGCTGATA	oncogene,tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	8	1	14	1	85702157	-	10	27033377	-	4.1688	1.658	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-C8-A12L-01A	ENSG00000109920	ENSG00000245532	FNBP4	NEAT1	ATTGCCTGAGGGAATAAAAGAAGAAGAAGAGAGATGGAGAAGAAAAGTAA*TTTAGGCTCCAGTTTTTGTTGTTGTTGTTAATAAAATGCAATGGAATGTA	lincrna,oncogene,cancer	BOWTIE+BLAT	CDS(truncated)/exonic(no-known-CDS)	0	5	1	22	11	47746265	-	11	65433266	+	7.5993	14.5729	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-C8-A12L-01A	ENSG00000196365	ENSG00000076984	LONP1	MAP2K7	CAACCCGGTGTTCCCGCGCTTTATCAAGATTATCGAG*CCCTGCAGCTCCCGCTGGCCAACGATGGGGGCAGCCG	known,oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	5	3	24	19	5719704	-	19	7909755	+	17.6277	8.3936	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-C8-A12L-01A	ENSG00000148120	ENSG00000158079	C9ORF3	PTPDC1	GGCGATCGGTTACATGGACCTCAGACCAGAGTGGCAG*ACTACCATGGCTGCAGGAGTCTTGCCTCAGAATGAAC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	4	2	24	9	94760580	+	9	94064734	+	1.0024	1.8563	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-C8-A12L-01A	ENSG00000171017	ENSG00000161091	LRRC8E	MFSD12	AGTGCGGGACAAGATGGAGGAGGAATGAAGCTGGGGTGGGGCCGTTTTAG*AACAGCGGAGCGTTCGTGTACGGCTCCATGAGCTTCTTGGATAAGGTGGC	18cancers	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	4	2	23	19	7900935	+	19	3546168	-	0.3132	20.4766	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-C8-A12L-01A	ENSG00000134247	ENSG00000134250	PTGFRN	NOTCH2	GTGTCTTCCCCAGCTGGTGTGGGTGTGACCTGGCTAG*GACAGTTCTGCACAGAGGATGTGGATGAATGCCTGCT	known,tcga,cell_lines,18cancers,chimerdb3seq,cancer,m3,tcga-cancer,exon-exon	BOWTIE	in-frame	0	4	4	24	1	116949572	+	1	119969744	-	64.4469	41.0697	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-C8-A12L-01A	ENSG00000136828	ENSG00000196814	RALGPS1	MVB12B	CGAAGCCTGAAGATGGTTCCAAGTATTCCCTATCTAG*TACGAGTACAGCTTCCGCACAGAGCAGAGCGCAGCCG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	4	3	23	9	127069356	+	9	126503177	+	2.3055	4.4673	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A0YG-01A	ENSG00000143164	ENSG00000197965	DCAF6	MPZL1	CTGGAGGACCCGTCCCGGCTGCGGAGTCGCTACCTGG*TGACAGCTGGAGTATCAGCCTTGGAAGTATATACGCC	known,tcga,cell_lines,18cancers,chimerdb3seq,m45,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	72	14	24	1	167937008	+	1	167765583	+	32.0736	99.9272	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A0YG-01A	ENSG00000198929	ENSG00000117501	NOS1AP	MROH9	TATCTTCAGGTGTAACGTCTTTAAATCCAAGAAGAAG*CTTCTGAATAACTTCTTCAAGGACCCTTTACCAGAAG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	37	9	24	1	162333125	+	1	171014117	+	1.2129	1.4736	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A0YG-01A	ENSG00000143179	ENSG00000143376	UCK2	SNX27	CCTTATAGGCGTCAGCGGGGGAACAGCTAGCGGCAAG*GAACCACGTGAATGTTGAGGGGGCGACACACAAGCAG	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	14	7	25	1	165827932	+	1	151638888	+	6.8827	5.1337	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A0YG-01A	ENSG00000152894	ENSG00000231312	PTPRK	AC007388.1	CAAGAGCCTCATTATCTACCACCCGAGATGCCCCAAG*AGTGGTTGATCATACTGTAAAACTCAAATGTGAAGGG	antisense,cancer,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	11	5	23	6	128397566	-	2	39599366	+	13.6916	0.6449	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A0YG-01A	ENSG00000139865	ENSG00000151338	TTC6	MIPOL1	GAGCGTCCTTGGCCAGAACTACGACATTACAATGGAA*GCAAAGTTGTTATCTATGCAACAAGCCAGAGAAACTG	known,tcga,prostates,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	10	3	25	14	37623003	+	14	37422855	+	1.3846	2.2419	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A0YG-01A	ENSG00000167232	ENSG00000137075	ZNF91	RNF38	AATATGAAGCAACATGAGATGGTGGATGAACCCACAG*GTAGTGTTGGTGCTTCTTTTCAGTGCCAGTCCATCCA	18cancers,m4,exon-exon	BOWTIE	CDS(truncated)/UTR	0	6	7	24	19	23373742	-	9	36424683	-	4.5997	12.5231	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A0YG-01A	ENSG00000054611	ENSG00000283406	TBC1D22A	DGCR5	TTCAAGCAGCTGCTTGCCGGCCCCAACACGGACCTTG*GGCACCAACTGGACAGAGGCCTCCGGTCAGCCTCACT	exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	4	4	25	22	46797620	+	22	19030782	+	3.9957	NA	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-A2-A0YG-01A	ENSG00000105738	ENSG00000136813	SIPA1L3	KIAA0368	GCAGTGAGCCGAGATCGCGCCACCGCACTCCAGCATGGGCGACAGAGCAA*TCATTCCAGCTCTGCTAGAGTCCTTAAGTGTATTGGAGCCCCAAGTTCTC	NA	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	14	19	38054587	+	9	111378665	-	13.3753	26.7603	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AN-A04D-01A	ENSG00000244754	ENSG00000189167	N4BP2L2	ZAR1L	CAACTTGGTGATGCCCATGACTGGAACCAGAACAGAG*ACCTGCTCAAAGTCTCATTGTTCCTGTCCTCAAAAGA	100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	36	7	23	13	32527408	-	13	32304022	-	0.5882	3.1815	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-AN-A04D-01A	ENSG00000244754	ENSG00000189167	N4BP2L2	ZAR1L	GTATAATGTTAATCAACTTGGTGATGCCCATGACTGGAACCAGAACAGAG*AAAGGTACATCTTGGCCAGGCATGGTGGCTCACTCTTGTAATCCCAGCGC	100K<gap<200K	BOWTIE+STAR	CDS(truncated)/intronic	0	36	2	19	13	32527408	-	13	32305123	-	0.5882	3.1815	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-AN-A04D-01A	ENSG00000186106	ENSG00000186501	ANKRD46	TMEM222	AAGCTGCCGCTGTCGCTGCTGCTCGTTCGAGTCGCAG*GTGGTTTTTCCCCATCATCGGCCACATGGGCATCTGC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	14	13	24	8	100559711	-	1	27330720	+	3.8915	14.051	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-AN-A04D-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	CCGCCTGCCTCAGCCTCCAAAGTAGCTGAGACTACAG*CAGTTTAAGTATAGTGTGCCTGGGTTGGGTGCGGTGG	antisense,m3,exon-exon	BOWTIE	exonic(no-known-CDS)/UTR	0	7	4	24	10	87246115	-	10	46593287	+	0.4047	0.0422	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AN-A04D-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	CCGGAGCTTCTCAGAAGACAGAGGGTTTTCTTTTGAG*ATTCCAGTTCTTTGATGAAAGTCTCTATTCCACCCAT	antisense,m3,exon-exon	BOWTIE	exonic(no-known-CDS)/UTR	0	7	2	24	10	87288442	-	10	46593989	+	0.4047	0.0422	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AN-A04D-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	CCGGAGCTTCTCAGAAGACAGAGGGTTTTCTTTTGAG*CAGTTTAAGTATAGTGTGCCTGGGTTGGGTGCGGTGG	antisense,m3,exon-exon	BOWTIE	exonic(no-known-CDS)/UTR	0	7	2	21	10	87288442	-	10	46593287	+	0.4047	0.0422	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AN-A04D-01A	ENSG00000132122	ENSG00000269113	SPATA6	TRABD2B	GGTGTTCCCGGACGCAGTAGATCCTGGAGATGTGGTTACACAGCTTGAAT*GACAAGATCTAAGCTCGAGCCTGAATTTATGGACCGCCATGGGGTGCTCT	NA	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	3	1	20	1	48451552	-	1	47881022	-	3.8797	0.2009	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000123130	ENSG00000184831	ACOT9	APOO	AGACATCCATGGAAGTGAAGATGCAAATGTTCCAG*GTAATTCAGAGGTCCGTGGGGCCAGCCAGCCTGAG	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	340	17	24	X	23721881	-	X	23880952	-	31.9629	78.1437	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000123130	ENSG00000184831	ACOT9	APOO	TGGCAGGATTCTTGAGGATCTTGACAGCTTGGGAG*TTATAGGTAAACATTGGAAACTCCATAGAATAAAT	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	340	16	24	X	23730527	-	X	23833612	-	31.9629	78.1437	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000123130	ENSG00000184831	ACOT9	APOO	CGGCAGCCTAGCGCAATGAGGCGGGCAGCACTGCG*GAAAAACTAGACCAGACCTCTGTTATCTTCTGTGA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	340	12	24	X	23743125	-	X	23833510	-	31.9629	78.1437	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000123130	ENSG00000184831	ACOT9	APOO	TTTGTAATGGTGGCTCGTGATTCTGAAAATAAAGG*GTAATTCAGAGGTCCGTGGGGCCAGCCAGCCTGAG	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	340	11	24	X	23713135	-	X	23880952	-	31.9629	78.1437	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000123130	ENSG00000184831	ACOT9	APOO	TGGCAGGATTCTTGAGGATCTTGACAGCTTGGGAG*GAAAAACTAGACCAGACCTCTGTTATCTTCTGTGA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	340	9	23	X	23730527	-	X	23833510	-	31.9629	78.1437	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000123130	ENSG00000184831	ACOT9	APOO	CGGCAGCCTAGCGCAATGAGGCGGGCAGCACTGCG*TTATAGGTAAACATTGGAAACTCCATAGAATAAAT	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	340	8	24	X	23743125	-	X	23833612	-	31.9629	78.1437	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000123130	ENSG00000184831	ACOT9	APOO	AGACATCCATGGAAGTGAAGATGCAAATGTTCCAG*CTTTCACTCTACTCAGTTCCTGAGGGTCAATCGAA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	340	2	18	X	23721881	-	X	23879034	-	31.9629	78.1437	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000123130	ENSG00000184831	ACOT9	APOO	ATGTTGTATATCTCGTATTTCATATTGCATCGTATCAGGAGGTACAGGTT*GTCTTTCTGTAGAACTGCCTAAGAGCCGGGAGAATTCATGCTTTTGAAAC	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K	BOWTIE+BLAT	intronic/UTR	0	340	1	22	X	23711801	-	X	23883962	-	31.9629	78.1437	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000123130	ENSG00000184831	ACOT9	APOO	CTTTATTTTTGTTTCAGTTCGAGATAAGTTGCGGGAGATAGTAGGAGCAT*ACAGCTATGACTATCTCCAAAATGCACCTCCTGGATTTTTTCCGAGACTT	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K	BOWTIE+BLAT	in-frame	0	340	1	20	X	23733185	-	X	23868688	-	31.9629	78.1437	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000123130	ENSG00000184831	ACOT9	APOO	CGGCAGCCTAGCGCAATGAGGCGGGCAGCACTGCG*GTAATTCAGAGGTCCGTGGGGCCAGCCAGCCTGAG	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	340	1	13	X	23743125	-	X	23880952	-	31.9629	78.1437	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000092929	ENSG00000167881	UNC13D	SRP68	GTGGAGCTTTGCTACATGAACACCAACTTGGTGCAGGAGAACTTCAGCAG*TACCATGGATTTGAAATGAACTCATCCTTGCTGTGAGCATCCAGGAGCCC	18cancers,chimerdb3seq,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	41	7	21	17	75832966	-	17	76039342	-	34.9329	17.1066	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000092929	ENSG00000167881	UNC13D	SRP68	CTCTCCTCCCACGGCCCCTCCTTCCTGGGCCCCAGCATCCGTTCTGAGGG*CCCTGTGAGCTGTGATTGATTGCCTTTGGTCAGTAATGCGTTCAGGAGTC	18cancers,chimerdb3seq,100K<gap<200K	BOWTIE+BLAT	UTR/UTR	0	41	1	23	17	75832874	-	17	76039441	-	34.9329	17.1066	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000177479	ENSG00000132153	ARIH2	DHX30	AAACAGCCAACTACATTAGTGCTCACACTAAAGAC*AGCCTGGGCCTGGTGGACAGGAACAACGAACCGCT	tcga,cell_lines,18cancers,chimerdb3seq,m11,tcga-cancer,exon-exon	BOWTIE	in-frame	0	15	8	23	3	48973816	+	3	47845700	+	8.2969	14.6475	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000152558	ENSG00000137675	TMEM123	MMP27	TGGGCTTCCACACAACTCCAGTGCTAACTCAACAG*GTTTGATGAAATGACCCAAACCATGGACAAAGGGT	known,tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	15	12	23	11	102448812	-	11	102693041	-	202.0409	7.3303	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000140694	ENSG00000085721	PARN	RRN3	CCAGGGATTTGATTTTAATAAAGTTTTTCGAAATG*ATCTTCCTGCAAATTTTGACACATGTCACAGAGCC	tcga,chimerdb3seq,m9,tcga-cancer,exon-exon	BOWTIE	in-frame	0	13	5	24	16	14617590	-	16	15084705	-	11.1519	34.2814	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000185630	ENSG00000162946	PBX1	DISC1	GTTTAATGTGTTGTGTGAAATCAAAGAAAAAACAG*AAACAAGTGTGAAGGAAAATACTATGAAGTACATG	oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	12	7	21	1	164563311	+	1	231958828	+	7.8257	5.552	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000171456	ENSG00000101337	ASXL1	TM9SF4	AACTGCCTGGCCGAATCAGCCTTTTCACGCTCAAG*GATTGGTTGCCGTGGTCTTTACTGCTTTTCTCCCT	tcga,cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	9	5	22	20	32369123	+	20	32133013	+	9.7814	30.8676	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000182541	ENSG00000184792	LIMK2	OSBP2	ACTGTCAACGAAACCTGGCACGGCTCTTGCTTCCG*ATGACTCTGGGGACGACGACGAGGCTACCACCCCA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	7	6	23	22	31225819	+	22	30870429	+	17.241	2.7455	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000149761	ENSG00000256481	NUDT22	AP006333.2	TCTTTTCCAGTGTCCTTCAGGAGATCTGTGATGAG*GAGCTGTCACTGCCTCTCTCCTTGATGGCGGGGTA	antisense,100K<gap<200K,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	7	3	24	11	64227666	+	11	64086914	+	3.49	2.0168	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000164970	ENSG00000196092	FAM219A	PAX5	AGGTGCCCACCGCGCACTCGGAGATGCAGCCGCTG*ACCACAGAGTATTCAGCCATGGCCTCGCTGGCTGG	cell_lines,18cancers,cancer,tumor,exon-exon	BOWTIE	in-frame	0	5	3	23	9	34458204	-	9	36923484	-	6.4625	4.7251	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000100151	ENSG00000100129	PICK1	EIF3L	ACAACGACTGCTACGCAGTGCTGCGGGATGCCGACGTCTTCCCCATCGAG*GGGGGACCTTCCTTGGAGCAGAGGTTTGAATCCTATTACAACTACTGCAA	cancer,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	5	2	20	22	38074967	+	22	37862969	+	8.3875	36.2805	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000121211	ENSG00000164144	MND1	ARFIP1	CAAGGAAACATAAGTTGGAGGTTCTGGAATCTCAG*GATTTGAAGCATTCATTACCATCTGGACTTGGTCT	18cancers,tcga-cancer,exon-exon	BOWTIE	in-frame	0	4	1	13	4	153358622	+	4	152863606	+	0.2714	10.6629	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000078114	ENSG00000138081	NEBL	FBXO11	AACATGCCATGGAGGTCAATAAACACCAGAGTAAT*ATGATGATGTGCCTGCAGATATGGTTGCAGAAGAA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	4	2	15	10	20880794	-	2	47839769	-	24.4764	10.7087	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000108774	ENSG00000141699	RAB5C	RETREG3	CCGGCCCCAAGTAACGCCGCCGCCCCGGAGCCGCC*TTGTCACTGTCATGATGTGGCCCCTTGCTGTGTAC	18cancers,cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	4	2	21	17	42154893	-	17	42585262	-	19.1147	44.3167	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000163125	ENSG00000136631	RPRD2	VPS45	AAGCACAATACAAAGAAGTAAAAGTGGTGGCTAAT*TGGACATATCAGGCCATGGTCCACGAACTACTAGG	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	4	1	14	1	150446401	+	1	150081342	+	9.8556	12.1805	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000074219	ENSG00000268006	TEAD2	PTOV1-AS1	CGCCTATGTCTTCGAGGTCTCCACCAGCGAGCGTGGGGCCCAGCATCACA*TCTCAAAAACAAGAATGTAATGTCGTGTGCTAACTAGGAGACCAATACTG	antisense,chimerdb3seq,m2	BOWTIE+BLAT	CDS(truncated)/intronic	0	4	4	23	19	49341347	-	19	49848110	-	66.9445	1.9579	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000074219	ENSG00000268006	TEAD2	PTOV1-AS1	TGAACAGCGTCCTGGAAAACTTCACCATCCTCCAG*TTTCACTCTTGCAGCCCAGACTGGTGTGCAATGGT	antisense,chimerdb3seq,m2,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	4	2	21	19	49342438	-	19	49844892	-	66.9445	1.9579	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000071564	ENSG00000065000	TCF3	AP3D1	CACGCCGCCTGTCAGCGGGGCCGACAGCCTCCTGG*AAATCTCCCAAGCCTAAGAAGAAGAAGCACAGGAA	oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	3	4	20	19	1621838	-	19	2111828	-	15.3172	14.633	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000163933	ENSG00000272886	RFT1	DCP1A	TATCTACGGAGGGACCATGCTTAGCTCAGGATCCG*TGTCGATATATAGTATCTGGTTTTATGACAAGAAT	18cancers,chimerdb3seq,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	2	3	23	3	53103953	-	3	53319473	-	7.3949	14.0684	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000187531	ENSG00000176155	SIRT7	CCDC57	AGGCTGCCAGCAGAGCAGACACCATCCTGTGTCTAGGGTCCAGCCTGAAG*CCCGAATGCTGGTGGAGCCTCCGCTGGAGATCACACAGGGCTCCAGTGAC	tcga,chimerdb3seq,tcga-cancer,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	14	17	81914294	-	17	82115258	-	7.7819	3.7169	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000084463	ENSG00000070019	WBP11	GUCY2C	GATAATCCGAGACATGGAGAAATTGGATGAAATGG*AAAATATAGAAAAGATTATGAACTTCGTCAGAAAA	10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	2	2	19	12	14799635	-	12	14656617	-	17.1273	1.1351	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-EW-A1PH-01A	ENSG00000156735	ENSG00000129559	BAG4	NEDD8	CTGGCCAGAGCCTGGTCGAGCCGGAGGAAGCCACCAG*ACGCTGACCGGAAAGGAGATTGAGATTGACATTGAAC	tcga,18cancers,chimerdb3seq,m50,tcga-cancer,exon-exon	BOWTIE	in-frame	0	115	20	24	8	38177139	+	14	24218431	-	29.4241	13.5359	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A1PH-01A	ENSG00000077380	ENSG00000224638	DYNC1I2	AC106900.1	GAAGCCAAGACTCTGGAGATGGCGCCGTGGGATCTAG*GTTGCCTGTGCTGCATGGAAGAACAGTTGACTTTGCT	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	94	15	25	2	171707377	+	2	173881690	-	22.7765	NA	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-EW-A1PH-01A	ENSG00000077380	ENSG00000224638	DYNC1I2	AC106900.1	CCAAGTGAAGCTGGAAGCCAAGACTCTGGAGATGGCGCCGTGGGATCTAG*GCTAAACTTGTGGGATTTTACTTGCTCTGGTCTCCAGTCCTAAAAAGAAA	lincrna	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	94	2	21	2	171707377	+	2	173884320	-	22.7765	NA	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-EW-A1PH-01A	ENSG00000077380	ENSG00000224638	DYNC1I2	AC106900.1	CCAAGTGAAGCTGGAAGCCAAGACTCTGGAGATGGCGCCGTGGGATCTAG*GGCCTGCTGTAGACAGAGCATGACATGTGAGTTCTCTCCTATTCTGTTCG	lincrna	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	94	1	23	2	171707377	+	2	173883488	-	22.7765	NA	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-EW-A1PH-01A	ENSG00000077380	ENSG00000224638	DYNC1I2	AC106900.1	TTTGTTTTAGGATCCTGCATACATGTTGGGACTTGCTTTTCAAAAGTTCA*GCTAAACTTGTGGGATTTTACTTGCTCTGGTCTCCAGTCCTAAAAAGAAA	lincrna	BOWTIE+BLAT;BOWTIE+STAR	intronic/intronic	0	94	1	19	2	171707997	+	2	173884320	-	22.7765	NA	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-EW-A1PH-01A	ENSG00000077380	ENSG00000224638	DYNC1I2	AC106900.1	CCAAGTGAAGCTGGAAGCCAAGACTCTGGAGATGGCGCCGTGGGATCTAG*ATCATGTCAAAGAAAACCCAGCCTCTGTGTGAAGGCAGAGTCCACTTTTG	lincrna	BOWTIE+STAR	CDS(truncated)/intronic	0	94	1	17	2	171707377	+	2	173883432	-	22.7765	NA	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-EW-A1PH-01A	ENSG00000147548	ENSG00000197140	NSD3	ADAM32	CAGTGTAACTAATTTTTATATGTTAACTGTTACCAAG*ATCCAGCTCAGAAGGCAGCACTCAGACATATGCCAGC	oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	83	16	25	8	38281467	-	8	39274312	+	29.9159	0.6346	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A1PH-01A	ENSG00000147548	ENSG00000197140	NSD3	ADAM32	CAGTGTAACTAATTTTTATATGTTAACTGTTACCAAG*ATCCAAATCAGAAGATAGTGCTGAAGCATATACTAGC	oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	83	5	21	8	38281467	-	8	39281136	+	29.9159	0.6346	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A1PH-01A	ENSG00000147548	ENSG00000197140	NSD3	ADAM32	ATGCAGATTGCGAATCAAGCGAGCCCACGAGAACAGT*ATCCAGCTCAGAAGGCAGCACTCAGACATATGCCAGC	oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	83	4	21	8	38281500	-	8	39274312	+	29.9159	0.6346	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A1PH-01A	ENSG00000147548	ENSG00000197140	NSD3	ADAM32	CAGTGTAACTAATTTTTATATGTTAACTGTTACCAAG*ATCCAAATCACAGGACAGTACCCAAACACAAAGCAGT	oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	83	4	17	8	38281467	-	8	39283586	+	29.9159	0.6346	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A1PH-01A	ENSG00000147548	ENSG00000197140	NSD3	ADAM32	ATGCAGATTGCGAATCAAGCGAGCCCACGAGAACAGT*ATCCAAATCAGAAGATAGTGCTGAAGCATATACTAGC	oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	83	3	19	8	38281500	-	8	39281136	+	29.9159	0.6346	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A1PH-01A	ENSG00000147548	ENSG00000197140	NSD3	ADAM32	CAGTGTAACTAATTTTTATATGTTAACTGTTACCAAG*AACCAGATCAGAAAGCAGCAGTCAAGCTGATACTAGC	oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	83	1	13	8	38281467	-	8	39275828	+	29.9159	0.6346	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A1PH-01A	ENSG00000118217	ENSG00000198574	ATF6	SH2D1B	TGTCCTACAAAGTACCATGAGAAATGTCGGTTCAGAT*AACAGTAACAGCGATTATGTGGATGTCTTGCCTTGAA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	69	15	25	1	161802272	+	1	162397315	-	34.3519	8.812	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A1PH-01A	ENSG00000118217	ENSG00000198574	ATF6	SH2D1B	CCGTGACTAAACCTGTCCTACAAAGTACCATGAGAAATGTCGGTTCAGAT*GCATAGGTCCAGAGCACCAAACTCTAGTGGACAATTCAGACTCTCCTGGT	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	69	1	20	1	161802272	+	1	162397209	-	34.3519	8.812	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A1PH-01A	ENSG00000105223	ENSG00000130402	PLD3	ACTN4	TGGGGCTGGGTCTCGGAGTGGGAGACGTGGAGTGCAG*CTGGAAGGATGGTCTTGCCTTCAATGCCCTGATCCAC	oncogene,18cancers,chimerdb3seq,exon-exon	BOWTIE	UTR/CDS(truncated)	0	13	6	24	19	40348768	+	19	38708117	+	169.9512	347.2154	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A1PH-01A	ENSG00000105223	ENSG00000130402	PLD3	ACTN4	CTAGGAGGGGCCGTCAGGCGGGGATACAGCCTGGAAG*CTGGAAGGATGGTCTTGCCTTCAATGCCCTGATCCAC	oncogene,18cancers,chimerdb3seq,exon-exon	BOWTIE	UTR/CDS(truncated)	0	13	2	24	19	40348724	+	19	38708117	+	169.9512	347.2154	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A1PH-01A	ENSG00000118007	ENSG00000229688	STAG1	ISPD-AS1	AGGAAAAAGAAAAAGGGGTCGTCCTGGCCGGCCTCCA*ATTTGATATCAAAGTAATGTCAAGTGCTTCTGACCCA	antisense,18cancers,cancer,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	13	5	20	3	136623146	-	7	16266227	+	4.3125	1.8148	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-EW-A1PH-01A	ENSG00000228801	ENSG00000253844	AC064807.1	AC064807.2	CCTCTACCTCTGCCTCCATGAGTAACTGGAACTACAG*GTTAATATTCATCTGTAGCCTGAGTGACCCCAAAAAG	lincrna,antisense,m9,10K<gap<100K,exon-exon	BOWTIE	exonic(no-known-CDS)/exonic(no-known-CDS)	0	10	6	22	8	51913180	+	8	52022416	+	22.7352	1.3126	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	antisense_RNA	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-EW-A1PH-01A	ENSG00000186575	ENSG00000070371	NF2	CLTCL1	CCAAGGCAGAAGACCTATCTGCATTTGAGCCCTCAAA*GATGCCATGCAGCATGCTGCAGAGTCGCGGGATGCTG	tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	9	3	24	22	29683064	+	22	19183611	-	25.7672	1.2943	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A1PH-01A	ENSG00000171793	ENSG00000224729	CTPS1	PCOLCE-AS1	CATCAGTGAAGGAGAAAATATCAATGTTCTGCCATGTTGAGCCTGAACAA*GGTCTGAGGAATCTGCAGGAAACAGTTTGCAAAAGCCATTGCTTTGGGCC	antisense	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	8	1	23	1	40991845	+	7	100593071	-	15.3975	0.0831	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-EW-A1PH-01A	ENSG00000171793	ENSG00000224729	CTPS1	PCOLCE-AS1	GAAAATATCAATGTTCTGCCATGTTGAGCCTGAACAA*CAGGGTCTGAGGAATCTGCAGGAAACAGTTTGCAAAA	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	8	1	13	1	40991845	+	7	100593074	-	15.3975	0.0831	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-EW-A1PH-01A	ENSG00000138771	ENSG00000130726	SHROOM3	TRIM28	CGTGGTCAGGAGGGGTTAAACTTCGGCTGAAGCACAG*GAGATGATCCCTACTCAAGTGCAGAGCCCCATGTGTC	oncogene,18cancers,exon-exon	BOWTIE	out-of-frame	0	5	3	24	4	76710287	+	19	58548862	+	4.6966	73.0337	TRUE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-EW-A1PH-01A	ENSG00000136891	ENSG00000237461	TEX10	AL359710.1	TCAAAGAGGATGGAACACTTCCAACAAACAATAGAAAACTTAACATAAAG*AACAGTAACAAGAAGACTGAAAGCAAGAACTCAGCCAACTATAAAAGACC	lincrna	BOWTIE+STAR	CDS(truncated)/intronic	0	4	1	16	9	100349184	-	9	99599889	-	7.2833	0.1579	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A0EY-01A	ENSG00000186111	ENSG00000266469	PIP5K1C	AC005288.1	CCGGGAGCTCTTTGGGATCCGGCCAGATGATTACTTG*AAACCAACGGGATAGGATTCAAAACTAGGTGACAAAC	antisense,m494,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	496	22	25	19	3660966	-	17	39405480	+	14.8038	0.288	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A0EY-01A	ENSG00000186111	ENSG00000266469	PIP5K1C	AC005288.1	CCTTCCGCTACTTCCGGGAGCTCTTTGGGATCCGGCCAGATGATTACTTG*GTACTTTTAATGTTTTTGCTTGACTTCAGCCAGTGGAATAAAAAAGCCTT	antisense,m494	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	496	10	25	19	3660966	-	17	39403670	+	14.8038	0.288	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A0EY-01A	ENSG00000186111	ENSG00000266469	PIP5K1C	AC005288.1	GCCCGAGGCTGCGCTCTTCCAGGGAGAACTAGCATGTGCTCCAGCCAGGG*AAACCAACGGGATAGGATTCAAAACTAGGTGACAAACTCATGAGAAATCC	antisense,m494	BOWTIE+BLAT;BOWTIE+STAR	intronic/exonic(no-known-CDS)	0	496	3	25	19	3659746	-	17	39405480	+	14.8038	0.288	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A0EY-01A	ENSG00000186111	ENSG00000266469	PIP5K1C	AC005288.1	CCTTCCGCTACTTCCGGGAGCTCTTTGGGATCCGGCCAGATGATTACTTG*AGCTGTTTTCTCCCAGCAAAAACTGATGCATTTGGTGAGTAACAATGGCA	antisense,m494	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	496	1	23	19	3660966	-	17	39403740	+	14.8038	0.288	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A0EY-01A	ENSG00000157106	ENSG00000134343	SMG1	ANO3	ACTATGTACCAGAATCAGTTGTTGGAGAAAATTAAAG*GTATCTGGCTTGGAATTCTCGAAGGAATCGGTATATT	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	36	7	22	16	18858170	-	11	26647709	+	5.7498	4.6458	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A0EY-01A	ENSG00000087299	ENSG00000168216	L2HGDH	LMBRD1	GCAGGAGGATATAAAAAAGAAGGAGCCATATTGTAGG*ATCAGTGTACTGTTACCCGGACATACCTATTCCTTCA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	32	4	19	14	50294115	-	6	69676541	-	8.1692	6.8828	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A0EY-01A	ENSG00000103067	ENSG00000103064	ESRP2	SLC7A6	CGCAGTGGCATGTCCCCTCCACCCTGCAAGCTGCCCT*GTCTGCTGACATTTGTGAACTGTGCCTATGTCAAGTG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	25	10	25	16	68231178	-	16	68287746	+	97.4728	5.673	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A0EY-01A	ENSG00000104447	ENSG00000197226	TRPS1	TBC1D9B	AAACAAGTCCAAGGATGAATCCCAGTCCCTGTTACGG*GGAATCATCGCAGAAGAGAACAAGAACCTGCAGCCCC	tcga,cell_lines,18cancers,chimerdb3seq,exon-exon	BOWTIE	in-frame	0	14	5	21	8	115587001	-	5	179894614	-	25.8226	18.9848	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A0EY-01A	ENSG00000128487	ENSG00000178307	SPECC1	TMEM11	GGCAACCACTCAGGACGGCCCGAGGATCCGGAACCAG*GGTGAGCTTGTCGGCCACAGACTGCTACATTGTGCAT	tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	8	8	24	17	20156236	+	17	21198840	-	2.7578	171.1926	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-B6-A0RT-01A	ENSG00000105379	ENSG00000105370	ETFB	LIM2	GGTCATCGCCGTCAGCTGTGGGCCTGCACAGTGCCAG*CCCTTTTCGTCGTGTTGGCCTTGGCCATCTACACTGG	tcga,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	79	16	24	19	51354150	-	19	51380639	-	2.2904	6.6437	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-B6-A0RT-01A	ENSG00000213639	ENSG00000158019	PPP1CB	BABAM2	CTGAACGTGGACAGCCTCATCACCCGGCTGCTGGAGG*CTGCACATCATTGACTCCTGGGCCCAACTGTGACCGA	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	64	11	22	2	28752176	+	2	27929832	+	61.1688	14.6807	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-B6-A0RT-01A	ENSG00000174238	ENSG00000167693	PITPNA	NXN	AACCTGGCACAAACCAGATCTTGGCACGCAGGAGAAT*CTCAAACTTTGGAACAAATACCGAATTTCCAACATTC	cell_lines,18cancers,exon-exon	BOWTIE	in-frame	0	27	6	22	17	1541566	-	17	826078	-	18.6372	6.2836	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0RT-01A	ENSG00000174238	ENSG00000167693	PITPNA	NXN	TGATTAAAATTGAAACCTGGCACAAACCAGATCTTGGCACGCAGGAGAAT*AGCGGACACGGAAAAGCTCACCCTGCCGACTTGGAATTTATAATAGCATT	cell_lines,18cancers	BOWTIE+STAR	CDS(truncated)/intronic	0	27	1	19	17	1541566	-	17	847069	-	18.6372	6.2836	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0RT-01A	ENSG00000164808	ENSG00000253844	SPIDR	AC064807.2	GCCGTCCCCAGGACACTGTCCGGATCTTCCCTCCCTG*GTTAATATTCATCTGTAGCCTGAGTGACCCCAAAAAG	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	21	6	23	8	47440542	+	8	52022416	+	5.8244	1.2674	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0RT-01A	ENSG00000164808	ENSG00000253844	SPIDR	AC064807.2	GGCTACCTCAGGGGCCGTCCCCAGGACACTGTCCGGATCTTCCCTCCCTG*GCTGGAGCGCAGTGGTGTGATCTCAGCTCACTGCAACCTCTCTACCTCCC	lincrna	BOWTIE+BLAT	CDS(truncated)/intronic	0	21	1	20	8	47440542	+	8	52005581	+	5.8244	1.2674	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0RT-01A	ENSG00000187079	ENSG00000112186	TEAD1	CAP2	GAGGAGACTCTCCCTGGAAAACTTCCCTTCCCTTTCG*GCAGAAATGGTGCACAGTGCTTTCCAGGCCCAGCGGG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	16	3	22	11	12675561	+	6	17462996	+	5.125	5.9582	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-B6-A0RT-01A	ENSG00000105707	ENSG00000078304	HPN	PPP2R5C	TCATTAACAAGAGGCAGTGACATGGCGCAGAAGGAGG*TTGAGGCTGTGAAGCTGGGCAGGGTTTCAGCTGAGCT	tcga,18cancers,chimerdb3seq,m12,tcga-cancer,exon-exon	BOWTIE	in-frame	0	14	3	20	19	35042522	+	14	101836169	+	2.2215	13.5653	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-B6-A0RT-01A	ENSG00000105707	ENSG00000078304	HPN	PPP2R5C	GTCAGCCAGGGAATCATTAACAAGAGGCAGTGACATGGCGCAGAAGGAGG*GAGTGTATTCAAAGCACATTCACAGTAAGGAAAAAAAAAATGCAGCCTGT	tcga,18cancers,chimerdb3seq,m12,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	14	2	21	19	35042522	+	14	101835031	+	2.2215	13.5653	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-B6-A0RT-01A	ENSG00000122299	ENSG00000189067	ZC3H7A	LITAF	ACCGCTGTCATATCCAGGAACACAGGAGCAATATGCG*GTAAAATGTCGGTTCCAGGACCTTACCAGGCGGCCAC	18cancers,chimerdb3seq,tumor,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	10	6	23	16	11781425	-	16	11556735	-	8.6549	51.6829	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0RT-01A	ENSG00000122299	ENSG00000189067	ZC3H7A	LITAF	CTGCCTTCTGCCGCCGGCCGGCGCGTCGTCCCCACAG*GTAAAATGTCGGTTCCAGGACCTTACCAGGCGGCCAC	18cancers,chimerdb3seq,tumor,100K<gap<200K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	10	1	13	16	11797124	-	16	11556735	-	8.6549	51.6829	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0RT-01A	ENSG00000110697	ENSG00000167791	PITPNM1	CABP2	GCCTTTGCCTCCCCAGTGGAGGCAGAGGGAACGCCAG*GTGGCGGAAAGGTGGACTTTGAAGACTTCGTGGAGCT	tcga,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	9	3	20	11	67499723	-	11	67520160	-	9.8399	0.3855	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-B6-A0RT-01A	ENSG00000125648	ENSG00000109667	SLC25A23	SLC2A9	TGTGGAGGACGTGCTGTATTTCTGGAAGCATTCCACG*TGACCTCATGTCAAGAAGGCAGACCTGCAGAAATGAA	18cancers,cancer,m3,exon-exon	BOWTIE	CDS(complete)/UTR	0	4	7	23	19	6456420	-	4	9771369	-	4.8785	1.1774	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0RT-01A	ENSG00000125648	ENSG00000109667	SLC25A23	SLC2A9	ATTCGCTGGAAAATGTGGAGGACGTGCTGTATTTCTGGAAGCATTCCACG*GTGTCCTGTGTTCCAGGAGAGCCCTGGGCTGGCTCCTAGTGCAGCCGTTA	18cancers,cancer,m3	BOWTIE+BLAT;BOWTIE+STAR	CDS(complete)/intronic	0	4	1	24	19	6456420	-	4	9777837	-	4.8785	1.1774	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Breast	TCGA-B6-A0RT-01A	ENSG00000159023	ENSG00000132549	EPB41	VPS13B	GGCGCGGAGCCAGAACGCGGTCGGCCCGGTCCCCGCCGCACCCAGCCCAG*ATCATCTGTAGTTACTTGTCTCAAAGCATAGAACTAAAAGTCGTTCAGCA	18cancers	BOWTIE+STAR	UTR/CDS(truncated)	0	3	2	25	1	28887210	+	8	99817561	+	7.8738	4.7768	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0RT-01A	ENSG00000143458	ENSG00000143443	GABPB2	C1ORF56	AAACTGGCGGGCTCCGTGGAAGCGTGGCCGGCAGCGTCCCGGACGAGGAG*AGCACCACCAGTACCAGGACCACCACTACCCCCTTCCCCACCATCCACCT	10K<gap<100K	BOWTIE+STAR	UTR/CDS(truncated)	0	2	1	23	1	151070934	+	1	151048679	+	9.6713	3.6186	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A152-01A	ENSG00000100211	ENSG00000100226	CBY1	GTPBP1	GGGGAGCGCTTGGACCCCGGCTTCTGGGACGCGTCAG*CTGGTTCTAGTGAGCCCTACATCAGAGCAGTATGACA	18cancers,chimerdb3seq,10K<gap<100K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	134	17	22	22	38656750	+	22	38708845	+	6.2997	32.588	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A152-01A	ENSG00000100211	ENSG00000100226	CBY1	GTPBP1	GGGGAGCGCTTGGACCCCGGCTTCTGGGACGCGTCAG*ATGGGACTGAGTATGGGCTGAGTGAAGCTGACATGGA	18cancers,chimerdb3seq,10K<gap<100K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	134	12	25	22	38656750	+	22	38715907	+	6.2997	32.588	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A152-01A	ENSG00000100211	ENSG00000100226	CBY1	GTPBP1	GACTCACTGTGCAATTCTGTGCATGTACAGTGGCCAG*CTGGTTCTAGTGAGCCCTACATCAGAGCAGTATGACA	18cancers,chimerdb3seq,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	134	3	24	22	38665685	+	22	38708845	+	6.2997	32.588	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-E2-A152-01A	ENSG00000100211	ENSG00000100226	CBY1	GTPBP1	AAACCAGAGATTCCGCCCTTGTTTTCTTAGAATTAAA*CTGGTTCTAGTGAGCCCTACATCAGAGCAGTATGACA	18cancers,chimerdb3seq,10K<gap<100K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	134	2	23	22	38657143	+	22	38708845	+	6.2997	32.588	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0WX-01A	ENSG00000135373	ENSG00000228061	EHF	AC131571.1	CAACAGCCACAGCTATTGGATTTCCCACCCAGAATCTTTAGGTAAATGAG*ACAGGTTCTCATTTTGTGGCCCAGGATGAAGTGCAGTGACACAACTGAAC	antisense	BOWTIE+BLAT;BOWTIE+STAR	UTR/intronic	0	93	21	25	11	34621228	+	11	31689440	-	32.5554	1.9852	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0WX-01A	ENSG00000135373	ENSG00000228061	EHF	AC131571.1	TATTGGATTTCCCACCCAGAATCTTTAGGTAAATGAG*GTTCTCATTTTGTGGCCCAGGATGAAGTGCAGTGACA	antisense,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	93	10	21	11	34621228	+	11	31689436	-	32.5554	1.9852	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0WX-01A	ENSG00000135373	ENSG00000228061	EHF	AC131571.1	CTGCCTTTGTTACTGGGAAACCGAACGCGGCGCTGTGGCTTTCAGCTTGG*ACAGGTTCTCATTTTGTGGCCCAGGATGAAGTGCAGTGACACAACTGAAC	antisense	BOWTIE+BLAT;BOWTIE+STAR	UTR/intronic	0	93	5	25	11	34624317	+	11	31689440	-	32.5554	1.9852	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0WX-01A	ENSG00000135373	ENSG00000228061	EHF	AC131571.1	TGGGAAACCGAACGCGGCGCTGTGGCTTTCAGCTTGG*GTTCTCATTTTGTGGCCCAGGATGAAGTGCAGTGACA	antisense,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	93	4	25	11	34624317	+	11	31689436	-	32.5554	1.9852	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0WX-01A	ENSG00000135373	ENSG00000228061	EHF	AC131571.1	AGAGAAGAGGATTGGTCCTGCTTTTAAGCCTAGCTGAAATTCTTTTCAAG*ACAGGTTCTCATTTTGTGGCCCAGGATGAAGTGCAGTGACACAACTGAAC	antisense	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	93	2	18	11	34632652	+	11	31689440	-	32.5554	1.9852	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0WX-01A	ENSG00000135373	ENSG00000228061	EHF	AC131571.1	CAACAGCCACAGCTATTGGATTTCCCACCCAGAATCTTTAGGTAAATGAG*ACACTATAAATGACACATTATGAAAAGAAGTGTTTCAGAGAGTATCATGT	antisense	BOWTIE+STAR	UTR/intronic	0	93	2	16	11	34621228	+	11	31656969	-	32.5554	1.9852	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0WX-01A	ENSG00000135373	ENSG00000228061	EHF	AC131571.1	GGGATTGCCATCTGAAGACAGAGGCAGGAGGGCAGCCACACCTTGCCCAG*ACAGGTTCTCATTTTGTGGCCCAGGATGAAGTGCAGTGACACAACTGAAC	antisense	BOWTIE+STAR	intronic/intronic	0	93	1	16	11	34624386	+	11	31689440	-	32.5554	1.9852	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0WX-01A	ENSG00000135373	ENSG00000228061	EHF	AC131571.1	CAACAGCCACAGCTATTGGATTTCCCACCCAGAATCTTTAGGTAAATGAG*ACCACCAACATTTCCCTGGTATATGGAGGAGGTGGAGAACAGAGTATTGT	antisense	BOWTIE+STAR	UTR/intronic	0	93	1	14	11	34621228	+	11	31689983	-	32.5554	1.9852	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0WX-01A	ENSG00000135503	ENSG00000257379	ACVR1B	AC023509.1	CCCCAAGATTATTTAAAGATCCCACCACTGGACTGTATTCCCGGCCCTTG*AGTGGTGCACGTATCAACATCTCAGAAGGGAATTGTCCTGAGAGAATTAT	cancer,m2	BOWTIE+BLAT;BOWTIE+STAR	intronic/exonic(no-known-CDS)	0	6	4	23	12	51952771	+	12	53455885	+	5.4756	0	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-B6-A0WX-01A	ENSG00000135503	ENSG00000197111	ACVR1B	PCBP2	GCCGGCAGCGGCGGGTCCGGGCCCCGGGGGGTCCAGG*AGTGGTGCACGTATCAACATCTCAGAAGGGAATTGTC	cancer,m2,exon-exon	BOWTIE	out-of-frame	0	6	3	24	12	51951834	+	12	53455885	+	5.4756	16.7098	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A25B-01A	ENSG00000198231	ENSG00000136492	DDX42	BRIP1	ATCTGAATACACACAGCCCACTCCAATACAGTGCCAG*CCCCCTGGCCACTGTTCTAGGTGCTGTTGTTCTACTA	tcga,cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	34	9	25	17	63806654	+	17	61808757	-	40.0108	8.8309	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A25B-01A	ENSG00000154217	ENSG00000171634	PITPNC1	BPTF	AACCAAGTATGAGGACAACAAAGGAAGCAATGACACC*GTATAGACTTCAGACAGTAAAGTCCTTAGCTGGAGTG	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	17	6	25	17	67578257	+	17	67918714	+	4.3283	21.913	TRUE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A25B-01A	ENSG00000132589	ENSG00000108733	FLOT2	PEX12	GGGCCTGGGCCTGGTGGTGTATCTCCGACACTCAGAG*GTTCTTGCAGAATCAAATCCCACCCACTATGGCTTCT	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	11	14	24	17	28888945	-	17	35577591	-	50.0544	11.5372	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A25B-01A	ENSG00000029725	ENSG00000108381	RABEP1	ASPA	GTCATGGCGCAGCCGGGCCCGGCTTCCCAGCCTGACG*GAAAAGAATTTCCTCCCTGCGCCATTGAGGTCTATAA	tcga,cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	9	6	21	17	5282520	+	17	3494350	+	24.2332	4.5021	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A25B-01A	ENSG00000186283	ENSG00000116191	TOR3A	RALGPS2	GGGCTGAGTCTCCATGGACTATCTTTCTGTTTCTCAG*GTTCCTACAAACTTGATGACTTTTGAGTAGAAGCCTG	cancer,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	9	2	25	1	179088089	+	1	178916330	+	16.2461	32.8331	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A25B-01A	ENSG00000185420	ENSG00000162851	SMYD3	TFB2M	GGAGTCGTGGCGTCGTCTGCGACCGCTGCCTTCTCGG*GAGCCTTGGTCATCATTTGATATATACACCCGGAAAG	tcga,chimerdb3seq,cancer,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	6	2	19	1	246507054	-	1	246548607	-	10.7566	30.7347	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A25B-01A	ENSG00000126653	ENSG00000198720	NSRP1	ANKRD13B	ATCAGTGTTTGGGAATGATTCTGATGATGATGATGAG*GTGGACATCGAGCAGCTGGATCCCCGCGGCCGGACTC	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	5	5	22	17	30118173	+	17	29607742	+	16.4087	12.6565	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A25B-01A	ENSG00000143258	ENSG00000143217	USP21	NECTIN4	CACTAAGGAAGAAGAGCTAGAGTCGGAGAATGCCCCA*AGTGAAGAGCCCGAGGGCCGCAGTTACTCCACGCTGA	oncogene,tcga,chimerdb3seq,cancer,m3,tcga-cancer,exon-exon	BOWTIE	in-frame	0	4	2	20	1	161164250	+	1	161072885	-	10.576	21.1383	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A25B-01A	ENSG00000156650	ENSG00000182010	KAT6B	RTKN2	GACAATCATTGCTTCAAGAATGCTGACCCTTGTAGAA*ATATTCGAATACCACTAATGTGGAAAGACTCTGATCA	tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	2	3	23	10	75025249	+	10	62241195	-	3.6907	2.4211	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A25B-01A	ENSG00000103199	ENSG00000140632	ZNF500	GLYR1	TAGTGTCTGGAATGTGGCCTTCCACGGTTGCCCCACTTTGTCTTTCTAAG*GATCTCACCATCCCGGAGTCTAGTACCGTGAAGGGGATGATGGCCGGACC	10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	2	1	20	16	4751299	-	16	4823907	-	1.3858	21.2591	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A25B-01A	ENSG00000103199	ENSG00000140632	ZNF500	GLYR1	AAACCCCATCTCTACTAAAAATACAAAAAAATTAGCCGGGTGTGGTGGCA*CGCGCCTGTGGTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTGG	10K<gap<100K	BOWTIE+BLAT	intronic/intronic	0	2	1	17	16	4756664	-	16	4825799	-	1.3858	21.2591	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A25B-01A	ENSG00000103199	ENSG00000140632	ZNF500	GLYR1	GTCTGGCCTGTGCTGCGTGGGAGCCACTGGTCTGTGCACATCCACGGTGG*GATCTCACCATCCCGGAGTCTAGTACCGTGAAGGGGATGATGGCCGGACC	10K<gap<100K	BOWTIE+STAR	UTR/CDS(truncated)	0	2	1	16	16	4751222	-	16	4823907	-	1.3858	21.2591	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A2-A3XX-01A	ENSG00000104447	ENSG00000180233	TRPS1	ZNRF2	GGCTGCCGAGGGTGTTCTTGACGATTAATCAACAG*AGGATGTACTGAGTAAAGATGCTGGGGAATGTGCA	tcga,18cancers,chimerdb3seq,exon-exon	BOWTIE	UTR/CDS(truncated)	0	34	3	23	8	115668545	-	7	30355728	+	72.1086	8.2601	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A2-A3XX-01A	ENSG00000104447	ENSG00000180233	TRPS1	ZNRF2	AGCGGGGCGCAGACTAGGCACCAGCATGCAGAGTA*AGGATGTACTGAGTAAAGATGCTGGGGAATGTGCA	tcga,18cancers,chimerdb3seq,exon-exon	BOWTIE	in-frame	0	34	2	20	8	115667874	-	7	30355728	+	72.1086	8.2601	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-GM-A2DF-01A	ENSG00000139842	ENSG00000057593	CUL4A	F7	TCAGTGGATTCTATGCTCAGTCTCACGGGCAGAGTCAAGGTGTCAGCCAG*AAGCTGTTCTGGATTTCTTACAGTGGTGAGTGGATGATCACCACCAGTCC	oncogene,18cancers,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	54	6	24	13	113219488	+	13	113113752	+	51.9439	93.3383	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-GM-A2DF-01A	ENSG00000139842	ENSG00000057593	CUL4A	F7	TCAGTGGATTCTATGCTCAGTCTCACGGGCAGAGTCAAGGTGTCAGCCAG*ATGGGGACCAGTGTGCCTCAAGTCCATGCCAGAATGGGGGCTCCTGCAAG	oncogene,18cancers,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	54	2	22	13	113219488	+	13	113113847	+	51.9439	93.3383	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-GM-A2DF-01A	ENSG00000139842	ENSG00000057593	CUL4A	F7	TCAGTGGATTCTATGCTCAGTCTCACGGGCAGAGTCAAGGTGTCAGCCAG*GTCCACAGCTCAGCGACAGAAGAGTCAGGGTTGAACCTCGGGTGTTCTGA	oncogene,18cancers,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	UTR/intronic	0	54	2	21	13	113219488	+	13	113113476	+	51.9439	93.3383	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-GM-A2DF-01A	ENSG00000139842	ENSG00000057593	CUL4A	F7	AGACCACGTCCAGGCACAGATCCTTCCGTTTAGAGAATATCCTTTTTTTG*AAGCTGTTCTGGATTTCTTACAGTGGTGAGTGGATGATCACCACCAGTCC	oncogene,18cancers,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	54	1	22	13	113219062	+	13	113113752	+	51.9439	93.3383	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-GM-A2DF-01A	ENSG00000139842	ENSG00000057593	CUL4A	F7	CGTAACCCAGTCAAGGAATGATGACCTTCGTATTCACAGCCTCGTTCACA*TGGTGAGTGGATGATCACCACCAGTCCTGCCTGCAACCCTTCTCAGCTTA	oncogene,18cancers,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	54	1	21	13	113219773	+	13	113113775	+	51.9439	93.3383	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-GM-A2DF-01A	ENSG00000139842	ENSG00000057593	CUL4A	F7	TATGGAGACACCCACTTATCAGCGCACAGTTGTGTCTGTCAGGAGGCCAG*AAGCTGTTCTGGATTTCTTACAGTGGTGAGTGGATGATCACCACCAGTCC	oncogene,18cancers,10K<gap<100K	BOWTIE+BLAT	UTR/CDS(truncated)	0	54	1	20	13	113219431	+	13	113113752	+	51.9439	93.3383	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-GM-A2DF-01A	ENSG00000152767	ENSG00000126216	FARP1	TUBGCP3	CACTTAATATAACAGTTTTCTTTCTATTAAAAAATAATGACAAAACACAC*ACACACACACACACACAGACACACACACACACACACACACACACACATAC	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer	BOWTIE+BLAT	UTR/intronic	0	48	1	17	13	98401421	+	13	112487100	-	1.3925	21.8374	TRUE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-GM-A2DF-01A	ENSG00000126216	ENSG00000152767	TUBGCP3	FARP1	GATATATGATGGGGAGCTTGAGGACACTTACCACGAA*AATCAGTTGTCTGGAAACCTGCTGAGGAAATTCAAAA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	48	11	24	13	112545699	-	13	98446098	+	21.8374	1.3925	FALSE	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-GM-A2DF-01A	ENSG00000095787	ENSG00000134882	WAC	UBAC2	TAATCCAAGCAATAACCCAAGCAAAACTTCAGATGCA*CCTGGCACCTGTGTTTGCTCTGTTTGTACCATTTTAC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	38	9	25	10	28583505	+	13	99314097	+	12.1746	58.1766	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-GM-A2DF-01A	ENSG00000144674	ENSG00000109971	GOLGA4	HSPA8	TACAGAGCAACTTGATGAAGGTACACCCAATAGAGAG*ACTGTTACCAATGCTGTGGTCACAGTGCCAGCTTACT	tcga,cell_lines,18cancers,chimerdb3seq,m21,tcga-cancer,exon-exon	BOWTIE	in-frame	0	23	8	23	3	37251484	+	11	123060268	-	12.6753	108.5876	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-GM-A2DF-01A	ENSG00000137478	ENSG00000204922	FCHSD2	UQCC3	AACATCAAGCAGAATGTGATTTGCTTGAAGATATGAG*AGTTGAGGGGATGGAGAGGGATGTGTATGTGTGTAGA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	9	4	22	11	73140031	-	11	62671284	+	9.3583	4.6088	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-GM-A2DF-01A	ENSG00000137478	ENSG00000204922	FCHSD2	UQCC3	AACATCAAGCAGAATGTGATTTGCTTGAAGATATGAG*GAGATGCCACTGCAGGACCCAAGGAGCAGGGAGGAGG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	9	2	24	11	73140031	-	11	62671953	+	9.3583	4.6088	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-GM-A2DF-01A	ENSG00000155957	ENSG00000155974	TMBIM4	GRIP1	AGCAGCGTGGCCTCCGCCACCGTGCACATCCGAATGG*TGTCCTTAGCCTCCAGCACAGTAGGATTGGCTGGGCA	18cancers,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	4	4	23	12	66169855	-	12	66445508	-	7.6539	5.2357	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-GM-A2DF-01A	ENSG00000231889	ENSG00000112335	TRAF3IP2-AS1	SNX3	GGAGGCGGGGGCAGCCGCTGAGACGGTTTTTCACAAG*GTCGTAGTTCCCCCGCTCCCTGGGAAAGCGTTTTTGC	antisense,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	2	6	24	6	111483665	+	6	108214622	-	0.4027	92.0616	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000123130	ENSG00000184831	ACOT9	APOO	TTTGGCAGGATTCTTGAGGATCTTGACAGCTTGGGAG*TTATAGGTAAACATTGGAAACTCCATAGAATAAATCA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	1282	24	25	X	23730527	-	X	23833612	-	30.8741	100.1921	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000123130	ENSG00000184831	ACOT9	APOO	GAAGACATCCATGGAAGTGAAGATGCAAATGTTCCAG*GTAATTCAGAGGTCCGTGGGGCCAGCCAGCCTGAGCT	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	1282	23	25	X	23721881	-	X	23880952	-	30.8741	100.1921	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000123130	ENSG00000184831	ACOT9	APOO	CACGGCAGCCTAGCGCAATGAGGCGGGCAGCACTGCG*TTATAGGTAAACATTGGAAACTCCATAGAATAAATCA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	1282	18	25	X	23743125	-	X	23833612	-	30.8741	100.1921	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000123130	ENSG00000184831	ACOT9	APOO	TTTGGCAGGATTCTTGAGGATCTTGACAGCTTGGGAG*GAAAAACTAGACCAGACCTCTGTTATCTTCTGTGAAA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	1282	14	25	X	23730527	-	X	23833510	-	30.8741	100.1921	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000123130	ENSG00000184831	ACOT9	APOO	CACGGCAGCCTAGCGCAATGAGGCGGGCAGCACTGCG*GAAAAACTAGACCAGACCTCTGTTATCTTCTGTGAAA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	1282	12	25	X	23743125	-	X	23833510	-	30.8741	100.1921	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000123130	ENSG00000184831	ACOT9	APOO	CATTTGTAATGGTGGCTCGTGATTCTGAAAATAAAGG*GTAATTCAGAGGTCCGTGGGGCCAGCCAGCCTGAGCT	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	1282	8	24	X	23713135	-	X	23880952	-	30.8741	100.1921	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000123130	ENSG00000184831	ACOT9	APOO	GAAGACATCCATGGAAGTGAAGATGCAAATGTTCCAG*CTTTCACTCTACTCAGTTCCTGAGGGTCAATCGAAGT	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	1282	4	20	X	23721881	-	X	23879034	-	30.8741	100.1921	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000123130	ENSG00000184831	ACOT9	APOO	GGTTGCAGTGAGCTGAGATCGCGCCCCTGCACTCCAGCCTGGGCAACACA*GAAAAACTAGACCAGACCTCTGTTATCTTCTGTGAAATCATCCTACAAGC	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K	BOWTIE+STAR	intronic/UTR	0	1282	2	21	X	23741708	-	X	23833510	-	30.8741	100.1921	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000123130	ENSG00000184831	ACOT9	APOO	TCTCCATCGCGCGCACGGCAGCCTAGCGCAATGAGGCGGGCAGCACTGCG*AGATGGGGTTTTACCATGTTGGTCAGGCTGGTCTCGAACTCCTGACCTCG	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K	BOWTIE+BLAT	CDS(truncated)/intronic	0	1282	1	24	X	23743125	-	X	23869782	-	30.8741	100.1921	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000184831	ENSG00000123130	APOO	ACOT9	TATTGAATGTATTAAATTGGCTTTCTTCTTCAGGAAAAACTAGACCAGAC*CTCAGTTTCCCTCCGCCGACTAGCGCGCGGGGCCCGGTTCTCCATCGCGC	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K	BOWTIE+BLAT	UTR/UTR	0	1282	1	18	X	23833494	-	X	23743212	-	100.1921	30.8741	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-A7-A13D-01A	ENSG00000167881	ENSG00000092929	SRP68	UNC13D	CAGTAATGCGTTCAGGAGTCCACACCAGGCACAGATGGGGCCTTGAAACG*CTCGCCACCTCCCCCTCTCCTCCCACGGCCCCTCCTTCCTGGGCCCCAGC	18cancers,chimerdb3seq,100K<gap<200K	BOWTIE+BLAT	UTR/UTR	0	227	1	19	17	76039362	-	17	75832937	-	25.5882	52.8123	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000092929	ENSG00000167881	UNC13D	SRP68	GTGGAGCTTTGCTACATGAACACCAACTTGGTGCAGGAGAACTTCAGCAG*TACCATGGATTTGAAATGAACTCATCCTTGCTGTGAGCATCCAGGAGCCC	18cancers,chimerdb3seq,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	227	16	25	17	75832966	-	17	76039342	-	52.8123	25.5882	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000092929	ENSG00000167881	UNC13D	SRP68	CTCTCCTCCCACGGCCCCTCCTTCCTGGGCCCCAGCATCCGTTCTGAGGG*CCCTGTGAGCTGTGATTGATTGCCTTTGGTCAGTAATGCGTTCAGGAGTC	18cancers,chimerdb3seq,100K<gap<200K	BOWTIE+BLAT	UTR/UTR	0	227	4	25	17	75832874	-	17	76039441	-	52.8123	25.5882	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000092929	ENSG00000167881	UNC13D	SRP68	GTGGAGCTTTGCTACATGAACACCAACTTGGTGCAGGAGAACTTCAGCAG*TAATGCGTTCAGGAGTCCACACCAGGCACAGATGGGGCCTTGAAACGCTT	18cancers,chimerdb3seq,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	227	3	22	17	75832966	-	17	76039408	-	52.8123	25.5882	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000143033	ENSG00000122406	MTF2	RPL5	TCCAGCAGTGTTACTGCTATTGTGGAGGCCCTGGAGA*ATGGAGGAGATGTATAAGAAAGCTCATGCTGCTATAC	ribosomal,tcga,18cancers,chimerdb3seq,m8,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	125	17	25	1	93115618	+	1	92840551	+	8.8318	183.3439	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000171456	ENSG00000101337	ASXL1	TM9SF4	TAAACTGCCTGGCCGAATCAGCCTTTTCACGCTCAAG*GATTGGTTGCCGTGGTCTTTACTGCTTTTCTCCCTGA	tcga,cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	46	8	24	20	32369123	+	20	32133013	+	7.7271	44.6638	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000152558	ENSG00000137675	TMEM123	MMP27	TCTGGGCTTCCACACAACTCCAGTGCTAACTCAACAG*GTTTGATGAAATGACCCAAACCATGGACAAAGGGTTC	known,tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	40	18	25	11	102448812	-	11	102693041	-	143.743	7.2382	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000152558	ENSG00000137675	TMEM123	MMP27	AGGCTGATGTCATCAATATCAGTAGTAAATCATCAAG*GTTTGATGAAATGACCCAAACCATGGACAAAGGGTTC	known,tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(no-known-start-or-end)/CDS(truncated)	0	40	2	16	11	102448236	-	11	102693041	-	143.743	7.2382	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000140694	ENSG00000085721	PARN	RRN3	AGCCAGGGATTTGATTTTAATAAAGTTTTTCGAAATG*ATCTTCCTGCAAATTTTGACACATGTCACAGAGCCTT	tcga,chimerdb3seq,m8,tcga-cancer,exon-exon	BOWTIE	in-frame	0	31	13	23	16	14617590	-	16	15084705	-	10.3614	27.0999	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000140694	ENSG00000085721	PARN	RRN3	GGACCTTCAGTCTCTGCATTAACAAATGGTTTTGACACTCCAGAAGAGAG*GTGTGGGAAGACATGAGTGCTGAAGAGCTACAGGAGTTCAAGAAACCCAT	tcga,chimerdb3seq,m8,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	31	1	18	16	14628191	-	16	15063252	-	10.3614	27.0999	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000177479	ENSG00000132153	ARIH2	DHX30	TGAAACAGCCAACTACATTAGTGCTCACACTAAAGAC*AGCCTGGGCCTGGTGGACAGGAACAACGAACCGCTTA	tcga,cell_lines,18cancers,chimerdb3seq,m23,tcga-cancer,exon-exon	BOWTIE	in-frame	0	24	7	22	3	48973816	+	3	47845700	+	7.1107	14.0664	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000254986	ENSG00000175115	DPP3	PACS1	CAAGCCTGCTCTAGAGCGCTTCCTGCGGAGACTTCAG*GAAATCACTGACCAGGACATGTTTGGAGATGCCAGCA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	19	7	24	11	66497477	+	11	66230548	+	13.0648	12.6521	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000185630	ENSG00000162946	PBX1	DISC1	TTGTTTAATGTGTTGTGTGAAATCAAAGAAAAAACAG*AAACAAGTGTGAAGGAAAATACTATGAAGTACATGGA	oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	19	3	25	1	164563311	+	1	231958828	+	5.2858	3.7216	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000163125	ENSG00000136631	RPRD2	VPS45	TGAAGCACAATACAAAGAAGTAAAAGTGGTGGCTAAT*TGGACATATCAGGCCATGGTCCACGAACTACTAGGCA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	15	3	25	1	150446401	+	1	150081342	+	12.12	9.477	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000163125	ENSG00000136631	RPRD2	VPS45	TGAAGCACAATACAAAGAAGTAAAAGTGGTGGCTAAT*AATATGTACCTGAACTTTGCTGAGATTGGTAGCAATA	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	15	1	13	1	150446401	+	1	150081884	+	12.12	9.477	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	FALSE	Breast	TCGA-A7-A13D-01A	ENSG00000055483	ENSG00000035862	USP36	TIMP2	CGCAGTAGGACAGCAGGCCCAAGTCTGCACATCCCAG*TGATCAGGGCCAAAGCGGTCAGTGAGAAGGAAGTGGA	cancer,10K<gap<100K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	14	2	25	17	78838587	-	17	78873919	-	9.8888	65.4639	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000117713	ENSG00000117682	ARID1A	DHDDS	GAACCTGAGCCTTCAGTCAAGACCCTCCAGCTTGCCT*GCAGGCCCAATGCCGAAACACATTGCATTCATAATGG	cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	13	4	24	1	26732792	+	1	26438168	+	9.0104	11.63	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000150967	ENSG00000111361	ABCB9	EIF2B1	CATCATCTACGAGTTTGTCCTGGGAGATTGTATGGAG*ATTGGAACCAACCAGATGGCTGTGTGTGCCAAAGCAC	18cancers,tcga-cancer,exon-exon	BOWTIE	in-frame	0	11	5	25	12	122944391	-	12	123622761	-	1.3234	9.2577	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000149761	ENSG00000256481	NUDT22	AP006333.2	ACTCTTTTCCAGTGTCCTTCAGGAGATCTGTGATGAG*GAGCTGTCACTGCCTCTCTCCTTGATGGCGGGGTATG	antisense,100K<gap<200K,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	8	6	21	11	64227666	+	11	64086914	+	3.8336	1.682	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000071564	ENSG00000065000	TCF3	AP3D1	CACACGCCGCCTGTCAGCGGGGCCGACAGCCTCCTGG*AAATCTCCCAAGCCTAAGAAGAAGAAGCACAGGAAGG	oncogene,tcga,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	8	3	21	19	1621838	-	19	2111828	-	19.2499	19.4925	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000144036	ENSG00000144040	EXOC6B	SFXN5	ACATTCAGACAAAATTGGAGAGACTGCCATGAAGCAA*CTCTGGAGTGCACAGAAAATCAAGCAGGCTATTCTAC	tcga,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	6	7	25	2	72718103	-	2	73023214	-	4.39	1.7991	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000132510	ENSG00000182896	KDM6B	TMEM95	CTGTGATCGGTGCGTGCCGTCCTGCGCAAGTCAGACTGCCGCGTCCCCGC*GTCTCCTGCAGGGGGCAGCACCACGCTGTACAACTGCTCCACCTGCAAGG	18cancers,tcga-cancer	BOWTIE+BLAT	intronic/CDS(truncated)	0	6	4	22	17	7852106	+	17	7356185	+	15.1222	15.6492	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000132510	ENSG00000182896	KDM6B	TMEM95	AGCACTACTGGGAGACCATCAGCGCTTTCTGTGATCG*GTCCCACCACCTCCAAGCAAAAAGTGGCTTGTGAAGA	18cancers,tcga-cancer,exon-exon	BOWTIE	in-frame	0	6	2	18	17	7852065	+	17	7356599	+	15.1222	15.6492	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000121211	ENSG00000164144	MND1	ARFIP1	TGCAAGGAAACATAAGTTGGAGGTTCTGGAATCTCAG*GATTTGAAGCATTCATTACCATCTGGACTTGGTCTCT	18cancers,tcga-cancer,exon-exon	BOWTIE	in-frame	0	6	2	24	4	153358622	+	4	152863606	+	0.0582	7.0497	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000078114	ENSG00000138081	NEBL	FBXO11	TAAACATGCCATGGAGGTCAATAAACACCAGAGTAAT*ATGATGATGTGCCTGCAGATATGGTTGCAGAAGAATC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	6	4	22	10	20880794	-	2	47839769	-	11.4848	5.5985	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000163933	ENSG00000272886	RFT1	DCP1A	GATATCTACGGAGGGACCATGCTTAGCTCAGGATCCG*TGTCGATATATAGTATCTGGTTTTATGACAAGAATGA	18cancers,chimerdb3seq,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	6	5	24	3	53103953	-	3	53319473	-	6.9053	12.0634	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000130699	ENSG00000130700	TAF4	GATA5	AACCCGACCAACATCCAGAACTTCCAGCTGCCCCCAG*GTGCCGCGGCCTCTGGCTATGAAGAAGGAAAGCATCC	18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	6	5	23	20	62064451	-	20	62465921	-	2.7313	2.6317	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000187531	ENSG00000176155	SIRT7	CCDC57	AGGCTGCCAGCAGAGCAGACACCATCCTGTGTCTAGGGTCCAGCCTGAAG*CCCGAATGCTGGTGGAGCCTCCGCTGGAGATCACACAGGGCTCCAGTGAC	tcga,chimerdb3seq,tcga-cancer,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	4	2	21	17	81914294	-	17	82115258	-	5.821	2.959	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000187531	ENSG00000176155	SIRT7	CCDC57	AGCAGACACCATCCTGTGTCTAGGGTCCAGCCTGAAG*AGCTCCCAGCTCCTCCAGCAGCCGACAGGAGGCCCGT	tcga,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	4	1	13	17	81914294	-	17	82101866	-	5.821	2.959	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-A7-A13D-01A	ENSG00000181617	ENSG00000187533	FDCSP	PRR27	CAGCGTCAGAGAGAAAGAACTGACTGAAACGTTTGAG*GGTCAATCAAAATGAAGCTTCTCCTTTGGGCCTGCAT	18cancers,10K<gap<100K,exon-exon	BOWTIE	UTR/UTR	0	3	5	24	4	70226182	+	4	70154365	+	96576.9508	0.6784	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000182541	ENSG00000184792	LIMK2	OSBP2	GGACTGTCAACGAAACCTGGCACGGCTCTTGCTTCCG*ATGACTCTGGGGACGACGACGAGGCTACCACCCCAGC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	3	5	23	22	31225819	+	22	30870429	+	17.8315	3.2516	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000100151	ENSG00000100129	PICK1	EIF3L	ACAACGACTGCTACGCAGTGCTGCGGGATGCCGACGTCTTCCCCATCGAG*GGGGGACCTTCCTTGGAGCAGAGGTTTGAATCCTATTACAACTACTGCAA	cancer,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	3	1	18	22	38074967	+	22	37862969	+	9.2111	39.5225	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000100154	ENSG00000227117	TTC28	HORMAD2-AS1	TCAGTTGGTACTCGCCATGAAACTCAAAGATCGAGAG*GTCTTGCCCTGTCATCCAGGCTGGAGTGCAATGGATC	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	3	2	23	22	28296198	-	22	30018729	-	0.7052	0.0122	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000089597	ENSG00000065029	GANAB	ZNF76	GACCTGGGTTGATATATCTTCCAACACTGCCGGGAAG*ATTTGTGACCCAGAAGGAAATCTCTGACCTCAGCTGT	18cancers,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	2	2	18	11	62632565	-	6	35281056	+	121.9076	2.967	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000241839	ENSG00000180357	PLEKHO2	ZNF609	CCTCTGCCAGGCCCAGCTGCTGGTCTATGAGAATGAG*ATGGAGTCCCCTGTTTCCACACCAGCAGTGCTGCCAA	chimerdb3seq,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	2	3	25	15	64848742	+	15	64622827	+	5.748	5.2193	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000076382	ENSG00000173065	SPAG5	FAM222B	GGACAGTAGCACACAGACTGACACATCTCACAGTGGG*TGTGAGCCACTGCCCCATGTTGTGTTGATGCCAATCT	tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	2	3	24	17	28591698	-	17	28766707	-	9.2261	27.7555	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000076382	ENSG00000173065	SPAG5	FAM222B	GGACAGTAGCACACAGACTGACACATCTCACAGTGGG*GTGCTGAGGAGTCATGGAAGAGTTTTTAAACCAGTGT	tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	2	2	22	17	28591698	-	17	28834326	-	9.2261	27.7555	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-A7-A13D-01A	ENSG00000118965	ENSG00000055917	WDR35	PUM2	CTCTATGAGGGATGTGTGGACACTGCACTGAAGACAG*GCTATCAAGTACTAGCTCCAACTGCCTATTATGATCA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	2	2	20	2	19930396	-	2	20283486	-	2.6766	22.8466	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000108848	ENSG00000141371	LUC7L3	C17ORF64	CCTGCGGAATTGTTCACAAATACACGTTCTGATCTTG*GTGACATTCTGCGCCTCGGATGCGCCGGAGAGGTCCT	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	152	22	25	17	50737026	+	17	60429362	+	28.4605	13.5778	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000108848	ENSG00000141371	LUC7L3	C17ORF64	CAGAACCCTGGACAGGCTCAGGATTTGGAGGCACCAG*GATGCTCTGGCGGTTCATCTCCCTCTTCTCGGAGCTG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	152	4	23	17	50737479	+	17	60426718	+	28.4605	13.5778	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000108848	ENSG00000141371	LUC7L3	C17ORF64	CCTGCGGAATTGTTCACAAATACACGTTCTGATCTTG*ATTCTTTAAGGGAGCTTTCTCAAAAACCAAAACTCAA	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	152	3	23	17	50737026	+	17	60431181	+	28.4605	13.5778	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000047932	ENSG00000099204	GOPC	ABLIM1	TCAAAGTGCTGACTCTGGTACCATTAAGGCAAAATTG*GCAGGTGACAAACATTACCACCCCAGCTGTGCACGAT	oncogene,tcga,cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	73	13	25	6	117578900	-	10	114491878	-	8.1755	16.8722	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000047932	ENSG00000099204	GOPC	ABLIM1	AGCCCAGTCTGTGTCTCAAATCAACCACAAGCTGGAG*GCAGGTGACAAACATTACCACCCCAGCTGTGCACGAT	oncogene,tcga,cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	73	2	16	6	117602004	-	10	114491878	-	8.1755	16.8722	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000170836	ENSG00000110092	PPM1D	CCND1	AAGATGCCATCTCAATGTGCCAGGACCAAGAGGAGAAAAAATACCTGATG*TGACCTGTTTATGAGATGCTGGTTTTCTACCCAACGGCCCTGCAGCCAGC	oncogene,18cancers,cancer,tumor	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	68	13	24	17	60648082	+	11	69652174	+	36.6961	139.8206	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000170836	ENSG00000110092	PPM1D	CCND1	AAGATGCCATCTCAATGTGCCAGGACCAAGAGGAGAAAAAATACCTGATG*GTAGATGTGTAACCTCTTCACCTTATTCATGGCTGAAGTCACCTCTTGGT	oncogene,18cancers,cancer,tumor	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	68	3	23	17	60648082	+	11	69651902	+	36.6961	139.8206	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000170836	ENSG00000110092	PPM1D	CCND1	GCTTCCCAAAGTGCTGGGATTACAAGCGCAAGCCACCGCGACCGACCGGC*CTCAACCATCCTGGCTGCGGCGTCTGTCTGAACCACGCGGGGGCCTTGAG	oncogene,18cancers,cancer,tumor	BOWTIE+BLAT;BOWTIE+STAR	intronic/UTR	0	68	1	19	17	60638671	+	11	69654158	+	36.6961	139.8206	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000170836	ENSG00000110092	PPM1D	CCND1	AAGATGCCATCTCAATGTGCCAGGACCAAGAGGAGAAAAAATACCTGATG*GTTGCTGTTTCACAATACCTCATGCTTCACTTAGCCATGGTGGACCCAGC	oncogene,18cancers,cancer,tumor	BOWTIE+STAR	CDS(truncated)/UTR	0	68	1	16	17	60648082	+	11	69653481	+	36.6961	139.8206	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000110660	ENSG00000203799	SLC35F2	CCDC162P	GCCTGCTGCGCAGGATAAAAGGCAAACTCTTCACCTG*ATGAGAAGCCGGCTTGCCCAGGAGCGCAGTGTGAAGC	pseudogene,18cancers,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	38	10	25	11	107858658	-	6	109348427	+	6.2003	1.8553	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	transcribed_unitary_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000110660	ENSG00000203799	SLC35F2	CCDC162P	GCCTGCTGCGCAGGATAAAAGGCAAACTCTTCACCTG*GCTCAACTGCTGAAGGAGTTAGAACATAGAGTGACCC	pseudogene,18cancers,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	38	10	23	11	107858658	-	6	109343987	+	6.2003	1.8553	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	transcribed_unitary_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000110660	ENSG00000203799	SLC35F2	CCDC162P	GCACGGACTTCGGTTCGGGGCTCAACACGCACACCAG*GCTCAACTGCTGAAGGAGTTAGAACATAGAGTGACCC	pseudogene,18cancers,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	38	3	20	11	107858501	-	6	109343987	+	6.2003	1.8553	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	transcribed_unitary_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000005156	ENSG00000266101	LIG3	AC004408.1	GGACTGGAAATCTGCCACTAACCTTCCCCAACTCAAG*TTCCGACCCCAGAGCAGGAGGGAAGACGGGCAGGGCG	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	28	11	23	17	35001403	+	17	39177204	+	10.9112	0.0764	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000005156	ENSG00000266101	LIG3	AC004408.1	GATCTACTATCCTGACTTCATCGTCCCAGACCCAAAG*TTCCGACCCCAGAGCAGGAGGGAAGACGGGCAGGGCG	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	28	10	24	17	34999856	+	17	39177204	+	10.9112	0.0764	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000005156	ENSG00000266101	LIG3	AC004408.1	GCAGAAGGGAAGCTGAGTAACTCCAACAGCAAAGATG*TTCCGACCCCAGAGCAGGAGGGAAGACGGGCAGGGCG	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	28	8	25	17	35002104	+	17	39177204	+	10.9112	0.0764	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000196712	ENSG00000234751	NF1	AP002381.1	AAAAACATAAAGCAAAAAGCAAATAAAGCCCCCCACCACACAAAAAAAGC*ATACAAATTTTTTGAGGTTATCCTCATTGATCCATTCCATAAAGCTATCA	pseudogene,cancer,tumor,m16	BOWTIE+BLAT	intronic/exonic(no-known-CDS)	0	27	9	24	17	31232256	+	11	72940875	+	40.1117	5.718	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	processed_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000171475	ENSG00000170832	WIPF2	USP32	GCGGCAGAGGATTCGCTCCCAGAGCAGCTGCGGCCAG*TTACAGATGTAGAGCTAAAACGACTGAAGGATGCTTT	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	24	5	24	17	40219492	+	17	60345608	-	29.4617	89.7658	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000171475	ENSG00000170832	WIPF2	USP32	AGCTGCGGCCAGGTCGGAAAGAGGCCGGGGCGGCTGG*TTACAGATGTAGAGCTAAAACGACTGAAGGATGCTTT	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	24	1	14	17	40219517	+	17	60345608	-	29.4617	89.7658	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000159063	ENSG00000170832	ALG8	USP32	GGGTGACTCTTCTCAAATGCCTTCTCATCCCCACATA*TTACAGATGTAGAGCTAAAACGACTGAAGGATGCTTT	18cancers,cancer,exon-exon	BOWTIE	out-of-frame	0	19	3	25	11	78139494	-	17	60345608	-	73.4714	89.7658	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000175155	ENSG00000149269	YPEL2	PAK1	AAAACAACAAAAGGAACAGATCCTTGACCGCATGGCGGCAGCCCACCTTG*CTGACTTTGGATTCTGTGCACAGATAACCCCAGAGCAGAGCAAACGGAGC	oncogene,18cancers,cancer	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	16	4	21	17	59397488	+	11	77336282	-	49.1732	35.8454	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000175155	ENSG00000149269	YPEL2	PAK1	CCAACCCAGTGTCCACGTGAACGCCATTCAACCGAACATTCTTCCCAAGC*CTGACTTTGGATTCTGTGCACAGATAACCCCAGAGCAGAGCAAACGGAGC	oncogene,18cancers,cancer	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	16	2	21	17	59397255	+	11	77336282	-	49.1732	35.8454	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000196712	ENSG00000263798	NF1	AC018521.1	TTTGTGATCTTTTAAGTTAGCTATAGAAGCCATCTTCTCATTCTGCTGTG*CTCCAGAAGGTGTTGCCAGGGGCCCAGATGCCCTGACACTGCTTGAATAC	cancer,tumor,m7	BOWTIE+STAR	intronic/exonic(no-known-CDS)	0	15	3	18	17	31291773	+	17	47978829	+	40.1117	0	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000196712	ENSG00000108465	NF1	CDK5RAP3	AAGCTGGGAATCCTATTTTTTATTATGTTGCACGGAG*CTTGAGATCTTCTTAGCCCAGAGAGCAGTGGAGTTGA	tcga,cell_lines,18cancers,chimerdb3seq,cancer,tumor,m7,tcga-cancer,exon-exon	BOWTIE	in-frame	0	15	4	21	17	31265339	+	17	47980593	+	40.1117	0.4274	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000196712	ENSG00000108465	NF1	CDK5RAP3	AAGCTGGGAATCCTATTTTTTATTATGTTGCACGGAG*GTATGTGGACCGAGTGACTGAATTCCTCCAGCAAAAG	tcga,cell_lines,18cancers,chimerdb3seq,cancer,tumor,m7,tcga-cancer,exon-exon	BOWTIE	in-frame	0	15	3	23	17	31265339	+	17	47981163	+	40.1117	0.4274	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000196712	ENSG00000108465	NF1	CDK5RAP3	TCTATGTATAAGTGTGCCCATGCCATTCAAACCCATGTTGTTCAAGGGTC*ATGTGGGCCAGCTGTTATGGTAGGAGGGCTCTAGGGGGATCGGGGCCCTG	tcga,cell_lines,18cancers,chimerdb3seq,cancer,tumor,m7,tcga-cancer	BOWTIE+BLAT	intronic/intronic	0	15	1	21	17	31292631	+	17	47978426	+	40.1117	0.4274	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000141376	ENSG00000162105	BCAS3	SHANK2	ATTCGAGCGGCTAGAATCTTGCCTGCTCCACAGTTTG*GTTAACAATGAGAATGTTGTCAAAGTCGGCCACAGGC	18cancers,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	14	3	22	17	60747279	+	11	70502931	-	3.3051	3.3951	FALSE	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000137478	ENSG00000126351	FCHSD2	THRA	TGCTTATTAAATAGAGCAGTTCTTGCCACCCAGTCTTGTATTCTGTCTTT*GTTGGGGAGCTGTACCCTTTGTCCCCCTCCTACCCGCCACACCTGCCTGT	oncogene,18cancers,cancer	BOWTIE+BLAT	UTR/intronic	0	14	2	25	11	72837047	-	17	40073176	+	20.9903	15.3278	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000162105	ENSG00000141376	SHANK2	BCAS3	GTGGGGTGGCGTGGCAAGCCGGACTAAGGACCGGGGACTTCTTGATTGAG*ACGGAGTCTCGCTCTGTCGCCCAGGCCGGAGTGCAGTGGCGCGATCTCGG	18cancers,cancer,tumor,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	14	1	18	11	70659828	-	17	61329362	+	3.3951	3.3051	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000162105	ENSG00000141376	SHANK2	BCAS3	GTGGGGTGGCGTGGCAAGCCGGACTAAGGACCGGGGACTTCTTGATTGAG*ACGGAGTCTCGCTCTGTCGCCCAGGTTGGAGTGCAGTGGCACGATCTCAG	18cancers,cancer,tumor,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	14	1	18	11	70659828	-	17	61186732	+	3.3951	3.3051	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000162105	ENSG00000141376	SHANK2	BCAS3	GTGGGGTGGCGTGGCAAGCCGGACTAAGGACCGGGGACTTCTTGATTGAG*ACGGAGTCTCGCTCTGTCACCCAGGCTGGAGTGCAGTGGTGCGATCTCAG	18cancers,cancer,tumor,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	14	1	18	11	70659828	-	17	60880996	+	3.3951	3.3051	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000162105	ENSG00000141376	SHANK2	BCAS3	GTGGGGTGGCGTGGCAAGCCGGACTAAGGACCGGGGACTTCTTGATTGAG*ACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGTGCGGTCTCGG	18cancers,cancer,tumor,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	14	1	18	11	70659828	-	17	61267079	+	3.3951	3.3051	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000162105	ENSG00000141376	SHANK2	BCAS3	GTGGGGTGGCGTGGCAAGCCGGACTAAGGACCGGGGACTTCTTGATTGAG*ACGGAGTCTCGCTCTGTCACCCAGGGAGGAGTGCAGTGGCATGATCTCGG	18cancers,cancer,tumor,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	14	1	18	11	70659828	-	17	61234909	+	3.3951	3.3051	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000162105	ENSG00000141376	SHANK2	BCAS3	GTGGGGTGGCGTGGCAAGCCGGACTAAGGACCGGGGACTTCTTGATTGAG*ACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGAAGTGGTGTGATCTCGG	18cancers,cancer,tumor,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	14	1	18	11	70659828	-	17	61107108	+	3.3951	3.3051	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000162105	ENSG00000141376	SHANK2	BCAS3	GTGGGGTGGCGTGGCAAGCCGGACTAAGGACCGGGGACTTCTTGATTGAG*ACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGTGCGACCTTGG	18cancers,cancer,tumor,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	14	1	18	11	70659828	-	17	61170314	+	3.3951	3.3051	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000162105	ENSG00000141376	SHANK2	BCAS3	GTGGGGTGGCGTGGCAAGCCGGACTAAGGACCGGGGACTTCTTGATTGAG*ACGGAGTCTCGCTCTGTCGCCCAGGCCGGACTGCGGACTGCAGTGGCGCA	18cancers,cancer,tumor,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	14	1	18	11	70659828	-	17	60975016	+	3.3951	3.3051	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000068097	ENSG00000214517	HEATR6	PPME1	ACGATCAGCTATAGAAGCATCCAAGGATAAAGACAAG*CCCTGGAAGAAAGCGGGACTTTTCCCCTGTTCCTTGG	18cancers,exon-exon	BOWTIE	out-of-frame	0	10	4	22	17	60047309	-	11	74203728	+	93.4218	7.9276	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000173065	ENSG00000170832	FAM222B	USP32	GAGTGATGCTGTGTTCTTCACTGCATGATTTCAAAAG*TTACAGATGTAGAGCTAAAACGACTGAAGGATGCTTT	18cancers,cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	3	2	23	17	28790378	-	17	60345608	-	3.8821	89.7658	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000087157	ENSG00000079616	PGS1	KIF22	ACCGCCTCGGCAGGAACCGGGACCGCCAGCGCAGGAG*GAGCTGGTCGCTGTCGGCTAAGCAAGATTGGAGCTAC	18cancers,chimerdb3seq,exon-exon	BOWTIE	in-frame	0	3	4	21	17	78378808	+	16	29796893	+	7.0045	29.3796	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000108423	ENSG00000266826	TUBD1	AC011195.2	GCCTACTTATTCTGCAGAAAGCTCATTTCACTACAGACGAAATCCACTAG*GGCCTCGACCTCCTTGACAAGGTTGCCAAAATGTTATCGCAGCTTGACTT	NA	BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	3	1	25	17	59878103	-	17	58661461	-	60.4111	0.4812	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A18R-01A	ENSG00000130349	ENSG00000104237	C6ORF203	RP1	GCGGCCGCGGGGAGGGACGAGAGGGCCTGACGTACAG*GTAATGGATGGTTTCTTGGGAGTATTGTTGTTAAGTC	exon-exon	BOWTIE	UTR/CDS(truncated)	0	2	2	20	6	107028271	+	8	54865835	+	12.289	0.2323	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-BH-A18R-01A	ENSG00000147862	ENSG00000167258	NFIB	CDK12	TCTCCCTCCCTTCCCTCCTTACTTTCTCTCTCTCTCTCTTTCTCTCTCTC*TCTCTTTCCTTTTTTGCTGATGTGTGCTCTCTCTCTCTCTTTCTCTCTCT	oncogene,cancer	BOWTIE+BLAT	intronic/UTR	0	2	1	16	9	14388475	-	17	39532062	+	13.7663	47.0819	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-A8-A075-01A	ENSG00000165675	ENSG00000147481	ENOX2	SNTG1	TGAGATCAATTCTTGGAGAACACAAAGAAGTGTGATG*ACTGCTCTCCAGAATGTTGAGATTGCCCGAGAAGTGA	exon-exon	BOWTIE	UTR/UTR	0	2	2	23	X	130901684	-	8	50172561	+	2.8517	0.062	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A18U-01A	ENSG00000147548	ENSG00000156011	NSD3	PSD3	AGGCTGGGGCCTCAGGACCAAAAGGAGCATTAAGAAG*GCTCTGTACAACTCAATCAAGAATGAGAAGCTTGAAT	oncogene,tcga,cell_lines,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	213	23	25	8	38288487	-	8	18655685	-	86.929	72.3258	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A18U-01A	ENSG00000253802	ENSG00000168615	AC105999.2	ADAM9	GAGAGTTGGCACTTAGGGATGAAGAAATCATCTTCTG*GCTTTCAACAGACCTCACATCTTTCTTCTTATGAAAT	lincrna,oncogene,cancer,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	52	7	25	8	40343278	-	8	39007886	+	465.9958	47.1738	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A18U-01A	ENSG00000253802	ENSG00000168615	AC105999.2	ADAM9	GAGTTGACCCTGGGCTTTCAAAAAACTGTTCTTTCAG*GCTTTCAACAGACCTCACATCTTTCTTCTTATGAAAT	lincrna,oncogene,cancer,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	52	3	22	8	40333874	-	8	39007886	+	465.9958	47.1738	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A18U-01A	ENSG00000253802	ENSG00000168615	AC105999.2	ADAM9	TAAGAGAAAGGCAGAGTTGACCCTGGGCTTTCAAAAAACTGTTCTTTCAG*ACGGAGTCTCCCTCGGAGGTTGCCCAGGCTGGAGTGCAGTGGTGCAATCT	lincrna,oncogene,cancer	BOWTIE+BLAT;BOWTIE+STAR	exonic(no-known-CDS)/intronic	0	52	2	24	8	40333874	-	8	39002856	+	465.9958	47.1738	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-BH-A18U-01A	ENSG00000164080	ENSG00000187672	RAD54L2	ERC2	GAGTGCTGTCCCTTGGAACAGGAGGAGTAAGATTGAG*CTATTAGAAGGGCTGAATAAAGGGAACATGCAGCTCT	tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	UTR/UTR	0	14	8	24	3	51541650	+	3	55511276	-	3.6753	0.5976	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Breast	TCGA-BH-A18U-01A	ENSG00000156110	ENSG00000198739	ADK	LRRTM3	ATTGATACCAATGGAGCTGGAGATGCATTTGTTGGAG*ATACCTTTATCAATGAATGTGTCAACCTTTCTGGCAT	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	12	2	19	10	74670269	+	10	67097587	+	11.1838	0.229	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-BH-A18U-01A	ENSG00000183023	ENSG00000171428	SLC8A1	NAT1	GGAGAGCCCCGCCTGGTGGAGATGAGTGAGAAGAAAG*GGGATCATGGACATTGAAGCATATCTTGAAAGAATTG	cancer,exon-exon	BOWTIE	out-of-frame	0	2	1	13	2	40178387	-	8	18222042	+	0.841	1761.6566	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AR-A0TU-01A	ENSG00000049323	ENSG00000249258	LTBP1	AC079193.2	GGCTTTCAAGCCCCACAGGATGGGCAAGGGTGTGTGG*GGGAGCATGTCTTGAACCAGAGCCAATGTGGGTTTCC	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	11	8	22	2	33342963	+	8	17149505	+	5.515	0.64	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Breast	TCGA-AR-A0TU-01A	ENSG00000140350	ENSG00000129295	ANP32A	LRRC6	GATTCATTTAGAGCTGCGGAACAGGACGCCCTCTGAT*GATGTGAAGAGCTGGCAAAACTTGACCTGACTGTGAA	cancer,exon-exon	BOWTIE	out-of-frame	0	6	2	24	15	68820698	-	8	132638107	-	3.7914	9.7085	TRUE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-AR-A0TU-01A	ENSG00000129295	ENSG00000140350	LRRC6	ANP32A	GCTTTAAACAACATTGAAAAAATAGAAAACTTGGAAG*GTGAAAGAACTTGTCCTGGACAACAGTCGGTCGAATG	cancer,exon-exon	BOWTIE	out-of-frame	0	6	4	22	8	132656830	-	15	68787919	-	9.7085	3.7914	FALSE	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Breast	TCGA-AR-A0TU-01A	ENSG00000049323	ENSG00000104219	LTBP1	ZDHHC2	GGTTTCTCAATCTCTGCAGATGGCCGTACGTGTGAAG*TGTCCATGGAAAACACTGGCGAACAAGTTGTGTGCCT	tcga-cancer,exon-exon	BOWTIE	in-frame	0	5	2	21	2	33315269	+	8	17184789	+	5.515	2.9268	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-AR-A0TU-01A	ENSG00000104219	ENSG00000049323	ZDHHC2	LTBP1	TGGTCCTACTACGCCTACGCCATCCAGCTGTGCATAG*ATGTGAATGAATGTGAACTGCTCAGTGGGGTGTGTGG	tcga-cancer,exon-exon	BOWTIE	in-frame	0	5	2	24	8	17156853	+	2	33347367	+	2.9268	5.515	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Breast	TCGA-AR-A0TU-01A	ENSG00000104219	ENSG00000049323	ZDHHC2	LTBP1	TGGTCCTACTACGCCTACGCCATCCAGCTGTGCATAG*ATATTGATGAATGTGTAAACAACACTGTTTGTGACAG	tcga-cancer,exon-exon	BOWTIE	in-frame	0	5	2	16	8	17156853	+	2	33342838	+	2.9268	5.515	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-G2-A3IE-01A	ENSG00000223704	ENSG00000249740	LINC01422	OSMR-AS1	CTAGTTCATGCGGTGGACCTGCTGGGTGGCCTCAG*GTTTTCAGTGATGTTGAGAGTCAACAGGAAATTAA	lincrna,exon-exon	BOWTIE	exonic(no-known-CDS)/exonic(no-known-CDS)	0	3	2	19	22	26862105	+	5	38796469	-	0.5183	0.0238	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	lincRNA	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-G2-A3IE-01A	ENSG00000141447	ENSG00000260719	OSBPL1A	AC009133.3	TCCACCCGCCAGCATCCTTAGCGAGGACGAGTTCTATGATGCGCTGTCAG*ACCCTGCACTTGATGGATCAGCTGGCACCACCCAGATCAATAAACTGGCT	antisense,m2	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	3	1	19	18	24239220	-	16	29747995	+	0.7255	3.2495	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-G2-A3IE-01A	ENSG00000140262	ENSG00000184007	TCF12	PTP4A2	GTTTAGCATTTCATTTTTACCAAATTTTGATGAAAAGCAAACAAAAAAAA*AAATCTCTCTATAAAATGAATAAAATGTTTAAGAAAAGAGAAAGAGAAAA	oncogene,cancer	BOWTIE+STAR	intronic/UTR	0	2	1	16	15	57203000	+	1	31908690	-	3.9694	44.7454	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-BT-A3PK-01A	ENSG00000175221	ENSG00000181588	MED16	MEX3D	GGTGGCCAGCGACACACAGTTCTACCCTGGCCTCG*GCTGCAAGATCAAGGCCCTGCGGGCCAAGACAAAC	exon-exon	BOWTIE	in-frame	0	10	2	19	19	881559	-	19	1556923	-	13.4838	10.3797	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-GC-A3RD-01A	ENSG00000147889	ENSG00000174197	CDKN2A	MGA	CCATGCCCGCATAGATGCCGCGGAAGGTCCCTCAG*CTATATGTGAGACAGAGCCTGAACAGCCTGTTCGA	tcga,cell_lines,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	29	2	20	9	21970902	-	15	41727180	+	0.818	6.0072	FALSE	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-GC-A3RD-01A	ENSG00000174197	ENSG00000147889	MGA	CDKN2A	GAAAGAGAAAAAGAAGAGAAAGAAGCTAGAATACA*ACATCCCCGATTGAAAGAACCAGAGAGGCTCTGAG	tcga,cell_lines,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	29	11	24	15	41713496	+	9	21968242	-	6.0072	0.818	TRUE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-GC-A3RD-01A	ENSG00000116478	ENSG00000124299	HDAC1	PEPD	ATGGAGAGTACTTCCCAGGAACTGGGGACCTACGG*CCTCTTCGAGCACTACTGCTACTCCCGGGGCGGCA	oncogene,tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	7	3	24	1	32327677	+	19	33413643	-	30.3049	10.4048	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-GC-A3RD-01A	ENSG00000116478	ENSG00000124299	HDAC1	PEPD	GTTACACCATTCGTAACGTTGCCCGGTGCTGGACATATGAGACAGCTGTG*GGGCCACCCTCCATGAGTGTGCCACAAGCCTTGTGGATGCACCTGTGACA	oncogene,tcga,chimerdb3seq,tcga-cancer	BOWTIE+BLAT	CDS(truncated)/intronic	0	7	2	24	1	32330883	+	19	33447252	-	30.3049	10.4048	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-GC-A3RD-01A	ENSG00000176623	ENSG00000176571	RMDN1	CNBD1	CTCTCAGGCTGCTGTGGTTCATGCCACAGCCAAAG*CCGGAGTATGAGCAATATCTTATCAGCTCACGATA	exon-exon	BOWTIE	in-frame	0	3	1	13	8	86506995	-	8	86905081	+	11.5605	0.1192	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-FD-A3B4-01A	ENSG00000163995	ENSG00000074211	ABLIM2	PPP2R2C	GCATCCGCTGTGACAGCTGTGAGAAATACATCACGGGGCGCGTGCTGGAG*AATACCTTCTGCTGGCCGGGTGCAATGGCTCACGCCTGTAATCCCAGCAC	tcga,chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	6	1	19	4	8077628	-	4	6500460	-	2.3364	15.677	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-FD-A3SN-01A	ENSG00000010322	ENSG00000163939	NISCH	PBRM1	TGTGGGGCTTTTCGACCAGCATTTCCGGCTGACGG*GTAGGAAGAGTGGCATTTCTCCTAAAAAATCAAAA	tcga,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	4	2	18	3	52490833	+	3	52609955	-	11.6728	3.7914	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-CU-A0YN-01A	ENSG00000139636	ENSG00000099337	LMBR1L	KCNK6	GACCCGCTTCAAGAAGCCTGCTGAGTTCACCACAG*GCTATGGGTACACAACGCCACTGACTGATGCGGGC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	61	12	23	12	49106961	-	19	38326593	+	5.914	38.2231	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-CU-A0YN-01A	ENSG00000139636	ENSG00000099337	LMBR1L	KCNK6	AACAGCTATTCCACGAGAGGATCCGCGAGTGTATT*GCTATGGGTACACAACGCCACTGACTGATGCGGGC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	61	10	22	12	49110484	-	19	38326593	+	5.914	38.2231	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-CU-A0YN-01A	ENSG00000139636	ENSG00000099337	LMBR1L	KCNK6	GTGGATGATGAAGATGCCACCGTCAACAAGATTGC*GCTATGGGTACACAACGCCACTGACTGATGCGGGC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	61	4	21	12	49105924	-	19	38326593	+	5.914	38.2231	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-CU-A0YN-01A	ENSG00000139636	ENSG00000099337	LMBR1L	KCNK6	GACCCGCTTCAAGAAGCCTGCTGAGTTCACCACAG*ATACGAGGCTGGCCATGCCATGTGGGAGATGGAGT	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	61	2	22	12	49106961	-	19	38325043	+	5.914	38.2231	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-CU-A0YN-01A	ENSG00000166704	ENSG00000160439	ZNF606	RDH13	CATGGCATGAAGTTGGAAAGATATATATGGGATGATCCTTGGTTCTCCAG*TCCATACTCTACATCTCAGCCAGAAAAGAAGAAATTCTAAAACATGTATC	tcga,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	52	6	23	19	57980162	-	19	55067715	-	3.3332	6.1709	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-CU-A0YN-01A	ENSG00000166704	ENSG00000160439	ZNF606	RDH13	AGTGGAGCAGGCATGTCCTCAACGCACTTGTCCAG*AATTTCACTCTGTCGCCAGGCTGGAATGCAGTAGG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	52	4	22	19	57988207	-	19	55064412	-	3.3332	6.1709	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-CU-A0YN-01A	ENSG00000166704	ENSG00000160439	ZNF606	RDH13	TACTCAACATACAAGCACTTACACTGCAGAGAAACCCTATGACTACAATG*ACACAGGAGGGGGAGAGAAAGAGGGAGAGAGCAATGAGAGAGATATGAGA	tcga,chimerdb3seq,tcga-cancer	BOWTIE+BLAT	CDS(truncated)/intronic	0	52	1	22	19	57979470	-	19	55068036	-	3.3332	6.1709	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-CU-A0YN-01A	ENSG00000048052	ENSG00000243004	HDAC9	AC005062.1	TCTGATTCTCATGATGAGCTCACCTGCACAGCCTG*ATCGCTTCTTGACCTGCACAACTTTCTGATTTGAT	exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	2	6	23	7	18162349	+	7	20045561	-	4.015	0.2608	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	sense_overlapping	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-BT-A0YX-01A	ENSG00000224186	ENSG00000173801	C5ORF66	JUP	TGATGGAACCAGGTGACCCGCAGCCTCCGGGCCAG*GCAACCATCGGCTTGATCAGGAATCTGGCCCTGTG	antisense,oncogene,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	146	20	24	5	135174172	+	17	41758870	-	0.8526	378.0552	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-BT-A0YX-01A	ENSG00000224186	ENSG00000173801	C5ORF66	JUP	TCTAGATTTCAAAAGGCCCTTTCAGAATTGGAAGACTTTTGCCTTGAATG*GCAACCATCGGCTTGATCAGGAATCTGGCCCTGTGCCCAGCCAACCATGC	antisense,oncogene	BOWTIE+STAR	intronic/CDS(truncated)	0	146	1	17	5	135195519	+	17	41758870	-	0.8526	378.0552	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-BT-A0YX-01A	ENSG00000224186	ENSG00000173801	C5ORF66	JUP	TGGATTCTAGGCTTCCATAATGGCCTTGTCTTCTCCAGGGGATCCTACAG*GCAACCATCGGCTTGATCAGGAATCTGGCCCTGTGCCCAGCCAACCATGC	antisense,oncogene	BOWTIE+STAR	intronic/CDS(truncated)	0	146	1	16	5	135195265	+	17	41758870	-	0.8526	378.0552	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-G2-A2ES-01A	ENSG00000149948	ENSG00000174099	HMGA2	MSRB3	GCAAAAACAAGAGTCCCTCTAAAGCAGCTCAAAAG*TGTGGTGCTCACCTTGGGCACATTTTTGATGATGG	known,oncogene,tcga,cell_lines,chimerdb3seq,cancer,tumor,exon-exon	BOWTIE	in-frame	0	362	22	24	12	65828087	+	12	65463155	+	4.0478	11.5474	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-G2-A2ES-01A	ENSG00000149948	ENSG00000174099	HMGA2	MSRB3	CGTCCGGTGTTGATGGTGGCAGCGGCGGCAGCCTAAGCAACAGCAGCCCT*TGATGATGGGCCTCGTCCAACTGGGAAAAGATACTGCATAAATTCGGCTG	known,oncogene,tcga,cell_lines,chimerdb3seq,cancer,tumor	BOWTIE+BLAT	UTR/CDS(truncated)	0	362	1	19	12	65825137	+	12	65463181	+	4.0478	11.5474	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-G2-A2ES-01A	ENSG00000134759	ENSG00000134775	ELP2	FHOD3	TGCTGTTCGACTCTGGTCTAAAAAGGGTCCAGAAG*AAAAACTATACAACTCCAGCGGACGAGATTTGAGA	cell_lines,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	8	4	24	18	36138426	+	18	36501932	+	3.301	1.7501	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-G2-A2ES-01A	ENSG00000104327	ENSG00000103342	CALB1	GSPT1	CCTTCTCTCCTTGTCTCTACCCCTTCTCTGCTTTTCTGGGGGAGGGACAA*ACAAGAGAACATGCAATGTTGGCAAAGACAGCAGGTGTAAAACACCTAAT	cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	14	8	90094892	-	16	11886877	-	142.1841	23.9796	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-DK-A3X1-01A	ENSG00000109667	ENSG00000051180	SLC2A9	RAD51	GCTACAACCTGTCGGTGGTGAATGCCCCCACCCCG*GCTGAGGCAGCTAAATTAGTTCCAATGGGTTTCAC	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	8	4	22	4	10018975	-	15	40706177	+	0.6904	9.843	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-DK-A3X1-01A	ENSG00000064042	ENSG00000141522	LIMCH1	ARHGDIA	GAAGAAGGGTGCCTCCTCCCTGTCTTGATCCTACTTCCTTCAAGAATCTT*GCGCCTACGGCTATCCTCGCGCGGCGCGGAGGCCCCAGCCCCTGGAGG	NA	BOWTIE+BLAT	intronic/UTR	0	3	3	23	4	41559378	+	17	81870788	-	5.016	33.1585	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-BT-A2LB-01A	ENSG00000166783	ENSG00000174628	MARF1	IQCK	CCGACTTGCCCCCCAGGTTACCACTAAAAATGCCA*TGAAATGCAAAATGGAGGACGATGCAGTACCTGCA	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	141	16	24	16	15630332	-	16	19856487	+	7.3727	0.8786	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BT-A2LB-01A	ENSG00000166783	ENSG00000174628	MARF1	IQCK	ACACACTGCTCCAGCCACAGTGGTTCTTGTGTCAA*TGAAATGCAAAATGGAGGACGATGCAGTACCTGCA	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	141	9	23	16	15631381	-	16	19856487	+	7.3727	0.8786	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BT-A2LB-01A	ENSG00000166783	ENSG00000174628	MARF1	IQCK	TTGAAGAGTTCATTTCCGACTTGCCCCCCAGGTTACCACTAAAAATGCCA*AAAGGCAGGGGCTGGGTGCGGTGGCTCATACCTGTAATCTCAGCGCTTTG	tcga,cell_lines,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	141	2	22	16	15630332	-	16	19849471	+	7.3727	0.8786	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BT-A20T-01A	ENSG00000121316	ENSG00000111269	PLBD1	CREBL2	CAGCAGTAGTCGCCTCTCTTTCAGCAGTTACCCAG*GTGGTTGGAGGCAAAGTAAAGAAGCCCGGTAAACG	tcga,18cancers,chimerdb3seq,tumor,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	7	3	21	12	14535659	-	12	12635777	+	24.0245	6.2047	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-BT-A20T-01A	ENSG00000143614	ENSG00000117419	GATAD2B	ERI3	GGCGAGCTAGCCGGGAGTTACACCGCCACCGCCAG*GAAATCATCGAGTTCCCCATCCTAAAGCTAAATGG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	3	2	22	1	153922733	-	1	44319744	-	5.5797	25.8878	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-DK-A3IN-01A	ENSG00000182541	ENSG00000093009	LIMK2	CDC45	AGGTCAGGTTTGCCAAAGGAATCGCCTCCGGAATG*ACAAAGAACCGGCGCTGCAAACTGCTGCCCCTGGT	tcga,chimerdb3seq,m36,tcga-cancer,exon-exon	BOWTIE	in-frame	0	38	8	23	22	31268200	+	22	19516527	+	30.5547	15.4539	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-DK-A3IN-01A	ENSG00000169762	ENSG00000169744	TAPT1	LDB2	CGACCGGCGGCGGGAGAGGCGCCGGGGCCGCACAG*CTATCGGCAGGACCCTCATCCCCCGTTACTTTAGC	tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	7	2	24	4	16226259	-	4	16595875	-	2.5434	3.6797	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-DK-A3IN-01A	ENSG00000099991	ENSG00000183454	CABIN1	GRIN2A	TGGCCTTCCTCTACACCTACAGCAAGACCCACCGG*ATTTATGGTCAATGTTACATGGGATGGCAAAGACT	oncogene,tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	5	3	16	22	24119698	+	16	9891100	-	28.7711	0.2448	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BL-A13J-01A	ENSG00000115464	ENSG00000170264	USP34	FAM161A	TTCTGGAGCTTCAGAAAATGTTTACATATTTAATG*AAAAATGCAAGAATGGCAGCAGAAAAGCATTATTC	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	37	6	22	2	61259711	-	2	61827258	-	6.6537	3.7189	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BL-A13J-01A	ENSG00000187676	ENSG00000175664	B3GLCT	TEX26	GCAGGCTGGGCCTTAAGTATTCCACTTGTAAACAA*ATAGACAAATTATTGATCGCTTTATTCGTACTCAC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	34	5	24	13	31261082	+	13	30974846	+	3.7573	1.4139	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BL-A13J-01A	ENSG00000121390	ENSG00000196199	PSPC1	MPHOSPH8	CAAGAGTTGCAAAAACGGAAGCAAATACAACTAAG*ATGGCAGGCAGCAGATTCTGAGTTTGGGCATGGAC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	8	1	14	13	19741565	-	13	19658995	+	7.2429	14.3099	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BL-A13J-01A	ENSG00000143198	ENSG00000143179	MGST3	UCK2	ATGTTTCCAAGGCCCGCAAGAAGTACAAAGTGGAG*TCTTCCGTGTGTGCTAAGATCGTGCAGCTCCTGGG	18cancers,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	6	2	23	1	165649964	+	1	165890204	+	22.5216	8.2461	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-BL-A13J-01A	ENSG00000143198	ENSG00000143179	MGST3	UCK2	TTTTGTTCTGCTCCAGCTGTTCGAAGGTGATCCAG*TCTTCCGTGTGTGCTAAGATCGTGCAGCTCCTGGG	18cancers,100K<gap<200K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	6	2	20	1	165631293	+	1	165890204	+	22.5216	8.2461	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-DK-A1A3-01A	ENSG00000153879	ENSG00000173809	CEBPG	TDRD12	GAGGCCGCCTGGGGGCAGGCGGGCTAGAGGAGCAG*ACCTGCCAAGAAGTGGGACAATGCAGCTATTCAGT	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	11	9	23	19	33373895	+	19	32748476	+	15.5273	9.0487	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-DK-A1A3-01A	ENSG00000085832	ENSG00000154222	EPS15	CC2D1B	CCATGGCTGCGGCGGCCCAGCTCTCTCTGACACAG*AATATAAAAGATGAGTTCCATGACAACGGGGCCCT	cancer,tumor,m3,exon-exon	BOWTIE	CDS(truncated)/UTR	0	4	2	22	1	51519199	-	1	52346203	-	17.0822	4.6453	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-DK-A1A3-01A	ENSG00000116285	ENSG00000169641	ERRFI1	LUZP1	GGAGGGCGCCGCGGGGCAGCCGCCGCTCCTCCGGG*GTCAAGAGACAACTGCCTTTGAAAGAGAGTGAGTG	tcga,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	UTR/UTR	0	3	2	22	1	8026158	-	1	23109127	-	20.9092	15.1871	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-DK-A1A3-01A	ENSG00000116285	ENSG00000169641	ERRFI1	LUZP1	GGAGGGCGCCGCGGGGCAGCCGCCGCTCCTCCGGG*GGGACATTGAATAAACCTGAGTATTGTGTGCCTGT	tcga,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	UTR/UTR	0	3	1	14	1	8026158	-	1	23109650	-	20.9092	15.1871	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-DK-A1A3-01A	ENSG00000117298	ENSG00000127481	ECE1	UBR4	CGCTGCCCACCTGGCTCACCCATGAACCCGCCTCACAAGTGCGAAGTCTG*AACCCGAGCAACTTCCCGAGAAGAGAAGAACCTCCAAGGCTTTCTGGAAC	NA	BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	2	2	21	1	21219959	-	1	19081573	-	28.8894	5.8781	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-FD-A3SL-01A	ENSG00000161405	ENSG00000008838	IKZF3	MED24	AGAAGGCCCAGCCAATGAAGATGAAGACATAGGAG*CCAACCTGTTCCTGCTCATCTCCTCCATCCTGGGG	cell_lines,18cancers,cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	26	11	23	17	39829387	-	17	40019933	-	2.3924	10.4267	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-BT-A20R-01A	ENSG00000204498	ENSG00000204420	NFKBIL1	MPIG6B	AGAAGCAAGAAACTTCGGGGCTGCAGCCTCAGGATGAGGCAGAAGGAAGG*CTTCTCTGGACGGCCGCCCTGGGGACCGGGTGAATCTCTCCTGCGGAGGA	100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	4	2	24	6	31558670	+	6	31723639	+	16.0952	4.3445	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-BT-A20R-01A	ENSG00000204498	ENSG00000204420	NFKBIL1	MPIG6B	AGAAGCAAGAAACTTCGGGGCTGCAGCCTCAGGATGAGGCAGAAGGAAGG*GGTCTGGCTGGCTCTGTCGCCCAGGCTGGAGTGCAATGGCCTGATCACAG	100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	UTR/UTR	0	4	1	22	6	31558670	+	6	31723004	+	16.0952	4.3445	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-GV-A3QH-01A	ENSG00000170017	ENSG00000147010	ALCAM	SH3KBP1	CTGCCTCTTGATCTCCGCCACCGTCTTCAGGCCAG*AAAGACCAGAGAGAGAGCCAAAACTGGATTTACAG	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	73	13	23	3	105367481	+	X	19588802	-	28.8258	10.9403	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-GV-A3QH-01A	ENSG00000134852	ENSG00000135220	CLOCK	UGT2A3	GGAGGGAAGAAGCCGGAGCCGCCGCAAGCCACACG*GAAATGGAAAATTTTGTCCAGAGTTCAGGGGAAGA	tcga,chimerdb3seq,m9,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	61	15	24	4	55546482	-	4	68932759	-	2.5388	25.6598	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-GV-A3QH-01A	ENSG00000134852	ENSG00000135220	CLOCK	UGT2A3	AGGAAATCTGGCCGCCGCCGCCGCGAGCGCTCCCG*GAAATGGAAAATTTTGTCCAGAGTTCAGGGGAAGA	tcga,chimerdb3seq,m9,tcga-cancer,exon-exon	BOWTIE;BOWTIE+BLAT	UTR/CDS(truncated)	0	61	15	24	4	55546782	-	4	68932759	-	2.5388	25.6598	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-GV-A3QH-01A	ENSG00000134852	ENSG00000135220	CLOCK	UGT2A3	GGAGGGAAGAAGCCGGAGCCGCCGCAAGCCACACG*GTGTTATGGAGGTACAAAGGAAAAAAACCATCCAC	tcga,chimerdb3seq,m9,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	61	2	23	4	55546482	-	4	68931242	-	2.5388	25.6598	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-GV-A3QH-01A	ENSG00000134852	ENSG00000135220	CLOCK	UGT2A3	AGGAAATCTGGCCGCCGCCGCCGCGAGCGCTCCCG*GAAAGTTATACCAGAAAACCAAGCTCTCTTAAGCC	tcga,chimerdb3seq,m9,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	61	2	20	4	55546782	-	4	68943378	-	2.5388	25.6598	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-GV-A3QH-01A	ENSG00000134852	ENSG00000135220	CLOCK	UGT2A3	TTATATTCTTTGAAAGTGTTTGTAGCTTTGTAGAGGTCCTCTTGTTGATG*GAAATGGAAAATTTTGTCCAGAGTTCAGGGGAAGATGGTATTGTGGTGTT	tcga,chimerdb3seq,m9,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	61	1	22	4	55545678	-	4	68932759	-	2.5388	25.6598	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-GV-A3QH-01A	ENSG00000134852	ENSG00000135220	CLOCK	UGT2A3	GGGAAACTTTTCTTTCTTTTGAGGAAATCAAACATGAACCCCAGTGAAAG*GAAAGTTATACCAGAAAACCAAGCTCTCTTAAGCCATGGCATCTGTATCT	tcga,chimerdb3seq,m9,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	61	1	22	4	55544210	-	4	68943378	-	2.5388	25.6598	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-GV-A3QH-01A	ENSG00000134852	ENSG00000135220	CLOCK	UGT2A3	CTCTTCGGGCGTCCGGGATCCCCTGGCGCGGCTCCGTGCTGCCTAACGGG*GAAATGGAAAATTTTGTCCAGAGTTCAGGGGAAGATGGTATTGTGGTGTT	tcga,chimerdb3seq,m9,tcga-cancer	BOWTIE+BLAT	UTR/CDS(truncated)	0	61	1	19	4	55547005	-	4	68932759	-	2.5388	25.6598	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-GV-A3QH-01A	ENSG00000172197	ENSG00000146038	MBOAT1	DCDC2	AAGGTTTCCACAGCTTGCCAGAACCTTCTCCCACA*GTAAAACCAGTAATCCATAGCAGGATCAACGTGTC	exon-exon	BOWTIE	in-frame	0	25	6	22	6	20126517	-	6	24302044	-	33.6189	4.493	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-GV-A3QH-01A	ENSG00000170185	ENSG00000112116	USP38	IL17F	TTAGCTTTCAGCATTCTCCAGAGGCGTTCCATTTG*TGTCACTTGGGACCCCAACCGGTACCCCTCGGAAG	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	14	8	23	4	143197924	+	6	52237168	-	22.6362	1.2768	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-GV-A3QH-01A	ENSG00000250903	ENSG00000246982	GMDS-AS1	Z84485.1	GGGGCAGCGTGCTGCATCTCAGCCAACTCCAGGAG*AACTCCATGGCAATGTTTTGAGGATTAAAGAGGAG	lincrna,antisense,exon-exon	BOWTIE	exonic(no-known-CDS)/exonic(no-known-CDS)	0	8	3	19	6	2248926	+	6	36158941	-	0.2088	0.7982	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	lincRNA	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-GV-A3QF-01A	ENSG00000131941	ENSG00000124299	RHPN2	PEPD	GTGCGGATGAGGACCGGAGCGGAAAACCTTCTGAA*CCTCTTCGAGCACTACTGCTACTCCCGGGGCGGCA	known,tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	80	15	22	19	33044249	-	19	33413643	-	9.8635	46.0242	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-GV-A3QF-01A	ENSG00000130699	ENSG00000130702	TAF4	LAMA5	CCCGACCAACATCCAGAACTTCCAGCTGCCCCCAG*ACCTCCCAGGAGCTACACTGCCTGATGTGGGCCTG	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	75	14	23	20	62064451	-	20	62310311	-	4.0287	23.9452	TRUE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-GV-A3QF-01A	ENSG00000130699	ENSG00000130702	TAF4	LAMA5	CCCGACCAACATCCAGAACTTCCAGCTGCCCCCAG*GTCCTGCTGCGGGCGGATGACGGAGCAGGGGAGTT	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	75	3	22	20	62064451	-	20	62310081	-	4.0287	23.9452	TRUE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Bladder	TCGA-GV-A3QF-01A	ENSG00000165671	ENSG00000254035	NSD1	AC104117.3	CAGTTTGACACCACAGGCTGAGCTCCCTGAACCAG*GATGCTGCTGTGAAGATGTAATGGGTGGAGCCTCA	antisense,oncogene,cancer,tumor,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	39	9	22	5	177212195	+	5	178989747	+	2.6198	2.1138	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-GV-A3QF-01A	ENSG00000167900	ENSG00000187775	TK1	DNAH17	CCGCCTATACCAAGAGGCTCGGCACAGAGAAGGAG*GTGAAGGCCGTGCTGGACGACATCCTGGAGAAGAT	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	25	5	23	17	78175050	-	17	78427108	-	87.0301	0.5002	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-GV-A3QF-01A	ENSG00000143252	ENSG00000198358	SDHC	AL354714.1	AACCGTCCTCTGTCTCCCCACATTACTATCTACAG*AATTCCAGTTTTTCCGTCTCCAAATAGCCGGGGTT	antisense,cancer,m14,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	15	6	23	1	161328497	+	1	160945066	+	59.8198	0.1563	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-GV-A3QF-01A	ENSG00000075643	ENSG00000134775	MOCOS	FHOD3	CGAGCTGCGGGCGCGCGAGTTCAGCCGCCTGGCAG*ATACAGCAATTTTGGCAATAACTCTTATCACTCCT	oncogene,tcga,cell_lines,chimerdb3seq,cancer,tumor,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	3	2	22	18	36187681	+	18	36658075	+	5.4567	2.8703	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-GV-A3QF-01A	ENSG00000146070	ENSG00000112782	PLA2G7	CLIC5	ACCTTAGAACCCTGAAACAAGAGGAGGAGACACATATACGAAATGAGCAG*AAGAGAACGGGAATGAAGTAAGATCAGAAAATAAAGGAAGAAATAGAAAG	NA	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	3	4	23	6	46711496	-	6	46016587	-	14.5525	0.1814	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-GV-A3QF-01A	ENSG00000143190	ENSG00000033122	POU2F1	LRRC7	AGATGAGAGTTCAGCCGCGGCGGCAGCAGCAGCAG*GATGGAGAACCTAATAAGGGGAAGGAATCCCCCGC	exon-exon	BOWTIE	out-of-frame	0	3	1	14	1	167220958	+	1	69678381	+	4.6075	0.1956	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01A	ENSG00000248485	ENSG00000158864	PCP4L1	NDUFS2	CTCGCGCGCCCTGTCCGGCTGCGGAGATGAGCGAG*ACTTCCATGGAGTCACTGATTCATCACTTTAAGTT	tcga,cell_lines,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	26	8	23	1	161258983	+	1	161213380	+	5.0097	27.3596	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-BL-A0C8-01A	ENSG00000105556	ENSG00000101391	MIER2	CDK5RAP1	CAGCAACCTGCACTTGAACCGGCACTGTGAGAAGA*GCTGCATGGCTGAGAGGTTGAAGGAGGAGATTCTC	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	22	13	23	19	325635	-	20	33387533	-	4.6658	13.5157	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01A	ENSG00000147257	ENSG00000132170	GPC3	PPARG	GTTCTTAATTATTCAGAATGCTGCGGTTTTCCAAG*AAATGACCATGGTTGACACAGAGATGCCATTCTGG	oncogene,cell_lines,cancer,exon-exon	BOWTIE	in-frame	0	21	13	23	X	133953050	-	3	12379704	+	2365.2732	291.7952	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01A	ENSG00000177697	ENSG00000177106	CD151	EPS8L2	TCGCTGGTATCCTCGCCTACGCCTACTACCAGCAG*AGCAGAGGAAGAAGTATTCCAACTCCAACGTCATC	tcga,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	17	13	24	11	836843	+	11	710422	+	42.2413	11.74	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01A	ENSG00000008294	ENSG00000120265	SPAG9	PCMT1	GATCAACTAGAATCCACAGCTCATAGTAGAATTAG*AAAATGGAATCATCAAGACAGATAAAGTATTTGAA	oncogene,tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	15	5	22	17	51047375	-	6	149771162	+	85.857	17.9986	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01A	ENSG00000008294	ENSG00000120265	SPAG9	PCMT1	ACTTGAGCTGAAAGCGAAAAACTATGCTGACCAGA*AAAATGGAATCATCAAGACAGATAAAGTATTTGAA	oncogene,tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	15	2	21	17	51079584	-	6	149771162	+	85.857	17.9986	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01A	ENSG00000247596	ENSG00000053108	TWF2	FSTL4	GCGCCGAGCCATGGCGCACCAAACGGGCATCCACG*GACTTTGGAGAGGATGATTCCCTGTACATCACCAA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	10	6	24	3	52238992	-	5	133233537	-	7.0641	3.7016	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01A	ENSG00000083307	ENSG00000197872	GRHL2	FAM49A	TGAAGTCTCCCACAGTGAAGGGCCTGATGGAAGCG*GTTTGCTGGGATGGGAAACCTGCTCAAAGTCCTTA	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	5	3	23	8	101649499	+	2	16588129	-	19.7511	21.0959	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01A	ENSG00000083307	ENSG00000197872	GRHL2	FAM49A	TGAAGTCTCCCACAGTGAAGGGCCTGATGGAAGCG*ATGCTCAGCCTACAGAAGGAGAGAGAGAAATCTGG	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	5	1	14	8	101649499	+	2	16565767	-	19.7511	21.0959	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01A	ENSG00000143748	ENSG00000011376	NVL	LARS2	AGATGGAGAAATTGAAGCTGTCCTGCAAAAGAAAG*GCCTGGCGCTGGTGCCGAGGAAGCTCTGTGCCCAC	cell_lines,tcga-cancer,exon-exon	BOWTIE	in-frame	0	4	3	18	1	224305034	-	3	45541829	+	5.1715	3.1098	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01A	ENSG00000133961	ENSG00000258603	NUMB	AC005225.2	GCAGTGGCGCTTGAGTTGGTCGGGGGCAGCGGCAG*ATTTTTTACCATTGAGATGTTTATGGAAGAAAGTT	antisense,100K<gap<200K,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	2	5	22	14	73458493	-	14	73619816	-	6.3608	0.0666	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-FT-A3EE-01A	ENSG00000156675	ENSG00000215262	RAB11FIP1	KCNU1	GATCTGCACCGCGACCAGGGCCGCAGGAAGACGCA*GACTCTTCAACATGATGTAGAACAAGATTCTGACC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	76	12	23	8	37899071	-	8	36905708	+	8.9198	9.9183	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-FT-A3EE-01A	ENSG00000020181	ENSG00000104687	ADGRA2	GSR	CCGCCCTCAGCCCCCATGCCCAGCACATCTCAGTG*GTGAATGTTGGATGTGTACCCAAAAAGGTAATGTG	cell_lines,18cancers,exon-exon	BOWTIE	in-frame	0	29	8	21	8	37834128	+	8	30712088	-	4.2002	18.0793	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-FT-A3EE-01A	ENSG00000020181	ENSG00000104687	ADGRA2	GSR	AGAAATTTTTGGGTTATGTCGACCAGATCAAAGAG*GTGAATGTTGGATGTGTACCCAAAAAGGTAATGTG	cell_lines,18cancers,exon-exon	BOWTIE	in-frame	0	29	2	14	8	37833837	+	8	30712088	-	4.2002	18.0793	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-GD-A3OP-01A	ENSG00000235106	ENSG00000160271	LINC00094	RALGDS	ACTCTCCACCCAGCTCCCAGGCTGCCCCACGGGAC*AGCTCCACGCAGGAGATCGGTGAGGAGCTGATCAA	oncogene,cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	6	2	22	9	134026090	+	9	133112152	-	3.3053	1.1529	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-E5-A2PC-01A	ENSG00000141027	ENSG00000239704	NCOR1	CDRT4	AACCATCTTTTATAATGGGAGGCTCCATCTCACAG*GAATCTGAACCTGTGATGTTAAGAAATCAGTAAAT	cell_lines,cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	32	7	19	17	16086282	-	17	15440285	-	1.6929	0.009	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-E5-A2PC-01A	ENSG00000141027	ENSG00000239704	NCOR1	CDRT4	AACCATCTTTTATAATGGGAGGCTCCATCTCACAG*GACTCACAGAAAACACTGGACTTCCCCGGAAGCTA	cell_lines,cancer,exon-exon	BOWTIE	out-of-frame	0	32	3	22	17	16086282	-	17	15438200	-	1.6929	0.009	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Bladder	TCGA-E5-A2PC-01A	ENSG00000189308	ENSG00000145284	LIN54	SCD5	CGCGCGACCAGGAGGCGGCGGCGCCGCCGGCTTTG*CCTACTTCTGCTTCCTCCTGGCCGCTCTGGGTGTG	100K<gap<200K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	16	5	23	4	83012792	-	4	82705413	-	2.1326	6.6709	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-E5-A2PC-01A	ENSG00000189308	ENSG00000145284	LIN54	SCD5	GAGCCCGAGGGAGGAGAAAGCGGCAGCCGCTGGAG*CCTACTTCTGCTTCCTCCTGGCCGCTCTGGGTGTG	100K<gap<200K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	16	2	14	4	83010484	-	4	82705413	-	2.1326	6.6709	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-E5-A2PC-01A	ENSG00000186047	ENSG00000231607	DLEU7	DLEU2	GCTGCCAGTAAACACCAACTGTTCAAGTGAAATAGTAAATCCAAATGTGC*CTCTGTCTCCTACAAGCTGATGTATTTGGCAGGGTTACTATTTCCCAGGG	antisense,cancer	BOWTIE+BLAT;BOWTIE+STAR	UTR/intronic	0	3	1	24	13	50712538	-	13	49997763	-	0.0353	0.2361	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-CF-A27C-01A	ENSG00000177084	ENSG00000185046	POLE	ANKS1B	CGCGCGGACCCAGGCGCGGATGGCGAGGCCAGCAG*GTTTTAAAAATCAATTTGATTGGCCACAGGAAACG	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	4	6	22	12	132687254	-	12	98832136	-	1.6486	1.2602	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-CF-A27C-01A	ENSG00000198722	ENSG00000153707	UNC13B	PTPRD	ACTGCCACGACTTATACAGCCGCCAGTACCAGCTG*CACCTCCAAGGTTTACACGAACACCCGTTGATCAG	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	2	2	23	9	35386293	+	9	8636844	-	1.2328	1.2168	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	FALSE
TRUE	FALSE	Bladder	TCGA-G2-A2EF-01A	ENSG00000002549	ENSG00000079785	LAP3	DDX1	CAGGGAAGACTCGAACCTTTTATGGTCTGCATCAG*AATGCTGAACTGAAATTTAACTTCGGTGAAGAGGA	tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	293	23	24	4	17581814	+	2	15606150	+	119.9131	25.047	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-G2-A2EF-01A	ENSG00000105810	ENSG00000188175	CDK6	HEPACAM2	TTCCAGAGCCTGGAGTGCCCACTGAAACCATAAAG*ATCCCAAGCAGGTCTGTTCCAGCCTCTGATTGTGT	known,oncogene,tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	155	19	24	7	92774696	-	7	93192363	-	13.0269	6.5564	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-G2-A2EF-01A	ENSG00000198131	ENSG00000142396	ZNF544	AC020915.1	GGACCTGTGCAGGGCAGAGCAGGAGGCCCCCCGAG*ACCCCAGCAGAACGACACTGGCAACTGCTAGAGGA	m7,10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/CDS(no-known-start-or-end)	0	10	4	23	19	58246794	+	19	58312021	+	4.8976	0.5617	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-G2-A2EF-01A	ENSG00000198131	ENSG00000142396	ZNF544	AC020915.1	GGACCTGTGCAGGGCAGAGCAGGAGGCCCCCCGAG*GAGATGGACAAACCGTGTGGGTGCCCTCCAGGTGT	m7,10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/CDS(no-known-start-or-end)	0	10	3	21	19	58246794	+	19	58312166	+	4.8976	0.5617	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-G2-A2EF-01A	ENSG00000178149	ENSG00000114302	DALRD3	PRKAR2A	CCTGGCACTCTGATGACTGCCCCTGAGTACTACGA*ACTAAATCAAACAAGGATGGTGGGAACCAGGAGGT	100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	9	4	23	3	49016774	-	3	48752317	-	2.6512	8.3432	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-G2-A2EF-01A	ENSG00000091164	ENSG00000168702	TXNL1	LRP1B	TCCAGACTCGCCGTGGTCAAGTTCACCATGAGAGG*GTGATAGTTAAATCTGGGCCAGGGACTTTCCTCAG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	5	3	24	18	56638343	-	2	140541971	-	3.1404	2.2417	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-G2-A2EF-01A	ENSG00000274425	ENSG00000104883	AC114271.1	PEX11G	GCTCCCTGAAGACGTACATTAAGGCCAGTACGATAGTCACCACGCCCAGG*GACAGCGCTCTGGTGCATCCCTGAGACCCCTCGTTCCTCTATGCCCTCTG	antisense	BOWTIE+STAR	exonic(no-known-CDS)/intronic	0	3	1	15	19	10334013	+	19	7483599	-	0.0581	3.7154	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-G2-A2EF-01A	ENSG00000249859	ENSG00000253438	PVT1	PCAT1	ATGCACGTTCCATCCGGCGCTCAGCTGGGCTTGAG*ATCCAGCCACCTCTTGGGATGCACACGTTTCTCTT	lincrna,oncogene,18cancers,chimerdb3seq,cancer,oesophagus,exon-exon	BOWTIE	exonic(no-known-CDS)/exonic(no-known-CDS)	0	3	3	21	8	127890998	+	8	127006555	+	0.8208	0.1965	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	lincRNA	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-FD-A3N5-01A	ENSG00000131558	ENSG00000232053	EXOC4	AC078845.1	TGAAGGTGCTGGGAGTGCAGCGGCCTCTCCTACAG*TATCTTACAGAGCAAGACTGCAGATCAAGATTTTC	lincrna,cancer,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	8	4	16	7	133817544	+	7	136242150	+	8.3833	0.9813	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-DK-A1A6-01A	ENSG00000131620	ENSG00000248844	ANO1	AP003555.1	GTTTGTCACTGAGCTCCGAAGGCCGGTAGCTGTCAGAGCCAAAGACATCG*GCCTCTGAGCCCAGGCTAAGCCATCATATCCCCTGTGACCTGCAGGTATA	lincrna	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	21	7	22	11	70171039	+	11	70057857	-	8.2534	3.4155	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-DK-A1A6-01A	ENSG00000131620	ENSG00000248844	ANO1	AP003555.1	GTTTGTCACTGAGCTCCGAAGGCCGGTAGCTGTCAGAGCCAAAGACATCG*GTATACATCTAGATGGCCTGAAGCAACTGACGAACCACAAAAGAAGTGAA	lincrna	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	21	6	23	11	70171039	+	11	70057812	-	8.2534	3.4155	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-DK-A1A6-01A	ENSG00000131620	ENSG00000248844	ANO1	AP003555.1	CCGAAGGCCGGTAGCTGTCAGAGCCAAAGACATCG*GACATCTAGCACAATGTTGAAAAGTATGGCCCAGA	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	21	6	20	11	70171039	+	11	70056535	-	8.2534	3.4155	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-DK-A1A6-01A	ENSG00000104375	ENSG00000175581	STK3	MRPL48	CCGGCCGCCATGGAGCAGCCGCCGGCGCCTAAGAG*GTGCTGTGCCTGAGGAACAATACCATTTTTAAGCA	known,ribosomal,tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	6	4	18	8	98825515	-	11	73805027	+	6.8246	13.6532	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-DK-A1A6-01A	ENSG00000060688	ENSG00000121753	SNRNP40	ADGRB2	GATGGAAGCAAAATAGCAGCTGGCTCAGCCGACAG*GTGAGGAGCCGGAAGAGGAACCGAAAGTGAAAACC	tcga,chimerdb3seq,m4,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	5	5	19	1	31267871	-	1	31744731	-	12.2179	38.9219	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-DK-A1A6-01A	ENSG00000132549	ENSG00000099331	VPS13B	MYO9B	TGAAGCTTTGATAAATGAAATCTTCCTAAGTATAG*GGAGGACATCACCTACCGGCTGCCGGAGCTGGACC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	5	4	22	8	99193057	+	19	17211647	+	5.0563	16.4407	FALSE	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-DK-A1A6-01A	ENSG00000170485	ENSG00000110075	NPAS2	PPP6R3	CTGGGGGACTGCAGTCCCCAAGGAGACCCTGCCACATGCTGGCCCTTTGA*CTCGGGGAGTACAGACAGTGAGGAAAGTACAGACTCTGAAGAAGAAGATG	NA	BOWTIE+BLAT	UTR/CDS(truncated)	0	3	1	23	2	100996498	+	11	68596097	+	11.4658	138.6272	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-BT-A3PH-01A	ENSG00000075702	ENSG00000126264	WDR62	HCST	GGTGCTGTGCCTGGAGTACTCCAAGCCAGAGACGG*TGGCTGCAGCTCAGACGACTCCAGGAGAGAGATCA	tcga,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	101	13	23	19	36084744	+	19	35903351	+	3.3701	1.691	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BT-A3PH-01A	ENSG00000075702	ENSG00000126264	WDR62	HCST	GGCCCATGATGCTGAGGTGCTGTGCCTGGAGTACTCCAAGCCAGAGACGG*TTCCTCTGGACTTCTCTGGACCACAGTCCTCTGCCAGACCCCTGCCAGAC	tcga,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	101	1	22	19	36084744	+	19	35902533	+	3.3701	1.691	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BT-A3PH-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	GCCTGCCTCAGCCTCCAAAGTAGCTGAGACTACAG*CAGTTTAAGTATAGTGTGCCTGGGTTGGGTGCGGT	antisense,m2,exon-exon	BOWTIE	exonic(no-known-CDS)/UTR	0	19	5	23	10	87246115	-	10	46593287	+	0.8553	0.0181	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-BT-A3PH-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	GCCTGCCTCAGCCTCCAAAGTAGCTGAGACTACAG*ATTCCAGTTCTTTGATGAAAGTCTCTATTCCACCC	antisense,m2,exon-exon	BOWTIE	exonic(no-known-CDS)/UTR	0	19	3	23	10	87246115	-	10	46593989	+	0.8553	0.0181	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-BT-A3PH-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	GCCTGCCTCAGCCTCCAAAGTAGCTGAGACTACAG*GTGTGTTTGTCAAAGTGTCTCTGATGAACCACAAC	antisense,m2,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	19	2	23	10	87246115	-	10	46585598	+	0.8553	0.0181	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01A	ENSG00000147257	ENSG00000132170	GPC3	PPARG	GTTCTTAATTATTCAGAATGCTGCGGTTTTCCAAG*AAATGACCATGGTTGACACAGAGATGCCATTCTGG	oncogene,cell_lines,cancer,exon-exon	BOWTIE	in-frame	0	87	14	24	X	133953050	-	3	12379704	+	2928.5378	190.9765	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01A	ENSG00000177697	ENSG00000177106	CD151	EPS8L2	TCGCTGGTATCCTCGCCTACGCCTACTACCAGCAG*AGCAGAGGAAGAAGTATTCCAACTCCAACGTCATC	tcga,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	53	12	24	11	836843	+	11	710422	+	50.1245	14.8759	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01A	ENSG00000177697	ENSG00000177106	CD151	EPS8L2	TCGCTGGTATCCTCGCCTACGCCTACTACCAGCAG*TCCCAACTGGACGGGAGGCTGTGGGTCCTGCCCGT	tcga,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	53	2	23	11	836843	+	11	710357	+	50.1245	14.8759	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01A	ENSG00000177697	ENSG00000177106	CD151	EPS8L2	TTCTGCTGGAGATCATCGCTGGTATCCTCGCCTACGCCTACTACCAGCAG*AGGTCCACGGAGCAGCCTCCCTCCGCTTGACTCCACCTTCCCTTGTGGGT	tcga,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K	BOWTIE+STAR	CDS(truncated)/UTR	0	53	1	16	11	836843	+	11	710303	+	50.1245	14.8759	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-BL-A0C8-01A	ENSG00000105556	ENSG00000101391	MIER2	CDK5RAP1	CAGCAACCTGCACTTGAACCGGCACTGTGAGAAGA*GCTGCATGGCTGAGAGGTTGAAGGAGGAGATTCTC	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	52	15	24	19	325635	-	20	33387533	-	4.8298	14.7241	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-BL-A0C8-01A	ENSG00000105556	ENSG00000101391	MIER2	CDK5RAP1	CTCTTCTGCCTCCTCCGACACCGAGGAGGACTCTCTTCCTGCCAACAAAT*GTGTGAGCCTCAGCAGCGATTTCATTGCTGGCTTTTGTGGTGAGACGGAG	tcga,cell_lines,chimerdb3seq,tcga-cancer	BOWTIE+STAR	in-frame	0	52	1	18	19	326515	-	20	33370629	-	4.8298	14.7241	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01A	ENSG00000248485	ENSG00000158864	PCP4L1	NDUFS2	CTCGCGCGCCCTGTCCGGCTGCGGAGATGAGCGAG*ACTTCCATGGAGTCACTGATTCATCACTTTAAGTT	tcga,cell_lines,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	42	12	24	1	161258983	+	1	161213380	+	4.7555	30.6433	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01A	ENSG00000248485	ENSG00000158864	PCP4L1	NDUFS2	AGTCTCATCTCCAGAAACAAGGATCAGCCTTTCCAAGTGAAGTCAGTCTG*ACTTCCATGGAGTCACTGATTCATCACTTTAAGTTGTATACTGAGGGCTA	tcga,cell_lines,chimerdb3seq,tcga-cancer,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	42	2	24	1	161259792	+	1	161213380	+	4.7555	30.6433	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01A	ENSG00000248485	ENSG00000158864	PCP4L1	NDUFS2	ATTGGAATCGGCTGTAGAGTCCGGAAGCGGGGATGCTGAGCTCTCAGGTG*ACTTCCATGGAGTCACTGATTCATCACTTTAAGTTGTATACTGAGGGCTA	tcga,cell_lines,chimerdb3seq,tcga-cancer,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	42	1	21	1	161259259	+	1	161213380	+	4.7555	30.6433	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01A	ENSG00000008294	ENSG00000120265	SPAG9	PCMT1	GATCAACTAGAATCCACAGCTCATAGTAGAATTAG*AAAATGGAATCATCAAGACAGATAAAGTATTTGAA	oncogene,tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	18	2	21	17	51047375	-	6	149771162	+	37.2531	17.2785	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01A	ENSG00000181610	ENSG00000108395	MRPS23	TRIM37	CAAGACATCTGGTACCACGAGGATCGGATTAGAGC*ATACACATTCCAGTTTTCCTGATGGTGAACAAATA	ribosomal,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	17	5	20	17	57849240	-	17	58999459	-	7.0463	7.3529	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01A	ENSG00000247596	ENSG00000053108	TWF2	FSTL4	GCGCCGAGCCATGGCGCACCAAACGGGCATCCACG*GACTTTGGAGAGGATGATTCCCTGTACATCACCAA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	10	4	19	3	52238992	-	5	133233537	-	7.1095	3.6315	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01A	ENSG00000145819	ENSG00000213585	ARHGAP26	VDAC1	CTACAACTCGAACAAAGACAGCCAGAGTGAAGGGA*GCTAAAGTGAACAACTCCAGCCTGATAGGTTTAGG	cancer,tumor,exon-exon	BOWTIE	out-of-frame	0	8	3	20	5	143014116	+	5	133973848	-	1.4299	120.9609	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01A	ENSG00000143748	ENSG00000011376	NVL	LARS2	AGATGGAGAAATTGAAGCTGTCCTGCAAAAGAAAG*GCCTGGCGCTGGTGCCGAGGAAGCTCTGTGCCCAC	cell_lines,tcga-cancer,exon-exon	BOWTIE	in-frame	0	5	4	23	1	224305034	-	3	45541829	+	2.9449	2.0017	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01A	ENSG00000148143	ENSG00000171530	ZNF462	TBCA	AGCTACCCCGGCTGAAGAAGTGGAAGACTCCAATG*GTTGGTCAAAGAAAAAGTGATGTATGAAAAAGAGG	exon-exon	BOWTIE	in-frame	0	5	2	18	9	106939107	+	5	77708347	-	3.4119	20.7881	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01A	ENSG00000233836	ENSG00000268362	AC139769.1	AC092279.1	ACGCACAGCCAGGACATCCTGGAACCTGGGAAAGG*AAGGCATTGAGACATGGCTGGGCTCAGCACTAAGA	pseudogene,lincrna,exon-exon	BOWTIE	exonic(no-known-CDS)/exonic(no-known-CDS)	0	2	1	14	19	23763134	+	19	24063816	+	6.4481	2.1455	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	transcribed_unprocessed_pseudogene	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01A	ENSG00000164946	ENSG00000026751	FREM1	SLAMF7	CAAACAGCAGCCATTCTGAGAGGAGACATGATGAG*GGTCAGCAGCCTCTGGACCCGTGAAAGAGCTGGTC	tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	2	2	20	9	14851284	-	1	160748194	+	0.4915	0.6268	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-BL-A13J-01B	ENSG00000187676	ENSG00000175664	B3GLCT	TEX26	GCAGGCTGGGCCTTAAGTATTCCACTTGTAAACAA*ATAGACAAATTATTGATCGCTTTATTCGTACTCAC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	15	7	24	13	31261082	+	13	30974846	+	5.9692	1.2043	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BL-A13J-01B	ENSG00000157483	ENSG00000137845	MYO1E	ADAM10	CATCCATCCATCAGTGATCAGTGATGTCCAACAGAATTTTGTGGCATGTG*ACATTTCAACCTACGAATGAAGAGGGACACTTCCCTTTTCAGTGATGAAT	NA	BOWTIE+STAR	intronic/CDS(truncated)	0	6	1	16	15	59234175	-	15	58682314	-	11.1662	84.3565	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Bladder	TCGA-FD-A3SP-01A	ENSG00000122406	ENSG00000122483	RPL5	CCDC18	CAGCATATTGTACTGGCCTGCTGCTGGCCCGCAGG*GTTTCTATGCTTGAGTCTGCTCAACAGCAGGCAGC	ribosomal,m2,exon-exon	BOWTIE	in-frame	0	37	6	23	1	92834913	+	1	93192000	+	298.3585	10.3146	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-FD-A3SP-01A	ENSG00000151240	ENSG00000057608	DIP2C	GDI2	CGTGCAGACCTCGATGGACGCCTACACCCCTCCAG*GCTAAGTGCTATTTATGGAGGTACCTATATGCTGA	cancer,exon-exon	BOWTIE	out-of-frame	0	5	1	14	10	440871	-	10	5773941	-	7.1075	92.229	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-FD-A3SP-01A	ENSG00000097033	ENSG00000198691	SH3GLB1	ABCA4	GAAACCAGAAGGGCAAGGTGCCAATTACCTACTTAGAACTGCTCAATTAA*TGCTTTGGCCTCCTGGGAGTGAATGGTGCCGGCAAAACAACCACATTCAA	NA	BOWTIE+STAR	UTR/CDS(truncated)	0	4	1	16	1	86743235	+	1	94007740	-	45.2368	0.7006	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-FD-A3SP-01A	ENSG00000108100	ENSG00000151150	CCNY	ANK3	CCTGCAGCACATCAGCGACCGGGAGAACATAGACG*CATCTAACATTCACAAGGGAATTTGATTCAGATTC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	3	2	17	10	35337207	+	10	60114331	-	13.197	0.4148	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-FD-A3SP-01A	ENSG00000167522	ENSG00000141012	ANKRD11	GALNS	GAGCCGTCGCGGAGCCGCGCAGCCCTCGGAGCACG*CGAGGGCGGCACTGCTCACAGGACGGCTACCCATC	cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	2	6	22	16	89490245	-	16	88841971	-	3.8303	12.1512	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-FD-A3SP-01A	ENSG00000167522	ENSG00000141012	ANKRD11	GALNS	TTTGTCGGTGAACAACGCAGAGCTGATGCAGACAT*CGAGGGCGGCACTGCTCACAGGACGGCTACCCATC	cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	2	3	20	16	89431256	-	16	88841971	-	3.8303	12.1512	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-G2-A2EJ-01A	ENSG00000105778	ENSG00000122507	AVL9	BBS9	TGGTGGTCGGATTTCACCACAAGAAGGGCTGCCAG*TGATTTAAAGGGAGTGATAGTCACTCTGAGTGATG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	27	10	24	7	32495802	+	7	33336441	+	1.7706	3.2637	FALSE	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-DK-A1AC-01A	ENSG00000160551	ENSG00000023287	TAOK1	RB1CC1	TGTGTGGTCTCTTGGAATAACATGTATTGAACTAG*ACCAATTTTAACACTGTTTTAACAAGAGAGAAAAT	tcga,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	78	14	24	17	29482288	+	8	52642812	-	21.4464	26.2026	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-DK-A1AC-01A	ENSG00000168300	ENSG00000126858	PCMTD1	RHOT1	CGGATATTTAAGTACAATGGTGGGCTTAATTTTAG*GCTGCCTTTAATATTGGTTGGGAACAAATCTGATC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	63	13	24	8	51860845	-	17	32182757	+	20.7077	18.0902	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-DK-A1AC-01A	ENSG00000168300	ENSG00000126858	PCMTD1	RHOT1	AGCGCCTGGCCTGCGCGCCGCTGCCCGCGCCACAG*GCTGCCTTTAATATTGGTTGGGAACAAATCTGATC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	63	2	23	8	51898930	-	17	32182757	+	20.7077	18.0902	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-DK-A1AC-01A	ENSG00000168300	ENSG00000126858	PCMTD1	RHOT1	GTATTTTACCTCTGCTTTCCATAACTGAATGGAGTATCAGAACCACGAAG*GCTGCCTTTAATATTGGTTGGGAACAAATCTGATCTGGTGGAATATAGTA	tcga,chimerdb3seq,tcga-cancer	BOWTIE+BLAT	intronic/CDS(truncated)	0	63	2	23	8	51857493	-	17	32182757	+	20.7077	18.0902	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-DK-A1AC-01A	ENSG00000168300	ENSG00000126858	PCMTD1	RHOT1	ACCTGGGAAGTGGAACCGGATATTTAAGTACAATG*GCTGCCTTTAATATTGGTTGGGAACAAATCTGATC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	63	2	19	8	51860861	-	17	32182757	+	20.7077	18.0902	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-DK-A1AC-01A	ENSG00000168300	ENSG00000126858	PCMTD1	RHOT1	GTATCAGAACCACGAAGGCAAGTTATTCTGATAAACTCTTTGTGATTCAG*GCTGCCTTTAATATTGGTTGGGAACAAATCTGATCTGGTGGAATATAGTA	tcga,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	63	1	23	8	51857460	-	17	32182757	+	20.7077	18.0902	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-DK-A1AC-01A	ENSG00000168300	ENSG00000126858	PCMTD1	RHOT1	GTGTTTTGTGACTGAGCTTTAATTGAGGAGAACCTGTTGACTTGTAAATT*GCTGCCTTTAATATTGGTTGGGAACAAATCTGATCTGGTGGAATATAGTA	tcga,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	63	1	16	8	51879569	-	17	32182757	+	20.7077	18.0902	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-DK-A1AC-01A	ENSG00000110066	ENSG00000176658	KMT5B	MYO1D	AAATCTGACAGTTTTTCTCACAACAACCCTGTGAG*GTAAATCGATTTAGTAAGGTGGAAGACAGAGCAAT	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	31	6	23	11	68180132	-	17	32638835	-	10.8294	3.3103	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-DK-A1AC-01A	ENSG00000188807	ENSG00000171621	TMEM201	SPSB1	GCTTTGCCAGGTCCGAAGCGGGCCCCTCTCTGTCCTGCCTCTTTTCACCT*GCAACCCATGAGAAGAGGTTTGCGTAGTGACAAGTCCAGAAACTGTGTGC	tcga,chimerdb3seq,tcga-cancer	BOWTIE+BLAT	UTR/intronic	0	9	1	20	1	9602376	+	1	9342301	+	7.3042	12.8289	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-E7-A3X6-01A	ENSG00000084754	ENSG00000115137	HADHA	DNAJC27	CCGCTTTTCTGCCTTCAGGATCCTCCGCTCCCGAG*GGATGAAGTCAATAAAGCGTATCGGAAACTTGCTG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	6	1	13	2	26244530	-	2	24947748	-	29.2713	2.6513	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-GV-A3JZ-01A	ENSG00000112079	ENSG00000096654	STK38	ZNF184	AAGCAGAAACCTGGAAAAGAAATAGACGTCAGCTA*GAAGCGGTGACTTTCAAGGATGTGATAGTGGACTT	known,tcga,exon-exon	BOWTIE	in-frame	0	21	14	24	6	36506583	-	6	27457409	-	29.0385	20.6765	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-GV-A3JZ-01A	ENSG00000153292	ENSG00000112818	ADGRF1	MEP1A	CCCTCGAGTTCTGGTGTGAAGAGATAAATCACCAG*GAGATGATGACCACAATTGGAAAATTGCCCATGTG	oncogene,tcga,chimerdb3seq,m9,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	11	3	18	6	47042191	-	6	46833074	+	4.4501	1.8706	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-GV-A3JZ-01A	ENSG00000145996	ENSG00000172348	CDKAL1	RCAN2	AATCCACTGATAGAAATCATTTCCATCAATACCGG*GAATGAGGGGAGAATCATACTTCATCGGAATGAGG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	7	2	20	6	20781265	+	6	46456978	-	11.0739	4.8365	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-GV-A3JZ-01A	ENSG00000118620	ENSG00000185774	ZNF430	KCNIP4	TATGAAGAGACATGCGATGGTAGATCAACCCCCAG*ACAGCGTGGAAGATGAACTGGAGATGGCCACCGTC	tcga,chimerdb3seq,m3,tcga-cancer,exon-exon	BOWTIE	in-frame	0	4	3	23	19	21034184	+	4	20850667	-	1.5077	0.2013	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-GV-A3JZ-01A	ENSG00000118620	ENSG00000185774	ZNF430	KCNIP4	AAAAGAGCCCTGGAATATGAAGAGACATGCGATGGTAGATCAACCCCCAG*TTATGACCACAGCATCTGGAAATGCATGCACATATGGTCCTAGTCAAGAG	tcga,chimerdb3seq,m3,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	4	1	22	19	21034184	+	4	21348226	-	1.5077	0.2013	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-GV-A3JZ-01A	ENSG00000118620	ENSG00000185774	ZNF430	KCNIP4	AAAAGAGCCCTGGAATATGAAGAGACATGCGATGGTAGATCAACCCCCAG*TCCCACCACTCCCCAATACCAGAAGAGCTATGTTATTAAGAGGAAGACAT	tcga,chimerdb3seq,m3,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	4	1	19	19	21034184	+	4	21457566	-	1.5077	0.2013	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-GV-A3JZ-01A	ENSG00000145996	ENSG00000065882	CDKAL1	TBC1D1	TGGACAGCTAGCTGCTTATGGCTATAAAATTACAG*ATTATTCAGAGCTGGGAGAGCTTCCCCCACGATCT	oncogene,tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	3	4	21	6	20548705	+	4	38089932	+	11.0739	11.9235	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-GV-A3JZ-01A	ENSG00000159023	ENSG00000060642	EPB41	PIGV	GGCGCGGAGCCAGAACGCGGTCGGCCCGGTCCCCGCCGCACCCAGCCCAG*ATCACCATGCAGAAGCCTTCTCTCCTCCTCGCCTGGCCCCCTCAGGCTTT	tcga,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	3	2	17	1	28887210	+	1	26794138	+	10.2707	2.88	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	FALSE	Bladder	TCGA-GV-A3JZ-01A	ENSG00000159023	ENSG00000060642	EPB41	PIGV	GTGGCGGGCGCAGGAGCCCGGCCCCGGAGCCACCG*GCCCTCTTCAATGCCATCATCCCAGATCACCATGC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	3	2	16	1	28914768	+	1	26794113	+	10.2707	2.88	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-DK-A3IQ-01A	ENSG00000173821	ENSG00000175866	RNF213	BAIAP2	TCCTTCTCACCGTTCCGGGAACAAATGCTAGATAC*GAGACGTTCTCTTCCAGATGGCTGAAGTCCACAGG	cell_lines,cancer,tumor,exon-exon	BOWTIE	out-of-frame	0	7	3	16	17	80298518	+	17	81084832	+	6.1129	7.6452	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Bladder	TCGA-DK-A3IQ-01A	ENSG00000120071	ENSG00000073969	KANSL1	NSF	GGAGCACTCAGACCTGTCAATGGAGTTATTAACAC*GGCCGCAAGCTTCTTATCATTGGGACCACTAGCCG	tcga-cancer,exon-exon	BOWTIE	in-frame	0	2	5	19	17	46067549	-	17	46749773	+	1.8035	6.1907	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Bladder	TCGA-FD-A3B7-01A	ENSG00000164164	ENSG00000106153	OTUD4	CHCHD2	AGTGAAATATCAGATTCAGAGGATGACAGTTGCAA*CCGGGCCCCTCAGATGAGAGCTGCACCCAGGCCAG	cell_lines,exon-exon	BOWTIE	in-frame	0	6	4	22	4	145159503	-	7	56104475	-	37.8444	647.7738	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-DK-A1A7-01A	ENSG00000130940	ENSG00000172869	CASZ1	DMXL1	GCTGCCACGCCGCTCTGCGAGTGGGTCTGTCTTCTGCCTGGGCGGTGGCA*AACTGCCTTTTGACCCAGCAATCCCATTACTGGCTATGTACCTAGAGGAG	NA	BOWTIE+BLAT	intronic/intronic	0	2	1	22	1	10790066	-	5	119142653	+	1.5328	2.9209	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-DK-A1A7-01A	ENSG00000083168	ENSG00000253452	KAT6A	AC100818.1	CTCCAGTGTCCCTTCTTCCACATGAAAAGGATAAG*ATGCTCAGAGGCCCCATGCCTGATGAGTCAGTGGA	lincrna,oncogene,cancer,tumor,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	2	1	13	8	42048378	-	8	35944244	+	5.2879	0.0284	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-G2-A2EC-01A	ENSG00000158019	ENSG00000138101	BABAM2	DTNB	TACCCCAAGCTGTACTTGTCACCTCGAATTGAGCA*GTTACAGTATAGCCAGGATATACCCAGTCACTTGG	cell_lines,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	32	4	22	2	28129380	+	2	25455494	-	6.2724	3.5085	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Bladder	TCGA-G2-A2EC-01A	ENSG00000158019	ENSG00000138101	BABAM2	DTNB	TACCCCAAGCTGTACTTGTCACCTCGAATTGAGCA*TGTTCTGGACAGTCCTAGCCGACTGGATGAGGAAC	cell_lines,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	32	2	21	2	28129380	+	2	25451635	-	6.2724	3.5085	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Bladder	TCGA-G2-A2EC-01A	ENSG00000158805	ENSG00000197912	ZNF276	SPG7	CCTCTTCCCTGATGGCCGCGTCTTCATGGAAGTAGGAGAGAAGACTAGAG*GAGAGGCGGGAGATTTTTGAGCAGCACCTGAAGAGCCTGAAGCTGACCCA	100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	10	5	24	16	89739295	+	16	89546658	+	1.6299	3.1391	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-DK-A1AE-01A	ENSG00000148842	ENSG00000280693	CNNM2	SH3PXD2A-AS1	ATACTATGGCGTGATGGCCCTGACAGCCTCTCCAG*ATACTCATGCTGAGGGAAGCCAGCTTCCATGTTGT	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	24	9	23	10	103068722	+	10	103749782	+	0.9406	3.0846	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-GC-A3I6-01A	ENSG00000088325	ENSG00000101294	TPX2	HM13	AAAAAAGAGTTGCGGGAGGCTGTCGGCTAATAACG*AATGCTTCAGACATGCCTGAAACAATCACCAGCCG	known,tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	551	23	24	20	31739621	+	20	31527484	+	113.794	102.7486	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-GC-A3I6-01A	ENSG00000088325	ENSG00000101294	TPX2	HM13	CCCGCGGCGGGTTGGCTCGCGCTTCGTTGTCAGATCTGAGGCGAGGCTAG*AATGCTTCAGACATGCCTGAAACAATCACCAGCCGGGATGCCGCCCGCTT	known,tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	551	3	16	20	31739347	+	20	31527484	+	113.794	102.7486	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-GC-A3I6-01A	ENSG00000088325	ENSG00000101294	TPX2	HM13	CCCGCGGCGGGTTGGCTCGCGCTTCGTTGTCAGATCTGAGGCGAGGCTAG*GATCTGCTGGAGAAAGGCCTCGAAGCAAACAACTTTGCCATGCTGGGACT	known,tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K	BOWTIE+STAR	UTR/CDS(truncated)	0	551	2	15	20	31739347	+	20	31554760	+	113.794	102.7486	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-GC-A3I6-01A	ENSG00000101294	ENSG00000171552	HM13	BCL2L1	GTGCTGGGAATCCTGGCCCTGTCCCACACCATCAG*GATACTTTTGTGGAACTCTATGGGAACAATGCAGC	known,oncogene,cell_lines,cancer,exon-exon	BOWTIE	out-of-frame	0	57	10	24	20	31538261	+	20	31666086	-	102.7486	482.5042	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-GC-A3I6-01A	ENSG00000101294	ENSG00000171552	HM13	BCL2L1	GCTGCACACTCTTGGGGCTCTACCTCTTTTTCAAA*GATACTTTTGTGGAACTCTATGGGAACAATGCAGC	known,oncogene,cell_lines,cancer,exon-exon	BOWTIE	in-frame	0	57	4	23	20	31527582	+	20	31666086	-	102.7486	482.5042	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-GC-A3I6-01A	ENSG00000176406	ENSG00000164929	RIMS2	BAALC	AAGAAAGAAGAGGAGAAGGAGCAGTCCGTGCTCAA*GCATGCTGGAAGATGGACTGCCCTCCAATGGTGTG	oncogene,tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	19	7	22	8	103501062	+	8	103212919	+	1.6696	7.9329	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	FALSE	Bladder	TCGA-GC-A3I6-01A	ENSG00000176406	ENSG00000164929	RIMS2	BAALC	AAGAAAGAAGAGGAGAAGGAGCAGTCCGTGCTCAA*GCTAAAAGAGATGCTAAGAGAATGCCTGCAAAAGA	oncogene,tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	19	5	24	8	103501062	+	8	103227989	+	1.6696	7.9329	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-GC-A3I6-01A	ENSG00000135899	ENSG00000187957	SP110	DNER	TGACCCAGAAGAGCCCCAGGAGGTGTCCAGCACACCTTCAGACAAGAAAG*GGCTCTGACCCCAAATTGAGACTTGTGTGACACATAAGCATAGGCAGTGC	cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	20	2	230209931	-	2	229654693	-	4.1571	0.8372	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-DK-A1A5-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	GGAGCTTCTCAGAAGACAGAGGGTTTTCTTTTGAG*AGAGCCAGCAGCTGGGCCGAGTGGTGGTGGGCCCC	antisense,m2,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	7	1	14	10	87288442	-	10	46587505	+	0.5846	0.104	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-GD-A2C5-01A	ENSG00000043514	ENSG00000134259	TRIT1	NGF	CCCTTGCATCCTTTGGCTTCATGCTGACCAGGCAG*AGTTTTGGCCAGTGGTCGTGCAGTCCAAGGGGCTG	exon-exon	BOWTIE	CDS(truncated)/UTR	0	13	1	13	1	39850119	-	1	115293750	-	71.8501	5.5631	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-FD-A3SR-01A	ENSG00000109756	ENSG00000145247	RAPGEF2	OCIAD2	GAAGGACCCAATTGACCGGACAGATGATGACATTG*ACACTGGGTCAAGGAGTAAGCAGAGGATAAACAAC	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	95	18	23	4	159314768	+	4	48904611	-	5.1594	21.9247	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-FD-A3SR-01A	ENSG00000040933	ENSG00000071073	INPP4A	MGAT4A	TCTGGACGAAGCATGCACAGACGGAGATCATTGAG*GAAAATTTGAGAATGGTGTTGCAGAAGGAATGGTG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	63	13	24	2	98533495	+	2	98625835	-	11.4401	55.2051	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-FD-A3SR-01A	ENSG00000104365	ENSG00000156687	IKBKB	UNC5D	GGGGATTTGGAAATGTCATCCGATGGCACAATCAG*GAACTGACAATGGCGAAGCCCTTCCCGAATCCATC	known,tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	26	7	22	8	42272205	+	8	35549292	+	7.2818	6.8147	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-FD-A3SR-01A	ENSG00000099817	ENSG00000197050	POLR2E	ZNF420	ACCTACCGGCTGGTGCAGTAGCTACCGCCTGACAG*ACTTGCCTTCAAGGTGTGCAAGTAAGGACTTATCT	tcga,chimerdb3seq,m15,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	18	8	23	19	1089472	-	19	37127128	+	22.1087	9.3077	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-GV-A3JW-01A	ENSG00000138867	ENSG00000231405	GUCD1	AL008638.1	GTCACAATTTCATTTGTTGATCCCGGCACCGCCAG*AGACGAGCATGTACAGGAAGCACCCGGGCTGTGCA	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	52	11	21	22	24555615	-	22	27159458	+	24.1615	10.0191	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-GV-A3JW-01A	ENSG00000138867	ENSG00000231405	GUCD1	AL008638.1	GGAGGCGGAGGCAGCGGGGCCGCCGCTCGAGCCCG*AGACGAGCATGTACAGGAAGCACCCGGGCTGTGCA	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	52	2	19	22	24554949	-	22	27159458	+	24.1615	10.0191	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-GV-A3JW-01A	ENSG00000129255	ENSG00000138867	MPDU1	GUCD1	CGACCAACTTTTCGTTCAGTGGGACTTGCTTCACG*GGGACTTTGTGCAACTGCCTGTGCCCGTCATCCAG	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	27	9	22	17	7583965	+	22	24549001	-	24.1567	24.1615	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-GV-A3JW-01A	ENSG00000129255	ENSG00000138867	MPDU1	GUCD1	CGACCAACTTTTCGTTCAGTGGGACTTGCTTCACG*GTACCTGGGCCAGCTGGACGACAGTGAGTTTGAGA	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	27	2	17	17	7583965	+	22	24548073	-	24.1567	24.1615	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-GV-A3JW-01A	ENSG00000048471	ENSG00000130287	SNX29	NCAN	GCAGGCAGCGGGCTTTGCCAGCAAAACCGAAACAG*TGCACTCAGATCCCTGTGAGAACAACCCTTGTCTT	tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	12	6	21	16	12027444	+	19	19233789	+	1.7693	2.6277	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-FD-A3B6-01A	ENSG00000170425	ENSG00000185666	ADORA2B	SYN3	GTCGACAGATACCTGGCCATCTGTGTCCCGCTCAG*GTCACAGCCCCACACTTCCCGGTGGTAGTCAAGCT	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	16	9	24	17	15945583	+	22	32596736	-	27.1204	5.1098	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-FD-A3B6-01A	ENSG00000126821	ENSG00000258689	SGPP1	LINC01269	TTTCTATGGTCCTCCTCACCTATGGCCGCTGGCAG*GTTTATGAGCAGGAACCATTGCTTAAGAAATACTC	lincrna,m2,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	4	1	13	14	63727261	-	14	70712010	+	7.5604	1.0632	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-K4-A3WS-01A	ENSG00000088305	ENSG00000149599	DNMT3B	DUSP15	GGGTCCAGTGGTTTGGCGATGGCAAGTTCTCCGAG*GTACTTCCTGGACTCTACCTCGGAAACTTCATTGA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	12	2	23	20	32789012	+	20	31869597	-	8.3282	1.4257	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-K4-A3WS-01A	ENSG00000140199	ENSG00000248079	SLC12A6	DPH6-AS1	ACTGGATCCACCCAGTGACCGGACTTCTCACCCCCAGGATGTCATCGAGG*AGATGATGTTTCCCTATGTTGCCTAAGCTGGTTTCGAACTCCTGGGCTCA	lincrna	BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	3	1	17	15	34336410	-	15	35856480	+	2.4269	0.1115	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-K4-A3WS-01A	ENSG00000105357	ENSG00000215301	MYH14	DDX3X	GCTTGAGCCCAGGAGTTCGGGACCATCCTGGGCATGGCAAAACCCCATCC*CGATCTAGAGTTCGTCCTTGCGTGGTTTATGGTGGTGCCGATATTGGTCA	NA	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	2	2	24	19	50211811	+	X	41344248	+	15.4675	12.8809	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-K4-A3WS-01A	ENSG00000105357	ENSG00000215301	MYH14	DDX3X	ATTCAAACCCAGGAGTGTGGTCCTCCAGGCCACCCTACTCCACATGCCCG*AGTGTAAGGGGATAGGTAGAAATAGAGATGAAAGGCACTAAGATGTCCTA	NA	BOWTIE+BLAT	intronic/UTR	0	2	1	21	19	50224028	+	X	41336355	+	15.4675	12.8809	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-K4-A3WS-01A	ENSG00000172943	ENSG00000227517	PHF8	LINC01483	ATCATTCACTGTGAGGGATGTTGAACACTATGTTG*GTGCCCAAAGGAGAGAGAGAATAAACTTGAACATT	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	2	3	20	X	54017661	-	17	69845440	+	3.6133	0.102	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-BT-A2LA-01A	ENSG00000102572	ENSG00000125247	STK24	TMTC4	ACTCCCCGGTGCAGTCGGGCCTGCCCGGCATGCAG*GAATCTGAAGCTTTATTCCTCAAGGCAATTAAAGC	known,tcga,18cancers,chimerdb3seq,m21,tcga-cancer,exon-exon	BOWTIE	in-frame	0	23	4	23	13	98576745	-	13	100606427	-	8.5527	9.0115	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BT-A2LA-01A	ENSG00000086544	ENSG00000167578	ITPKC	RAB4B	CCTCTACCCTGGGCTTCCGGATCGAGGGCATCAAG*ACTTCCTCTTCAAATTCCTGGTGATTGGCAGTGCA	18cancers,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	8	2	20	19	40733364	+	19	40780019	+	52.6301	1.069	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-BT-A2LA-01A	ENSG00000148541	ENSG00000138311	FAM13C	ZNF365	GAATTTGAAGAACAGTTTTTTAAACAAACAGGAAG*ATTTTTGGCCATATAAACCACCATCTTTCGGGGTT	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	7	4	21	10	59251575	-	10	62623103	+	2.6602	0.8878	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BT-A2LA-01A	ENSG00000198265	ENSG00000154263	HELZ	ABCA10	CACTAATGAACTACAGTGCTGGTGAGATGTGTAAG*CTATTGCTCTGCAATATTTACTTTACCCTGTTAAT	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/UTR	0	4	2	19	17	67243784	-	17	69227285	-	3.479	0.6733	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BT-A2LA-01A	ENSG00000101246	ENSG00000243319	ARFRP1	FGF14-IT1	AGGCCCTGCAGCGGCAGCCTTTCCACAGGGCGCAGCGGCGGCCTTTCGAG*ATTCTAGATACAAGTTTCTTATCAGGTATATGATTTAGAAGTATTTTATC	NA	BOWTIE+BLAT	UTR/intronic	0	2	2	24	20	63700181	-	13	102382260	-	5.6008	0.1272	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	sense_intronic	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-BT-A2LA-01A	ENSG00000108825	ENSG00000108306	PTGES3L-AARSD1	FBXL20	GTGGGACCCATGTGAGCAATCTCAGTGACCTTCAG*ATGTTCTCAAATAGTGATGAAGCTGTAATCAATAA	exon-exon	BOWTIE	in-frame	0	2	1	13	17	42956204	-	17	39343241	-	0	3.1159	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-BT-A20W-01A	ENSG00000112977	ENSG00000150753	DAP	CCT5	AAAGACAAGGATGACCAGGAATGGGAAAGCCCCAG*GGTCAACAGTTGTCACCGACAGATGGCTGAGATTG	cell_lines,exon-exon	BOWTIE	in-frame	0	70	10	21	5	10748175	-	5	10258111	+	455.6552	189.4301	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Bladder	TCGA-BT-A20W-01A	ENSG00000112977	ENSG00000150753	DAP	CCT5	AAAGACAAGGATGACCAGGAATGGGAAAGCCCCAG*TCCTGGCTGGTGCCTTGTTAGAAGAAGCGGAGCAA	cell_lines,exon-exon	BOWTIE	out-of-frame	0	70	5	19	5	10748175	-	5	10255955	+	455.6552	189.4301	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Bladder	TCGA-BT-A20W-01A	ENSG00000092439	ENSG00000140319	TRPM7	SRP14	GCTGCCCTTCCGGAGTCCGCCCCGTGAGGAGAATG*TTCCTGACGGAGCTGACCAGACTTTTCCAGAAGTG	m16,exon-exon	BOWTIE	in-frame	0	69	9	24	15	50686531	-	15	40038948	-	6.7745	235.3122	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Bladder	TCGA-BT-A20W-01A	ENSG00000092439	ENSG00000140319	TRPM7	SRP14	GCTGCCCTTCCGGAGTCCGCCCCGTGAGGAGAATG*GGGCTTAAGCGGAGGGAGTCGAGCCAGCGTCGCCG	m16,exon-exon	BOWTIE	CDS(truncated)/UTR	0	69	2	23	15	50686531	-	15	40039153	-	6.7745	235.3122	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-BT-A20W-01A	ENSG00000006831	ENSG00000151065	ADIPOR2	DCP1B	CTCAGCGGTGGCTCCCAAGAAGTCCGAGACACGCG*TGTCCATCTATGGAATTTGGTTTTATGATAAGGAA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	38	8	22	12	1691191	+	12	1967910	-	24.4454	32.4854	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BT-A20W-01A	ENSG00000006831	ENSG00000151065	ADIPOR2	DCP1B	TCCGAGACACGCGGTGAGGCGGCGACGGGCTCCGG*TGTCCATCTATGGAATTTGGTTTTATGATAAGGAA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	38	8	22	12	1691213	+	12	1967910	-	24.4454	32.4854	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BT-A20W-01A	ENSG00000006831	ENSG00000151065	ADIPOR2	DCP1B	CCGTGGCTCCCACGCTGCTATTCAAAACTTCCTGG*TGTCCATCTATGGAATTTGGTTTTATGATAAGGAA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	38	6	21	12	1702982	+	12	1967910	-	24.4454	32.4854	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-BT-A20W-01A	ENSG00000029534	ENSG00000284697	ANK1	AC006511.5	ACTCAGAGAATGAAGTGTCTCTTGTTTCAGGCCATCAGAGGGGGCAAGCC*CGAATCACTTCAAAAGGGAAGACTGCCTATATCAAACTCGAGGATAAAGT	NA	BOWTIE+BLAT	CDS(truncated)/exonic(no-known-CDS)	0	5	1	21	8	41672407	-	12	8089982	+	0.6422	0.0142	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-BT-A20W-01A	ENSG00000272168	ENSG00000122224	CASC15	LY9	CGGTAGGAGACTTTCTGGATGGGGAAGATTTCCAG*GTGGTGCCACCACCACAACAGAATGATCTTGAGAT	lincrna,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	4	1	13	6	21783708	+	1	160827748	+	0.6183	0.3372	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-BT-A20W-01A	ENSG00000150753	ENSG00000250921	CCT5	LINC02063	AGCAAATACAATGAGAACATCACTTGGACCAAATG*GGGTCCTGAGTTTCCTCAATGGCATTCTAATCCAT	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	3	2	21	5	10254205	+	5	4143247	+	189.4301	1.5698	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-BT-A20W-01A	ENSG00000052126	ENSG00000254115	PLEKHA5	AC090572.3	GAAGAAACGCTGGTTTGTGCTTTCTGACCTTTGCCTCTTTTATTATAGAG*GTTGAATCTACTGATGCACTTGTTAGAAATAAAAAAAAATTGCAAGCATG	antisense	BOWTIE+STAR	CDS(truncated)/intronic	0	3	1	15	12	19261021	+	8	86750238	+	3.6028	0.3902	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-BT-A20W-01A	ENSG00000143850	ENSG00000142156	PLEKHA6	COL6A1	CGCCTTCCAGCGCTTCACCGGACTGGACACTAGGCGCCTGGTTCCAAGGC*CCCGCGGCAGGCCTGGCCCCAACCGGCCCTTCCTGCCCTTTGCTATGCAG	NA	BOWTIE+BLAT	intronic/intronic	0	3	3	23	1	204370344	-	21	46002168	+	6.9927	78.2479	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-DK-A1AD-01A	ENSG00000102189	ENSG00000169372	EEA1	CRADD	ACACAGTGGACGTCAATAATGAAAGCTCTTCAGAG*GTGACAGATTGACTGGGATCCCCTCGCACATCCTC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	49	12	24	12	92891629	-	12	93849970	+	3.0308	4.1503	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-DK-A1AD-01A	ENSG00000102189	ENSG00000169372	EEA1	CRADD	CAGCAACTCCTATAAACACAGTGGACGTCAATAATGAAAGCTCTTCAGAG*GTGACTACTGAGCTTGGTGGCAGAATTGAGAATAAAGACTCCCTGACTTC	tcga,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	49	1	23	12	92891629	-	12	93712906	+	3.0308	4.1503	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-DK-A1AD-01A	ENSG00000162755	ENSG00000105176	KLHDC9	URI1	GGCCATCGCACCTGCCTTTGGAATGATCAGCTTTACCTGGTTGGGGGTTT*GTGGTCACTAACTGCCAAGAGAGAATCCAGCATTGGTGAGTGAAAGATGG	oncogene	BOWTIE+BLAT	out-of-frame	0	10	1	21	1	161100169	+	19	29971193	+	1.2628	48.4606	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-DK-A1AD-01A	ENSG00000135365	ENSG00000175220	PHF21A	ARHGAP1	GCTGCCAGGGGGGACAGCCAGCCAGCAGCAGGAGG*GTTTCTCTTAAGGTTCTGCAGGGCAAGGCTGTCTG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/UTR	0	7	2	18	11	46120935	-	11	46696156	-	2.3649	29.5275	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	FALSE	Bladder	TCGA-DK-A1AD-01A	ENSG00000070413	ENSG00000206028	DGCR2	Z99774.1	CTCCTTGGAAGGTCGCTGGGAGGTGGCATTCAAAG*AGAAAAGGCCATGTGAGGACATAGTGAGAAGGTGC	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	4	3	21	22	19063202	-	22	26669438	-	26.1561	0.1998	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-DK-A1AD-01A	ENSG00000205209	ENSG00000012061	SCGB2B2	ERCC1	CGGACACATAACAAGCAGCAGTGAGGACACCAAAG*CCTCCGCTACCACAACCTGCACCCAGACTACATCC	cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	3	1	13	19	34675630	-	19	45419197	-	0.0338	13.9533	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Bladder	TCGA-BT-A0S7-01A	ENSG00000127328	ENSG00000111581	RAB3IP	NUP107	AACGATTAAAAGAAGAACTCGCAAAAGCTCAGAGG*ATTTGGATGTTGCAACAATAACAAAAACTGTAGTT	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	429	22	24	12	69756663	+	12	68731607	+	7.5778	31.2961	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BT-A0S7-01A	ENSG00000127328	ENSG00000111581	RAB3IP	NUP107	AACGATTAAAAGAAGAACTCGCAAAAGCTCAGAGG*GAGGATCGTTTAAAAATTGATGTAATTGACTGGTT	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	429	7	23	12	69756663	+	12	68732637	+	7.5778	31.2961	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BT-A0S7-01A	ENSG00000127328	ENSG00000111581	RAB3IP	NUP107	AACGATTAAAAGAAGAACTCGCAAAAGCTCAGAGG*CATCAAAAAAGCACGAAGCTGCAAAAGAAGTATTT	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	429	2	22	12	69756663	+	12	68733452	+	7.5778	31.2961	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-BT-A0S7-01A	ENSG00000127328	ENSG00000111581	RAB3IP	NUP107	GATCTGCCTGGGCATGTGGCAGAGAGGATCTCTAATTTTTGTGGTAGCAG*ATTTGGATGTTGCAACAATAACAAAAACTGTAGTTGAGAATATTCGAAAG	tcga,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	429	1	19	12	69765775	+	12	68731607	+	7.5778	31.2961	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BT-A0S7-01A	ENSG00000127328	ENSG00000111581	RAB3IP	NUP107	AGACGTTTAAATTGTGCGGAAATATCTAGTATCAG*CATCAAAAAAGCACGAAGCTGCAAAAGAAGTATTT	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	429	1	14	12	69755659	+	12	68733452	+	7.5778	31.2961	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BT-A0S7-01A	ENSG00000100393	ENSG00000128285	EP300	MCHR1	TCCGGCCCTCTCGGCGTCCGCCAGCGATGGCACAG*GATCACCTCCTCGCACGGGGAGCATCTCCTACATC	tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	68	14	24	22	41093098	+	22	40680949	+	12.2656	18.4119	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BT-A0S7-01A	ENSG00000175782	ENSG00000274979	SLC35E3	AC020656.2	ATGGTGAACTTATCAATTTATTGGATCATTGGGAACACTTCACCTGTCAC*ATTCACCCATGTCATTGCATGTATCAAAAGTCCATTTTTTTGCTGAGTAC	lincrna	BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	2	2	16	12	68759239	+	12	69326728	-	18.3427	0.1704	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-BL-A3JM-01A	ENSG00000173473	ENSG00000088538	SMARCC1	DOCK3	AGCATGTCACCAACCCGGCCTTCACCAAACTCCCT*GGGATCTTTCCTGCAAATTACATTCACTTGAAAAA	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	8	7	21	3	47772817	-	3	50890026	+	24.4962	5.2944	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-FD-A3SQ-01A	ENSG00000141258	ENSG00000072134	SGSM2	EPN2	GCATGAAGACAGCAGCCACATCATTGCTTTATGTG*CCACCTCCCCGCGAGTGTCCTCCGAGCTGGAGCAA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	54	13	24	17	2343620	+	17	19309885	+	5.1213	3.7472	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-FD-A3SQ-01A	ENSG00000141258	ENSG00000072134	SGSM2	EPN2	CGCAGGAGCTTACATTCTGTTGGGGAGACAGACAGGAAACAAATGCGCAA*CCACCTCCCCGCGAGTGTCCTCCGAGCTGGAGCAAGCCCGGCCCCAGACT	tcga,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	54	1	18	17	2344660	+	17	19309885	+	5.1213	3.7472	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-FD-A3NA-01A	ENSG00000134375	ENSG00000163435	TIMM17A	ELF3	GACAGCTATTAAAACCAGGGCTCCACAGTTAGGAG*GTAGCCTCATGGCTGCAACCTGTGAGATTAGCAAC	cell_lines,10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	32	12	24	1	201957574	+	1	202011129	+	16.5995	51.0568	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-FD-A3NA-01A	ENSG00000134375	ENSG00000163435	TIMM17A	ELF3	GGGGTTTCATGCAGGAGAAACCCATCAAGCCGATTGGGCTCTTCTCCAAG*GTAGCCTCATGGCTGCAACCTGTGAGATTAGCAACATTTTTAGCAACTAC	cell_lines,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	intronic/UTR	0	32	1	22	1	201958271	+	1	202011129	+	16.5995	51.0568	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-FD-A3NA-01A	ENSG00000134375	ENSG00000163435	TIMM17A	ELF3	AAAAAGGACATTAGCAAACTAAGGAAATCTGAATTAAGTATGGACTTCAG*GGTTGGGCAAAGCAGAGTAGCTGGGAGTGTAAGGAGAGGACCCTCGTCCC	cell_lines,10K<gap<100K	BOWTIE+BLAT	intronic/UTR	0	32	1	22	1	201960101	+	1	202011044	+	16.5995	51.0568	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-FD-A3NA-01A	ENSG00000111679	ENSG00000110811	PTPN6	P3H3	AACTCCGTACCTTACAGGTCTCCCCGCTGGACAAT*GCTCGGGTGCGTCCTCGCTGTGGGCGCCTTGTGGC	tcga,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	25	3	22	12	6957785	+	12	6839000	+	21.0234	18.0408	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-FD-A3NA-01A	ENSG00000143653	ENSG00000162852	SCCPDH	CNST	TGGAAAGTTTCCTGACTATACATTCAGGACCTGAG*AGAGTAAAACTTGTCTCGGCACAGAGTCAAGTAAA	tcga,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	20	6	23	1	246744125	+	1	246647139	+	226.1537	7.9112	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-FD-A3NA-01A	ENSG00000143653	ENSG00000162852	SCCPDH	CNST	GTACTTTGACTGCTGTGGAAAGTTTCCTGACTATACATTCAGGACCTGAG*GCTGGAGTGCAATGGCGTGATCTCAGGTAACCGCAGCCTCCGCCTCCCGG	tcga,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K	BOWTIE+STAR	CDS(truncated)/intronic	0	20	1	19	1	246744125	+	1	246646526	+	226.1537	7.9112	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-FD-A3NA-01A	ENSG00000143653	ENSG00000162852	SCCPDH	CNST	CGGAACATAACTGACACATTGGTTCTTTGGAGAGGATCTCAGGACTCATT*AGAGTAAAACTTGTCTCGGCACAGAGTCAAGTAAAGAAAGCCAACATACA	tcga,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K	BOWTIE+STAR	intronic/CDS(truncated)	0	20	1	14	1	246747980	+	1	246647139	+	226.1537	7.9112	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-FD-A3NA-01A	ENSG00000055332	ENSG00000115816	EIF2AK2	CEBPZ	AGATTTGACCTTCCTGACATGAAAGAAACAAAGTATACTGTGGACAAGAG*GGCCCCAGCAGATTGGATGGTGCCCACTCACATTTGAATGCAGATCTTCC	known,tcga,18cancers,chimerdb3seq,cancer,tcga-cancer,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	9	1	18	2	37135484	-	2	37206105	-	12.8083	10.2553	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-FD-A3NA-01A	ENSG00000068097	ENSG00000267095	HEATR6	AC025048.1	CTGCAGCACCTGATCAGAGAGCACCAGTCTTCTTG*TTTCCCCGGCGATGGTGTCCTGGACTGAAGAGACT	lincrna,10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	2	2	23	17	60055515	-	17	60136227	-	5.284	0	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-HQ-A2OE-01A	ENSG00000167962	ENSG00000103544	ZNF598	C16ORF62	GCTACTGCGCCGTGTGCCGCGAGGAGCTGCGCCAG*TGGACTCCAACGACAGCCTCTACGGGGGAGACTCC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	92	11	23	16	2009524	-	16	19691353	+	16.7918	5.161	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-HQ-A2OE-01A	ENSG00000131374	ENSG00000228956	TBC1D5	SATB1-AS1	GGGAATAGGAGCTGGGGAGCCCTTCTGCGCCACAG*GTGGAAGAGTAAACTGTTCCTGTTTCTCCATCTTG	exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	36	7	24	3	17742481	-	3	18526387	+	12.5962	0.813	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-HQ-A2OE-01A	ENSG00000131374	ENSG00000228956	TBC1D5	SATB1-AS1	AGGTTCAAGCGATTCTCCTGCGTCAGCCTCCTGAGGAGCTGGGACTACAG*GTGGAAGAGTAAACTGTTCCTGTTTCTCCATCTTGACAGGAAGCAGAAGT	NA	BOWTIE+STAR	intronic/exonic(no-known-CDS)	0	36	1	22	3	17729582	-	3	18526387	+	12.5962	0.813	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-HQ-A2OE-01A	ENSG00000140983	ENSG00000255395	RHOT2	AP001972.4	CCACTGGTGAATGGGGGGACCACGCAGGGGCCCAG*GTCCCAAGATAAAGAACGCCATTCAGGAATCGTGC	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	31	8	21	16	670175	+	11	75133929	-	56.3495	3.7711	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-HQ-A2OE-01A	ENSG00000140983	ENSG00000255395	RHOT2	AP001972.4	AGACGGACGAGGAGCTGCGGGAGGAGATCCACAAG*GTCCCAAGATAAAGAACGCCATTCAGGAATCGTGC	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	31	4	17	16	668699	+	11	75133929	-	56.3495	3.7711	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-HQ-A2OE-01A	ENSG00000166004	ENSG00000161996	CEP295	WDR90	AGAGAATGTCTGTGGTGATGACTATGATGAAGCAG*GATGGCGTCGTGCGGGCAGGGCAGTGTGCGGCTCT	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	18	4	20	11	93706897	+	16	655307	+	3.2016	15.1632	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-HQ-A2OE-01A	ENSG00000198131	ENSG00000104983	ZNF544	CCDC61	GGACCTGTGCAGGGCAGAGCAGGAGGCCCCCCGAG*CAACCTTGGCCATGGACCAGCCGGCTGGCCTGCAG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	17	8	24	19	58246794	+	19	46003008	+	2.5657	5.1046	FALSE	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-HQ-A2OE-01A	ENSG00000125450	ENSG00000232724	NUP85	TRIM80P	TTGTTGGCAGCCTTTGAGTTTGACATCCATCAAGTAATCAAAGAGTGCAG*TCTTCCTCCTGGCACCAGTGGCCACAGGCTTCTGCAGAGGAGCGCTCAGG	pseudogene,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	CDS(complete)/exonic(no-known-CDS)	0	12	3	21	17	75226157	+	17	75079053	+	16.9135	0.3413	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	unitary_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-HQ-A2OE-01A	ENSG00000185022	ENSG00000100151	MAFF	PICK1	CTTGCAGCCCCCCAAACTGGGACCGAATGACCCTGGGAAGGGGAACTTGG*ATGGGCTTGTCAAGAGGCTAGAGGAGCTGGAGCGGACCGCTGAGCTATAC	cancer,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	3	1	20	22	38215077	+	22	38070838	+	27.013	11.4416	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-HQ-A2OE-01A	ENSG00000213390	ENSG00000052749	ARHGAP19	RRP12	GAAGGGGAGGTGCCAGCCCGCGAATCCGGCCGGAG*TAATGCACACGAATCCGGAAGTGACGCCAGAAGAA	known,tcga,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	1	2	24	10	97292572	-	10	97401368	-	7.5784	14.1331	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Bladder	TCGA-DK-A3X2-01A	ENSG00000089356	ENSG00000248385	FXYD3	TARM1	GAAGGTGACCCTGGGCCTGCTTGTGTTCCTGGCAG*GACTGTGCGTGGGCCAAGGAGACACAAGGGGAGAT	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	142	12	22	19	35119416	+	19	54075918	-	1.8511	24.571	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-DK-A3X2-01A	ENSG00000089356	ENSG00000248385	FXYD3	TARM1	GAAGGTGACCCTGGGCCTGCTTGTGTTCCTGGCAG*GGTCACTGCCCAAGCCGTCCCTCAGTGCCTGGCCC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	142	6	23	19	35119416	+	19	54075114	-	1.8511	24.571	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-DK-A3X2-01A	ENSG00000120784	ENSG00000007306	ZFP30	CEACAM7	GATATTAGAGAACTATAGCAACTTGGTGTCACTGG*CCTCGCTTTTAACCTTCTGGAACCTGCCAAACAGT	tcga,chimerdb3seq,cancer,m38,tcga-cancer,exon-exon	BOWTIE	in-frame	0	39	11	24	19	37644610	-	19	41687221	-	1.125	14.6126	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-DK-A3X2-01A	ENSG00000120784	ENSG00000007306	ZFP30	CEACAM7	TTTGTACAGAGATGTGATATTAGAGAACTATAGCAACTTGGTGTCACTGG*GGAAACTCCATGAGCACAGGGGCCACGTCTGTCCTGCTTTTTGTGGAATC	tcga,chimerdb3seq,cancer,m38,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	39	1	21	19	37644610	-	19	41691215	-	1.125	14.6126	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-DK-A3X2-01A	ENSG00000065526	ENSG00000142634	SPEN	EFHD2	GTGCGGGAAGAGAAGATCATCGAGCATTTCAAACG*GTATGATGCCGGGCGGGACGGCTTCATCGACCTGA	tcga,chimerdb3seq,m29,tcga-cancer,exon-exon	BOWTIE	in-frame	0	30	7	23	1	15848150	+	1	15425871	+	16.4494	58.7912	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-DK-A3X2-01A	ENSG00000167632	ENSG00000123908	TRAPPC9	AGO2	TTTCTATAGAGAGAGGAATTAAAACGCTGGAAGCAAGGCCCAGTTGAAAG*GTGGTGGGCAGCATGGACGCCCACCCCAATCGCTACTGCGCCACCGTGCG	tcga,cell_lines,chimerdb3seq,tcga-cancer,10K<gap<100K	BOWTIE+STAR	intronic/CDS(truncated)	0	10	3	24	8	140456799	-	8	140541358	-	4.2387	8.4985	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Bladder	TCGA-DK-A3X2-01A	ENSG00000167632	ENSG00000123908	TRAPPC9	AGO2	TGGGCTCCCGCTCCGGGCCCGGGGCCACCGGCTGT*GTGGTGGGCAGCATGGACGCCCACCCCAATCGCTA	tcga,cell_lines,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	10	2	23	8	140457639	-	8	140541358	-	4.2387	8.4985	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-DK-A3X2-01A	ENSG00000125450	ENSG00000180901	NUP85	KCTD2	AAGATCCAGCCAATGGCCGCCAGTTCAGCAGCCAG*GATGAGACAGGAGCCTATCTGATTGACAGGGACCC	tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	9	3	21	17	75213119	+	17	75049220	+	23.9304	17.9865	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-DK-A3X2-01A	ENSG00000116661	ENSG00000215910	FBXO2	C1ORF167	GCGGGGGGGCTGCCCTCCAGGCCTCTCTTGGTCCA*CTCCTTCTTCCAGGGCCTGCAGCAGCGGATGCTGC	exon-exon	BOWTIE	UTR/CDS(truncated)	0	2	2	22	1	11648092	-	1	11778660	+	1.4713	0.0922	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01B	ENSG00000177697	ENSG00000177106	CD151	EPS8L2	TCGCTGGTATCCTCGCCTACGCCTACTACCAGCAG*AGCAGAGGAAGAAGTATTCCAACTCCAACGTCATC	tcga,chimerdb3seq,cancer,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	21	10	24	11	836843	+	11	710422	+	18.0361	16.3499	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01B	ENSG00000120265	ENSG00000008294	PCMT1	SPAG9	TAGGTTTCCAAGCAACAATCAGTGCTCCACACATG*TTAGCAGACTTGAAGAAAGAGAAGCAGAACTGAAG	oncogene,tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	19	3	15	6	149773169	+	17	51056482	-	23.9408	93.0341	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01B	ENSG00000120265	ENSG00000008294	PCMT1	SPAG9	GACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCGG*ATGATCTACCCGCCTTGGCCTCCCGAAGTGCTTGAATTACAGGCGTGAGC	oncogene,tcga,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/UTR	0	19	2	23	6	149797049	+	17	50964369	-	23.9408	93.0341	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01B	ENSG00000120265	ENSG00000008294	PCMT1	SPAG9	ACAAAAAAAATTTAGCCGGGTATGGTGGTGCCTGCCTGTAATCCCAGCGA*TTTAGGAGGCTGAGGCAGATGGATTGCTTGAGCCCAGGAGTTCAAGACCA	oncogene,tcga,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/UTR	0	19	1	15	6	149809148	+	17	50965023	-	23.9408	93.0341	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01B	ENSG00000008294	ENSG00000120265	SPAG9	PCMT1	GATCAACTAGAATCCACAGCTCATAGTAGAATTAG*AAAATGGAATCATCAAGACAGATAAAGTATTTGAA	oncogene,tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	19	5	24	17	51047375	-	6	149771162	+	93.0341	23.9408	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-BL-A0C8-01B	ENSG00000105556	ENSG00000101391	MIER2	CDK5RAP1	CAGCAACCTGCACTTGAACCGGCACTGTGAGAAGA*GCTGCATGGCTGAGAGGTTGAAGGAGGAGATTCTC	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	17	9	23	19	325635	-	20	33387533	-	5.1203	17.954	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-BL-A0C8-01B	ENSG00000105556	ENSG00000101391	MIER2	CDK5RAP1	GTTCCAAGCTGACCTCAGCAACCTGCACTTGAACCGGCACTGTGAGAAGA*GTTTTAGCAAGTATTATAGGCTAGAAGAGAGGGAAAGGGTTCAAGTGTAG	tcga,cell_lines,chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	17	1	17	19	325635	-	20	33388246	-	5.1203	17.954	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01B	ENSG00000083307	ENSG00000197872	GRHL2	FAM49A	TGAAGTCTCCCACAGTGAAGGGCCTGATGGAAGCG*GTTTGCTGGGATGGGAAACCTGCTCAAAGTCCTTA	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	8	3	19	8	101649499	+	2	16588129	-	26.4858	22.3391	FALSE	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01B	ENSG00000147257	ENSG00000132170	GPC3	PPARG	GTTCTTAATTATTCAGAATGCTGCGGTTTTCCAAG*AAATGACCATGGTTGACACAGAGATGCCATTCTGG	oncogene,cell_lines,cancer,exon-exon	BOWTIE	in-frame	0	5	5	23	X	133953050	-	3	12379704	+	1400.4294	328.7462	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Bladder	TCGA-BL-A0C8-01B	ENSG00000147257	ENSG00000132170	GPC3	PPARG	GTTCTTAATTATTCAGAATGCTGCGGTTTTCCAAG*ATTTGAAAGAAGCCAACACTAAACCACAAATATAC	oncogene,cell_lines,cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	5	3	24	X	133953050	-	3	12312380	+	1400.4294	328.7462	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01B	ENSG00000233080	ENSG00000183822	LINC01399	NCF4-AS1	TCAGCAAACAATGGCAAGGCAGAGCCACCAGAAAG*TATTCCTCCCACAGATGAGGAAACTGGAGCTTGGA	pseudogene,antisense,exon-exon	BOWTIE	exonic(no-known-CDS)/exonic(no-known-CDS)	0	3	1	14	22	35194857	-	22	36848017	-	2.648	0.978	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	transcribed_processed_pseudogene	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01B	ENSG00000247596	ENSG00000053108	TWF2	FSTL4	GCGCCGAGCCATGGCGCACCAAACGGGCATCCACG*GACTTTGGAGAGGATGATTCCCTGTACATCACCAA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	3	2	22	3	52238992	-	5	133233537	-	2.6049	3.1581	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01B	ENSG00000164144	ENSG00000137460	ARFIP1	FHDC1	TTTTTTTTTTTTTTTTTGAGACAGAGTCTCACTCTGTCGCCCAGGCTGGA*TGCAGTGATCTCAGCTCGCTGCAACCTCCACCTCCCGGATTCAAGCGATT	known,cosmic,tcga,chimerdb3kb,chimerdb3seq,tcga-cancer,10K<gap<100K	BOWTIE+STAR	intronic/intronic	0	2	1	17	4	152781286	+	4	152955542	+	25.2764	8.4596	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-BL-A0C8-01B	ENSG00000164144	ENSG00000137460	ARFIP1	FHDC1	TTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGA*TGCAGTGATCTCAGCTCGCTGCAACCTCCACCTCCCGGATTCAAGCGATT	known,cosmic,tcga,chimerdb3kb,chimerdb3seq,tcga-cancer,10K<gap<100K	BOWTIE+STAR	intronic/intronic	0	2	1	17	4	152815795	+	4	152955542	+	25.2764	8.4596	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-DK-A2I6-01A	ENSG00000161395	ENSG00000131748	PGAP3	STARD3	CCCCCATGTACCACACCTGTGTGGCCTTCGCCTGG*ACCAACACAGGCATCCGTAAGAACTTGGAGCAGGA	tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	97	13	24	17	39684597	-	17	39657008	+	31.5281	43.2611	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-DK-A2I6-01A	ENSG00000161395	ENSG00000131748	PGAP3	STARD3	GTTCACCAGGCCACATTTGTCTGTTTCAGGCTGGACCTGTCGGGACGACT*GGTCTGACAATGAATCAGATGAAGAAGTTGCTGGGAAGAAAAGTTTCTCT	tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer	BOWTIE+STAR	in-frame	0	97	2	18	17	39685999	-	17	39659051	+	31.5281	43.2611	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-DK-A2I6-01A	ENSG00000106266	ENSG00000002822	SNX8	MAD1L1	TCCTGAAGCATGTGGAGTATGAGGTTTCCAGCCAG*GAGCGGGACGGTATGCGGGCCATCCTGGGGTCCTA	cell_lines,chimerdb3seq,cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	23	4	22	7	2278100	-	7	2014642	-	3.0905	0.0237	TRUE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-DK-A2I6-01A	ENSG00000101773	ENSG00000141510	RBBP8	TP53	AACTGCTTGGGCACACGTGTAAGGAATGTGAAATT*CAGCCAGACTGCCTTCCGGGTCACTGCCATGGAGG	tcga,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	8	6	24	18	23016924	+	17	7676622	-	4.5985	4.6043	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-DK-A2I6-01A	ENSG00000102547	ENSG00000104324	CAB39L	CPQ	TTGATATTGCTTCAGATGCCTTTGCTACTTTCAAG*GCATTACAGCAGAAGTTCTGGTGGTGACCTCTTTC	exon-exon	BOWTIE	out-of-frame	0	6	5	23	13	49350744	-	8	96834973	+	46.9827	13.6056	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Bladder	TCGA-DK-A2I6-01A	ENSG00000132549	ENSG00000214511	VPS13B	HIGD1C	CTGGGCAGACCAGAAGTCCACATGGCCCTGGACGTGGTTCTGGTGAGGGG*CTAAAGCAATGGTTTAACATAAGTGACTTTGTGAGGTTGGGGATTGAATT	NA	BOWTIE+BLAT	CDS(truncated)/intronic	0	2	1	23	8	99871513	+	12	50966795	+	2.9911	0.1154	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-CF-A1HS-01A	ENSG00000146950	ENSG00000169891	SHROOM2	REPS2	TGCCTTCACAGCTGGGCGAACTCCCATCCAGCACG*CTACCAAGTCAGGATTGTTACCCCCACCACCTGCG	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	8	4	22	X	9912587	+	X	17103718	+	12.3264	1.57	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-CF-A1HS-01A	ENSG00000139926	ENSG00000115310	FRMD6	RTN4	CTTCTTCTGGTTGGAAACTTGTCAAATTTCATCAG*TTGTTGACCTCCTGTACTGGAGAGACATTAAGAAG	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	7	3	22	14	51570410	+	2	54987698	-	18.0476	57.1684	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-CF-A1HS-01A	ENSG00000139926	ENSG00000115310	FRMD6	RTN4	GGATGTCTTTGGCTTGTTGAGCAGTGGCAGTCCAGCCCCAGCAGGACCTG*TTGTTGACCTCCTGTACTGGAGAGACATTAAGAAGACTGGAGTGGTGTTT	tcga,chimerdb3seq,cancer,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	7	1	21	14	51620726	+	2	54987698	-	18.0476	57.1684	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-CF-A1HS-01A	ENSG00000058272	ENSG00000181163	PPP1R12A	NPM1	GTCTCCTCCACAACAGAGGTCAGGGAGAGACGCAG*GCTATTCAAGATCTCTGGCAGTGGAGGAAGTCTCT	oncogene,cancer,tumor,m2,exon-exon	BOWTIE	out-of-frame	0	6	7	23	12	79805592	-	5	171410527	+	5.1775	94.6369	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-CF-A1HS-01A	ENSG00000164327	ENSG00000164588	RICTOR	HCN1	CGGCGAGGAGAACGTCCCGCTGGATCTGACCCGAG*GTTTTACTGGGATTTAATAATGCTTATAATGATGG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	5	2	23	5	39074111	-	5	45645608	-	4.6257	0.0658	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-CF-A1HS-01A	ENSG00000173327	ENSG00000235126	MAP3K11	AC128709.2	CTTAGGATCTCCTTCCACACCCCCAGCACTCAATG*ATGACGTAACTACGGCTTTGGGATGTTACGCAACG	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	3	2	22	11	65605761	-	3	197457783	-	7.835	1.5235	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-FD-A3SS-01A	ENSG00000198522	ENSG00000196096	GPN1	AC079610.1	AGCAGTACATGAAGTTCCCTTTCCTGCCAATATTG*GTCAAGCTGATGCAAGAGATGGTTTCCCATGGTCT	lincrna,m54,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	63	5	22	2	27629952	+	2	213278531	-	11.832	11.7836	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-FD-A3SS-01A	ENSG00000198522	ENSG00000196096	GPN1	AC079610.1	GATCAACCTGGATCCAGCAGTACATGAAGTTCCCTTTCCTGCCAATATTG*AATTTTTCCCTCAACATGTGAGAATTATGGGAGTACAATTCAAGATGATA	lincrna,m54	BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	63	1	17	2	27629952	+	2	213277025	-	11.832	11.7836	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-FD-A3SS-01A	ENSG00000259080	ENSG00000196096	AC074091.1	AC079610.1	GATCAACCTGGATCCAGCAGTACATGAAGTTCCCTTTCCTGCCAATATTG*AATTTTTCCCTCAACATGTGAGAATTATGGGAGTACAATTCAAGATGATA	lincrna,m16	BOWTIE+BLAT;BOWTIE+STAR	exonic(no-known-CDS)/exonic(no-known-CDS)	0	19	2	22	2	27629952	+	2	213277025	-	0	11.7836	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	processed_transcript	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-FD-A3SS-01A	ENSG00000146350	ENSG00000146374	TBC1D32	RSPO3	ACACTCAGACTCAAGATCTGCAAGTTTTCCTAAAA*TGCATCCTAACGTTAGTCAAGGCTGCCAAGGAGGC	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	3	2	16	6	121090853	-	6	127148648	+	1.0704	0.4494	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-DK-A3IV-01A	ENSG00000100991	ENSG00000078814	TRPC4AP	MYH7B	ACCAGATGTTCCTGCTGAAGCGAGGCCTCTTGGAG*GTGTTCTTCAAGGCTGGGCTTCTAGGCGTCCTGGA	cell_lines,exon-exon	BOWTIE	in-frame	0	316	18	24	20	35007550	-	20	34993334	+	643.6033	50.6292	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-DK-A3IV-01A	ENSG00000100991	ENSG00000078814	TRPC4AP	MYH7B	GTCATGAAGAAGGAGCCAGCAGAGTCGTCTTTCAG*GGATGCGCTGTTCACCATCCAGTGGAACATCCGTG	cell_lines,exon-exon	BOWTIE	in-frame	0	316	2	22	20	35008664	-	20	34994146	+	643.6033	50.6292	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-DK-A3IV-01A	ENSG00000100991	ENSG00000078814	TRPC4AP	MYH7B	CCATGCCAGGCCCTGGTGGGGGCAGCCACGTTGACACCTTCACCCTGTCC*CATGGCTGTGGCGGTCACACTGGGCAGGGTTCATGCGGATGGTTGGGGGT	cell_lines	BOWTIE+BLAT	intronic/intronic	0	316	2	22	20	35006588	-	20	34993254	+	643.6033	50.6292	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-DK-A3IV-01A	ENSG00000100991	ENSG00000078814	TRPC4AP	MYH7B	CCACCTCCTATGCAGACCAGATGTTCCTGCTGAAGCGAGGCCTCTTGGAG*GACATCAGCGTGTGGCCCGGAGGGGTAGCGATGGCACCCAGTGTCTTCCA	cell_lines	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	316	1	20	20	35007550	-	20	34993673	+	643.6033	50.6292	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-DK-A3IV-01A	ENSG00000088325	ENSG00000088320	TPX2	REM1	TGAAGGAGATACTCAAAACATAGATTCATGGTTTG*GATAAAAGCTGGAGCCAGGAGTCATGCCTGCAGGG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	24	8	24	20	31757582	+	20	31482287	+	66.5911	1.259	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-DK-A3IV-01A	ENSG00000088325	ENSG00000088320	TPX2	REM1	TTCATCCTTGGATGATGAAGGAGATACTCAAAACATAGATTCATGGTTTG*GCATAAAGAACCATATGGCAAGACTAAACCCTCCTCAGAAACAAGACAAA	tcga,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	24	5	23	20	31757582	+	20	31481903	+	66.5911	1.259	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-DK-A3IV-01A	ENSG00000006715	ENSG00000187258	VPS41	NPSR1	AGGATGCAGCTAGCTGCATGACAGTCCATGACAAG*GTTGTGCTGCTCTACGCCTCTACCTACGTCCTGGT	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	22	2	19	7	38869146	-	7	34811770	+	6.3418	1.763	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-DK-A3IV-01A	ENSG00000122545	ENSG00000229618	SEPT7	AC011287.1	ATACAGAAAATCGGTGAAGAGAGGTTTTGAATTCACGCTTATGGTAGTGG*GGTTTTCTACATGTAAAATCATGACATCTGCAAACAAAGGTAATTTTACC	lincrna	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	8	3	19	7	35832900	+	7	13004984	+	5.7514	1.4993	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-DK-A3IV-01A	ENSG00000122545	ENSG00000229618	SEPT7	AC011287.1	ATACAGAAAATCGGTGAAGAGAGGTTTTGAATTCACGCTTATGGTAGTGG*GATTGAATTCACAGGTCCATGTTGTATTTCGTTGTCATGTCTCCTTGGTT	lincrna	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	8	1	23	7	35832900	+	7	13043466	+	5.7514	1.4993	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-DK-A3IV-01A	ENSG00000122545	ENSG00000229618	SEPT7	AC011287.1	ATACAGAAAATCGGTGAAGAGAGGTTTTGAATTCACGCTTATGGTAGTGG*GCTTTTGAGCCTCACAAGACTTTGAGATTTTATGGATATGAAACCTGCTA	lincrna	BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	8	1	20	7	35832900	+	7	13101506	+	5.7514	1.4993	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-DK-A3IV-01A	ENSG00000011426	ENSG00000106536	ANLN	POU6F2	CTTATTGGACTTATCCAGATGATGAGAAACGCAAG*GATCCAATGATAGCTGGACAAGTCAGTAAGCCCTT	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	3	3	22	7	36443862	+	7	39085860	+	6.2892	0.2257	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-FD-A3B5-01A	ENSG00000176571	ENSG00000175354	CNBD1	PTPN2	TGAGATGGCAATCATTGAAGATAAGGACCTATTTG*GCCAAGATTGACAGACACCTAATATTCATGACTTG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	6	2	16	8	87353786	+	18	12785844	-	0.7438	6.5894	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-CU-A3YL-01A	ENSG00000135040	ENSG00000050555	NAA35	LAMC3	CTCTACAGTATGCACGAGTACTATTACATATATTG*CCACAGAGACACCGCCACCAAGATCGCAGCCACTG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	11	3	24	9	86013897	+	9	131075831	+	2.6925	4.9062	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-CU-A3YL-01A	ENSG00000135040	ENSG00000050555	NAA35	LAMC3	CTCTACAGTATGCACGAGTACTATTACATATATTG*CTGCACCAGGAGGCCAGAGCCGCCCTGACCCAGGC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	11	2	21	9	86013897	+	9	131082059	+	2.6925	4.9062	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-BT-A20X-01A	ENSG00000188906	ENSG00000061987	LRRK2	MON2	AGTGAGTTGCTGTTTGCTCCATAGGCTTACATTAG*CATACCTCCAGATAATCTCTCTATTCAAGAGTTTC	exon-exon	BOWTIE	out-of-frame	0	2	2	19	12	40243681	+	12	62578445	+	0.4679	1.7766	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-DK-A3IM-01A	ENSG00000125977	ENSG00000101421	EIF2S2	CHMP4B	ACTTCTTTTGTCAACTTTACAGATATCTGTAAACT*CGGCCCTCCAGGCACTGAAGCGTAAGAAGAGGTAT	m3,exon-exon	BOWTIE	out-of-frame	0	5	2	17	20	34096657	-	20	33848467	+	66.1934	129.4321	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-DK-A3IM-01A	ENSG00000125977	ENSG00000101421	EIF2S2	CHMP4B	GGGTCTTGCTGTGTTGCCCAGGAGGGCTTGTTTTATTAGTGCATTCAGAG*CGGCCCTCCAGGCACTGAAGCGTAAGAAGAGGTATGAGAAGCAGCTGGCG	m3	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	5	1	18	20	34096231	-	20	33848467	+	66.1934	129.4321	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-DK-A3IM-01A	ENSG00000249859	ENSG00000196911	PVT1	KPNA5	ATTAAAGTTTTACAAGATTTAACCTGTCATCAAGACCTGGGATTTTGGTG*CAGGTTTGTGGAGGTCCTTAGGAGGTTAACAAACTCCTGAAATTGCATGC	lincrna,oncogene,cancer	BOWTIE+STAR	exonic(no-known-CDS)/intronic	0	4	1	14	8	128010444	+	6	116715212	+	2.1878	1.1809	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-DK-A3IM-01A	ENSG00000132549	ENSG00000186106	VPS13B	ANKRD46	ATTCACTAAACACTGCAATACAAGCTTGGCAACAG*AGAAGGACACTGAGGCTTGGAAGCTTTGCAAGGCA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	4	2	15	8	99779031	+	8	100510639	-	4.5609	7.4041	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-G2-A3VY-01A	ENSG00000197562	ENSG00000260228	RAB40C	AC009119.1	GCACCATCTTCAGGTCCTACTCCAGGGGCGCTCAG*GGAGGCAGTCAATGGTGAATGCTGGCCTCGCTGAT	antisense,m137,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	144	16	24	16	618260	+	16	83790204	-	25.715	2.4976	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-G2-A3VY-01A	ENSG00000197562	ENSG00000260228	RAB40C	AC009119.1	GCCAGGGCCGGTTCTGCACCATCTTCAGGTCCTACTCCAGGGGCGCTCAG*ATGTCAAAGAAAGAAATGCAGATCCTTCAGTTCAACTCTCAGTTGCAGTA	antisense,m137	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	144	11	22	16	618260	+	16	83790315	-	25.715	2.4976	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-G2-A3VY-01A	ENSG00000197562	ENSG00000260228	RAB40C	AC009119.1	CTGCTGGACGGCCGGCGCGTGAAGCTGGAGCTCTG*GGAGGCAGTCAATGGTGAATGCTGGCCTCGCTGAT	antisense,m137,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	144	5	24	16	617268	+	16	83790204	-	25.715	2.4976	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-G2-A3VY-01A	ENSG00000069248	ENSG00000113361	NUP133	CDH6	CTGTAGAAGTCACTCAATATAATCCACCTTTTCAG*GTATTATCAAGACAGCTTTGCTCAACATGGATCGA	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	13	3	22	1	229489955	-	5	31299464	+	9.4383	0.5894	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-G2-A3VY-01A	ENSG00000082068	ENSG00000151062	WDR70	CACNA2D4	ATAAAGGGAGAATTTATGACTTGCTCAAATGATGC*AATCTGGTGGAAGCTGCCGAGGAGGCCGACCTGAA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	12	3	22	5	37516590	+	12	1909965	-	7.0542	1.9563	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-G2-A3VY-01A	ENSG00000196151	ENSG00000115159	WDSUB1	GPD2	TAGAGAACTTATGAAAGATCCGGTCATCGCATCAG*GCTAAGAAATGGCATTTCAAAAGGCAGTGAAAGGG	tcga,chimerdb3seq,m5,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	7	3	23	2	159248372	-	2	156476098	+	16.9641	36.9573	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-G2-A3VY-01A	ENSG00000104472	ENSG00000147481	CHRAC1	SNTG1	ACCAGGAGGCGTTGGTGCTCACGGCCAAGGCCACG*GAAAGAACGGTGACCATCAGAAGACAAACAGTAGG	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	2	2	23	8	140511646	+	8	50438543	+	23.6724	0.6324	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-GD-A3OS-01A	ENSG00000137693	ENSG00000149972	YAP1	CNTN5	GCAAAGACATCTTCTGGTCAGAGATACTTCTTAAA*TCATCTCTAGGTATCCATGGAAGATTGCTTCCAGG	oncogene,cancer,tumor,exon-exon	BOWTIE	CDS(truncated)/UTR	0	84	13	23	11	102114394	+	11	99049591	+	138.9642	0.4884	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-GD-A3OS-01A	ENSG00000135956	ENSG00000136738	TMEM127	STAM	AGCAGCACCATCCCAGCCCTGGGGCCTGCTGACTG*ACCTAAGGATTGTCTTCGGTCTATTATGAGAAGAG	tcga,chimerdb3seq,tumor,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	50	5	24	2	96265869	-	10	17684675	+	17.2074	14.5603	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-GD-A3OS-01A	ENSG00000167112	ENSG00000107147	TRUB2	KCNT1	CACCAGCGTACCCTCTTTCATCAACCATCCACTGG*GGTCCAGGTGGAGTTCTACGTCAACGAGAACACCT	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	40	11	24	9	128321599	-	9	135750098	+	4.0441	5.4275	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-GD-A3OS-01A	ENSG00000082175	ENSG00000172900	PGR	FLJ42102	TAGAAAGTGCTGTCAGGCTGGCATGGTCCTTGGAG*GCATGACTGTTGAATCTGGAGAAGGAATGACACAC	pseudogene,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	30	9	23	11	101091760	-	11	71393958	-	0.2768	1.1969	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	transcribed_unitary_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-GD-A3OS-01A	ENSG00000082175	ENSG00000172900	PGR	FLJ42102	TAGAAAGTGCTGTCAGGCTGGCATGGTCCTTGGAG*GTGCTGTTTGAGATTTTCAACATACCTGCCCTGTA	pseudogene,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	30	2	21	11	101091760	-	11	71395350	-	0.2768	1.1969	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	transcribed_unitary_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-GD-A3OS-01A	ENSG00000082175	ENSG00000172900	PGR	FLJ42102	CCCAGCATGTCGCCTTAGAAAGTGCTGTCAGGCTGGCATGGTCCTTGGAG*CTAACCGAGGAGTCCTTTCTCTGTACGCCTCTGGCCAGACCTTCGGTGAG	pseudogene	BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	30	1	18	11	101091760	-	11	71395310	-	0.2768	1.1969	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	transcribed_unitary_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-GD-A3OS-01A	ENSG00000082175	ENSG00000172900	PGR	FLJ42102	CCCAGCATGTCGCCTTAGAAAGTGCTGTCAGGCTGGCATGGTCCTTGGAG*GGAAAAACACCCCTGGCATCCACACGAAGGCCATCCAGAGCATCACTTCC	pseudogene	BOWTIE+STAR	CDS(truncated)/intronic	0	30	1	15	11	101091760	-	11	71389515	-	0.2768	1.1969	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	transcribed_unitary_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-GD-A3OS-01A	ENSG00000152292	ENSG00000140396	SH2D6	NCOA2	GAGCAAAGGTTCCGGAACAGGGCAGGGCAGGACAG*GCCCTTGATGGGTTCTTCTTTGTAGTGAACCTGGA	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	27	10	24	2	85422690	+	8	70170379	-	0.0172	7.0956	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-GD-A3OS-01A	ENSG00000170962	ENSG00000137692	PDGFD	DCUN1D5	CAAAGCTTTGCGCAACGCCAACCTCAGGCGAGATG*GGCCTGTTCTTCTTGATGAATTTGTTGAGTGGCAA	tumor,exon-exon	BOWTIE	in-frame	0	19	7	24	11	104163804	-	11	103062414	-	6.8883	24.2031	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Bladder	TCGA-GD-A3OS-01A	ENSG00000144021	ENSG00000152292	CIAO1	SH2D6	CAACCTCCTGGCCACTTGCAGCCGAGATAAGAGCGTTTGGGTCTGGGAAG*GGGCAGAATCTGGGCAGCGGGGGAATGGATCAAGCTGAAAGACAGCTAAA	m6	BOWTIE+BLAT	CDS(truncated)/intronic	0	11	4	22	2	96267736	+	2	85421960	+	27.4167	0.0172	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-GD-A3OS-01A	ENSG00000120594	ENSG00000118640	PLXDC2	VAMP8	CACGGACCAGTTTCAGTTCGCCGATGGGAAACCCGGAGACCAAATCCTTG*GGACAACCCTCCATAAATGTGTGCCAAGAGGGTCTCCTTTCCTGTCTTCC	cancer	BOWTIE+STAR	CDS(truncated)/UTR	0	7	2	20	10	19817191	+	2	85581754	+	4.3939	91.661	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-GD-A3OS-01A	ENSG00000120594	ENSG00000118640	PLXDC2	VAMP8	GTTCGCCGATGGGAAACCCGGAGACCAAATCCTTG*GAGGAAGCCAGTGAAGGTGGAGGAAATGATCGTGT	cancer,exon-exon	BOWTIE	out-of-frame	0	7	2	18	10	19817191	+	2	85579009	+	4.3939	91.661	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Bladder	TCGA-BT-A20U-01A	ENSG00000115760	ENSG00000049323	BIRC6	LTBP1	AGGCTAACACCAATGGAGGCTTTACTTCAGACAAG*AGTGACTCCTCTTTCTTCCCAGAGTGTGGTGATTC	known,tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	10	2	16	2	32445668	+	2	33110582	+	4.6926	7.9389	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-CU-A0YR-01A	ENSG00000104517	ENSG00000253661	UBR5	ZFHX4-AS1	GAGACTCTAGGCAGGCTGGCAGGCAACACCTTAGG*GTGTGTTGCTGGCAATATGTGGCCCCAGGGGAGAG	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	7	5	22	8	102360071	-	8	76502846	-	19.0784	0.0959	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-CU-A0YR-01A	ENSG00000240849	ENSG00000277449	TMEM189	CEBPB-AS1	ATCTTCGGCACCTTCACCAACCAGATCCACAAGTGGTCGCACACGTACTT*TCGGCCCTGCCACACTGTGTGACCTTGGGTGAGTCACTTCACTTCTCCCA	antisense,10K<gap<100K	BOWTIE+BLAT	CDS(truncated)/exonic(no-known-CDS)	0	6	5	21	20	50128088	-	20	50190025	-	9.3178	0.2528	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-GV-A3JV-01A	ENSG00000144711	ENSG00000154764	IQSEC1	WNT7A	AGCGAGAAATCTTCCTGTTCAACGACCTCCTGGTG*TGGCTTCTCCTCAGTGGTAGCTCTGGGCGCAAGCA	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	602	19	24	3	12913428	-	3	13875173	-	104.5802	48.5595	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-GV-A3JV-01A	ENSG00000144711	ENSG00000154764	IQSEC1	WNT7A	AATGAAGCTAGAGGACTTCATCAAGAACCTCCGAG*TGGCTTCTCCTCAGTGGTAGCTCTGGGCGCAAGCA	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	602	16	24	3	12920430	-	3	13875173	-	104.5802	48.5595	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-GV-A3JV-01A	ENSG00000144711	ENSG00000154764	IQSEC1	WNT7A	GCTCAGAAAGTGGAGCGGCTCATAGAGGCGTTCAG*TGGCTTCTCCTCAGTGGTAGCTCTGGGCGCAAGCA	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	602	7	24	3	12922120	-	3	13875173	-	104.5802	48.5595	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-GV-A3JV-01A	ENSG00000144711	ENSG00000154764	IQSEC1	WNT7A	AATGAAGCTAGAGGACTTCATCAAGAACCTCCGAG*GGAGCCGGGAGGCTGCGTTCACCTACGCCATCATT	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	602	2	23	3	12920430	-	3	13854803	-	104.5802	48.5595	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-GV-A3JV-01A	ENSG00000132170	ENSG00000144711	PPARG	IQSEC1	GGCAATATTTATTGCTGTCATTATTCTCAGTGGAG*CGTCGAGGGCGAGGCCCCCAGCAGTGAGACTGGCA	oncogene,cancer,exon-exon	BOWTIE	out-of-frame	0	59	6	24	3	12417154	+	3	12941865	-	335.1018	104.5802	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-GV-A3JV-01A	ENSG00000126777	ENSG00000139946	KTN1	PELI2	AAATTGAGCAGCTTAAACAACAAAACTACCAACAG*GTACAATGGTGCTTTACCCAATGGAGATAGAGGAC	cancer,tcga-cancer,exon-exon	BOWTIE;BOWTIE+BLAT	out-of-frame	0	11	3	23	14	55658614	+	14	56178335	+	29.1316	2.3657	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-GV-A3JV-01A	ENSG00000267795	ENSG00000078328	SMIM22	RBFOX1	GCTCCCCCGGGCCCCGCAGGGAAAGCCCCAGGAAG*GATCTACTGTGCCTGCCATACAGCCTGGTTGAGGG	exon-exon	BOWTIE	in-frame	0	5	3	22	16	4796033	+	16	5467216	+	5.483	0.0781	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-GV-A3JV-01A	ENSG00000267795	ENSG00000078328	SMIM22	RBFOX1	GCAGGGAAAGCCCCAGGAAGGTGAGCCCCTGGAAG*GATCTACTGTGCCTGCCATACAGCCTGGTTGAGGG	exon-exon	BOWTIE	in-frame	0	5	2	23	16	4796048	+	16	5467216	+	5.483	0.0781	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-GV-A3JV-01A	ENSG00000267795	ENSG00000078328	SMIM22	RBFOX1	ACTGCTGCTGCTGCAGCTCCCCCGGGCCCCGCAGGGAAAGCCCCAGGAAG*GCGAGGAAGATGCCTCTGAGTGATGAAGATTCACATTCGAGGAAGGCACA	NA	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	5	1	19	16	4796033	+	16	5460755	+	5.483	0.0781	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-GV-A3JV-01A	ENSG00000267795	ENSG00000078328	SMIM22	RBFOX1	GCTCCCCCGGGCCCCGCAGGGAAAGCCCCAGGAAGGTGAGCCCCTGGAAG*GGCGCCACGAGAGGCCTCCTCTGTTTGTGCCCCATCATGTCTCCAGCATT	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	5	1	16	16	4796048	+	16	5464632	+	5.483	0.0781	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-FD-A3N6-01A	ENSG00000072415	ENSG00000171723	MPP5	GPHN	CGAAGATAATCAACCTCTAGCCGGGCTTGTTCCAG*TTATCATGTGATGTAAAACTTGATCCTCGTCCAGA	known,tcga,cell_lines,18cancers,chimerdb3seq,cancer,tcga-cancer,oesophagus,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	7	5	20	14	67312710	+	14	67179578	+	3.3978	6.584	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-CU-A3QU-01A	ENSG00000133056	ENSG00000143850	PIK3C2B	PLEKHA6	GCCCCAGTCTGCTGGTTAAGGGAATTGTGCCCAGG*GTGACTGTGTGCTGGGTGGATGAGGCCGAGGCCAG	known,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	9	2	18	1	204442526	-	1	204261508	-	14.1742	14.1103	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-CU-A3QU-01A	ENSG00000185947	ENSG00000186094	ZNF267	AGBL4	CTAAGACGCCAGGGCATCCCGGAAGCTGGGAAATG*CAACAACGAAAGCTTGACCTCCTGACGATAACCAG	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	7	2	15	16	31873969	+	1	48867230	-	4.1451	0.6263	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-CU-A3QU-01A	ENSG00000047056	ENSG00000065809	WDR37	FAM107B	AGCTGCCGACACCCCAGCCTGTTGCTGACACTAGT*GAAGAAGAATTTCGAGAAGAACCTAAATGCCTCGA	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	3	2	24	10	1096246	+	10	14667691	-	2.975	25.3401	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-CU-A0YO-01A	ENSG00000091009	ENSG00000189339	RBM27	SLC35E2B	TTGTGCTGATCAACTTGATGTCTTTTTACAAAAAG*CGTCGCCAGCACCGTGAAACATGCCTTGTCCATCT	tcga,chimerdb3seq,m20,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	22	8	24	5	146219103	+	1	1666019	-	3.9103	6.0959	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-CU-A0YO-01A	ENSG00000168118	ENSG00000125835	RAB4A	SNRPB	CAAGATGTCGCAGACGGCCATGTCCGAAACCTACG*ACGGTGGGCAAGAGCAGCAAGATGCTGCAGCATAT	tcga,chimerdb3seq,m14,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	15	5	21	1	229271370	+	20	2467758	-	13.0965	78.7731	FALSE	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-CU-A0YO-01A	ENSG00000125835	ENSG00000168118	SNRPB	RAB4A	CGGCGGGTATCAGAGCCATCAGAACCGCCACCATG*ATTTTTTGTTTAAGTTCTTGGTTATTGGAAATGCA	tcga,chimerdb3seq,m14,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	15	2	18	20	2470688	-	1	229286486	+	78.7731	13.0965	FALSE	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Bladder	TCGA-CU-A0YO-01A	ENSG00000112297	ENSG00000164494	CRYBG1	PDSS2	GTTCCTTACTTCTAGAGTCTGGAATATTTAAAAAG*GCTCAAGAAAAAGGAAGATTGGACTATGCTAAGTT	exon-exon	BOWTIE	in-frame	0	8	2	24	6	106451832	+	6	107193854	-	23.2824	6.8928	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-CU-A0YO-01A	ENSG00000164494	ENSG00000112297	PDSS2	CRYBG1	TTGGAAGAGATTTGTGGATTAAACAGATCGGAGAG*TCCAGAGCACAACCTCCAGAAGACAACAGAAGGAA	exon-exon	BOWTIE	in-frame	0	8	2	18	6	107210439	-	6	106511430	+	6.8928	23.2824	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-CU-A0YO-01A	ENSG00000134453	ENSG00000197746	RBM17	PSAP	CGCGGCTCATGGGCAGAGTCGGCCGGGCGGGCCGG*CTCTAGCCGGCCCGGTCCTTGGACTGAAAGAATGC	cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	2	8	24	10	6089193	+	10	71834505	-	6.4952	273.4775	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BT-A3PJ-01A	ENSG00000089902	ENSG00000196663	RCOR1	TECPR2	AACTAGACATGGAATTGGTTTCAGTCAAACGACAG*CCCGCCGGGGTCAGCTTGGTCAGCGTCCATTCCAG	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	in-frame	0	20	5	24	14	102714617	+	14	102496979	+	7.6563	5.0672	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BT-A3PJ-01A	ENSG00000066933	ENSG00000140488	MYO9A	CELF6	AGGGGGCTGCGGTGGCCACCGCGGCGGAGCCCGAG*ATGAATCGTCCGATCCAAGTGAAGCCAGCTGCCAG	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	UTR/CDS(complete)	0	14	2	24	15	72117680	-	15	72304794	-	1.6731	0	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BT-A3PJ-01A	ENSG00000066933	ENSG00000260729	MYO9A	AC009690.1	AGGGGGCTGCGGTGGCCACCGCGGCGGAGCCCGAG*AGGACCGAAAGCTGTTTGTGGGGATGCTGGGCAAG	100K<gap<200K,exon-exon	BOWTIE	UTR/UTR	0	10	4	24	15	72117680	-	15	72290255	-	1.6731	0	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-BT-A3PJ-01A	ENSG00000100345	ENSG00000146648	MYH9	EGFR	CAGGCCATGTCGGCCAGGAGGGGGTGAGCCCTCTAGGGTGGCTGGGCCCA*GGCTGCAGTGACATCACCTGAGGAGCTTTTAAAAGCTTGAAGCCCAGCTA	oncogene,cancer,tumor,m6	BOWTIE+BLAT	UTR/UTR	0	7	1	20	22	36319801	-	7	55210383	+	558.0929	431.4223	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-BT-A3PJ-01A	ENSG00000131236	ENSG00000084072	CAP1	PPIE	CCGCTCATCACTGTTCGCGCAGATTAATCAGGGGGAGAGCATTACACATG*GTGGACCTGTGCCACAGAGGAATTAAGTAACCTTCCCATGGTCACATAGC	18cancers	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	4	9	24	1	40067717	+	1	39717633	+	172.6459	10.5573	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-BT-A3PJ-01A	ENSG00000146648	ENSG00000189403	EGFR	HMGB1	TCGTTCTGCTGACAACATGACATGTTTCTATAACTTGAAAAAAGCAAGCA*GAAGATGAGGAAGATGAAGAGGATGAGGAGGAGGAGGAAGATGAAGAAGA	oncogene,cancer,tumor	BOWTIE+STAR	intronic/CDS(truncated)	0	3	1	14	7	55131395	+	13	30461440	-	431.4223	49.4831	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-FD-A3SM-01A	ENSG00000156675	ENSG00000020181	RAB11FIP1	ADGRA2	TGACAATGAGGATGAGTCCTCCTCGGCCTCGGATG*GGACCTGAGGAACAACATCATCAGCACAGTGCAGC	m13,exon-exon	BOWTIE	out-of-frame	0	14	3	22	8	37877109	-	8	37828888	+	53.1103	7.7784	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-DK-A2I2-01A	ENSG00000278540	ENSG00000276234	ACACA	TADA2A	TGGTGGTCTACTCTGATGTCAATCTTGAGGGCTAG*ATGATCCCTCTGATAAGCCACCTTGCCGAGGCTGC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	5	5	19	17	37406262	-	17	37423509	+	12.8187	7.6876	FALSE	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	FALSE	Bladder	TCGA-DK-A2I2-01A	ENSG00000242741	ENSG00000143156	LINC02005	NME7	GATATGAACTCATCAGCAGAAATGTGAGTTCTTCCCAGCTTCTCCGTGCT*GTTCAATACTTCTTCAAGATCTTGGATAATTAGTGGTGTGGAAAGTAAAG	lincrna	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	3	2	21	3	73810110	+	1	169132817	-	0.0681	3.6468	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-FD-A3B3-01A	ENSG00000157168	ENSG00000253452	NRG1	AC100818.1	ATCAGTATCCACAGAAGGAGCAAATACTTCTTCAT*ATGCTCAGAGGCCCCATGCCTGATGAGTCAGTGGA	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	11	1	13	8	32616885	+	8	35944244	+	1.2861	1.3106	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-FD-A3B3-01A	ENSG00000057608	ENSG00000167625	GDI2	ZNF526	AGTACGACGTGATCGTGCTGGGCACCGGCCTGACG*GCTGCCGTGGGGTGTGTGTAGGCTTCAGAGACATG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	4	3	20	10	5813214	-	19	42224215	+	128.4565	3.4357	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-FD-A3B3-01A	ENSG00000005175	ENSG00000079387	RPAP3	SENP1	GACCAGAATCTACTGGCATCTTCATCTTGGACTCCCCATCCTCCAGAACT*ATCATCAATTTCTACATGAATATGCTGATGGAGCGAAGTAAAGAGAAGGG	NA	BOWTIE+STAR	UTR/CDS(truncated)	0	3	1	19	12	47661969	-	12	48049132	-	44.6962	9.0134	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-CF-A3MH-01A	ENSG00000164258	ENSG00000262352	NDUFS4	LINC02564	GTAGCTGCCCTTTCCGTTTCCAGGGTTCCGACCAG*ATGAGGCCTCACTCTGTCACCCAGGTTGGGGTGGA	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	5	3	19	5	53560760	+	18	15617	+	14.6193	0.0377	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-FD-A3SO-01A	ENSG00000105329	ENSG00000089327	TGFB1	FXYD5	CCTACATTTGGAGCCTGGACACGCAGTACAGCAAG*CTCATCCCACTGATGACACCACGACGCTCTCTGAG	oncogene,tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	32	10	24	19	41332128	-	19	35164156	+	19.1546	37.8669	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-FD-A3SO-01A	ENSG00000130204	ENSG00000165966	TOMM40	PDZRN4	CACCCTGGGGAACCCAGACGTCCTCGTGGGTTCAG*GTCAATGGGAAGGATCTTTCAAAGGCCACTCATGA	tcga,chimerdb3seq,m10,tcga-cancer,exon-exon	BOWTIE	in-frame	0	18	4	20	19	44894066	+	12	41506456	+	18.8535	0.2922	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-FD-A3SO-01A	ENSG00000130204	ENSG00000165966	TOMM40	PDZRN4	CTTCACAGCAGCCGTCACCCTGGGGAACCCAGACGTCCTCGTGGGTTCAG*AATCTTGCTTTGTCACCCAGGAGTGCAATGGCATGATCTCAGCTCACTGC	tcga,chimerdb3seq,m10,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	18	1	21	19	44894066	+	12	41421228	+	18.8535	0.2922	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-C4-A0F7-01A	ENSG00000088876	ENSG00000101266	ZNF343	CSNK2A1	GTGATGCTGGAGAATTACAGGAATCTTCTCTCATTGG*AGCCCCAGTTTGAGGGACAGCGGGATATCCACCATGC	oncogene,18cancers,cancer,m69,exon-exon	BOWTIE	in-frame	0	70	14	25	20	2492699	-	20	473950	-	5.5669	9.0939	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-C4-A0F7-01A	ENSG00000088876	ENSG00000101266	ZNF343	CSNK2A1	CCTCATCATACACGAGCGGACGCACTCTGGAGAGAAGCCTTATGTGTGTG*AGCCCCAGTTTGAGGGACAGCGGGATATCCACCATGCTGCTGTGAGACTC	oncogene,18cancers,cancer,m69	BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	70	4	25	20	2483559	-	20	473950	-	5.5669	9.0939	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-C4-A0F7-01A	ENSG00000256566	ENSG00000101266	AL049650.1	CSNK2A1	TCTATACAAAGAAGTGATGCTGGAGAATTACAGGAATCTTCTCTCATTGG*GGAGTCATTCCTCCCTTCCTCTTTGTTGACAGAGCCCCAGTTTGAGGGAC	oncogene,cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	55	2	25	20	2492699	-	20	473982	-	0	9.0939	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-C4-A0F7-01A	ENSG00000100280	ENSG00000100077	AP1B1	GRK3	TGGCCCTGCGCAACATCAATCTCATCGTGCAGAAAAG*TGGCACCCATGGGTACATGGCTCCCGAGGTGCTGCAG	known,oncogene,tcga,18cancers,tcga-cancer,exon-exon	BOWTIE	in-frame	0	55	7	24	22	29354650	-	22	25695107	+	12.4864	2.7188	TRUE	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-C4-A0F7-01A	ENSG00000100077	ENSG00000100280	GRK3	AP1B1	CCTGCGATTTTTCCAAAAAGAAGCCTCATGCGAGTGT*GCCTGAGATCCTGAAGCATGAGATGAAGGTGTTCTTC	known,oncogene,tcga,18cancers,tcga-cancer,exon-exon	BOWTIE	in-frame	0	55	9	24	22	25690283	+	22	29351825	-	2.7188	12.4864	FALSE	TRUE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-C4-A0F7-01A	ENSG00000152104	ENSG00000117697	PTPN14	NSL1	TGCCAAATGTGTCATGGCTTCAGCAAGAGGCCACAAG*CCCCTCATATGGAAAATTTGAAATGCAGAGGGGAAAC	18cancers,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	55	12	25	1	214451805	-	1	212739601	-	1.9469	2.0984	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-C4-A0F7-01A	ENSG00000181827	ENSG00000166035	RFX7	LIPC	CTGCAAAACTGTACAATCTAAAGTGGACTGCATTTTG*AGCCATTTGGAAGAAGAGCTCAAGCTGTTGAAACAAA	18cancers,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	39	8	23	15	56179270	-	15	58538333	+	2.8951	5.5413	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-C4-A0F7-01A	ENSG00000181827	ENSG00000166035	RFX7	LIPC	TTTCTCTTTCTTTTAGCAAAACTGTACAATCTAAAGTGGACTGCATTTTG*AGCTGGTCAAGCAAGAAGAGCACTGGACTACGCATCAAGACCTGGGGTGC	18cancers,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	UTR/intronic	0	39	4	24	15	56179270	-	15	58495122	+	2.8951	5.5413	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-C4-A0F7-01A	ENSG00000181827	ENSG00000166035	RFX7	LIPC	CCAGCGCGCTGCAACACAAGATCAAGAACTCCATCTG*AGCCATTTGGAAGAAGAGCTCAAGCTGTTGAAACAAA	18cancers,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	39	3	23	15	56243125	-	15	58538333	+	2.8951	5.5413	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-C4-A0F7-01A	ENSG00000181827	ENSG00000166035	RFX7	LIPC	CTGCAAAACTGTACAATCTAAAGTGGACTGCATTTTG*GTGGACGGCGTGCTAGAAAACTGGATCTGGCAGATGG	18cancers,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	39	2	21	15	56179270	-	15	58541785	+	2.8951	5.5413	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-C4-A0F7-01A	ENSG00000181827	ENSG00000166035	RFX7	LIPC	TTTCTCTTTCTTTTAGCAAAACTGTACAATCTAAAGTGGACTGCATTTTG*TATCATCCCCAGATTCTTATCACTGGTGTGACTACCTCTTCTGAAGACAT	18cancers,tcga-cancer	BOWTIE+STAR	UTR/intronic	0	39	1	17	15	56179270	-	15	58533115	+	2.8951	5.5413	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-C4-A0F7-01A	ENSG00000140262	ENSG00000124151	TCF12	NCOA3	CCAACTACACTGGGAAGCAGTCAATTCAGTGGATCAG*GATCAAAATACTTGCTGGATGGTGGACTCAGAGACCA	oncogene,18cancers,cancer,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	23	9	25	15	56921098	+	20	47583183	+	6.3216	8.8068	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-C4-A0F7-01A	ENSG00000140262	ENSG00000124151	TCF12	NCOA3	CCAACTACACTGGGAAGCAGTCAATTCAGTGGATCAG*TTGCTGATGTATATTCAAGATGAGTGGATTAGGAGAA	oncogene,18cancers,cancer,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	23	2	24	15	56921098	+	20	47622229	+	6.3216	8.8068	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-C4-A0F7-01A	ENSG00000183032	ENSG00000151338	SLC25A21	MIPOL1	GAGGTGGAAGGATCGCTTGAAGCCAGGACAGGAGCAGCCTGGACAACAAG*ATACCAGCATTGCCACCGGTGGGTAGAACACTAAGTGGGCTCTTGGAGTC	tcga,cell_lines,chimerdb3seq,tcga-cancer	BOWTIE+BLAT	intronic/UTR	0	14	1	23	14	37073415	-	14	37212230	+	1.0366	3.3883	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-C4-A0F7-01A	ENSG00000150281	ENSG00000099385	CTF1	BCL7C	TCTTAACTCTTGGACCCTCCTCGTCTGCATGGTAACTCCGTCTGAGTCTA*TGTAGCCGGGCATGTCAATCCCGTTGCTGTGTCTATGTGCATGGTAGTGA	tcga,chimerdb3seq,tcga-cancer	BOWTIE+STAR	UTR/UTR	0	4	1	14	16	30903050	+	16	30894932	-	2.2166	8.0157	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-C4-A0F7-01A	ENSG00000003147	ENSG00000019991	ICA1	HGF	GGAGACGCCCGGCAGCCGGGACGGTCGGGGACGCCTG*TTGAATGCATGACCTGCAATGGGGAGAGTTATCGAGG	cancer,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	4	1	14	7	8262000	-	7	81745120	-	5.7399	1.6473	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-CF-A3MG-01A	ENSG00000162105	ENSG00000184154	SHANK2	LRTOMT	GGAGGTCCAGTGTAAGCCCAGGGACAGCCAGGCAG*ATCTGGTAAATGAGGAGCCAAGGACAGGACTACGA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	16	7	24	11	70798443	-	11	72093496	+	1.8399	4.2592	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-G2-A3IB-01A	ENSG00000111726	ENSG00000234741	CMAS	GAS5	AATGGGCCTGTGCTGGAAAGAAGTGGCATATCTTG*GGTTTTTAATGACCACAACAAGCAAGCATGCAGCT	cancer,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	24	12	23	12	22062434	+	1	173864304	-	51.0663	17.5962	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-G2-A3IB-01A	ENSG00000168439	ENSG00000117697	STIP1	NSL1	AACGGGGTTCCGGACCGCGCTGCGCTATGGAGCAG*ATTCTGACATCAAAGTACTTGAAGATCAGTTTGAT	cell_lines,exon-exon	BOWTIE	out-of-frame	0	6	2	21	11	64186270	+	1	212784493	-	103.0121	1.8509	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Bladder	TCGA-BT-A20P-01A	ENSG00000113742	ENSG00000170091	CPEB4	HGNC:24955	GCTTGAACAGGGCTGACAACATTTTTCCTTTTCCG*ATGAGGACACTGAGGCACAGGAAGTCAAGAAACCT	10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	17	1	14	5	173890858	+	5	174242682	+	2.5838	1.6889	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-FD-A3SJ-01A	ENSG00000067560	ENSG00000007402	RHOA	CACNA2D2	GCGCGAAGAGGCTGGACTCGGATTCGTTGCCTGAG*AGACTGGCTGATGCTGCAGAGAACTTCCAGAAAGC	oncogene,tcga,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	32	6	24	3	49411820	-	3	50394168	-	69.8402	6.057	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-FD-A3SJ-01A	ENSG00000112294	ENSG00000254389	ALDH5A1	RHPN1-AS1	ATCCTCTGGTGTCCAAAATTTCCTTTACTGGTTCAACAACTACAGGAAAG*AGCTTGTTTCCTGGACTGACCTATTTTCAGAACCTACTTTCAAAACCAGC	antisense	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	24	4	23	6	24515310	+	8	143368072	-	11.2979	4.7398	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-FD-A3SJ-01A	ENSG00000112294	ENSG00000254389	ALDH5A1	RHPN1-AS1	ATCCTCTGGTGTCCAAAATTTCCTTTACTGGTTCAACAACTACAGGAAAG*GCTTCTTGGTTCAGCAGACAGAGGCCATTGGGAAGTTAAGAGAGGCTCTC	antisense	BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	24	1	18	6	24515310	+	8	143366764	-	11.2979	4.7398	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-FD-A3SJ-01A	ENSG00000058799	ENSG00000137547	YIPF1	MRPL15	AGTTACTGGGAAATGATGACTCTGACAAAACTGAG*ACATTGTATGCAAACCTGTTCCATTCTTTCTTCGT	ribosomal,tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	22	6	21	1	53883113	-	8	54147382	+	41.0952	52.1912	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-FD-A3SJ-01A	ENSG00000058799	ENSG00000137547	YIPF1	MRPL15	GGTGGGGGAAACAGGCAAACAGACCATTACTTTCC*ACATTGTATGCAAACCTGTTCCATTCTTTCTTCGT	ribosomal,tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	22	2	19	1	53882943	-	8	54147382	+	41.0952	52.1912	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-FD-A3SJ-01A	ENSG00000047315	ENSG00000240423	POLR2B	LINC00636	CCCGACCCACCAGTACTATATGGGTTAGCATGCTGGCAAGAGGAGGACAG*GCAGCCACCAGCCTTCCAGGAAGCTAAGCAGTATTGAAAGGAAGTTGAAG	lincrna	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	16	9	24	4	56995409	+	3	107908203	+	13.5617	3.1281	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-FD-A3SJ-01A	ENSG00000047315	ENSG00000240423	POLR2B	LINC00636	CCCGACCCACCAGTACTATATGGGTTAGCATGCTGGCAAGAGGAGGACAG*ACTAATTTGGTGCCCTTGAGAGCCTGCTGCCACACTGTGTCAAGGAGGAA	lincrna	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	16	8	23	4	56995409	+	3	107906642	+	13.5617	3.1281	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-FD-A3SJ-01A	ENSG00000047315	ENSG00000240423	POLR2B	LINC00636	CTATATGGGTTAGCATGCTGGCAAGAGGAGGACAG*GCTCCCACAGGCAAGAGCACATCCTACTGGACCTG	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	16	3	20	4	56995409	+	3	107923631	+	13.5617	3.1281	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-FD-A3SJ-01A	ENSG00000257261	ENSG00000227869	AC008014.1	AC073486.1	ATCAAACCAAACCAAGCAAACCACGGGGAATGGAG*ATGTAAAGCCTCTGTTAATACTTTTCCTGTTAACA	lincrna,m13,exon-exon	BOWTIE	exonic(no-known-CDS)/exonic(no-known-CDS)	0	14	2	22	12	46387972	+	7	125461481	+	0.5225	NA	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-FD-A3SJ-01A	ENSG00000257261	ENSG00000227869	AC008014.1	AC073486.1	ATCAAACCAAACCAAGCAAACCACGGGGAATGGAG*GGCCTTTCTCTGTTGCCCAGGCTGGAGTGCAGTGA	lincrna,m13,exon-exon	BOWTIE	exonic(no-known-CDS)/exonic(no-known-CDS)	0	14	2	20	12	46387972	+	7	125466270	+	0.5225	NA	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-FD-A3SJ-01A	ENSG00000182795	ENSG00000183814	C1ORF116	LIN9	TTTCTTTTCTCTCTTCAGCCCCCAACCCAGTGGAG*ACCAGATTATCAAAAATTCTCATGATTAAAAAGGA	tcga,chimerdb3seq,tumor,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	13	2	18	1	207032579	-	1	226250919	-	25.3526	4.249	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-FD-A3SJ-01A	ENSG00000196428	ENSG00000114279	TSC22D2	FGF12	AGCATAGCTATTCCTGTTGATGGTGATGAAGACAG*GATGTTTTCACTCCAGAATGCAAATTCAAGGAATC	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	13	2	21	3	150411308	+	3	192170656	-	4.339	1.4652	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-FD-A3SJ-01A	ENSG00000109670	ENSG00000283408	FBXW7	MIR548A1HG	CCACTTTCTCGGCGCCGCGGCTCTTTTCTAAAAGT*ACAGAAGAAGGAGATGCCAGTGACAAGCAAAGTAA	lincrna,cancer,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	6	5	21	4	152534941	-	6	18535848	+	1.5656	0.4685	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-FD-A3SJ-01A	ENSG00000153093	ENSG00000156687	ACOXL	UNC5D	TGACTCCCATGGCCAGCACGAGGATCAGGAATCAG*GAACTGACAATGGCGAAGCCCTTCCCGAATCCATC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	5	2	22	2	111092966	+	8	35549292	+	3.6057	0.4433	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-FD-A3SJ-01A	ENSG00000153093	ENSG00000156687	ACOXL	UNC5D	TAGAACATAAATACTTGACTCCCATGGCCAGCACGAGGATCAGGAATCAG*CTCTTCAGGTGATCTGGAGGTGACGCAGATTCAGCTACACACTCATCTCT	tcga,chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	5	1	15	2	111092966	+	8	35424653	+	3.6057	0.4433	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-FD-A3SJ-01A	ENSG00000101868	ENSG00000165182	POLA1	CXORF58	TGCACTGGAGAAACTTACTACCGATCATGAGAAAG*ATTACTTCATTGGAGGGAAAATGAATCGTTCCTCA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	5	2	17	X	24930549	+	X	23910283	+	1.5093	1.1013	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-FD-A3SJ-01A	ENSG00000183722	ENSG00000215483	LHFPL6	LINC00598	CGCGGGAGGGAAGGTGGCCGCCGCCCGCCAGCCAT*AATACCATCGGAGCTCCTCTGGAACATGTCCTTGT	lincrna,cancer,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	3	2	19	13	39602883	-	13	40350302	-	7.8884	0.2578	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-K4-A3WV-01A	ENSG00000253363	ENSG00000104755	AC090809.1	ADAM2	GTTGATGGTGTGGCACTACTGCCTGTTCTTCAAAG*AAACTTTTTACCCCATAATTTTAGAGTTTACAGTT	lincrna,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	42	8	24	8	36701821	-	8	39824897	-	62.9229	44.4328	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-K4-A3WV-01A	ENSG00000253363	ENSG00000104755	AC090809.1	ADAM2	AACCCTATGATGGCAAGCAGTCATAAGGATGAATG*TCATTTCAGTGGTGTGAAGATCTTTAGTAACTGCA	lincrna,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	42	2	24	8	36774146	-	8	39769575	-	62.9229	44.4328	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-K4-A3WV-01A	ENSG00000253363	ENSG00000104755	AC090809.1	ADAM2	GGTCATGGAAGCACTGTTGATGGTGTGGCACTACTGCCTGTTCTTCAAAG*GAGTTGTTCCCTTTCCAAAGGCCCTTTATTAGAACCTGCTTATAGTGGAG	lincrna	BOWTIE+BLAT	exonic(no-known-CDS)/intronic	0	42	1	21	8	36701821	-	8	39790841	-	62.9229	44.4328	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-K4-A3WV-01A	ENSG00000079691	ENSG00000172543	CARMIL1	CTSW	AAAGGAATAAGAAGCAGCAACCCACCCAAGCAGCG*AGCATGCTCACCGCCTGGACATCTTTGCCCACAAC	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	19	4	21	6	25581439	+	11	65881407	+	28.0529	6.2191	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-K4-A3WV-01A	ENSG00000079691	ENSG00000172543	CARMIL1	CTSW	CCAAGTTAAGGCCAAAAAGGAATAAGAAGCAGCAACCCACCCAAGCAGCG*GGGGCTGATCTGTGTGTGCCTTTTAGCCCAGACTGCCTGTGCCTTGTCAT	tcga,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	19	1	22	6	25581439	+	11	65880997	+	28.0529	6.2191	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-K4-A3WV-01A	ENSG00000172543	ENSG00000079691	CTSW	CARMIL1	GGACATCTTTGCCCACAACCTGGCCCAGGCTCAGAGGCTGCAGGAGGAGG*AGAAGCTGGAACACTTTACCAAGTTAAGGCCAAAAAGGAATAAGAAGCAG	tcga,chimerdb3seq,tcga-cancer	BOWTIE+BLAT	in-frame	0	19	1	23	11	65881472	+	6	25581372	+	6.2191	28.0529	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-K4-A3WV-01A	ENSG00000172543	ENSG00000079691	CTSW	CARMIL1	TGCCCACAACCTGGCCCAGGCTCAGAGGCTGCAGGAGGAGGACTTGGGCA*GAGCTCGGGATTTATCTCTGAGTTGCCCTCTGAAGAGGGGAAGAAGCTGG	tcga,chimerdb3seq,tcga-cancer	BOWTIE+BLAT	out-of-frame	0	19	1	20	11	65881481	+	6	25581331	+	6.2191	28.0529	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-K4-A3WV-01A	ENSG00000054690	ENSG00000171723	PLEKHH1	GPHN	GGAGCAGGTGGGATCCCTTCAAGATGCGCTAGAAG*GTCACAGTGCTGTCGATATCACCAAGGTGGCTAGA	tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	in-frame	0	10	7	22	14	67562035	+	14	67058649	+	5.3343	5.3874	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-K4-A3WV-01A	ENSG00000155324	ENSG00000247828	GRAMD2B	TMEM161B-AS1	AAGAGCTTACAGCTAACATAGTGAAATTAGAAAAG*GAGTGGGTGGACATTTGGCATCCAGGATGTGGTTC	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	7	4	23	5	126488892	+	5	88417187	+	14.5423	0.0429	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-K4-A3WV-01A	ENSG00000065526	ENSG00000162458	SPEN	FBLIM1	TCAATCAGCAGCAGCAGTAGTACCAGCAGTGACAG*AGCTGGCCTGAACCTCCAGGACTTCAGCCCTTCTA	tcga,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	6	3	23	1	15876678	+	1	15764496	+	4.1505	18.7334	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-K4-A3WV-01A	ENSG00000065526	ENSG00000162458	SPEN	FBLIM1	TCAATCAGCAGCAGCAGTAGTACCAGCAGTGACAG*CAGAGCTGGCCTGAACCTCCAGGACTTCAGCCCTT	tcga,chimerdb3seq,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/UTR	0	6	2	18	1	15876678	+	1	15764493	+	4.1505	18.7334	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-K4-A3WV-01A	ENSG00000215262	ENSG00000253363	KCNU1	AC090809.1	CAGGCTTGTGTACCTTCCTAACATCTCTATTTGTGGAGCAAAACAAAAAG*GACCTGAAGTCAGCAGGGCTGGGAGTCAGGAAAGTGATGGATGGCAAGTA	lincrna	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	4	3	23	8	36836945	+	8	36635389	-	8.5697	62.9229	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-K4-A3WV-01A	ENSG00000215262	ENSG00000253363	KCNU1	AC090809.1	CAGGCTTGTGTACCTTCCTAACATCTCTATTTGTGGAGCAAAACAAAAAG*GTCCCAACTTCTTTATTGTGAGTGACCTGCTACAGAAGAGACTGCTGTCC	lincrna	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	4	2	22	8	36836945	+	8	36635284	-	8.5697	62.9229	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-BT-A2LD-01A	ENSG00000164944	ENSG00000165078	VIRMA	CPA6	TATTTTTAGATACTTTTAAACACCCGAGCGCTGAG*TGATAAAGTGATAAGATTTATTCCCAAAACAGAAG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	9	2	19	8	94553385	-	8	67624251	-	5.6905	3.7846	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-BT-A2LD-01A	ENSG00000105176	ENSG00000198597	URI1	ZNF536	GTGGTCACTAACTGCCAAGAGAGAATCCAGCATTG*GTGAGAAACCCTACAAGTGTCCGCACTGTGACTAT	oncogene,exon-exon	BOWTIE	out-of-frame	0	5	2	23	19	29971227	+	19	30547943	+	175.3237	3.1905	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-BT-A2LD-01A	ENSG00000131051	ENSG00000138738	RBM39	PRDM5	ACACGAGCACCACAGGCGCCCGAAGGCCGGAACAG*GAAGGAGAAAACATTTTCTATTTGGCAGTTGAAGA	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	4	3	23	20	35741941	-	4	120821345	-	15.9764	1.2211	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-BT-A2LD-01A	ENSG00000083307	ENSG00000189042	GRHL2	ZNF567	CTGGCTGCGTCCTATTGGAAGTGCGCGGGGCCGCCCTTTTGCTTTCCCCG*GGATCAGTGTCTTTCAATGATGTGACTGTGGACTTCACTCAGGAGGAGTG	NA	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	15	8	101494079	+	19	36712386	+	46.5911	3.2512	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-G2-A2EL-01A	ENSG00000204120	ENSG00000185038	GIGYF2	MROH2A	GCGGAAACGCAGACACTGAACTTTGGGCCTGAATG*GACATCTGTCTCAAAATGGCCTTCATGAAGAGTGT	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	15	7	23	2	232735238	+	2	233810794	+	0.1048	2.7813	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-BT-A20N-01A	ENSG00000110075	ENSG00000137693	PPP6R3	YAP1	ATATTGCTGACTTTACTTGAGACACGACGACCAAC*TGGCACCTATCACTCTCGAGATGAGAGTACAGACA	oncogene,tcga,cell_lines,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	44	5	19	11	68558679	+	11	102227469	+	8.7771	16.7487	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-BT-A20N-01A	ENSG00000198740	ENSG00000169288	ZNF652	MRPL1	GCAGTACTTCGACGAACACATGAAAACACACACTG*ATTTTAAACTGCCTATGGGTAGTTGCTTTCACTTA	ribosomal,exon-exon	BOWTIE	CDS(truncated)/UTR	0	15	3	23	17	49311312	-	4	77906946	+	2.7628	15.3311	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Bladder	TCGA-BT-A20N-01A	ENSG00000115008	ENSG00000255512	IL1A	AP005135.1	CACGGCTGCTGCATTACATAATCTGGATGAAGCAG*GTCCACAGAAGTGGTTTCTGCCAATCTTTGAAGAG	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	9	3	19	2	112779496	-	11	135061947	-	23.9762	1.1629	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-BT-A20N-01A	ENSG00000115008	ENSG00000255512	IL1A	AP005135.1	CAATGATCAGTACCTCACGGCTGCTGCATTACATAATCTGGATGAAGCAG*AGCTCCAGGGCATAAGGAACCCATAGACTTCTCCTTGCCTCCTCAGTGGG	lincrna	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	9	1	24	2	112779496	-	11	135066325	-	23.9762	1.1629	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-BT-A20N-01A	ENSG00000115008	ENSG00000255512	IL1A	AP005135.1	CAATGATCAGTACCTCACGGCTGCTGCATTACATAATCTGGATGAAGCAG*TCTACGATCGATTGTAAATTGAGATAAACATGCAAACAAACAACTGAACA	lincrna	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	9	1	23	2	112779496	-	11	135066990	-	23.9762	1.1629	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-CF-A1HR-01A	ENSG00000164715	ENSG00000235419	LMTK2	AC010149.1	TTTTCGATGATGTCACAGTCTACCTGTTTGACCAG*GCTAAATTTTCGTCAACATTCCGGTGTAGTTGGCA	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	10	4	24	7	98194572	+	2	230520673	-	8.711	0.7747	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-BT-A20V-01A	ENSG00000103043	ENSG00000186153	VAC14	WWOX	AAGCTCCTGGAGGTCAGAGGCCCTTTCATCATCAG*CAACAGGGAGCTGCCACCACCGTGTACTGTGCTGC	tcga,cell_lines,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	32	15	24	16	70731495	-	16	79211608	+	9.2496	9.9088	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BT-A20V-01A	ENSG00000103043	ENSG00000186153	VAC14	WWOX	AGCTAAGGAACCAGCTGAAGGACCTGAAGACCCTG*CAACAGGGAGCTGCCACCACCGTGTACTGTGCTGC	tcga,cell_lines,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	32	6	21	16	70698637	-	16	79211608	+	9.2496	9.9088	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BT-A20V-01A	ENSG00000103043	ENSG00000186153	VAC14	WWOX	AGGTTGCCCCTTCATACTGGTTGCTGATGCTTCTGACATGAAACAGACAG*CAACAGGGAGCTGCCACCACCGTGTACTGTGCTGCTGTCCCAGAACTGGA	tcga,cell_lines,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+STAR	UTR/CDS(truncated)	0	32	1	21	16	70731301	-	16	79211608	+	9.2496	9.9088	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BT-A20V-01A	ENSG00000103043	ENSG00000186153	VAC14	WWOX	CCACAGAGCTCTTCCAGCTAAGGAACCAGCTGAAGGACCTGAAGACCCTG*TCTGCAGGCCCCGCCTGGCCCACCCAGTCCTTCTTAGAAGATGATGACCT	tcga,cell_lines,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	32	1	17	16	70698637	-	16	79016759	+	9.2496	9.9088	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BT-A20V-01A	ENSG00000130939	ENSG00000198597	UBE4B	ZNF536	AGCGTGGCTTCCTTTGGTGCCAGCTCTTTGTCTAG*GTCACAGGCCTTTCCAGTGCCGCTACTGTCCCTAC	18cancers,exon-exon	BOWTIE	out-of-frame	0	15	7	24	1	10105744	+	19	30710757	+	10.3833	2.1996000000000002	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BT-A20V-01A	ENSG00000110047	ENSG00000149124	EHD1	GLYAT	GATCCTGTCTGGAGAGAAGCAGCGGATCAGCAGAG*GAAGTCACACTTCTTTTCTAAGGTCACATGAGGAC	exon-exon	BOWTIE	CDS(truncated)/UTR	0	4	2	18	11	64874421	-	11	58640676	-	5.8383	0.1142	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-CU-A3KJ-01A	ENSG00000198265	ENSG00000154240	HELZ	CEP112	GCCACAAAATCAGCATCAGGAGAAGGATCAACATGAGCAAAATCGAAATG*ATGAAGACTGGCCAGACCGAGAGAGAAGAGGTGGCTTTGGTGTTCTTCAG	tcga,chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	14	1	23	17	67120405	-	17	65713979	-	2.7162	1.6237	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-CU-A3KJ-01A	ENSG00000198265	ENSG00000154240	HELZ	CEP112	GCCACAAAATCAGCATCAGGAGAAGGATCAACATGAGCAAAATCGAAATG*AACAATCCCGACTGAGCACCTGACCCTGGCTTCTCTTCAGGTTCCAGACT	tcga,chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	14	1	16	17	67120405	-	17	65715296	-	2.7162	1.6237	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-CU-A3KJ-01A	ENSG00000068383	ENSG00000171811	INPP5A	CFAP46	AGACTGTATGAACTGGACATCTCGTTCCCTCCCAG*ACGAGGCTTCTCAGACCTTGAAGGACAAGCTGCTG	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	13	9	23	10	132765846	+	10	132808904	-	3.9682	0.1258	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BL-A13J-01A	ENSG00000187676	ENSG00000175664	B3GLCT	TEX26	GCAGGCTGGGCCTTAAGTATTCCACTTGTAAACAA*ATAGACAAATTATTGATCGCTTTATTCGTACTCAC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	19	9	21	13	31261082	+	13	30974846	+	5.5959	0.6975	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BL-A13J-01A	ENSG00000121390	ENSG00000196199	PSPC1	MPHOSPH8	CAAGAGTTGCAAAAACGGAAGCAAATACAACTAAG*ATGGCAGGCAGCAGATTCTGAGTTTGGGCATGGAC	tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	9	2	24	13	19741565	-	13	19658995	+	9.5492	13.2006	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Bladder	TCGA-BL-A13J-01A	ENSG00000157483	ENSG00000137845	MYO1E	ADAM10	TCTCCAGAGTGTCTGGAGGAGGGACCAAAGTCCAG*ACATTTCAACCTACGAATGAAGAGGGACACTTCCC	exon-exon	BOWTIE	out-of-frame	0	6	2	22	15	59236585	-	15	58682314	-	11.695	85.5881	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-BL-A13J-01A	ENSG00000157483	ENSG00000137845	MYO1E	ADAM10	ATCATTGACAGAGAGAACCAGTGCGTCATTATCAG*ACATTTCAACCTACGAATGAAGAGGGACACTTCCC	exon-exon	BOWTIE	in-frame	0	6	2	19	15	59256284	-	15	58682314	-	11.695	85.5881	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-BL-A13J-01A	ENSG00000135040	ENSG00000259692	NAA35	AC104041.1	TTCTAGGCATGCTAAAAGATGTGGAGGATGACATGCAAAGAAGAGTAAAG*AGCAAACATAAGAGTGGCCTCCTCTACAAAAGGGACTCAAGATAGAAATC	lincrna,m4	BOWTIE+STAR	CDS(truncated)/intronic	0	5	2	20	9	85975157	+	15	81663171	-	10.2679	2.4601	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-BL-A13J-01A	ENSG00000143198	ENSG00000143179	MGST3	UCK2	ATGTTTCCAAGGCCCGCAAGAAGTACAAAGTGGAG*TCTTCCGTGTGTGCTAAGATCGTGCAGCTCCTGGG	18cancers,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	3	4	18	1	165649964	+	1	165890204	+	22.3686	9.4874	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-BL-A13J-01A	ENSG00000143198	ENSG00000143179	MGST3	UCK2	TTTTGTTCTGCTCCAGCTGTTCGAAGGTGATCCAG*TCTTCCGTGTGTGCTAAGATCGTGCAGCTCCTGGG	18cancers,100K<gap<200K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	3	3	20	1	165631293	+	1	165890204	+	22.3686	9.4874	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-BL-A13J-01A	ENSG00000099810	ENSG00000128805	MTAP	ARHGAP22	CAGATTATGACTGCTGGAAGGAGCACGAGGAAGCA*GTGGTGCCGGGGAGCGGGAGAAGGTGCCGGCCAAC	exon-exon	BOWTIE	out-of-frame	0	2	1	13	9	21854870	+	10	48479764	-	5.2701	0.553	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-BL-A13J-01A	ENSG00000067113	ENSG00000067248	PLPP1	DHX29	TGTCGAGGGAATGCAGAAAGAGTTAAGGAAGGCAG*GTTTTTCATCTTGAAGATATAATAGAAGAAACAGG	100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	2	3	24	5	55467869	-	5	55276406	-	35.2171	17.1312	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-DK-A1AB-01A	ENSG00000167114	ENSG00000228510	SLC27A4	AL359091.1	GAAGATTGCCAAGGATGTCTTCAAGAAGGGGGACCAGGCCTACCTTACTG*AATCTTTGGAGGATTGTCCTGTGGATGAAGTTGAAGATGCATTTCAGGGC	pseudogene,m11,10K<gap<100K	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	12	5	22	9	128355190	+	9	128444589	+	14.739	8.3618	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	processed_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-DK-A1AB-01A	ENSG00000167114	ENSG00000228510	SLC27A4	AL359091.1	GAAGATTGCCAAGGATGTCTTCAAGAAGGGGGACCAGGCCTACCTTACTG*GGCCTGGGAAAAGAAGATGAGGAAATTGAACAATTCAGTGATAAGACATT	pseudogene,m11,10K<gap<100K	BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	12	1	16	9	128355190	+	9	128444636	+	14.739	8.3618	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	processed_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-DK-A3IK-01A	ENSG00000170485	ENSG00000158435	NPAS2	CNOT11	AAAATTTGTAGGAAATTTTCGCTCTTACAACAATG*AACGCCAATCTGAATTGCCAACGCAAAGCAAAGCG	exon-exon	BOWTIE	in-frame	0	46	11	24	2	100949480	+	2	101262539	+	7.1868	50.4126	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Bladder	TCGA-DK-A3IK-01A	ENSG00000066739	ENSG00000092096	ATG2B	SLC22A17	CCTTCATTCTAGCAGTTTCAGTCTGTACCATAAAG*GGGCCGTGGCCTGGGCCTGATCATGGCTCTAGGGG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	36	6	22	14	96316533	-	14	23346936	-	2.4097	4.3631	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-DK-A3IK-01A	ENSG00000179091	ENSG00000185803	CYC1	SLC52A2	TCCCATCTACACAGATGTCTTAGAGTTTGACGATG*CTAGAAGAAGTCTTCACTTCCCAGGAGAGCCAAAG	exon-exon	BOWTIE	CDS(truncated)/UTR	0	25	9	23	8	144096744	+	8	144359184	+	91.3542	35.0192	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Bladder	TCGA-DK-A3IK-01A	ENSG00000151413	ENSG00000259076	NUBPL	AL049869.2	GCAGTTATCAGTCTCACAGAATATTCCTATAACAG*CTATCTCACTGTCTGTCTCACACTCACTGAGGGTG	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	14	2	19	14	31787873	+	14	64552888	-	2.2425	0.4409	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Bladder	TCGA-DK-A3IK-01A	ENSG00000049323	ENSG00000163803	LTBP1	PLB1	TTGGCCGGTGCTTCCAGGAAACCATTGGGTCACAG*ATGGAGCCAGCAGGAGAGAAAGATGAGCCATTGAG	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	13	3	21	2	33188851	+	2	28548860	+	20.8446	3.7757	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	NA	TRUE	TRUE
TRUE	FALSE	Bladder	TCGA-DK-A3IK-01A	ENSG00000187097	ENSG00000151413	ENTPD5	NUBPL	ATGGCTTTGGCTTTGCAGACAGCACAGTCTTACAG*GTGCTGTGATTGTCTCCACGCCCCAGGACATCGCA	oncogene,tumor,exon-exon	BOWTIE	in-frame	0	12	7	23	14	73970010	-	14	31826629	+	10.9761	2.2425	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Bladder	TCGA-DK-A3IK-01A	ENSG00000102908	ENSG00000198373	NFAT5	WWP2	GTCGGCCTTGATCCTAGCAACAACATGACACTGGC*TGAATGATGAACCCACAACAGCCACTGATCCCGAA	cell_lines,cancer,tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	10	4	22	16	69655799	+	16	69888039	+	2.7185	6.5077	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Bladder	TCGA-DK-A3IK-01A	ENSG00000157450	ENSG00000157470	RNF111	FAM81A	TGAAAACCACCAAAACAATCCAGCTGTTCCCTCAG*ATGTGAATTATTAAAAAGAAAATGGCCCAACGGAG	exon-exon	BOWTIE	CDS(truncated)/UTR	0	3	1	13	15	59031702	+	15	59458550	+	2.5563	0.8423	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-24-2290-01A	ENSG00000206199	ENSG00000144895	ANKUB1	EIF2A	ACACATACATATCTGTTACATATGGATGATATATGTGATATACATATGCA*TGATAATGTATTCAGAGTTTAACATGTTCCTTTTAGGTTCTCTCATCAAT	tcga,cell_lines,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/UTR	0	50	1	16	3	149919242	-	3	150567617	+	1.0068	14.6268	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-24-2290-01A	ENSG00000206199	ENSG00000144895	ANKUB1	EIF2A	CGGAAGATTGGAGAATCAGTCTTAGAGATTATGCAGCCAGAAACAACATC*AGTTGGAGAAAATTCAGAAAGAAACAGCCCTTCTCCAGGAGCTGGAAGAT	tcga,cell_lines,chimerdb3seq,tcga-cancer	BOWTIE+STAR	intronic/intronic	0	50	1	15	3	149784578	-	3	150583844	+	1.0068	14.6268	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-2290-01A	ENSG00000144895	ENSG00000206199	EIF2A	ANKUB1	ATGGTGAATGGACCACCACATTTTACAGAAAGCACAGTGTTTCCAAG*TGCCTTTAAAGAGAAACGATGGCTTCAGCAGTTAGAAATAGCAAGAG	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	50	24	29	3	150552425	+	3	149761613	-	14.6268	1.0068	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Ovarian	TCGA-24-2290-01A	ENSG00000030066	ENSG00000165923	NUP160	AGBL2	GAGAGTGGCAAGTTGTTCTCCGTAACCAGAAACAGGTTCATTCATTG*ATTCACATATGCTGAGTTTACCACATCTTAGGAGCAGACAGCTTCTT	10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	4	9	25	11	47847848	-	11	47704728	-	5.97	1.5516	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-2290-01A	ENSG00000030066	ENSG00000165923	NUP160	AGBL2	GAGAGTGGCAAGTTGTTCTCCGTAACCAGAAACAGGTTCATTCATTG*GGCCTATCAGTTTATCTTCAGCTGTGCACAGACAGATAGAAGCCATC	10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	4	8	30	11	47847848	-	11	47705917	-	5.97	1.5516	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Ovarian	TCGA-04-1514-01A	ENSG00000011260	ENSG00000259207	UTP18	ITGB3	TCGAGAACGACGAGGACGCGTTGCTGCGGCGTCTGCGAGGCCCGAGG*GGCCCAACATCTGTACCACGCGAGGTGTGAGCTCCTGCCAGCAGTGC	exon-exon	BOWTIE	out-of-frame	0	4	6	25	17	51260926	+	17	47274419	+	9.7333	1.8902	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Ovarian	TCGA-04-1514-01A	ENSG00000261404	ENSG00000284683	AC138627.1	AC087565.3	GCTCCTTTTTTGAAGCCATCTTTGCTCTGCTCTCCTCTGCTGCCCAG*GCTTCTGGACTTTTTGAATTCTGAAACCAAAAGAAGAATAAGTCGAA	lincrna,10K<gap<100K,exon-exon	BOWTIE;BOWTIE+STAR	exonic(no-known-CDS)/exonic(no-known-CDS)	0	3	3	26	16	74205905	-	16	73680240	-	0.0922	NA	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	lincRNA	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-04-1514-01A	ENSG00000149403	ENSG00000080546	GRIK4	SESN1	ACTACGCTTTGAAAATCTTACAGTTCACAAGGAATGGTTTTCGGCAG*GAACTTGGCATTAGAATTCCTCGACCACTAGGACAGGGACCAAGCAG	cell_lines,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	3	9	28	11	120875243	+	6	109002343	-	1.1648	5.9606	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Ovarian	TCGA-24-1552-01A	ENSG00000103197	ENSG00000114115	TSC2	RBP1	CTATTCTCTCAGGAACTCGCCGACATCTGTGTTGCCATCATTTTACCAGG*AAACGAACTGAACGTCTGAAACGAAGGTGGCGCGGCCTGGACAAACCTGA	cancer,tumor	BOWTIE+BLAT	intronic/UTR	0	30	24	34	16	2058874	+	3	139539829	-	8.8857	27.0224	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-1552-01A	ENSG00000103197	ENSG00000114115	TSC2	RBP1	GCATGGCTCTCTGGGGAGCCCACCGGCTCTATTCTCTCAGGAACTCGCCG*CCCCGCAGAGCCCCCTGTCCCCGGAGGGCGCTCATTTCCGGGCCGCCCAC	cancer,tumor	BOWTIE+BOWTIE2	out-of-frame	0	30	1	30	16	2058846	+	3	139539669	-	8.8857	27.0224	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-1552-01A	ENSG00000213965	ENSG00000021488	NUDT19	SLC7A9	AGCCGCCGCCCGTCTACCCCGACTTGGCGGAGGTGGTGGGCTACCAG*GTGCCCGTAGTCATTCCCGTCTTGATGACACTCATCTCTGTGTTTTT	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	27	25	30	19	32692674	+	19	32833323	-	25.675	0.9799	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Ovarian	TCGA-24-1552-01A	ENSG00000213965	ENSG00000021488	NUDT19	SLC7A9	GTGGGTTCTTGGTCTCGCTGACTTTAAGAATAAAGCCGCGGACCCTCGAA*GTGCCCGTAGTCATTCCCGTCTTGATGACACTCATCTCTGTGTTTTTGGT	tcga,cell_lines,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	27	1	27	19	32693179	+	19	32833323	-	25.675	0.9799	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Ovarian	TCGA-24-1552-01A	ENSG00000112992	ENSG00000177453	NNT	NIM1K	ACAATGCAAGGAGGTAGACATCCTTATCAGCACAGCACTTATTCCAG*AAAAGGTGGCCATTAAGATCCTGGACAAGACCAAGTTAGACCAGAAA	exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	16	18	29	5	43628387	+	5	43277057	+	6.1732	1.5176	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Ovarian	TCGA-24-1552-01A	ENSG00000112992	ENSG00000177453	NNT	NIM1K	TGGTGCTGAGCCCTTGGAGGTGGACTTGAAGGAATCTGGTGAGGGACAAG*ACCAAGTTAGACCAGAAAACCCAGAGGCTACTATCCCGAGAAATCTCCAG	NA	BOWTIE+BLAT;BOWTIE+BOWTIE2	out-of-frame	0	16	1	26	5	43628279	+	5	43277086	+	6.1732	1.5176	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Ovarian	TCGA-24-1552-01A	ENSG00000125868	ENSG00000185052	DSTN	SLC24A3	TTTGAAACAAAAGAATCCAGAAAAGAAGAGTTGATGTTTTTTTTGTG*GCCATATACATGTTCTATGCGCTGGCCATTGTGTGTGATGACTTCTT	m7,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	9	13	30	20	17601045	+	20	19580000	+	52.0827	2.8956	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-1552-01A	ENSG00000125868	ENSG00000185052	DSTN	SLC24A3	TGCAAGCTTTGAAACAAAAGAATCCAGAAAAGAAGAGTTGATGTTTTTTT*TTGGTGGCACCAGAACTACATTCTTCCCAGAGCACTGGCCTGTCGTGTAA	m7	BOWTIE+STAR	CDS(truncated)/intronic	0	9	2	18	20	17601041	+	20	19668095	+	52.0827	2.8956	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-1552-01A	ENSG00000185052	ENSG00000125868	SLC24A3	DSTN	TCAACATCCTGTGCATCATTGGTGTCTGTGGGCTCTTTGCTGGGCAG*GGCACCAGAACTAGCACCTCTGAAAAGTAAAATGATCTATGCAAGCT	m7,exon-exon	BOWTIE	out-of-frame	0	9	8	25	20	19585544	+	20	17604555	+	2.8956	52.0827	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-1552-01A	ENSG00000185052	ENSG00000125868	SLC24A3	DSTN	TGAGACACAGTAAGCACTATATTTATTTTTGCCGTTATTTTCTGCTCCAT*TTGCTGAAAAGTTAGGTGGATCCTTAATTGTAGCCTTTGAAGGATGCCCT	m7	BOWTIE+STAR	intronic/CDS(truncated)	0	9	1	14	20	19539556	+	20	17607091	+	2.8956	52.0827	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-1552-01A	ENSG00000185052	ENSG00000125868	SLC24A3	DSTN	GTTTCTCCAGCCCAAGGCTTAGTAAAAGGCTAATTAGGAAGTTGGCCAAT*AAGATTTTTGTTAAGCTCAGGATTTTAAATTACACAGTTCACAAACAGTA	m7	BOWTIE+STAR	intronic/UTR	0	9	1	14	20	19497454	+	20	17607385	+	2.8956	52.0827	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Ovarian	TCGA-24-1552-01A	ENSG00000170017	ENSG00000153832	ALCAM	FBXO36	CAAATGCCATTCACCTGCTCGGTGACATATTATGGACCATCTGGCCAGAA*TGAATTTTTTCCTGGCATTGTGTCGTCTGCGTCCAGCCATGAAGCTGGTG	NA	BOWTIE+STAR	CDS(truncated)/UTR	0	7	1	16	3	105534807	+	2	230011265	+	19.6656	0.4805	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-1552-01A	ENSG00000153832	ENSG00000170017	FBXO36	ALCAM	CGCCGCCTAGCAAAGACTATTACCAGTTACTGGTCACCCGGTCTCAG*GACTGCATCAAAACATGTAAACAAGGACCTCGGTAATATGGAAGAAA	exon-exon	BOWTIE;BOWTIE+BLAT	in-frame	0	7	9	29	2	229922609	+	3	105571852	+	0.4805	19.6656	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Ovarian	TCGA-24-1552-01A	ENSG00000153832	ENSG00000170017	FBXO36	ALCAM	CAGGTGGATCACGACGTCTGGAGTTGGAGACCAGCCTGACAAACATG*GACTGCATCAAAACATGTAAACAAGGACCTCGGTAATATGGAAGAAA	exon-exon	BOWTIE	in-frame	0	7	2	25	2	229932886	+	3	105571852	+	0.4805	19.6656	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Ovarian	TCGA-24-1552-01A	ENSG00000248932	ENSG00000140988	AC097103.2	RPS2	AGCTCCTGAAGGAAGCACTAAACATGGAAAGAAACAATTGGTACCAGCCA*TCATGATGGCTGGTATCGATGACTGCTACACCTCAGCCCGGGGCTGCACT	antisense,ribosomal	BOWTIE+STAR	intronic/CDS(truncated)	0	3	1	14	3	139406612	+	16	1962565	-	1.7798	937.6722	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-24-1552-01A	ENSG00000248932	ENSG00000140988	AC097103.2	RPS2	CTGCCATCTTGCTTCCCATTTTATGATGAGAAATATGGTGGTTACAAAGG*TCTGTGCTGGTACGCCTCATCCCTGCACCCAGGGGCACTGGCATCGTCTC	antisense,ribosomal	BOWTIE+STAR	intronic/CDS(truncated)	0	3	1	14	3	139419840	+	16	1962638	-	1.7798	937.6722	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-24-1552-01A	ENSG00000248932	ENSG00000140988	AC097103.2	RPS2	CAATTAAAAGACACAGACTGTCAAATTGGATAAAGAGTCAAGACCCATCG*CAAATGGCGGATGACGCCGGTGCAGCGGGGGGGCCCGGGGGCCCTGGTGG	antisense,ribosomal	BOWTIE+STAR	intronic/UTR	0	3	1	14	3	139406810	+	16	1964628	-	1.7798	937.6722	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-24-1552-01A	ENSG00000163617	ENSG00000181847	CCDC191	TIGIT	GGATGGGGCTGAATCGCTGGAAACGGTTCACAAGGAAGCCGAGTCCCAAG*ACCGTCTTTTCTCAGAGGCTCAGTTTTACCGTCCTATCTGCAGTCGGCTA	NA	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	in-frame	0	3	2	35	3	114056377	-	3	114293957	+	4.623	0.3092	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-1552-01A	ENSG00000140988	ENSG00000248932	RPS2	AC097103.2	CGCTGCAGCGGGCCTCTGCGTGGGCGGCGGGAATCCGCGGACATCGG*GAACATGGAGGAGACATATTTCCACCTATTTCTCTCCATAAGTATAA	antisense,ribosomal,exon-exon	BOWTIE;BOWTIE+STAR	UTR/exonic(no-known-CDS)	0	3	2	25	16	1964745	-	3	139423016	+	937.6722	1.7798	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-1552-01A	ENSG00000140988	ENSG00000248932	RPS2	AC097103.2	AAAAGCTGCTTCCCAGTAGGTCTCGTTCTTCTTTTCCGACAAAACAC*GAACATGGAGGAGACATATTTCCACCTATTTCTCTCCATAAGTATAA	antisense,ribosomal,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	3	2	23	16	1964807	-	3	139423016	+	937.6722	1.7798	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-1552-01A	ENSG00000140988	ENSG00000248932	RPS2	AC097103.2	GGCGGGAGCCCTTGTCTGGGTCTCGCGGGGGGCTGCCAGATGCGTAGGCC*GAGGCTGAGGAGTGGGGGTGTGCAGGGGAGAAGAAGGAGGAAGAGGAAGA	antisense,ribosomal	BOWTIE+STAR	UTR/intronic	0	3	1	15	16	1964663	-	3	139499886	+	937.6722	1.7798	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-1552-01A	ENSG00000140988	ENSG00000248932	RPS2	AC097103.2	ATGAAGATCAAGTCCCTGGAGGAGATCTATCTCTTCTCCCTGCCTATTAA*GGATCTCTGCTTCCTAACTCAGCATTTTGAACTTTCTTTTGAATTGCAGC	antisense,ribosomal	BOWTIE+STAR	CDS(truncated)/intronic	0	3	1	15	16	1964277	-	3	139454474	+	937.6722	1.7798	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-1552-01A	ENSG00000177469	ENSG00000141699	CAVIN1	RETREG3	AGGCCGAGCTGCTGCGGCGCCGCAACTTTAAAGTCATGATCTACCAG*GTTTTTTGCCCTGACATCTCTTCGTCTTGTGTTTTTACTTGCATTTG	100K<gap<200K,exon-exon	BOWTIE	out-of-frame	0	2	2	30	17	42422627	-	17	42592162	-	37.8072	10.2447	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-24-1552-01A	ENSG00000004534	ENSG00000230698	RBM6	AC105935.2	TGATGGCATGCCTGTAAAGAACTTGCAGTTGAAGGAGTATAACACAG*GTCACCATGGCCTGTACCAGGCCTCCGGCGGAGAAGCTGGGCACCAC	antisense,10K<gap<100K,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	2	5	28	3	49975392	+	3	49903431	+	5.6089	0.0321	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-04-1347-01A	ENSG00000197323	ENSG00000198691	TRIM33	ABCA4	GCTCAGCGTGCCCATCCCGGGGGGCAGCAACGGCGACATCCAGCAAG*GACTGATCTTTCACACCGCTCGTTCCTGCAGCCAGAAAGGAACTCTG	cancer,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	7	13	29	1	114510551	-	1	93993242	-	7.7802	0.7581	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Ovarian	TCGA-04-1347-01A	ENSG00000226688	ENSG00000225484	ENTPD1-AS1	NUTM2B-AS1	CCAGGGGTGTCCTATAGACTTTGTCATGGAGTGAAACAGAAACAAAT*GATTTAAACCTCAGACACAGGGAGCTGACCTATTCACCTTAGAATCC	antisense,exon-exon	BOWTIE	exonic(no-known-CDS)/exonic(no-known-CDS)	0	2	3	19	10	96089266	-	10	79692056	-	0.0992	0.5899	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-04-1347-01A	ENSG00000226688	ENSG00000225484	ENTPD1-AS1	NUTM2B-AS1	AACCCAGGTTCTTGGACTACAGGCTGGAGGCCAGCCCCTGGACAGCAAGG*ATTTAAACCTCAGACACAGGGAGCTGACCTATTCACCTTAGAATCCTCTG	antisense	BOWTIE+BOWTIE2	intronic/exonic(no-known-CDS)	0	2	1	32	10	95970596	-	10	79692055	-	0.0992	0.5899	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-04-1347-01A	ENSG00000225484	ENSG00000226688	NUTM2B-AS1	ENTPD1-AS1	TGTTGGACCTTCCGGAGCTTCTCAGAAGACAGAGGGTTTTCTTTTGAGGT*CTTATGAATATGTGAAAAAATGGTGCATAGACAGCGACATTCAGTGCAGC	antisense	BOWTIE+STAR	exonic(no-known-CDS)/intronic	0	2	1	21	10	79766269	-	10	95811916	-	0.5899	0.0992	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	antisense_RNA	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-1562-01A	ENSG00000196526	ENSG00000185774	AFAP1	KCNIP4	GCGGGACGGCACTTCATTATGACGATGTCCCGTGCATCAACGGCTCG*GATGAAAACATAATGCGCTCCATGCAGCTCTTTGAAAATGTGATTTA	cell_lines,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	21	24	29	4	7786194	-	4	20730129	-	2.9158	0.0626	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Ovarian	TCGA-24-1562-01A	ENSG00000196526	ENSG00000185774	AFAP1	KCNIP4	CTAATACCTCTTCTGTGGGGAGGGCGTCTCTCGGGCTCAACTCGCAG*GATGAAAACATAATGCGCTCCATGCAGCTCTTTGAAAATGTGATTTA	cell_lines,exon-exon	BOWTIE	in-frame	0	21	7	29	4	7781376	-	4	20730129	-	2.9158	0.0626	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Ovarian	TCGA-24-1562-01A	ENSG00000196526	ENSG00000185774	AFAP1	KCNIP4	AACCGGAAGACGGCTTTCCTGCTTCCTGCAGCAGAGGCTTGGGAGAAGAG*GATGAAAACATAATGCGCTCCATGCAGCTCTTTGAAAATGTGATTTAACT	cell_lines	BOWTIE+STAR	in-frame	0	21	2	30	4	7781574	-	4	20730129	-	2.9158	0.0626	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Ovarian	TCGA-24-1562-01A	ENSG00000196526	ENSG00000185774	AFAP1	KCNIP4	GCTTGTTCTCGCCGTCCAGAGCAAGGAACAGGCCGAGCAGTGGCTGAAGG*CTTTTGTGATCACCGCACCCGGAAGGGAGCCTTCCTCCCCTGAACTGCTC	cell_lines	BOWTIE+STAR	intronic/intronic	0	21	1	14	4	7838523	-	4	21173505	-	2.9158	0.0626	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Ovarian	TCGA-24-1562-01A	ENSG00000185774	ENSG00000196526	KCNIP4	AFAP1	ATTCTTCCCGGGCAACATGGAGCTAACTATGACTATTCCTATTCTACAAA*CAAGTAGGGCCTCTTTCCCAGCTTTCTTGCTTGCCTTCTGTGCAATATTT	cell_lines	BOWTIE+STAR	intronic/UTR	0	21	1	14	4	21171708	-	4	7762649	-	0.0626	2.9158	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-1562-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	GTTGGACCTTCCGGAGCTTCTCAGAAGACAGAGGGTTTTCTTTTGAG*GTGTGTTTGTCAAAGTGTCTCTGATGAACCACAACAAGTTTGTCAAG	antisense,m2,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	9	7	27	10	87288442	-	10	46585598	+	1.3855	0.0408	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-1562-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	CCGAAATGATCCGCCTGCCTCAGCCTCCAAAGTAGCTGAGACTACAG*ATTCCAGTTCTTTGATGAAAGTCTCTATTCCACCCATCAAGTCTGTG	antisense,m2,exon-exon	BOWTIE	exonic(no-known-CDS)/UTR	0	9	6	25	10	87246115	-	10	46593989	+	1.3855	0.0408	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-1562-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	GTTGGACCTTCCGGAGCTTCTCAGAAGACAGAGGGTTTTCTTTTGAG*ATTCCAGTTCTTTGATGAAAGTCTCTATTCCACCCATCAAGTCTGTG	antisense,m2,exon-exon	BOWTIE	exonic(no-known-CDS)/UTR	0	9	4	27	10	87288442	-	10	46593989	+	1.3855	0.0408	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-1562-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	CCGAAATGATCCGCCTGCCTCAGCCTCCAAAGTAGCTGAGACTACAG*GTGTGTTTGTCAAAGTGTCTCTGATGAACCACAACAAGTTTGTCAAG	antisense,m2,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	9	2	23	10	87246115	-	10	46585598	+	1.3855	0.0408	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-1562-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	CCGAAATGATCCGCCTGCCTCAGCCTCCAAAGTAGCTGAGACTACAG*AGAGCCAGCAGCTGGGCCGAGTGGTGGTGGGCCCCTACATGTACACC	antisense,m2,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	9	2	20	10	87246115	-	10	46587505	+	1.3855	0.0408	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-1562-01A	ENSG00000005339	ENSG00000262468	CREBBP	LINC01569	CTTGAAGAAAACTGGCAGACCTCGAAAAGAAAACAAATTCAGTGCTAAGA*AGTATCCGAAACATTGCCGTGTCAATCTCAGTGCGATGGGAGACTGCCGG	lincrna,cancer	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/intronic	0	6	9	31	16	3744894	-	16	4253622	-	15.2627	4.4453	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-1562-01A	ENSG00000005339	ENSG00000262468	CREBBP	LINC01569	GAAGAAAACTGGCAGACCTCGAAAAGAAAACAAATTCAGTGCTAAGA*GAACAAGGTCTCACCATGCTGCCCAAGCTGGTCTGAAAACTCTTGTC	lincrna,cancer,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	6	4	29	16	3744894	-	16	4252034	-	15.2627	4.4453	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-1562-01A	ENSG00000005339	ENSG00000262468	CREBBP	LINC01569	GAAGAAAACTGGCAGACCTCGAAAAGAAAACAAATTCAGTGCTAAGA*CATCTCCCGTGTCCCTCACAGCAGTTCTATGAGGCTGGCTGCCCTGT	lincrna,cancer,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	6	4	26	16	3744894	-	16	4246860	-	15.2627	4.4453	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-1562-01A	ENSG00000005339	ENSG00000262468	CREBBP	LINC01569	GAAGAAAACTGGCAGACCTCGAAAAGAAAACAAATTCAGTGCTAAGA*CCCTTTGAGGAACCGTTTGAGGTGTGGCACGATACAGCAAGTCAGCT	lincrna,cancer,exon-exon	BOWTIE;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	6	3	15	16	3744894	-	16	4247061	-	15.2627	4.4453	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-1562-01A	ENSG00000005339	ENSG00000262468	CREBBP	LINC01569	CTTGAAGAAAACTGGCAGACCTCGAAAAGAAAACAAATTCAGTGCTAAGA*TTCTATGAGGCTGGCTGCCCTGTTTGACAACTGAGGCCCGCATCTTCCCC	lincrna,cancer	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	6	1	36	16	3744894	-	16	4246836	-	15.2627	4.4453	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-1562-01A	ENSG00000005339	ENSG00000262468	CREBBP	LINC01569	CTATTATTTTGCAGTTTTGTGTGCGACAACTGCTTGAAGAAAACTGGCAG*TTCTATGAGGCTGGCTGCCCTGTTTGACAACTGAGGCCCGCATCTTCCCC	lincrna,cancer	BOWTIE+BOWTIE2	CDS(truncated)/exonic(no-known-CDS)	0	6	1	35	16	3744926	-	16	4246836	-	15.2627	4.4453	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-1562-01A	ENSG00000005339	ENSG00000262468	CREBBP	LINC01569	CTTGAAGAAAACTGGCAGACCTCGAAAAGAAAACAAATTCAGTGCTAAGA*CCTCCAGTGGTGCACTGAGTTGATCACGACCCTCACTCTTTCGGCCTGCA	lincrna,cancer	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/intronic	0	6	1	30	16	3744894	-	16	4247519	-	15.2627	4.4453	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-24-1562-01A	ENSG00000122786	ENSG00000080503	CALD1	SMARCA2	AAAGATTAAAAAGGACAAAGAACCCAAAGAAGAAGTTAAGAGCTTCATGG*GTCCTTTGTCCTTTGTATAAGAAGCCCAGTGTGAAGGATCTGAAATGTCT	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	17	7	134941152	+	9	2097288	+	24.2327	3.2737	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-24-1562-01A	ENSG00000114861	ENSG00000185567	FOXP1	AHNAK2	TCTAGATTGGATGTCCCAGCGTGGACAGATGAGCCCAGGGACCCTTGCCT*CTGCCTTTGGAAGCTCCCCCAATTTCAAAGGTCAGAGTGCATATTCAGGG	oncogene,cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	17	3	71522205	-	14	104939094	-	0.6998	12.5351	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-24-1562-01A	ENSG00000114861	ENSG00000185567	FOXP1	AHNAK2	AAAAGACGTGTGCCGGCATTCCCAGGTCAAAGTTTGCTAAGCAGGTTTCT*ACCCTGACTTCCACAAGACACCAGAATTCACACGGTACTCAGAGGCACTG	oncogene,cancer	BOWTIE+STAR	intronic/UTR	0	2	1	16	3	71448840	-	14	104937836	-	0.6998	12.5351	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-24-1562-01A	ENSG00000114861	ENSG00000185567	FOXP1	AHNAK2	ACAGAAGTATTATTTGTTCTTCTTTTCCTAGCCTATGAATTGAGGTGGAT*GTAAAGGCTACACACACATATGGAGCACCCCATCCCACAGCACATTACAT	oncogene,cancer	BOWTIE+STAR	intronic/UTR	0	2	1	14	3	71499878	-	14	104938013	-	0.6998	12.5351	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-24-1562-01A	ENSG00000114861	ENSG00000185567	FOXP1	AHNAK2	TGTGGACCATTTACTGACATATCTAGTTGAAGAGTCACTTAACACACTAG*GACTCAACACTCTAGGACTCAGGAGGGCACAGAAGAGGCTCCCATACAAG	oncogene,cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	14	3	71476096	-	14	104938837	-	0.6998	12.5351	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-24-1562-01A	ENSG00000114861	ENSG00000185567	FOXP1	AHNAK2	CTAAGTGGAAGAAAAAAAGTAGTTGCAAGCTGTTACAGAGCTGGACAGAA*AAGCTGACCTGCCTCTTCCCAAACATGATCTGTCTACCGAAGGTGACAGC	oncogene,cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	14	3	71085092	-	14	104940101	-	0.6998	12.5351	TRUE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-24-1562-01A	ENSG00000196535	ENSG00000163931	MYO18A	TKT	AGCGTGAATCCAAGACGCGCCTGGAAATCTCCAACCCCATCCCCATCAAG*TCCCTGGGCCAGGGCCTCGGGGCCGCTTGTGGGATGGCCTACACCGGCAA	NA	BOWTIE+STAR	in-frame	0	2	1	17	17	29166734	-	3	53240318	-	2.1898	39.0763	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-1562-01A	ENSG00000165495	ENSG00000157570	PKNOX2	TSPAN18	AGGCTTTCTATCCTCCATGCTGCTCACTAGAAAAGGGGCTGTGAACT*GTGAGCATCTCCTGGACCACCCTCAAGCTTCAGGTGAGCTGAGCTTC	exon-exon	BOWTIE;BOWTIE+STAR	UTR/UTR	0	2	2	17	11	125235115	+	11	44860328	+	0.6777	3.8203	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-1562-01A	ENSG00000134910	ENSG00000245832	STT3A	MIR4300HG	CTGTTTGCTGTCCTGAGATTTGAAAGTGTTATCCATGAGTTTGATCC*GTTGATTCTAAGGAAGCCAACAGCCGTGTTGTGAGTACCCAATGGAA	lincrna,exon-exon	BOWTIE;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	2	10	29	11	125597119	+	11	82356628	-	13.0977	0.2446	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-1562-01A	ENSG00000134910	ENSG00000245832	STT3A	MIR4300HG	CGTCTGTTTGCTGTCCTGAGATTTGAAAGTGTTATCCATGAGTTTGATCC*ATGTCTCCAAGATGTGCGTATCATGAGGTCAAGAGATCGAGACCATCCTG	lincrna	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	30	11	125597119	+	11	82589299	-	13.0977	0.2446	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-1562-01A	ENSG00000134910	ENSG00000245832	STT3A	MIR4300HG	CGTCTGTTTGCTGTCCTGAGATTTGAAAGTGTTATCCATGAGTTTGATCC*CTTAGATGCAACTCAGAGCAACTTGACCTTGAACTTCCATTCAAATCCTG	lincrna	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	27	11	125597119	+	11	82438437	-	13.0977	0.2446	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-2024-01A	ENSG00000131788	ENSG00000143839	PIAS3	REN	CCCTCTGAGCCTCCCGAGCCCTCTCTCCATTTCCCACAATTGTGCTG*GATCTTCCTCAAGAGAATGCCCTCAATCCGAGAAAGCCTGAAGGAAC	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	42	34	30	1	145859665	-	1	204162163	-	10.7597	29.9166	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Ovarian	TCGA-24-2024-01A	ENSG00000131788	ENSG00000143839	PIAS3	REN	TGGGGCGCCTGCGATGTCTCAAGATGGCGGAGCTGGGCGAATTAAAG*GATCTTCCTCAAGAGAATGCCCTCAATCCGAGAAAGCCTGAAGGAAC	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	42	18	30	1	145858967	-	1	204162163	-	10.7597	29.9166	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Ovarian	TCGA-24-2024-01A	ENSG00000131788	ENSG00000143839	PIAS3	REN	CCCTCTGAGCCTCCCGAGCCCTCTCTCCATTTCCCACAATTGTGCTG*GGCCTTCGCACGTTCTGTTCCTGCTGGGACTCTATTTCTTTGTCTTC	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	UTR/UTR	0	42	5	27	1	145859665	-	1	204173920	-	10.7597	29.9166	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Ovarian	TCGA-24-2024-01A	ENSG00000131788	ENSG00000143839	PIAS3	REN	TGGGGCGCCTGCGATGTCTCAAGATGGCGGAGCTGGGCGAATTAAAG*GGCCTTCGCACGTTCTGTTCCTGCTGGGACTCTATTTCTTTGTCTTC	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE;BOWTIE+STAR	CDS(truncated)/UTR	0	42	5	24	1	145858967	-	1	204173920	-	10.7597	29.9166	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Ovarian	TCGA-24-2024-01A	ENSG00000050767	ENSG00000146067	COL23A1	FAM193B	GATCCGGACTGCTCGGGAAGCTCCATCCGAATGTGTCTGCCCCCCAG*GCCCTGCCCAGGCTGAGCTGCTTCAGGGCGTCCTGAGGCCCTGACTG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	29	28	30	5	178560682	-	5	177520181	-	4.5637	6.7432	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Ovarian	TCGA-24-2024-01A	ENSG00000050767	ENSG00000146067	COL23A1	FAM193B	GGTCGGCAACCCCAGGAGACCACCCCCGCTGGCCCTGTCCTTGATGTCAG*GCCCTGCCCAGGCTGAGCTGCTTCAGGGCGTCCTGAGGCCCTGACTGCCA	tcga,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	intronic/UTR	0	29	1	30	5	178350977	-	5	177520181	-	4.5637	6.7432	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Ovarian	TCGA-24-2024-01A	ENSG00000050767	ENSG00000146067	COL23A1	FAM193B	CTTATGTGAGGCACCCAGTCATCAAATTCATAGAGACGGAAACCAGGATG*GCCCTGCCCAGGCTGAGCTGCTTCAGGGCGTCCTGAGGCCCTGACTGCCA	tcga,chimerdb3seq,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	intronic/UTR	0	29	1	24	5	178468940	-	5	177520181	-	4.5637	6.7432	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	FALSE	Ovarian	TCGA-24-2024-01A	ENSG00000146067	ENSG00000050767	FAM193B	COL23A1	AGAGCAGCAGCCTGACATCAACCTTGACCTGTCCCCTTTGACTTTGGGCT*ACTGCTCTCAGGAGCCACATGGGGGAAGGAAGGGAGGTCACTAAGCACCG	tcga,chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	29	1	16	5	177524860	-	5	178248361	-	6.7432	4.5637	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-2024-01A	ENSG00000248487	ENSG00000157388	ABHD14A	CACNA1D	GCAGCTACTGTCACAGAGGGGCTACCGGGCCGTGGCCCTTGACCTTCCAG*ATCCAGTGCCATCTCCGTTGTGAAGATTCTGAGGGTCTTAAGGGTCCTGC	exon-exon	BOWTIE+STAR	in-frame	0	2	1	16	3	51978374	+	3	53744740	+	4.2166	0.2432	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-24-2024-01A	ENSG00000157388	ENSG00000114786	CACNA1D	ABHD14A-ACY1	TTTGTAGGGACATGGGTGAAGCTGGAAACCATCATTCTGAGCAAACTATT*GGGTGGACATATATACACGCCTGCTGCCTGCCCTTGCCAGTGTGCCTGCC	NA	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	15	3	53397019	+	3	51989008	+	0.2432	0.0404	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-24-2024-01A	ENSG00000156639	ENSG00000167306	ZFAND3	MYO5B	AGCTCATGTCTCATTAATCACACCAACAAAAAGATCCTGTGGTACAG*TGCACAAGGGTCTGGATCCCTGACCCTGATGAGGTATGGCGCTCAGC	exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	2	4	22	6	38082457	+	18	50055378	-	23.7997	3.6959	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-13-0906-01A	ENSG00000104129	ENSG00000084733	DNAJC17	RAB10	ACCTGTACGCGCTGCTAGGCATTGAGGAGAAGGCAGCGGACAAAGAG*CATGCCAATGAAGATGTGGAAAGAATGTTACTAGGAAACAAGTGTGA	exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	26	14	29	15	40807369	-	2	26127144	+	2.2982	61.5324	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Ovarian	TCGA-13-0906-01A	ENSG00000084733	ENSG00000104129	RAB10	DNAJC17	GTAAAAGTTTTGAAAACATCAGCAAATGGCTTAGAAACATAGATGAG*GTAAAGAAGGCGTATAGGCAGAAGGCCCTCTCCTGCCACCCAGACAA	exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	26	15	27	2	26109906	+	15	40779997	-	61.5324	2.2982	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Ovarian	TCGA-13-0906-01A	ENSG00000084733	ENSG00000104129	RAB10	DNAJC17	GTAAAAGTTTTGAAAACATCAGCAAATGGCTTAGAAACATAGATGAG*ATAGGTTGCCCCAGTTTATATGCCCACCAAGAATGTGTAGAGTACCT	exon-exon	BOWTIE	in-frame	0	26	4	25	2	26109906	+	15	40780352	-	61.5324	2.2982	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Ovarian	TCGA-13-0906-01A	ENSG00000168000	ENSG00000278615	BSCL2	C11ORF98	CCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGTGGACGTGATCGG*GTCCAGTGCACGTGCCAACATTACACTGTCAGGGAAGAAGCGCAGAA	tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	15	25	29	11	62702468	-	11	62663333	-	1.7685	0.0282	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-13-0906-01A	ENSG00000168000	ENSG00000162194	BSCL2	LBHD1	TATATGCCGACAGTCAGCCACCTCAGCCCTGTGCATTTCTACTACAG*GTCCAGTGCACGTGCCAACATTACACTGTCAGGGAAGAAGCGCAGAA	tcga-cancer,10K<gap<100K,exon-exon	BOWTIE	out-of-frame	0	15	2	20	11	62705301	-	11	62663333	-	1.7685	0.258	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-13-0906-01A	ENSG00000234857	ENSG00000278615	HNRNPUL2-BSCL2	C11ORF98	GCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGTGGACGTGATCGG*GTCCAGTGCACGTGCCAACATTACACTGTCAGGGAAGAAGCGCAGAAAAC	10K<gap<100K,exon-exon	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	15	3	18	11	62702468	-	11	62663333	-	0	0.0282	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-13-0906-01A	ENSG00000234857	ENSG00000278615	HNRNPUL2-BSCL2	C11ORF98	AACAACCGAAACAAGCGTAACCGGCAGAACCGAAGCCGGGGCCAAGGCTA*AGACAGAGTCTCCCTCTGTTGCCCAGGCTGGAGTGAAGTGGCATGATCTC	10K<gap<100K	BOWTIE+BOWTIE2	CDS(truncated)/intronic	0	15	1	36	11	62716991	-	11	62664071	-	0	0.0282	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-13-0906-01A	ENSG00000151746	ENSG00000179241	BICD1	LDLRAD3	GACGCAGCAAAGGCAAACTTGGAAAGAGCAAGATCGGCAGCCCTAAA*AACCCGGCAGTGGGCAGGTGTTTGTGACTTCAGAGAACCAACTTGTG	exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	5	2	16	12	32337706	+	11	36227085	+	4.4308	6.9217	FALSE	TRUE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-13-0906-01A	ENSG00000077549	ENSG00000139644	CAPZB	TMBIM6	GTGAGACTCCATCTCAAAAAAAGACAAAAAAAAAAAAAAAAAAGAAAG*AAAAAAAAAAACACCTACTTTTAAAGAAAATACCTAACAGATTTTTAA	NA	BOWTIE+STAR	intronic/UTR	0	2	35	23	1	19452789	-	12	49764730	+	26.215	302.0395	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-13-0906-01A	ENSG00000077549	ENSG00000139644	CAPZB	TMBIM6	GGCAAGAAAATGGATTAAATATCTGAGCTGATACCTGTCCCACATACTGG*TTTGCACACATTACAGGTGGTGTGTTCTGTGATAATGAAAAGCATCAGAA	NA	BOWTIE+STAR	intronic/UTR	0	2	1	18	1	19467615	-	12	49762954	+	26.215	302.0395	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-13-0906-01A	ENSG00000077549	ENSG00000139644	CAPZB	TMBIM6	GGGGCAACATCTCCACCAAAAATACAAAAAAAAAAAAAAAAAAAAAAAGC*ACCTACTTTTAAAGAAAATACCTAACAGATTTTTAATATAGTTATCTCTA	NA	BOWTIE+STAR	intronic/UTR	0	2	1	15	1	19460573	-	12	49764742	+	26.215	302.0395	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-13-0906-01A	ENSG00000077549	ENSG00000139644	CAPZB	TMBIM6	GGGAGGATCACTTGGGACCAGCCTAGGCAACATAGTGAGACCCAATCTCT*GCAGTTCCTCATTCACATCAACAGAGCGAGGCTGTGATAACTTAGGAGGC	NA	BOWTIE+STAR	intronic/UTR	0	2	1	14	1	19467085	-	12	49763885	+	26.215	302.0395	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-13-0906-01A	ENSG00000069275	ENSG00000149639	NUCKS1	SOGA1	GTTCGGCAGCAGCGGTCCCATCGGCTGAAGTTCGGGGGGGGTGGGGCGCC*CTCTCTCTCCCTCCTCATTATCTGTGTCCCCTGTCTGTACCACAGATCAA	NA	BOWTIE+STAR	UTR/intronic	0	2	1	16	1	205750040	-	20	36810152	-	105.1267	9.1817	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-13-0906-01A	ENSG00000139644	ENSG00000077549	TMBIM6	CAPZB	CTCACCAGTTCAGAAGCATCCTAAGGAATAAAAGGGGGGGGGGGGGGGGC*CCGTGTGGTTTTTGTTCACCCGGGCCCCCCGTCTTCCTCCCTGTCCCCCC	NA	BOWTIE+STAR	intronic/UTR	0	2	1	15	12	49736021	+	1	19339293	-	302.0395	26.215	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-13-0906-01A	ENSG00000139644	ENSG00000077549	TMBIM6	CAPZB	GATGGCACCCTGAAGGAACGAGGCCCTGCTCGGAGACCAGACTCGGGAAA*CAGGATGCAGGGCACTCGTTTGGTGGTTGGGTTGGTTATGAGATGACTCG	NA	BOWTIE+STAR	UTR/intronic	0	2	1	15	12	49741763	+	1	19378353	-	302.0395	26.215	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-13-0906-01A	ENSG00000139644	ENSG00000077549	TMBIM6	CAPZB	GTAGTGGCTGTAAATATGTTCTTAAATTCTTTGATATCCCACCTTCAAAA*TACAAGTTGACCTCCACGGTGATGCTGTGGCTGCAGACCAACAAATCTGG	NA	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	15	12	49726260	+	1	19356724	-	302.0395	26.215	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-1632-01A	ENSG00000151322	ENSG00000139687	NPAS3	RB1	AACGGCACCCCGCAGAACGTCCAGGGCATCACCTCCTACCAGCAGCG*ACATTCAAACGTGTTTTGATCAAAGAAGAGGAGTATGATTCTATTAT	cancer,tumor,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	31	31	30	14	32935003	+	13	48464998	+	4.8932	13.6072	FALSE	FALSE	TRUE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Ovarian	TCGA-25-1632-01A	ENSG00000151322	ENSG00000139687	NPAS3	RB1	GCGCCCACCAAGCCCAGCTTTCAGCAGGATCCTTCCAGGCGAGAACG*ACATTCAAACGTGTTTTGATCAAAGAAGAGGAGTATGATTCTATTAT	cancer,tumor,exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	31	17	29	14	32939366	+	13	48464998	+	4.8932	13.6072	FALSE	FALSE	TRUE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Ovarian	TCGA-25-1632-01A	ENSG00000151322	ENSG00000139687	NPAS3	RB1	CAGCCCCGAGTAGCGGAGGAGTTGCAGCGAAGTCTGAGACGCCGCACAAG*ACATTCAAACGTGTTTTGATCAAAGAAGAGGAGTATGATTCTATTATAGT	cancer,tumor	BOWTIE+BOWTIE2;BOWTIE+STAR	intronic/CDS(truncated)	0	31	11	33	14	32935296	+	13	48464998	+	4.8932	13.6072	FALSE	FALSE	TRUE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Ovarian	TCGA-25-1632-01A	ENSG00000151322	ENSG00000139687	NPAS3	RB1	AGCCCTACTTTACTGGAGTCGTAGAGACCGAATGGAGGACCCCTTTTCAG*ACATTCAAACGTGTTTTGATCAAAGAAGAGGAGTATGATTCTATTATAGT	cancer,tumor	BOWTIE+BOWTIE2;BOWTIE+STAR	intronic/CDS(truncated)	0	31	1	22	14	32937702	+	13	48464998	+	4.8932	13.6072	FALSE	FALSE	TRUE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Ovarian	TCGA-25-1632-01A	ENSG00000139687	ENSG00000151322	RB1	NPAS3	CCAGGCGAGGTCAGAACAGGAGTGCACGGATAGCAAAACAACTAGAAAAT*AATTCTTGTATCATCCTTACTACCACTTCCCACCCTATTTCCCCTGCAGT	cancer,tumor	BOWTIE+STAR	CDS(truncated)/intronic	0	31	2	14	13	48362903	+	14	33623300	+	13.6072	4.8932	FALSE	FALSE	TRUE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-25-1632-01A	ENSG00000139687	ENSG00000151322	RB1	NPAS3	TATCTCCGGCTAAATACACTTTGTGAACGCCTTCTGTCTGAGCACCCAGA*TAGTTTTTTCTAATTCTGTGAAGAAAGTCAATGGTAGCTTGATGGGGATA	cancer,tumor	BOWTIE+STAR	CDS(truncated)/intronic	0	31	1	18	13	48459751	+	14	33662463	+	13.6072	4.8932	FALSE	FALSE	TRUE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-25-1632-01A	ENSG00000139687	ENSG00000151322	RB1	NPAS3	TACTTTTAGAATTGCTTGTTCTTTAAGGCTTTGACTTCATAAAAGTTTTC*ATATATTTGTTTACTTGTGCAATGCTAATATAGTAACTCGGCTGTCCTTT	cancer,tumor	BOWTIE+STAR	intronic/UTR	0	31	1	17	13	48323706	+	14	33803293	+	13.6072	4.8932	FALSE	FALSE	TRUE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-25-1632-01A	ENSG00000139687	ENSG00000151322	RB1	NPAS3	CCGCCGCGGAAAGGCGTCATGCCGCCCAAAACCCCCCGAAAAACGGCCGC*GGGACTGAAACTCCCTGGTCAGACTGAAAACAGCTCGTAAAATACTGTGA	cancer,tumor	BOWTIE+STAR	CDS(truncated)/intronic	0	31	1	14	13	48303944	+	14	33787128	+	13.6072	4.8932	FALSE	FALSE	TRUE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-25-1632-01A	ENSG00000139687	ENSG00000151322	RB1	NPAS3	ACTGCAAATGCAGAGACACAAGCAACCTCAGCCTTCCAGACCCAGAAGCC*AGAGAAAGAGAGGTAGAGAGGGAGAAAGAAATGGAGTGGTGAAAGAGAGA	cancer,tumor	BOWTIE+STAR	CDS(truncated)/intronic	0	31	1	14	13	48456311	+	14	33391591	+	13.6072	4.8932	FALSE	FALSE	TRUE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-25-1632-01A	ENSG00000139687	ENSG00000151322	RB1	NPAS3	ATGCAAAGTGAAGAATATAGACCTTAAATTCAAAATCATTGTAACAGCAT*GTGGAAGAGCCTTGGTACGGTTATCACTGTGGTAGCTATTTACTTCTAAT	cancer,tumor	BOWTIE+STAR	CDS(truncated)/intronic	0	31	1	14	13	48463806	+	14	33174337	+	13.6072	4.8932	FALSE	FALSE	TRUE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-25-1632-01A	ENSG00000139687	ENSG00000151322	RB1	NPAS3	TTGTGAACGCCTTCTGTCTGAGCACCCAGAATTAGAACATATCATCTGGA*AAAGAGTACAGATGTGCTCTTTTGCATTATGCATTAAGATTAATCAACCT	cancer,tumor	BOWTIE+STAR	CDS(truncated)/intronic	0	31	1	14	13	48459771	+	14	33221680	+	13.6072	4.8932	FALSE	FALSE	TRUE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-25-1632-01A	ENSG00000087253	ENSG00000102309	LPCAT2	PIN4	GCATTCAGCTTTGTATGCTTACTTTCTGCCAGCTCTTCACAAAGGTAGAA*GTAGAGATGGAGTCTCGCTATGTTGCCCAGGCTGGTCTTGAACTCCTGGC	NA	BOWTIE+BOWTIE2	CDS(truncated)/intronic	0	20	1	33	16	55537626	+	X	72188705	+	6.2778	8.4849	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-1632-01A	ENSG00000102309	ENSG00000087253	PIN4	LPCAT2	CAAGATGCCGCCCAAAGGAAAAAGTGGTTCTGGAAAAGCGGGGAAAG*TTTATGCCAGTTCAAGTACCAAATGATGAAGAAAAAAATGATCCTGT	exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	20	18	30	X	72181828	+	16	55545735	+	8.4849	6.2778	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-1632-01A	ENSG00000102309	ENSG00000087253	PIN4	LPCAT2	CAAGATGCCGCCCAAAGGAAAAAGTGGTTCTGGAAAAGCGGGGAAAG*AGCTCTGGGAATACCAGTAACAGATCATACCTATGAAGACTGCAGAT	exon-exon	BOWTIE	in-frame	0	20	2	30	X	72181828	+	16	55549277	+	8.4849	6.2778	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-1632-01A	ENSG00000163558	ENSG00000187033	PRKCI	SAMD7	GGCAGCGGGGACCATTCCCACCAGGTCCGGGTGAAAGCCTACTACCGCGG*CCAGAGAAGCTTCTGCAGTTGAAGGCCAGAAAGTCTTTGTATGGTTCTTC	oncogene,tumor	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/UTR	0	8	12	37	3	170222770	+	3	169911733	+	46.2261	4.1798	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Ovarian	TCGA-25-1632-01A	ENSG00000163558	ENSG00000187033	PRKCI	SAMD7	AGCGGGGACCATTCCCACCAGGTCCGGGTGAAAGCCTACTACCGCGG*AACTCCATTAGTGGCGAGAGATATTGAAGACAAACCCGGTGATGGCT	oncogene,tumor,exon-exon	BOWTIE	CDS(truncated)/UTR	0	8	6	29	3	170222770	+	3	169919458	+	46.2261	4.1798	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Ovarian	TCGA-25-1632-01A	ENSG00000104375	ENSG00000104361	STK3	NIPAL2	TTTTTCCTGATAACTGGAAAGTTCCTCAAGATGGAGACTTTGACTTT*ATTTTAGAAATATTAATTTTCTGCATTCTCCTGTATTTCTATAAAAG	chimerdb3seq,100K<gap<200K,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	4	3	28	8	98526742	-	8	98212501	-	1.7658	4.8281	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Ovarian	TCGA-25-1632-01A	ENSG00000156804	ENSG00000265817	FBXO32	FSBP	ACTTCTCAACTGCCATTCTGGATTCCAGAAGATTTAACTACGTGGTCCGG*TTCATTCGGCTCCTAAAGAAGTAGCAGTGTCCAAGGAACAAGAAGAGAAA	exon-exon	BOWTIE+STAR	out-of-frame	0	2	1	14	8	123531898	-	8	94411315	-	3.2158	0.3795	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-1632-01A	ENSG00000156804	ENSG00000197275	FBXO32	RAD54B	TCTCAACTGCCATTCTGGATTCCAGAAGATTTAACTACGTGGTCCGG*TTCATTCGGCTCCTAAAGAAGTAGCAGTGTCCAAGGAACAAGAAGAG	exon-exon	BOWTIE	in-frame	0	2	4	25	8	123531898	-	8	94411315	-	3.2158	0.3073	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-25-1632-01A	ENSG00000147316	ENSG00000104723	MCPH1	TUSC3	ATTGGTATGGGTTGATTTTTTTTTTTCAATCTCTGCAGCTTTGCCAGGGA*CCACCGGGAGCTTTCCCTTCCTTCTCCTGCTGCTGCTGCTCTGCATCCAG	cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	16	8	6511324	+	8	15540492	+	3.6967	17.9862	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-25-1632-01A	ENSG00000147316	ENSG00000104723	MCPH1	TUSC3	TCTCAGCTGCCATCAAGCCCTGCTCAGTTGAGCTGCAGAAGTCTTTCTAA*TATCCTTGTTTTCTCCTTTAAAAAATTGTGCAAACTAGAATATTTAGACT	cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	16	8	6445068	+	8	15672776	+	3.6967	17.9862	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-25-1632-01A	ENSG00000147316	ENSG00000104723	MCPH1	TUSC3	ATATTCATTCATCACCATCTTTCACTCACCTCGATAAATCAAGTCCTCAG*TTTCCACACAGATCATAGCAGCAATATATAGCTTTATCAGGGAAAAAACT	cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	15	8	6444589	+	8	15749323	+	3.6967	17.9862	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000010803	ENSG00000054116	SCMH1	TRAPPC3	GCGGCGGGAAGAGAGTGAGCCGCCCCGCGCCCCCGCCGCGCCCTCAG*AGCTCTGAGCTCTTCACCCTGACCTATGGTGCCCTGGTCACCCAGCT	exon-exon	BOWTIE;BOWTIE+STAR	UTR/CDS(truncated)	0	51	33	30	1	41242059	-	1	36140166	-	68.2993	124.5171	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000010803	ENSG00000054116	SCMH1	TRAPPC3	GCGGCGGGAAGAGAGTGAGCCGCCCCGCGCCCCCGCCGCGCCCTCAG*GTGGCGTTCAAGATGTACTTGGGCATCACTCCAAGCATTACTAATTG	exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	51	11	29	1	41242059	-	1	36137978	-	68.2993	124.5171	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000010803	ENSG00000054116	SCMH1	TRAPPC3	GCGGCGGGAAGAGAGTGAGCCGCCCCGCGCCCCCGCCGCGCCCTCAG*GTCCAGATGGCTGTGGAGGCCAAGTTTGTCCAGGACACCCTGAAAGG	exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	51	7	27	1	41242059	-	1	36137322	-	68.2993	124.5171	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Ovarian	TCGA-25-2400-01A	ENSG00000054116	ENSG00000010803	TRAPPC3	SCMH1	ACCTGCCCTTCTCTTGCGTTGGCTTACTGTGACCCAACCCAGTGTCTATT*GAGGGAGACTGCCCTGCTTTGGTCCCAGAGAGGCCCTCTGCAGATAGGCG	NA	BOWTIE+STAR	intronic/UTR	0	51	1	15	1	36145528	-	1	41027666	-	124.5171	68.2993	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000157191	ENSG00000142627	NECAP2	EPHA2	TGGACCTGGGCTTCAAGGAGGGCCAGACCATCAAGCTCAACATCGCA*GTGATGAAAGCCATCAATGATGGCTTCCGGCTCCCCACACCCATGGA	oncogene,tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	in-frame	0	16	24	30	1	16449201	+	1	16130419	-	8.8389	7.3596	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000157191	ENSG00000142627	NECAP2	EPHA2	CTCGCTTGGAGGAAACTAACATTTAATGAGCATCAGCTGAGGGCCAG*GTGATGAAAGCCATCAATGATGGCTTCCGGCTCCCCACACCCATGGA	oncogene,tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	16	2	29	1	16450241	+	1	16130419	-	8.8389	7.3596	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000115464	ENSG00000168754	USP34	FAM178B	AACGATGTGCGAGAACTGCGCAGACCTGGTGGAGGTGTTAAATGAAA*CTGCTGACATGGCCTCCAGAAACATCTTTGGGAGCCTTTGGTCTTCT	exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	10	23	30	2	61470650	-	2	96947902	-	13.8737	6.4017	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000115464	ENSG00000168754	USP34	FAM178B	CCGAACGATGTGCGAGAACTGCGCAGACCTGGTGGAGGTGTTAAATGAAA*ATGAAGACAAGCACCTGTGGTGCCCCTCACTGCAAGAAGTCAGGGAGGCA	exon-exon	BOWTIE+STAR	in-frame	0	10	1	15	2	61470650	-	2	96929320	-	13.8737	6.4017	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000113719	ENSG00000204764	ERGIC1	RANBP17	ACATGACGCATGTCATCCACAAGCTCTCCTTTGGGGACACGCTACAG*GTTGTACGCCTGAGGAGTGATGTACCCAGAGTTCCAGAGAAGGCTTG	oncogene,tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	4	12	30	5	172924109	+	5	171161407	+	17.5347	1.2231	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000113719	ENSG00000204764	ERGIC1	RANBP17	ACATGACGCATGTCATCCACAAGCTCTCCTTTGGGGACACGCTACAG*GTATATGCTCGTATGTCAGAAGTCTTAGGAATAACAGATGACAACCA	oncogene,tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE;BOWTIE+STAR	in-frame	0	4	9	25	5	172924109	+	5	171170130	+	17.5347	1.2231	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000113719	ENSG00000204764	ERGIC1	RANBP17	GCAACTTCCACGTGTCCACACACAGTGCCACAGCCCAGCCACAGAACCCA*AAGGAGAGATTGTTCAAATGATTGAATCAAGGAAGCTCCTGGGAAAACTG	oncogene,tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	4	1	14	5	172924061	+	5	171174396	+	17.5347	1.2231	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000182621	ENSG00000180769	PLCB1	WDFY3-AS2	GGACTGACCCTCAGGGATTTTTCTTTTACTGGACAGATCAAAACAAG*GACACAGCAAGAGGCAACATTTTGGAAGCAGAGGGCAACTCTCACTG	cancer,exon-exon	BOWTIE;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	4	7	30	20	8150371	+	4	85004230	+	2.8564	0.8359	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000182621	ENSG00000180769	PLCB1	WDFY3-AS2	GGACTGACCCTCAGGGATTTTTCTTTTACTGGACAGATCAAAACAAG*GTTTATGGGACTCCCCAGTACTCTCCATGTAGAGTCTAATGTAGAAT	cancer,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	4	2	24	20	8150371	+	4	85000691	+	2.8564	0.8359	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000182621	ENSG00000180769	PLCB1	WDFY3-AS2	CTCAGGGATTTTTCTTTTACTGGACAGATCAAAACAAGGTAAGAAATGAG*GACACAGCAAGAGGCAACATTTTGGAAGCAGAGGGCAACTCTCACTGGAA	cancer,exon-exon	BOWTIE+STAR	CDS(no-known-start-or-end)/exonic(no-known-CDS)	0	4	1	15	20	8150383	+	4	85004230	+	2.8564	0.8359	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000110844	ENSG00000248572	PRPF40B	EGFLAM-AS2	CCCTGACTGGCTGGAGAACTTGCCCATCCCACTGATGGCTCCTATCCCAT*TTTTAGATTTCTTCATATCCTTTCCCTTCCTCCATGTCACTAACACTTCA	antisense	BOWTIE+STAR	UTR/intronic	0	4	15	36	12	49633416	+	5	38401735	-	2.8617	5.8337	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000110844	ENSG00000248572	PRPF40B	EGFLAM-AS2	CGGGTGCGGACACCGCCAGCTCTGCTGTGGCTGGGACAGGCCCTCCG*GAAATTCTGTTTCTTGAAGGGAACTCCTCAGAGAAAAGGACCACAAG	antisense,exon-exon	BOWTIE;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	4	15	30	12	49632880	+	5	38401221	-	2.8617	5.8337	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-25-2400-01A	ENSG00000204764	ENSG00000113719	RANBP17	ERGIC1	GTTTAAAGTTCACAAAATTCTTTTTTTTTTTTTTTTTTTACATTAAGTTC*GCCTGTGTGCTGTGTGGCAACAGCATTCTGGTTCCCACTGCCAAGATCTC	oncogene,tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer	BOWTIE+STAR	intronic/UTR	0	4	1	17	5	170892159	+	5	172951591	+	1.2231	17.5347	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-25-2400-01A	ENSG00000204764	ENSG00000113719	RANBP17	ERGIC1	TAACATTAGTTGATAAAGTGATGGCAAGGTTTGAGAGCATTGACTCCAGT*GCCCTGGCCTCCCACGACTACATCCTGAAGATTGTGCCCACGGTTTATGA	oncogene,tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer	BOWTIE+STAR	intronic/intronic	0	4	1	15	5	171079437	+	5	172932435	+	1.2231	17.5347	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-25-2400-01A	ENSG00000204764	ENSG00000113719	RANBP17	ERGIC1	GAGCCAGGTACCTCAGCCGGAAATGCAGAAATCACCTGCATTCTGTGTTG*TTCCCTCAGGGGAACATCCCAGAATGCATATCGATCAGCTCTCAGCCAGG	oncogene,tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer	BOWTIE+STAR	intronic/UTR	0	4	1	14	5	171104009	+	5	172951124	+	1.2231	17.5347	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-25-2400-01A	ENSG00000204764	ENSG00000113719	RANBP17	ERGIC1	GTATGTATAGGCATTAGTCTTATACACTTGTTAGAGGTGGCAGCACATCT*CATCCTGGACTCATGCATCTTCACAGCCTCTGAGGCCTGGAAGAAGATCC	oncogene,tcga,cell_lines,chimerdb3seq,cancer,tcga-cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	4	1	14	5	170961810	+	5	172950747	+	1.2231	17.5347	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000163867	ENSG00000076864	ZMYM6	RAP1GAP	GACTTGGTTCCTATTCCAGTGCTCCTCCGGTAGCAGGGAGGCGACAGAAG*CGGGTCATCCGGAGCCGCAGCCAGTCCATGGATGCCATGGGGCTGAGCAA	cancer,exon-exon	BOWTIE+STAR	UTR/CDS(truncated)	0	4	1	16	1	35031815	-	1	21606197	-	0.7693	7.2445	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-25-2400-01A	ENSG00000233891	ENSG00000123427	AC007179.2	EEF1AKMT3	TTGATTTTCTTTAAAAAAAAAAAATACCAACTTATAAAGCAGAGCAGCTT*GTACTTAGTCTGTGTCCATGTGATCCAAAATTACCTTCCTATTGCATTTC	lincrna	BOWTIE+STAR	intronic/UTR	0	3	1	15	2	59552482	-	12	57781941	+	0.0465	9.9133	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000257921	ENSG00000233891	AC025165.3	AC007179.2	CGAACTGGGTGCGGGGACAGGCATCGTGGGGATCTTGGCAGCGCTGCAGG*ATTTCAAGAGAGAAGGCTGAAAAGGAAGGTGACTGGAATATTAAGAACTG	lincrna,exon-exon	BOWTIE+STAR	CDS(no-known-start-or-end)/exonic(no-known-CDS)	0	3	2	18	12	57773128	+	2	59238901	-	0	0.0465	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000257921	ENSG00000233891	AC025165.3	AC007179.2	CGAACTGGGTGCGGGGACAGGCATCGTGGGGATCTTGGCAGCGCTGCAGG*GAGAGGATAACAAAGGAAGCTGAGGAAGTCTGTTCTGGAGGCACCATGAC	lincrna	BOWTIE+STAR	CDS(no-known-start-or-end)/intronic	0	3	1	29	12	57773128	+	2	59249693	-	0	0.0465	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000123427	ENSG00000233891	EEF1AKMT3	AC007179.2	ACTGGGTGCGGGGACAGGCATCGTGGGGATCTTGGCAGCGCTGCAGG*ATTTCAAGAGAGAAGGCTGAAAAGGAAGGTGACTGGAATATTAAGAA	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	3	9	29	12	57773128	+	2	59238901	-	9.9133	0.0465	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000123427	ENSG00000233891	EEF1AKMT3	AC007179.2	ACTGGGTGCGGGGACAGGCATCGTGGGGATCTTGGCAGCGCTGCAGG*GCTTGCAGAGCTCAAACCATTACACCATTCAGAAGCTGGCTTTGGTA	lincrna,exon-exon	BOWTIE;BOWTIE+STAR	CDS(truncated)/exonic(no-known-CDS)	0	3	4	25	12	57773128	+	2	59241103	-	9.9133	0.0465	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000163468	ENSG00000091831	CCT3	ESR1	CCTCCCAAGTAGCTGGGACTATAGTCACGTGCCACCACGCCCAGCTAATT*AGGAGGCTGAGGCAGGAGAATCACTTGAACCTGGGAGGCAGAGGTTGCAG	cancer	BOWTIE+STAR	UTR/intronic	0	2	1	29	1	156333142	-	6	152022870	+	96.8899	18.7544	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000105810	ENSG00000131236	CDK6	CAP1	ATGGTGCACACCTGTAGTCCCAGCTACTTGGCAGGCTGAGGTGGGAAAAT*TCCTGGCCTCAAGTGATTGCCTGTGTTGCCCTCCCAAAGTGCTGGGATTA	oncogene,cancer	BOWTIE+STAR	intronic/intronic	0	2	1	18	7	92733937	-	1	40054881	+	3.8512	781.0826	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000105810	ENSG00000131236	CDK6	CAP1	TGACCTCCTAGTAACAGCTAAGAAACACTAGTAAATGACATTAACAGAGA*AAAAAAAAAAAAAAAAAAACCCACATGATTTCAAGGAGTCTGGCATTCCT	oncogene,cancer	BOWTIE+STAR	intronic/UTR	0	2	1	16	7	92795875	-	1	40072253	+	3.8512	781.0826	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000105810	ENSG00000131236	CDK6	CAP1	TTTCCACCCCCCCACCCCCAGCTTTTTTGTAATCATGACATTAATACTAA*AAAAAAAAAAAAAAAAAAACCCACATGATTTCAAGGAGTCTGGCATTCCT	oncogene,cancer	BOWTIE+STAR	intronic/UTR	0	2	1	16	7	92820944	-	1	40072253	+	3.8512	781.0826	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000105810	ENSG00000131236	CDK6	CAP1	CTATCACGAATGATGCCGCAGTGAATATTTGTTTACCTTCACTGCGTCAT*TTTCCAGATGGTTCTTCTAACCAAACTAATTTTTCACTGTTGACAAGCGA	oncogene,cancer	BOWTIE+STAR	intronic/UTR	0	2	1	14	7	92785063	-	1	40071957	+	3.8512	781.0826	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000091831	ENSG00000163468	ESR1	CCT3	CTTTGTCAGATGGATGGATTACAAAATTTTTCTCCCATTCTGTAGGTTGC*GTTCTGCTACTGCGAATTGATGACATCGTTTCAGGCCACAAAAAGAAAGG	cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	15	6	151779045	+	1	156309297	-	18.7544	96.8899	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000091831	ENSG00000163468	ESR1	CCT3	CTCAAAACGGAAAGAGTAGTGAGGATAATTCATGAGCAATGCGTGGCTTC*TAGATTTAGCTCAGCACTACCTTATGCGGGCCAATATCACAGCCATCCGC	cancer	BOWTIE+STAR	intronic/intronic	0	2	1	14	6	151875157	+	1	156317250	-	18.7544	96.8899	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000204060	ENSG00000158321	FOXO6	AUTS2	CCGCCCCTGGGCGCGGAGGTCGGACCGCTGCGGAAAGCGAAGAGCTCTCG*ATGGCTTTTATGATGTTCTGTGTTCCTTTGAAGGTTGATCAGGCATGAGT	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	15	1	41362181	+	7	70243342	+	68.3682	10.7217	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000164109	ENSG00000109339	MAD2L1	MAPK10	GGGAATCACCCTGCGCGGGAGCGCCGAAATCGTGGCCGAGTTCTTCT*GTATTTATGAGCCTCCATTTCTTATACTACTGCAGTGAACCAACATT	cancer,exon-exon	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	2	5	28	4	120066662	-	4	86194407	-	4.0728	0.1086	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000169288	ENSG00000251527	MRPL1	AC097110.1	GCAATCCGGAGTGCCCAACATGGCGGCGGCCGTAAGGTGCATGGGTAGAG*GGACATGGATGAAGCTGAAAACCATCATTCTCAGCAAACTAACACAGGAA	lincrna,ribosomal	BOWTIE+BLAT	CDS(truncated)/exonic(no-known-CDS)	0	2	14	37	4	77862879	+	4	65858762	+	12.7028	3.3869	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000169288	ENSG00000251527	MRPL1	AC097110.1	GGTGCTGAAAATGCCTCGTGCTGTTTCTGGTCTCTAGGTTTTTCAGAGGG*GACATGGATGAAGCTGAAAACCATCATTCTCAGCAAACTAACACAGGAAC	lincrna,ribosomal	BOWTIE+BOWTIE2	intronic/exonic(no-known-CDS)	0	2	1	25	4	77863014	+	4	65858763	+	12.7028	3.3869	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-25-2400-01A	ENSG00000174231	ENSG00000146729	PRPF8	NIPSNAP2	GGAATCCCGCTTTGAGAAGATGTATGAGAAGATCGACTTGACTCTGCTCA*TACATTTTCTCAAAAAAATTAGTATAGCTACAGAAAAGTATGCTTACATT	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	15	17	1675232	-	7	55994357	+	86.9282	26.9717	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-25-2400-01A	ENSG00000174231	ENSG00000146729	PRPF8	NIPSNAP2	TGGATTTGCTTGTATTGGGATTGCACCGGGCCAGTGAGATGGCTGGGCCC*ATCCATCTCACTGGATTGTCTCACTATATCACTCAGGCTCTAATTTTTGT	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	14	17	1674549	-	7	55954724	+	86.9282	26.9717	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-25-2400-01A	ENSG00000174231	ENSG00000146729	PRPF8	NIPSNAP2	ATTCATCGTGCAGTATTATGGCCTGGTGATGGATTTGCTTGTATTGGGAT*CAGAGTGGTCCCAGCCTTTCTTTGTAGACTGACTGCTTACTTCCTCGACA	NA	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	14	17	1674578	-	7	55995277	+	86.9282	26.9717	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-25-2400-01A	ENSG00000132670	ENSG00000127774	PTPRA	EMC6	AACCATGAACACCAGACCCGCAATCAGTAGGAGTACCCGCGGGGCCCTCT*TGCTCCTCATTCTCAAGGCGGGAAGGAGGTGGAACAAATATTTCAAATCA	cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	15	20	2867456	+	17	3669337	+	48.7102	2.6047	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000084070	ENSG00000130985	SMAP2	UBA1	TACAGTAAGCCAAGATCACACCATTGCACTCTAGACTGGGCGACAGAGCA*TCAGAGCAAGCTGATTGCAGGGAAGATCATCCCAGCCATTGCCACGACCA	NA	BOWTIE+STAR	intronic/intronic	0	2	1	16	1	40358531	+	X	47212986	+	141.7587	442.7795	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000130340	ENSG00000049618	SNX9	ARID1B	CTACTTTAAGGATTCAGAGTCAGCTGATGCAGGCGGCGCTCAGCGAGGAA*TTAGCAAGACTGTTTCAAGTACTGTTCAAGAATTATGATAAGATGAACAC	known,tcga,cell_lines,chimerdb3pub,chimerdb3seq,cancer,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	2	2	16	6	157902002	+	6	157012047	+	16.9578	3.9116	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000130340	ENSG00000049618	SNX9	ARID1B	GAAACTTCTTTATTTGACGACTAGAATAGAAATATCTTTCTAACAGGTCT*GCTGTGCAGAAAGGAAGCATTGGAAACTTGATAAGCTTCCTAGAGGATGG	known,tcga,cell_lines,chimerdb3pub,chimerdb3seq,cancer,tcga-cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	16	6	157828111	+	6	157207589	+	16.9578	3.9116	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000130340	ENSG00000049618	SNX9	ARID1B	GGGATGTGGGAGGGAAGGTGAGAGTTGGGCTAGAAGTGAGAGGCTACAGC*CAGCAGAGCAGTCCGTACCCAGGAGGTTCCTATGGCCCTCCAGGCCCACA	known,tcga,cell_lines,chimerdb3pub,chimerdb3seq,cancer,tcga-cancer	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	15	6	157774329	+	6	156829302	+	16.9578	3.9116	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-25-2400-01A	ENSG00000108639	ENSG00000270647	SYNGR2	TAF15	TCTGGGGTCGCATTCCGCACAAGCCTTTCATCAACATCTTAAAATAGTAA*AAAAAAAAAAAAAAAGATGATGTTCAAATGTATTATATGGAGGAATAGGA	oncogene,cancer,tumor	BOWTIE+STAR	UTR/intronic	0	2	1	17	17	78172923	+	17	35831407	+	76.1963	17.363	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-25-2400-01A	ENSG00000108639	ENSG00000270647	SYNGR2	TAF15	ACTCCGGACCCCAACACTGCCTACGCCTCCTACCCAGGTGCATCTGTGGA*GGAGGCTTGGGCATGTTTTAAAAGAGCCCCAGGTGATTCTAGTTTTTGGA	oncogene,cancer,tumor	BOWTIE+STAR	CDS(truncated)/intronic	0	2	1	14	17	78171863	+	17	35849205	+	76.1963	17.363	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-25-2400-01A	ENSG00000108639	ENSG00000270647	SYNGR2	TAF15	GAGTGTATTATAAAATCGTGGGGGAGATGCCCGGCCTGGGATGCTGTTTG*AATGATAAAAAATTTTGCAAGTGTTTTAGTTTTCTTTGGATATTAGAAAG	oncogene,cancer,tumor	BOWTIE+STAR	UTR/intronic	0	2	1	14	17	78172693	+	17	35819263	+	76.1963	17.363	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-25-2400-01A	ENSG00000108639	ENSG00000270647	SYNGR2	TAF15	AGAGAGGGCCCTCCCCTCTGCCCTGGACTTTCCCATGAGCCTCCTGGAAC*AAGAGAAAGAGAGGCATTAGTCTCTTCAGGACAACCAGTTTGGATCCTGC	oncogene,cancer,tumor	BOWTIE+STAR	UTR/UTR	0	2	1	14	17	78172012	+	17	35810390	+	76.1963	17.363	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Ovarian	TCGA-25-2400-01A	ENSG00000108639	ENSG00000270647	SYNGR2	TAF15	AGTGCCTCAGCTTCCCCCCGGCCCGGGTCAGGCCGTGGGAGCCGCTATTA*ATTACCTCTTCCCCTCCCCTCCATAACCCAATTCTCTTCTGTTGGACATG	oncogene,cancer,tumor	BOWTIE+STAR	UTR/intergenic	0	2	1	14	17	78172308	+	17	35807697	+	76.1963	17.363	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000164674	ENSG00000130338	SYTL3	TULP4	TTCATGCCACTTACACAGCTTCTTTGGGAATAGCATTTTTTTTTTTTTTT*TTTTTTTTTTTTTTAACCGTAAGTGCACGATGCAGGTGCATAGGCCCCAG	100K<gap<200K	BOWTIE+STAR	intronic/UTR	0	2	1	18	6	158673455	+	6	158511391	+	4.1852	2.9343	FALSE	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000130338	ENSG00000164674	TULP4	SYTL3	GAGAGGCACGGAGGAGCCGCTGGGGCTGCCGCCACGGCCGCCCGGAG*GGAAGTTTAATTAGCATTGACAGCACCTGTACAGAGATGGGCAATTT	100K<gap<200K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	2	5	22	6	158232303	+	6	158745480	+	2.9343	4.1852	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000130338	ENSG00000164674	TULP4	SYTL3	CGCACCCGGCCTAGACCCAATTTAGTCCTTTATGGATTTGAAATGATTTG*GGAAGTTTAATTAGCATTGACAGCACCTGTACAGAGATGGGCAATTTTGA	100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	33	6	158245333	+	6	158745480	+	2.9343	4.1852	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Ovarian	TCGA-25-2400-01A	ENSG00000130338	ENSG00000164674	TULP4	SYTL3	GCGGAGAGGCACGGAGGAGCCGCTGGGGCTGCCGCCACGGCCGCCCGGAG*AAATATGCATCAAGGCCTGTAAGAACCTTGCCTATGGAGAAGAAAAGAAG	100K<gap<200K	BOWTIE+STAR	UTR/CDS(truncated)	0	2	1	18	6	158232303	+	6	158745595	+	2.9343	4.1852	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Ovarian	TCGA-25-2400-01A	ENSG00000130985	ENSG00000084070	UBA1	SMAP2	AATGAGTTTAACAGCTGGTTTGTCAGGATGATTCTGTGTGTATGGTGCAT*AGCCAGGAGCTTCTGGGATGGTTGCCCCCATGGCCATGCCTGCAGGCTAT	NA	BOWTIE+STAR	intronic/CDS(truncated)	0	2	1	15	X	47207251	+	1	40416900	+	442.7795	141.7587	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-13-0727-01A	ENSG00000101266	ENSG00000256566	CSNK2A1	AL049650.1	TGTGTGAGCAGAGGGGAGAGCGGCCGCCGCCGCTGCCGCTTCCACCACAG*ACGGTGGGCAAGAGCAGCAAGATGCTGCAGCATATTGATTACAGGATGAG	oncogene,cancer,exon-exon	BOWTIE+BLAT;BOWTIE+STAR	UTR/CDS(truncated)	0	45	7	19	20	543672	-	20	2467758	-	10.7718	0	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-13-0727-01A	ENSG00000181143	ENSG00000174667	MUC16	OR7D4	AACACCAGTGTTGGCCCTCTGTACTCTGGCTGCAGACTGACCTCTCTCAG*AGATGGAGTCTTGCTATGTTGCCCAGGCTGGTCTTGAACTTCTGGTCTCA	cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	13	8	36	19	8910089	-	19	9210439	-	53.4485	2.4588	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Ovarian	TCGA-13-0727-01A	ENSG00000181143	ENSG00000174667	MUC16	OR7D4	AACACCAGTGTTGGCCCTCTGTACTCTGGCTGCAGACTGACCTCTCTCAG*ATGTCTTGCTCTGTTGCCCAAGCTGCAGTGAAGCGGCTCAGTCATAGCTC	cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	13	4	34	19	8910089	-	19	9210572	-	53.4485	2.4588	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Ovarian	TCGA-13-0727-01A	ENSG00000181143	ENSG00000174667	MUC16	OR7D4	AACACCAGTGTTGGCCCTCTGTACTCTGGCTGCAGACTGACCTCTCTCAG*CATTTCCCCATATCTAACAAGACTGCAATCAGATGTCAGCCAGGGTTGCA	cancer	BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR	CDS(truncated)/UTR	0	13	3	34	19	8910089	-	19	9211341	-	53.4485	2.4588	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Ovarian	TCGA-13-0727-01A	ENSG00000181143	ENSG00000174667	MUC16	OR7D4	CACTCCAGTAGATTTTGCTCTGCTTCCTTGCTGCACCTCCTAGGGATATC*TTTTTCTCTTTTAAAAAATGTGCTTGATGTGGGATTTTTGGTTGTTGTTA	cancer	BOWTIE+BOWTIE2	intronic/UTR	0	13	1	37	19	8909997	-	19	9213822	-	53.4485	2.4588	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Ovarian	TCGA-13-0727-01A	ENSG00000181143	ENSG00000174667	MUC16	OR7D4	AGAAAGACCAGCAGCTCTGAGGGGACCAGCTTAGCCACAGAGATGAGCAC*AGACTGAGATGGAGGTAGAGTATATCCTAACAATCTGACACTTTGCCCAC	cancer	BOWTIE+STAR	CDS(truncated)/UTR	0	13	1	16	19	8952351	-	19	9213016	-	53.4485	2.4588	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Ovarian	TCGA-13-0727-01A	ENSG00000181143	ENSG00000174667	MUC16	OR7D4	AATCACCACGAACAGACTGACAGCTACTCAATCAACAGCACCCAAAGGGA*GAGAAGAATATGTTGCACCTTTTTTTTTTTTTTTTTTTTTTTGAGATGGA	cancer	BOWTIE+STAR	CDS(truncated)/UTR	0	13	1	15	19	8972597	-	19	9211816	-	53.4485	2.4588	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Ovarian	TCGA-13-0727-01A	ENSG00000035403	ENSG00000229990	VCL	AC022400.2	GTGTGTTACAACTCACCTCTTGGGATGAAGATGCCTGGGCCAGCAAG*GTTAACGTTCTGAGGACCTCGTTATTTGCCAAGAACAAGCACAGGGG	antisense,cancer,100K<gap<200K,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	5	7	29	10	74074903	+	10	73846335	+	15.0937	0.64	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-04-1331-01A	ENSG00000145996	ENSG00000112699	CDKAL1	GMDS	AGAATATATGGCTGGACAGCTAGCTGCTTATGGCTATAAAATTACAG*ATTTCCTTTGACCTCGCTGAGTACACTGCGGACGTTGACGGAGTTGG	exon-exon	BOWTIE;BOWTIE+STAR	out-of-frame	0	4	6	24	6	20548705	+	6	1960966	-	8.9346	5.3683	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Ovarian	TCGA-04-1331-01A	ENSG00000145996	ENSG00000112699	CDKAL1	GMDS	GGCGACCTAACCTTGGTGACCGCAAGCGATCGGTTGTGAGAGAAAGAGCT*ATTTCCTTTGACCTCGCTGAGTACACTGCGGACGTTGACGGAGTTGGCAC	NA	BOWTIE+BOWTIE2;BOWTIE+STAR	intronic/CDS(truncated)	0	4	1	31	6	20577157	+	6	1960966	-	8.9346	5.3683	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-B0-5695-01A	ENSG00000172340	ENSG00000234323	SUCLG2	LINC01505	CGAAAATCTAGGCTTCGTTGGGCCTTTGAAAAGCCAG*GTCTGATTATAAAAGGAGAATTGGAGGCTTACCAAAC	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	5	2	19	3	67518247	-	9	106499487	+	20.3476	0.1647	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-B0-5695-01A	ENSG00000172340	ENSG00000234323	SUCLG2	LINC01505	CTCAGCGGATGGCCGAAAATCTAGGCTTCGTTGGGCCTTTGAAAAGCCAG*GAGGAAGTTTGACTTGCAAAGAAATGGAGAGTGAATGAAGCTGCAGGAAA	lincrna	BOWTIE+STAR	CDS(truncated)/intronic	0	5	1	19	3	67518247	-	9	106441862	+	20.3476	0.1647	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-B0-5695-01A	ENSG00000172340	ENSG00000234323	SUCLG2	LINC01505	CGAAAATCTAGGCTTCGTTGGGCCTTTGAAAAGCCAG*ACATTCTTATTCAAAAGAAAGAACACCGAAATTGACC	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	5	1	13	3	67518247	-	9	106603756	+	20.3476	0.1647	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Kidney	TCGA-B2-4102-01A	ENSG00000196240	ENSG00000224521	OR2T2	AC098483.1	CTTGTCCATTGGTGATATCCTTGACAATGTAGTTTAG*ATGATAAAGAAAAAATGAGGAAATGCTGTGAAGAACT	antisense,m11,10K<gap<100K,exon-exon	BOWTIE	UTR/exonic(no-known-CDS)	0	14	6	24	1	248446811	+	1	248562600	+	0.277	0.1492	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-B2-4102-01A	ENSG00000189283	ENSG00000152495	FHIT	CAMK4	ACATCCAGACGGTGGAAGGGAGAGAAAGAGAAAGAAG*GGGTGCTACATCCATTGTGTACAGATGCAAACAGAAG	known,tcga,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	11	5	24	3	61042047	-	5	111344024	+	1.0228	0.6838	TRUE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-B2-3924-01A	ENSG00000130396	ENSG00000120440	AFDN	TTLL2	GGCTGGACCTGTTCGAGATCAGCCAGCCGACCGAG*ATCTTTGAGAACCACCACCCCAGCCTTTACCCTTA	oncogene,cancer,tumor,m7,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	10	2	24	6	167827237	+	6	167338647	+	13.4865	3.7225	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Kidney	TCGA-CW-5585-01A	ENSG00000142599	ENSG00000107611	RERE	CUBN	ATGGTGAAACCCCGTCTCTACTAAAAATACAAAAAAAAAAAATTAGCCCG*GCATGGTGGCATGCACCCGTGGTTCCAGCTACACAGGAGGTTGAAGCAGG	oncogene,cancer	BOWTIE+STAR	intronic/UTR	0	2	2	22	1	8446833	-	10	16824211	-	24.4272	106.4424	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Kidney	TCGA-CW-5585-01A	ENSG00000142599	ENSG00000107611	RERE	CUBN	TGTTTGTTTGAAACAGAGTCTTACCCTGTCGCCCAGGCTGGAGTACAGTG*GTTAAGGCTGCAGTGAAACCCTGTGAATTAACCACTGTACTCCAGCCTGG	oncogene,cancer	BOWTIE+BLAT;BOWTIE+STAR	intronic/UTR	0	2	1	18	1	8454764	-	10	16824140	-	24.4272	106.4424	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Kidney	TCGA-CW-5585-01A	ENSG00000142599	ENSG00000107611	RERE	CUBN	TTATATTTGGAGACAAAGTTTCGCTCTGTCACCCAGGCTGGAGTACAGTG*GTTAAGGCTGCAGTGAAACCCTGTGAATTAACCACTGTACTCCAGCCTGG	oncogene,cancer	BOWTIE+STAR	intronic/UTR	0	2	1	18	1	8767925	-	10	16824140	-	24.4272	106.4424	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-B2-5633-01A	ENSG00000137494	ENSG00000181722	ANKRD42	ZBTB20	TGGTGCAGTCTCGGCTTGCTGCAACCTCTGCCTCCCGGATTCAAGCGATT*CTTCTGCCTCCCGGATTCAAGCATTTCTCATGCCTCAGGTTCCCAAGTAG	NA	BOWTIE+BLAT	UTR/intronic	0	2	1	21	11	83213997	+	3	114964351	-	4.8594	0.6796	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-AK-3428-01A	ENSG00000241684	ENSG00000144724	ADAMTS9-AS2	PTPRG	ACGACAGCGCACTGATGGAGCAGCCCAGTGTCTGGGG*TCGCCATCCTTCTGAAAGACGACTATTTTGTCAGTGG	antisense,18cancers,cancer,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	10	5	23	3	64685338	+	3	62003349	+	1.4564	5.8215	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-B2-3924-01B	ENSG00000130396	ENSG00000120440	AFDN	TTLL2	GGCTGGACCTGTTCGAGATCAGCCAGCCGACCGAG*ATCTTTGAGAACCACCACCCCAGCCTTTACCCTTA	oncogene,cancer,tumor,m3,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	4	2	23	6	167827237	+	6	167338647	+	26.512	11.3261	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-B2-3924-01B	ENSG00000130396	ENSG00000120440	AFDN	TTLL2	ACTGGAACGCCAACCGGCTGGACCTGTTCGAGATCAGCCAGCCGACCGAG*AGCCTGTCTTGGATGGAAGAAAGCACCAAAACTAGGAGCTGTCGGCTAAG	oncogene,cancer,tumor,m3,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/UTR	0	4	1	22	6	167827237	+	6	167328162	+	26.512	11.3261	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-B2-3924-01B	ENSG00000130396	ENSG00000120440	AFDN	TTLL2	ACTGGAACGCCAACCGGCTGGACCTGTTCGAGATCAGCCAGCCGACCGAG*GACGACATTTCCAGCTTCATCTTTGATCTTAACCCTCCCGGAGGCATACT	oncogene,cancer,tumor,m3,tcga-cancer	BOWTIE+STAR	CDS(truncated)/UTR	0	4	1	15	6	167827237	+	6	167358122	+	26.512	11.3261	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-CW-6087-01A	ENSG00000080845	ENSG00000124208	DLGAP4	TMEM189-UBE2V1	GCCCTCATGGCTTTGTGTCTGGAGCTCTTGAAGCAAT*TTGCAGGGGCTCTCATTGCTGACTTCTTGTCTGGCCT	exon-exon	BOWTIE	in-frame	0	4	2	19	20	36462599	+	20	50130947	-	11.8783	0	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-A3-3308-01A	ENSG00000167384	ENSG00000196739	ZNF180	COL27A1	TAAACTTATTAGGCATCAGGCAACTCATACTGAAGAGAAACTCTATGAAT*GGTGACTTAGGAGTGTTGGGTCCGATTGGCTACCCGGGACCCAAGGGCAT	18cancers	BOWTIE+BLAT;BOWTIE+STAR	out-of-frame	0	6	2	24	19	44476410	-	9	114231079	+	3.439	14.3531	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-A3-3308-01A	ENSG00000167384	ENSG00000196739	ZNF180	COL27A1	ATGCCTTACTCAACATCAGAGAACTCATACTGGAGAGAAACCATTTGAAT*GGTGACTTAGGAGTGTTGGGTCCGATTGGCTACCCGGGACCCAAGGGCAT	18cancers	BOWTIE+STAR	out-of-frame	0	6	1	18	19	44476578	-	9	114231079	+	3.439	14.3531	FALSE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-BP-4781-01A	ENSG00000065534	ENSG00000122584	MYLK	NXPH1	TATCTGACTTCTACGACATTGAGGAGAGATTAGGATC*GTCACATGTGCCAATTTAACGAACGGTGGAAAGTCAG	known,tcga,18cancers,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	8	3	25	3	123648971	-	7	8751008	+	5.7596	0.6925	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-B2-3924-01A	ENSG00000130396	ENSG00000120440	AFDN	TTLL2	CCGGCTGGACCTGTTCGAGATCAGCCAGCCGACCGAG*ATCTTTGAGAACCACCACCCCAGCCTTTACCCTTAAC	oncogene,cancer,tumor,m17,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	18	2	20	6	167827237	+	6	167338647	+	9.9705	2.9847	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-B2-3924-01A	ENSG00000130396	ENSG00000120440	AFDN	TTLL2	ACTGGAACGCCAACCGGCTGGACCTGTTCGAGATCAGCCAGCCGACCGAG*GACGACATTTCCAGCTTCATCTTTGATCTTAACCCTCCCGGAGGCATACT	oncogene,cancer,tumor,m17,tcga-cancer	BOWTIE+STAR	CDS(truncated)/UTR	0	18	1	25	6	167827237	+	6	167358122	+	9.9705	2.9847	FALSE	FALSE	TRUE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-B2-4101-01A	ENSG00000113391	ENSG00000189283	FAM172A	FHIT	TGGCACACAGATACCGTTTATTAAAAGAGCTGTGGCT*CTCCAGAAACATGACAAGGAGGACTTTCCTGCCTCTT	tcga,cell_lines,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	37	15	25	5	93958777	-	3	59752321	-	8.6875	2.1465	TRUE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-B2-4101-01A	ENSG00000113391	ENSG00000189283	FAM172A	FHIT	CAGATGGAACCAGAAAAGATACGAGGCTCTAGGAGAG*CTCCAGAAACATGACAAGGAGGACTTTCCTGCCTCTT	tcga,cell_lines,18cancers,chimerdb3seq,cancer,tumor,tcga-cancer,exon-exon	BOWTIE	in-frame	0	37	2	21	5	94050731	-	3	59752321	-	8.6875	2.1465	TRUE	TRUE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-A3-3363-01A	ENSG00000126870	ENSG00000106018	WDR60	VIPR2	TGATGCATATACAGCCAGTTGTGAAGATGATTTTGAA*ATCACGTTTTATATTCTGGTGAAGGCCATTTATACAC	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	16	9	24	7	158901816	+	7	159058578	-	10.849	1.1721	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-A3-3363-01A	ENSG00000126870	ENSG00000106018	WDR60	VIPR2	GAAGCTGGACCAGAGGCCGGGAGGCGAGGAAACCGTG*ATCACGTTTTATATTCTGGTGAAGGCCATTTATACAC	tcga,cell_lines,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	16	8	24	7	158891333	+	7	159058578	-	10.849	1.1721	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-A3-3363-01A	ENSG00000158623	ENSG00000013374	COPG2	NUB1	ACTAAAAATACAAAAAAATTGGCCGGGCGCGGTGGCTCACACCTGTAATC*CCAGCCTCCCTTCTGCATTTATTGCTGGAATTCTGAAAAATTTGTTTTTG	NA	BOWTIE+BLAT	intronic/UTR	0	2	1	21	7	130651786	-	7	151361075	+	15.2071	31.3585	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-CJ-5681-01A	ENSG00000125676	ENSG00000234052	THOC2	LINC01673	AAGCTCAAACAATAGACAGAGCCAAATATATCATGAA*GCCACTGTCTAGACCACAGGAAACCTGGTCAACAACA	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	83	12	24	X	123644575	-	21	27648665	+	6.0636	7.8009	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-CJ-5681-01A	ENSG00000125676	ENSG00000234052	THOC2	LINC01673	AAGCTCAAACAATAGACAGAGCCAAATATATCATGAA*AAACCTGAGCCTGAGAATTTGCTTATGGATTGTATAT	lincrna,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	83	8	20	X	123644575	-	21	27653356	+	6.0636	7.8009	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-CJ-5681-01A	ENSG00000180573	ENSG00000145685	HIST1H2AC	LHFPL2	CTCACTGCTTGTAGGTAGAAGGAAAAAAGGCACTAAG*GTGGCATTTTTCTGAAGTTGTTCATTAAGACTTCCCA	tcga,chimerdb3seq,m78,tcga-cancer,exon-exon	BOWTIE	UTR/UTR	0	79	10	24	6	26124749	+	5	78564871	-	28.9442	9.66	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-CJ-5681-01A	ENSG00000180573	ENSG00000145685	HIST1H2AC	LHFPL2	AGAGTCACCACAAGGCCAAGGGCAAGTGATTTGACAG*GTGGCATTTTTCTGAAGTTGTTCATTAAGACTTCCCA	tcga,chimerdb3seq,m78,tcga-cancer,exon-exon	BOWTIE	UTR/UTR	0	79	2	22	6	26124633	+	5	78564871	-	28.9442	9.66	FALSE	FALSE	FALSE	TRUE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-CJ-5681-01A	ENSG00000145685	ENSG00000180573	LHFPL2	HIST1H2AC	TCATGCAAGCGAGGGACCTGGGACTGCTCACAGCCAG*GTTGCAAAAGCTTCTCATTTCAGAGAGATGCCAGGAT	tcga,chimerdb3seq,m78,tcga-cancer,exon-exon	BOWTIE	UTR/UTR	0	79	12	25	5	78632264	-	6	26138054	+	9.66	28.9442	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-CJ-5681-01A	ENSG00000145685	ENSG00000180573	LHFPL2	HIST1H2AC	GTTAAGAAGCACCTCATGCAAGCGAGGGACCTGGGACTGCTCACAGCCAG*AAAATGTCTTCTGAGGCTGATCTGGTGTCTCACATCTGTAATCCCAGCAC	tcga,chimerdb3seq,m78,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	UTR/intronic	0	79	4	25	5	78632264	-	6	26127698	+	9.66	28.9442	FALSE	FALSE	TRUE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-CJ-5681-01A	ENSG00000150938	ENSG00000115353	CRIM1	TACR1	GTCTTGAGAAAAGGCCAGTGTTGTCCCTACTGCATAG*GTACATGGCCATCATACATCCCCTCCAGCCCCGGCTG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	33	12	25	2	36522313	+	2	75120768	-	20.0569	1.023	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-CJ-5681-01A	ENSG00000150938	ENSG00000115353	CRIM1	TACR1	ATCAACGTGGAAGGAAGTTGCTGCCCAATGTGTCCAG*GTACATGGCCATCATACATCCCCTCCAGCCCCGGCTG	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	33	10	25	2	36537546	+	2	75120768	-	20.0569	1.023	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-CJ-5681-01A	ENSG00000150938	ENSG00000115353	CRIM1	TACR1	TTTAGGGGAAGAGAAAGGAGAGGAAATGGCCAAGAAGTCCATAAGAAGTG*TACCTTCATGGCTGCAGTGGGGAAACCAGCCAGCATAGATTCTCCTTTGC	tcga,chimerdb3seq,tcga-cancer	BOWTIE+BLAT	intronic/intronic	0	33	1	20	2	36543943	+	2	75139489	-	20.0569	1.023	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-CJ-5681-01A	ENSG00000215533	ENSG00000009694	LINC00189	TENM1	CATGTTTGAATTTCAGATGTGTTCCTCAATGAATCAC*AGGACTGCCTAGACCCAATGTGTTCCAACCATGGCAT	exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	33	13	24	21	29194260	+	X	124641991	-	6.074	0.0954	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	sense_overlapping	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-CJ-5681-01A	ENSG00000160305	ENSG00000125676	DIP2A	THOC2	GAGAGCCTGGCTGAGCTGGAGCTGGAGCTGTCGGAAG*CTTCTTCCGGCTGATAATTGCATTATGGATGAACACA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	16	8	23	21	46459222	+	X	123668314	-	3.1844	6.0636	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-CJ-5681-01A	ENSG00000011677	ENSG00000147202	GABRA3	DIAPH2	TGACCTTTTGGGCCATGTTGTTGGGACAGAGATAATCCGGTCTAGTACAG*GTACTGTTGAGCCATGTTCCTTAACAAAAAGCTACAGCTTTACAAAGACT	tcga,chimerdb3seq,tcga-cancer	BOWTIE+STAR	CDS(truncated)/intronic	0	13	11	23	X	152208001	-	X	97348081	+	1.1289	0.913	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-CJ-5681-01A	ENSG00000011677	ENSG00000147202	GABRA3	DIAPH2	CATGTTGTTGGGACAGAGATAATCCGGTCTAGTACAG*AGGGTGATGAGACTGGTGTGATGGATAATCTTCTAGA	tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	13	1	14	X	152208001	-	X	97429650	+	1.1289	0.913	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-CJ-5681-01A	ENSG00000088247	ENSG00000068323	KHSRP	TFE3	CAGGTCCTGGCGGCCCCCAGCCGCCGCCCACGCAGCAGGGACAGCAGCAG*GCCCTCACCCCACCGCCGGGGCCCGCAAGTGCCCAGCCACTGCCTGCCCC	known,oncogene,cancer,tumor	BOWTIE+BLAT	in-frame	0	10	8	25	19	6415141	-	X	49038334	-	28.4195	30.3729	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-CJ-5681-01A	ENSG00000088247	ENSG00000068323	KHSRP	TFE3	CAATCTGGCCACTTGGGAAGAAAACGTCTATTTTTTCCCCTTCTCTGCAT*CCCAGGCCCTCACCCCACCGCCGGGGCCCGCAAGTGCCCAGCCACTGCCT	known,oncogene,cancer,tumor	BOWTIE+BLAT	UTR/CDS(truncated)	0	10	1	19	19	6414726	-	X	49038339	-	28.4195	30.3729	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-CJ-5681-01A	ENSG00000223692	ENSG00000125676	DIP2A-IT1	THOC2	ATCAGGATGTTCATTGATGGAAGTGAGATCATTAGAG*CTTCTTCCGGCTGATAATTGCATTATGGATGAACACA	exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	7	3	16	21	46463228	+	X	123668314	-	0.2958	6.0636	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	sense_intronic	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-CJ-5681-01A	ENSG00000142149	ENSG00000013619	HUNK	MAMLD1	GGTGCGCGAGGGGCTGCACGTGCTGACCGGGGAGAAG*GGAACTGTTAAGAGGAGACAAGAAGAAGACCACTTCC	known,tcga,chimerdb3seq,tcga-cancer,exon-exon	BOWTIE	in-frame	0	6	5	25	21	31873935	+	X	150469745	+	1.4658	3.7556	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-CJ-5681-01A	ENSG00000160199	ENSG00000101812	PKNOX1	H2BFM	GCAGCCGCTTGTCAGTGTGATGAAGATTGGCACCCAG*AACTTCATTATGTGCGATATGGCAACAGAGAAAGTGA	tcga,chimerdb3seq,cancer,tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	5	3	25	21	42974664	+	X	104040828	+	2.4139	5.9399	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-CJ-5681-01A	ENSG00000233818	ENSG00000142207	AP000695.2	URB1	GGGAATTAAAGCCAGCACCCAGTTAAAGCCAGTGAGGACAGCACTCCAAG*AGGAGCACATGTACCTGAAGGTCAGCAACTTCCTGCTGTCGCATGAGTAC	antisense	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	4	1	22	21	36478772	+	21	32322584	-	2.3647	6.5437	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Kidney	TCGA-CJ-5681-01A	ENSG00000111716	ENSG00000136881	LDHB	BAAT	GAGGGTGACACCAAGAAATCTGTAAGAGATCCACCCCCATGACCCAAACA*TCCCTAGTGTTGGAGGTGAGGCCTGGTGGGAGTTGTTTGGGTCATGGGGG	oncogene	BOWTIE+BLAT	intronic/UTR	0	3	1	21	12	21715428	-	9	101360741	-	7.2161	1357.2525	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Kidney	TCGA-CJ-5681-01A	ENSG00000111716	ENSG00000136881	LDHB	BAAT	GAGGGTGACACCAAGAAATCTGTAAGAGATCCACCCCCATGACCCAAACA*CTCCTCCCCATCCTCACACTCTTTCTTGCCTCCTCTCTCGCCATGTGAGA	oncogene	BOWTIE+BLAT	intronic/UTR	0	3	1	21	12	21715428	-	9	101360603	-	7.2161	1357.2525	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-CJ-5681-01A	ENSG00000173276	ENSG00000160224	ZBTB21	AIRE	GAAAGGGGCCCGGCGTCTGCCTCGAGACTGAAGACCG*GATGACACTGCCAGTCACGAGCCCGCTCTGCACAGGG	exon-exon	BOWTIE	UTR/CDS(truncated)	0	3	3	22	21	42010252	-	21	44296383	+	1.4831	0.4485	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Kidney	TCGA-HE-A5NK-01A	ENSG00000133030	ENSG00000141030	MPRIP	COPS3	AGCACGGCCTCTTGCGCTACGCCCTGGATGAGATG*AGTATGGGCTCACAAGAAGATGATTCAGGAAACAA	oncogene,tcga-cancer,exon-exon	BOWTIE	in-frame	0	49	7	22	17	17078076	+	17	17247151	-	3.2183	10.4734	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-B9-A44B-01A	ENSG00000077312	ENSG00000089847	SNRPA	ANKRD24	TATCAACAACCTCAATGAGAAGATCAAGAAGGATG*CTGCGGCTCAGCCCCACTGACCTTGGCTCCTGCCC	18cancers,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	13	3	22	19	40751481	+	19	4199683	+	21.4728	37.6975	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-B9-A44B-01A	ENSG00000077312	ENSG00000089847	SNRPA	ANKRD24	AAAAAAAGAACTCAATTATTGAAATCGGAAAGACTCTCTCACATTCTCAA*CTGCGGCTCAGCCCCACTGACCTTGGCTCCTGCCCGCCCTGCGGCCCCTG	18cancers,tcga-cancer	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	13	1	24	19	40752810	+	19	4199683	+	21.4728	37.6975	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-AL-3466-01A	ENSG00000109586	ENSG00000248388	GALNT7	AC093801.1	TCCGCCCATTTATGTTGGGTCTTCTCCAACTCTGAAG*ATTAAAAAAAATGTGTCACAAGAAAGTTTACAGAACC	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	7	2	24	4	173304118	+	4	176705903	+	6.1776	5.7999	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Kidney	TCGA-IA-A40X-01A	ENSG00000167522	ENSG00000090565	ANKRD11	RAB11FIP3	GGGCGCCAATGGGGAGCAGAAGGACTCGGACACAG*GCCTCACCCCCATGGCCAGTCTGTCATCACGGTGA	exon-exon	BOWTIE	out-of-frame	0	25	4	23	16	89305206	-	16	488851	+	3.5558	30.0264	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	FALSE	Kidney	TCGA-IA-A40X-01A	ENSG00000167522	ENSG00000090565	ANKRD11	RAB11FIP3	GTAGTGGGCTGCGGCTCAGACCCCACACCTGTGAGAGACACAGGCCTCTC*CCCCATGGCCAGTCTGTCATCACGGTGATCGGGGGCGAGGAGCACTTTGA	NA	BOWTIE+STAR	intronic/CDS(truncated)	0	25	1	14	16	89439944	-	16	488858	+	3.5558	30.0264	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Kidney	TCGA-IA-A40X-01A	ENSG00000066813	ENSG00000134250	ACSM2B	NOTCH2	CCTGCAGATGGCCTATTGTGGGACCTTGTGATCAT*CTCTAAAGTCTTTCTGGAAATTGACAACCGCCAGT	cell_lines,cancer,m2,exon-exon	BOWTIE	UTR/CDS(truncated)	0	18	8	23	16	20575422	-	1	119922778	-	15.1684	17.1521	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Kidney	TCGA-IA-A40X-01A	ENSG00000066813	ENSG00000134250	ACSM2B	NOTCH2	TCTCTCCAGAAAGACATCCTGAGAGGACTTGGCAG*CTCTAAAGTCTTTCTGGAAATTGACAACCGCCAGT	cell_lines,cancer,m2,exon-exon	BOWTIE	UTR/CDS(truncated)	0	18	1	14	16	20576207	-	1	119922778	-	15.1684	17.1521	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Kidney	TCGA-GL-A59R-01A	ENSG00000234768	ENSG00000130396	AL611929.1	AFDN	GGGGACACATTCGAACCTCAGCCAGGTACAAGCAG*GGTGCTGGTCAAGATAAACTAGGAATCTATGTGAA	lincrna,oncogene,cancer,tumor,exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	2	2	21	6	168194688	+	6	167943129	+	2.5535	13.1528	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-B9-4117-01A	ENSG00000173273	ENSG00000126858	TNKS	RHOT1	TCTAAATGTGAATTGCCATGCAAGTGATGGGCGAAAG*GCATGAAAACAGCCCTGGAAGTCTGCCCTGGCGCCTG	exon-exon	BOWTIE	out-of-frame	0	149	14	24	8	9680800	+	17	32253085	+	1.1701	7.0125	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-AL-A5DJ-01A	ENSG00000138495	ENSG00000114098	COX17	ARMC8	ATGCATGAGAGCCCTAGGATTTAAAATATGAAATG*CTTGATCATGATTTAAAACATGCTCACGAACTCCG	exon-exon	BOWTIE	UTR/CDS(truncated)	0	7	2	13	3	119675145	-	3	138245088	+	9.0574	1.9062	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-IA-A40Y-01A	ENSG00000138002	ENSG00000115207	IFT172	GTF3C2	GCTGAAGCTGAATTCATCAGAGCTGGTAAACCCAAGGAGGCAGTCCTCAT*CTTGAGTGTGCGTCAGAATCCCCTGAAGAGCTTGTTAAAACACAAGGTGC	10K<gap<100K	BOWTIE+STAR	CDS(truncated)/UTR	0	5	1	16	2	27454354	-	2	27350389	-	4.8789	17.467	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-IA-A40Y-01A	ENSG00000170832	ENSG00000077348	USP32	EXOSC5	CCAGCTACTCCGGAAGAAGAAGGACAAATTATTAG*GTGACACCTCTGTCCTGGCGGGTGTGTACGGGCCG	cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	2	1	13	17	60252381	-	19	41392980	-	6.6972	24.2533	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	FALSE
TRUE	TRUE	Kidney	TCGA-B3-4104-01A	ENSG00000151687	ENSG00000064933	ANKAR	PMS1	GCGTCCCTCTCCCGGACAAGAAAACAGCCATTCTAGA*ATATGAAGAGAAGGCTACTAAAGACTTGGAACGATAC	cancer,tumor,10K<gap<100K,exon-exon	BOWTIE	UTR/CDS(truncated)	0	16	1	14	2	189674830	+	2	189863743	+	0.4531	2.9371	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Kidney	TCGA-B9-4113-01A	ENSG00000215241	ENSG00000226711	LINC02449	FAM66C	ATTCCTGAGACAACGGAATTCTGGCGATGGAGCACAG*ATATAATACGTAAGTTTGGAGGTGGATGCTTTCAGCC	lincrna,antisense,m3,10K<gap<100K,exon-exon	BOWTIE	exonic(no-known-CDS)/exonic(no-known-CDS)	0	6	2	24	12	8235999	+	12	8215806	+	1.5697	1.093	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	lincRNA	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-B3-4103-01A	ENSG00000270105	ENSG00000185201	AC136475.8	IFITM2	AAGGTAATGGGATAATCCGGCTGCCTGGGCACCACAGTGAGGGTTATGGG*AGACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCA	lincrna	BOWTIE+BLAT	exonic(no-known-CDS)/UTR	0	2	2	21	11	322237	-	11	307677	+	0.1811	30.5888	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-B9-4116-01A	ENSG00000127914	ENSG00000166526	AKAP9	ZNF3	GGAGAGACAGAAGAAGCTGGAGGCCGGCAAAGCCAAG*TGCTTCCTCATTCTCTTTTAAAACCCGCTTCCCGCTG	oncogene,cancer,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	89	11	24	7	91941147	+	7	100077433	-	22.9568	35.8272	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-B9-4116-01A	ENSG00000127914	ENSG00000166526	AKAP9	ZNF3	GGAGAGACAGAAGAAGCTGGAGGCCGGCAAAGCCAAG*CATTGGCATCAACAAAAGTCAGAATTCCCGGGAACTT	oncogene,cancer,tcga-cancer,exon-exon	BOWTIE	CDS(truncated)/UTR	0	89	9	24	7	91941147	+	7	100079656	-	22.9568	35.8272	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-B9-4116-01A	ENSG00000127914	ENSG00000166526	AKAP9	ZNF3	GGAGAGACAGAAGAAGCTGGAGGCCGGCAAAGCCAAG*CTCTTCCTTCAAAAGTTCCTGCCTTTTCCGACAAGGA	oncogene,cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	89	6	25	7	91941147	+	7	100075630	-	22.9568	35.8272	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	FALSE	Kidney	TCGA-B9-4116-01A	ENSG00000128585	ENSG00000242593	MKLN1	AC006148.1	ACAAGTGGAGCTCCTTTTCCTCCACCTACCTTCCCGA*GTCATAGGAAATGAAACAGACTGCTGTTTTCATGAGT	antisense,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	41	7	25	7	131327997	+	7	124352816	+	9.9713	5.9631	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Kidney	TCGA-B9-4116-01A	ENSG00000128585	ENSG00000242593	MKLN1	AC006148.1	CCCTACGCGCTACACAAGTGGAGCTCCTTTTCCTCCACCTACCTTCCCGA*GTCTGACATTGGAATAATGCAGAACACTTGATTCAGGTCATAGAAGAAGC	antisense	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	41	3	23	7	131327997	+	7	124287289	+	9.9713	5.9631	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Kidney	TCGA-B9-4116-01A	ENSG00000128585	ENSG00000242593	MKLN1	AC006148.1	CCCTACGCGCTACACAAGTGGAGCTCCTTTTCCTCCACCTACCTTCCCGA*GCACCCATAGGATATTGAAAGTTATCAGGATATTCTTCCCACTCCAAGAT	antisense	BOWTIE+STAR	CDS(truncated)/intronic	0	41	2	23	7	131327997	+	7	124306478	+	9.9713	5.9631	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Kidney	TCGA-B9-4116-01A	ENSG00000128585	ENSG00000242593	MKLN1	AC006148.1	CCCTACGCGCTACACAAGTGGAGCTCCTTTTCCTCCACCTACCTTCCCGA*TTCTGGATGTTGGGAAGCAGAAGAACAAGGTGCCAGCAGATCCAGTGTCT	antisense	BOWTIE+STAR	CDS(truncated)/intronic	0	41	1	15	7	131327997	+	7	124334247	+	9.9713	5.9631	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	antisense_RNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-B9-4116-01A	ENSG00000091732	ENSG00000008277	ZC3HC1	ADAM22	ATGAGGGGATTGCCCCGGAAGAGGGAGGCGTGGACGC*TGATTTGCTGTCCTCTGAATACATAGAGAGACACATT	tcga-cancer,exon-exon	BOWTIE	in-frame	0	21	4	22	7	130051221	-	7	88075626	+	38.594	3.2847	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-B9-4116-01A	ENSG00000091732	ENSG00000008277	ZC3HC1	ADAM22	AATTGCACTTTCTGCCTGCTTCTAGAATTCCTCCAAG*TGATTTGCTGTCCTCTGAATACATAGAGAGACACATT	tcga-cancer,exon-exon	BOWTIE	UTR/CDS(truncated)	0	21	2	23	7	130048974	-	7	88075626	+	38.594	3.2847	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-B9-4116-01A	ENSG00000243797	ENSG00000105865	AC004917.1	DUS4L	GCCGGCTCCAACACACATCCTGTGGAGCGAGAGTTTG*GATCCATGATGACCTTAAAAGAACTGTAGATCTTTGT	exon-exon	BOWTIE	exonic(no-known-CDS)/CDS(truncated)	0	11	5	24	7	106760566	-	7	107576366	+	0.7879	2.9436	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	sense_overlapping	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Kidney	TCGA-B9-4116-01A	ENSG00000229413	ENSG00000282508	AC018638.1	LINC01002	CTCTCGCCCCACCGCGACCTCCCAGGCCCAAGTCCCTGCCTACCTCCCAG*CAGCTCTTGCCCCCACGGCGGCCTCCCGGGGCCAAGTCCCTGCCTGCCTC	pseudogene,m2	BOWTIE+BLAT	exonic(no-known-CDS)/exonic(no-known-CDS)	0	7	2	23	7	128653734	-	19	200566	-	54.0736	0.0896	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	processed_pseudogene	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Kidney	TCGA-B9-4116-01A	ENSG00000229413	ENSG00000282508	AC018638.1	LINC01002	TCCAGGCCCAGCTCTCGCCCCACCGCGACCTCCCAGGCCCAAGTCCCTGC*TGGGAGGTAGGCAGGGACTTGGGCCT	pseudogene,m2	BOWTIE+BLAT	exonic(no-known-CDS)/exonic(no-known-CDS)	0	7	1	24	7	128653745	-	19	198289	-	54.0736	0.0896	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	processed_pseudogene	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Kidney	TCGA-B9-4116-01A	ENSG00000229413	ENSG00000282508	AC018638.1	LINC01002	GGGAGTCTCCAGGCCCAGCTCTCGCCCCACCGCGACCTCCCAGGCCCAAG*CCCCTGCCTCAACAGGCCACCGTGAGGGAGGAACAGGATCGCACTCGGGC	pseudogene,m2	BOWTIE+BLAT	exonic(no-known-CDS)/exonic(no-known-CDS)	0	7	1	24	7	128653752	-	19	198342	-	54.0736	0.0896	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	processed_pseudogene	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Kidney	TCGA-B9-4116-01A	ENSG00000229413	ENSG00000282508	AC018638.1	LINC01002	GGCCCAGCTCTCGCCCCACCGCGACCTCCCAGGCCCAAGTCCCTGCCTAC*CTGAGAGAGGTCAGTGTGAGCCCCTTGCCTCACACCGGCCCCTCCCACGC	pseudogene,m2	BOWTIE+BLAT	exonic(no-known-CDS)/exonic(no-known-CDS)	0	7	1	24	7	128653741	-	19	200399	-	54.0736	0.0896	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	processed_pseudogene	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Kidney	TCGA-B9-4116-01A	ENSG00000229413	ENSG00000282508	AC018638.1	LINC01002	CTGTTGCCTCCCAGGGGAGTCTCCAGGCCCAGCTCTCGCCCCACCGCGAC*AGAGGTCAGCGTGAGCCCCTTGCCTCACACCGGCCCCTCCCACGCTGAGA	pseudogene,m2	BOWTIE+BLAT	exonic(no-known-CDS)/intronic	0	7	1	23	7	128653766	-	19	199036	-	54.0736	0.0896	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	processed_pseudogene	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Kidney	TCGA-B9-4116-01A	ENSG00000229413	ENSG00000282508	AC018638.1	LINC01002	GGCCCAGCTCTCGCCCCACCGCGACCTCCCAGGCCCAAGTCCCTGCCTAC*CTCCCAGGGGCCTCTCCAGGCCCAGCTCTTGCCCCCACGGCGGCCTCCCG	pseudogene,m2	BOWTIE+BLAT	exonic(no-known-CDS)/exonic(no-known-CDS)	0	7	1	23	7	128653741	-	19	200588	-	54.0736	0.0896	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	processed_pseudogene	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Kidney	TCGA-B9-4116-01A	ENSG00000229413	ENSG00000282508	AC018638.1	LINC01002	CTCTCGCCCCACCGCGACCTCCCAGGCCCAAGTCCCTGCCTACCTCCCAG*CCCTCCCACGCGGACAGAGGTCAGCCCGAGCCCCTTGTCTCACACCGGCC	pseudogene,m2	BOWTIE+BLAT	exonic(no-known-CDS)/intronic	0	7	1	22	7	128653734	-	19	199777	-	54.0736	0.0896	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	processed_pseudogene	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Kidney	TCGA-B9-4116-01A	ENSG00000229413	ENSG00000282508	AC018638.1	LINC01002	TCCAGGCCCAGCTCTCGCCCCACCGCGACCTCCCAGGCCCAAGTCCCTGC*CTTTCTCCAGCCAAGCTCTGAGGGCCCACCTCCTGCCTCCTGGTGGCCTG	pseudogene,m2	BOWTIE+BLAT	exonic(no-known-CDS)/exonic(no-known-CDS)	0	7	1	22	7	128653745	-	19	200688	-	54.0736	0.0896	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	processed_pseudogene	processed_transcript	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Kidney	TCGA-B9-4116-01A	ENSG00000282339	ENSG00000229413	AC010507.2	AC018638.1	AGTTGTCCTGAAGTCGGGCTCTCCCGGCCCTGCCTCCCAGCAAGTAAGCA*GCTCTTTTGGCTCAGCTCCCGCCGGCCTTTGTAGACCCCGAAGTTTCTGC	pseudogene,m2	BOWTIE+BLAT	exonic(no-known-CDS)/exonic(no-known-CDS)	0	6	1	21	19	200743	-	7	128653949	-	0	54.0736	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	transcribed_processed_pseudogene	processed_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Kidney	TCGA-B9-4116-01A	ENSG00000282339	ENSG00000229413	AC010507.2	AC018638.1	CCTTGCCTCCCAGGGGCCTCTCCAGGCCCAGCTCTTGCCCCCACGGCGGC*CTCCCAGGCCCAAGTCCCTGCCTACCTCCCAGCAGCCCGCGTGCGACCCT	pseudogene,m2	BOWTIE+BLAT	exonic(no-known-CDS)/exonic(no-known-CDS)	0	6	1	14	19	200545	-	7	128653765	-	0	54.0736	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	transcribed_processed_pseudogene	processed_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Kidney	TCGA-B9-4116-01A	ENSG00000229413	ENSG00000282339	AC018638.1	AC010507.2	CTGCAGACCCCGCTGTTGCCTCCCAGGGGAGTCTCCAGGCCCAGCTCTCG*CCCCACGGCGGCCTCCCGGGGCCAAGTCCCTGCCTGCCTCCCAGCAGCCC	pseudogene,m2	BOWTIE+STAR	exonic(no-known-CDS)/exonic(no-known-CDS)	0	6	2	22	7	128653778	-	19	200556	-	54.0736	0	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	processed_pseudogene	transcribed_processed_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Kidney	TCGA-B9-4116-01A	ENSG00000229413	ENSG00000282339	AC018638.1	AC010507.2	GGCCCAGCTCTCGCCCCACCGCGACCTCCCAGGCCCAAGTCCCTGCCTAC*CTCCTGCCTCCTGGTGGCCTGTACAGTTCTAGCACTGGTTGGAGAACAGC	pseudogene,m2	BOWTIE+STAR	exonic(no-known-CDS)/exonic(no-known-CDS)	0	6	1	23	7	128653741	-	19	200659	-	54.0736	0	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	processed_pseudogene	transcribed_processed_pseudogene	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-A4-A57E-01A	ENSG00000051382	ENSG00000156508	PIK3CB	EEF1A1	TTCTTCCACCACTGATTAAGACTCAGGTGGCAGGTATTAGGGATAATATT*CAAGAAGGCTGCTGGAGCTGGCAAGGTCACCAAGTCTGCCCAGAAAGCTC	oncogene,cancer,m2	BOWTIE+BLAT	intronic/CDS(truncated)	0	7	2	21	3	138826329	-	6	73517873	-	736.2726	615.8863	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-A4-A57E-01A	ENSG00000051382	ENSG00000156508	PIK3CB	EEF1A1	GCTGATTGAAACAAACATTTCTGAGGCTATTCTTCCACCACTGATTAAGA*GTGGTGGAAGAACGGTCTCAGAACTGTTTGTTTCAATTGGCCATTTAAGT	oncogene,cancer,m2	BOWTIE+BLAT	intronic/UTR	0	7	1	21	3	138826358	-	6	73517772	-	736.2726	615.8863	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-A4-A57E-01A	ENSG00000051382	ENSG00000156508	PIK3CB	EEF1A1	AACCTAAATGGCTGATTGAAACAAACATTTCTGAGGCTATTCTTCCACCA*CTAATACCTGCCACCCCACTCTTAATCAGTGGTGGAAGAACGGTCTCAGA	oncogene,cancer,m2	BOWTIE+BLAT	intronic/UTR	0	7	1	21	3	138826368	-	6	73517800	-	736.2726	615.8863	FALSE	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	TRUE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-A4-A57E-01A	ENSG00000114107	ENSG00000051382	CEP70	PIK3CB	AAGACCTCCAGAGGTATTTGTTTTAAAAGTTTACAAAGTATCATCCAGAA*TAGCTGGGACTACAGGCGTGTGCCACCTCGCCCAGCTAATTTTTGTATTT	cell_lines,10K<gap<100K	BOWTIE+BLAT	UTR/intronic	0	6	1	23	3	138500073	-	3	138795520	-	646.3354	736.2726	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Kidney	TCGA-A4-A57E-01A	ENSG00000114098	ENSG00000114107	ARMC8	CEP70	GTCCTAGCTACTGGGGAGGCTGAGGCAGGAGGATCACTTGAACCCAGGAG*GACCTCCAGAGGTATTTGTTTTAAAAGTTTACAAAGTATCATCCAGAATG	NA	BOWTIE+BLAT	intronic/CDS(truncated)	0	2	1	23	3	138293468	+	3	138500120	-	409.3182	646.3354	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-A4-A57E-01A	ENSG00000146592	ENSG00000051382	CREB5	PIK3CB	GGGAGGGATAGCATTAGGAGATATACCTAATGTAAATGACGAGTTAATGG*GTGATCTCTCTGAGTCCTGGCAACATCCAGCAAAACTACTGCTTATTCTC	NA	BOWTIE+BLAT	intronic/UTR	0	2	1	22	7	28590593	+	3	138654239	-	8.4946	736.2726	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-A4-A57E-01A	ENSG00000163453	ENSG00000051382	IGFBP7	PIK3CB	TTTTTGTGTGTTTTTTGGAGGGGTAGAGATGGGGTTTCACCGTGTTGCCC*TACAATAACAAGGTATTTGGTGAGGATTCAGTTGGAGTGATTTTTAAAAA	cancer	BOWTIE+BLAT	intronic/CDS(truncated)	0	2	1	20	4	57064148	-	3	138683735	-	181.1788	736.2726	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-A4-A57E-01A	ENSG00000158186	ENSG00000051382	MRAS	PIK3CB	CTTTGTGCCTGACTATGACCCCACCATTGAAGACTCCTACCTGAAACATA*TACATGGAATATTTTGATACAGGCATATAACATGTAATTATCGCATCAGG	oncogene	BOWTIE+BLAT	CDS(truncated)/UTR	0	2	1	23	3	138373043	+	3	138652856	-	674.0796	736.2726	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Kidney	TCGA-KN-8426-01A	ENSG00000169398	ENSG00000167632	PTK2	TRAPPC9	GAATGCTACAACTAAAAATAGCAGGTGCACCCGAG*ACCCTGGAAGCTGTCCTGAATTTCAAATACTCTGG	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	17	2	19	8	140803543	-	8	140024079	-	26.824	14.3878	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	FALSE	Kidney	TCGA-KN-8426-01A	ENSG00000169398	ENSG00000167632	PTK2	TRAPPC9	AAGGAATCAGTTACCTAACGGACAAGGGCTGCAAT*ACCCTGGAAGCTGTCCTGAATTTCAAATACTCTGG	tcga,cell_lines,18cancers,chimerdb3seq,tcga-cancer,100K<gap<200K,exon-exon	BOWTIE	in-frame	0	17	1	13	8	140818277	-	8	140024079	-	26.824	14.3878	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-KL-8341-01A	ENSG00000164929	ENSG00000104408	BAALC	EIF3E	GGACAGCGGCCCCGAAGCGGGCGGCCTGCACTCGG*CATGTTGGCAGATAAATTGAACATGACTCCAGAAG	oncogene,cancer,m4,exon-exon	BOWTIE	out-of-frame	0	50	14	24	8	103141057	+	8	108203503	-	80.4122	16.6274	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-KL-8341-01A	ENSG00000164929	ENSG00000104408	BAALC	EIF3E	AGGCTTCCAAGTGATGCTGATGCTGCTGGTCCAGAGGTCCTAGATCAGAG*CATGTTGGCAGATAAATTGAACATGACTCCAGAAGAAGCTGAAAGGTGGA	oncogene,cancer,m4	BOWTIE+BLAT;BOWTIE+STAR	intronic/CDS(truncated)	0	50	1	23	8	103155924	+	8	108203503	-	80.4122	16.6274	TRUE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-KL-8341-01A	ENSG00000169118	ENSG00000081014	CSNK1G1	AP4E1	CGCCTCATTTGCGCCTTGCAGCACTGCTGGACCAG*GTAGATGCTTCTTTATCTTTTCTGGATGGTTTTGT	known,tcga,18cancers,exon-exon	BOWTIE	UTR/CDS(truncated)	0	18	4	21	15	64355988	-	15	50968263	+	6.5172	4.424	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	FALSE
TRUE	TRUE	Kidney	TCGA-KL-8341-01A	ENSG00000187118	ENSG00000166415	CMC1	WDR72	AAAGGCCAAAGAGAGGTGTTCTGAACAAGTTCAAG*CTCCAGTCAGCCCGGTCAAGCATGACAGCAACTCA	cell_lines,18cancers,m7,tcga-cancer,exon-exon	BOWTIE	in-frame	0	10	6	21	3	28263380	+	15	53523322	-	3.7464	26.3433	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-KL-8341-01A	ENSG00000187118	ENSG00000166415	CMC1	WDR72	TTCTCGGCCCGCCGAGATGGCGCTCGACCCCGCAG*CTCCAGTCAGCCCGGTCAAGCATGACAGCAACTCA	cell_lines,18cancers,m7,tcga-cancer,exon-exon	BOWTIE	in-frame	0	10	2	18	3	28241812	+	15	53523322	-	3.7464	26.3433	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	non-validated	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-KL-8341-01A	ENSG00000164934	ENSG00000185634	DCAF13	SHC4	ACAGGAATATAGTACTGTACGATATGAGGCAAGCTACTCCTTTGAAAAAG*TTCTTTAGGGAAGCAATAAGTCGCCTGTGTGAAGCTGTCCCCGGGGCAAA	cancer	BOWTIE+BLAT	CDS(truncated)/intronic	0	7	1	24	8	103430689	+	15	48890819	-	21.8392	0.6226	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-KL-8341-01A	ENSG00000113504	ENSG00000171368	SLC12A7	TPPP	CCTGCTGGTTGGCATCTACTTCCCTTCCGTGACCG*CAACATGGCTGACAAGGCCAAGCCTGCCAAAGCTG	exon-exon	BOWTIE	CDS(truncated)/UTR	0	6	3	21	5	1081577	-	5	678064	-	19.5572	9.5791	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-KL-8341-01A	ENSG00000140025	ENSG00000258792	EFCAB11	AL137230.1	AAATTACCGGAAAGGACTGTTCTTGAGGTATTCAG*GGATCAGTTCTTTGCTCTTTGAAACGAGATGATCC	lincrna,100K<gap<200K,exon-exon	BOWTIE	CDS(truncated)/exonic(no-known-CDS)	0	2	1	13	14	89931541	-	14	89629136	-	1.8876	0	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-KL-8341-01A	ENSG00000047849	ENSG00000069667	MAP4	RORA	AACACTCCTAGCCAATGGTGGTCATGGAGTAGAAGGGAGCGATACTACAG*GTGTTTCTGAAAGAAAAGCAGCGGTGGAGCTTAAGAGCCAAGTCCACTGA	cancer	BOWTIE+STAR	CDS(truncated)/UTR	0	2	2	24	3	47977865	-	15	60494747	-	24.4393	5.3712	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-KN-8435-01A	ENSG00000276651	ENSG00000103657	AC007950.2	HERC1	CTTGCCAGTGCTGTTGGTTGCCTGATTTCCAGCCCCTGGAATACAGCCTG*ATGATTCCTCTTGATTCTTTTGTTGGCCAGAGTGCTGATGGCAAAATGGT	lincrna,18cancers,100K<gap<200K	BOWTIE+BLAT;BOWTIE+STAR	exonic(no-known-CDS)/CDS(truncated)	0	17	12	24	15	63500830	-	15	63615920	-	2.2625	9.9345	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	lincRNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-KL-8328-01A	ENSG00000088854	ENSG00000171873	C20ORF194	ADRA1D	CCTGGCGGCTCCAGCCGCGGGTCACCCTCCGTCAG*GCTCCTTGTTCCCGCAGCTGAAGCCATCGGAGGGC	tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	7	3	20	20	3407475	-	20	4222130	-	8.9617	1.5466	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	FALSE	Kidney	TCGA-KN-8425-01A	ENSG00000261404	ENSG00000284683	AC138627.1	AC087565.3	AAGCCATCTTTGCTCTGCTCTCCTCTGCTGCCCAG*GCTTCTGGACTTTTTGAATTCTGAAACCAAAAGAA	lincrna,10K<gap<100K,exon-exon	BOWTIE	exonic(no-known-CDS)/exonic(no-known-CDS)	0	2	1	14	16	74205905	-	16	73680240	-	0.2889	NA	FALSE	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	lincRNA	lincRNA	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-KO-8405-01A	ENSG00000223482	ENSG00000204176	NUTM2A-AS1	SYT15	GGAGCTTCTCAGAAGACAGAGGGTTTTCTTTTGAG*CAGTTTAAGTATAGTGTGCCTGGGTTGGGTGCGGT	antisense,m2,exon-exon	BOWTIE	exonic(no-known-CDS)/UTR	0	5	1	14	10	87288442	-	10	46593287	+	0.6133	0.0146	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	FALSE	antisense_RNA	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-KL-8323-01A	ENSG00000105929	ENSG00000054654	ATP6V0A4	SYNE2	AGCTCGGAGAGCTCGGATTGGTTCAGTTCAAAGAT*AATAAAGAAATTCATTTTCAAAGGAGGCGAACTAC	cancer,exon-exon	BOWTIE	in-frame	0	3	1	14	7	138771131	-	14	64174944	+	285.1043	15.9477	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	FALSE	FALSE
TRUE	TRUE	Kidney	TCGA-KM-8443-01A	ENSG00000113441	ENSG00000062194	LNPEP	GPBP1	CCGCGGCGGGGGGAAAATGGAGCCCTTCACCAATG*CAGCCTCGTCTAACCAAACTGACACGAATGCGCAC	cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	36	10	24	5	96936174	+	5	57249454	+	8.8769	12.042	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-KM-8443-01A	ENSG00000113441	ENSG00000062194	LNPEP	GPBP1	CCGCGGCGGGGGGAAAATGGAGCCCTTCACCAATG*ATTGTTAAAGGAAATGGGCTGGCAGGAAGACAGTG	cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	36	5	24	5	96936174	+	5	57261180	+	8.8769	12.042	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-KM-8443-01A	ENSG00000113441	ENSG00000062194	LNPEP	GPBP1	CCGCGGCGGGGGGAAAATGGAGCCCTTCACCAATG*TGTAATCGCTCAAATTCCTCTTCTCCTGTTGACAA	cancer,tcga-cancer,exon-exon	BOWTIE	out-of-frame	0	36	4	24	5	96936174	+	5	57249409	+	8.8769	12.042	FALSE	FALSE	FALSE	TRUE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	TRUE	validated	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-KM-8443-01A	ENSG00000136100	ENSG00000139679	VPS36	LPAR6	TTCATTGAAGAACAGGCGGCTGGAATTGGGAAGAG*GTGAAAACTCCAAAGCTTAACATTCTAACCACTCT	exon-exon	BOWTIE	CDS(truncated)/UTR	0	12	6	22	13	52439098	-	13	48389812	-	5.4698	0.7069	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE
TRUE	TRUE	Kidney	TCGA-KM-8443-01A	ENSG00000136100	ENSG00000139679	VPS36	LPAR6	CTTTCCCAAATTGTGTTCATTGAAGAACAGGCGGCTGGAATTGGGAAGAG*GCTGGTTTTGAACTCCTGGCTTCAAGAGATCCTCCCGCCTCAGCCCCACT	NA	BOWTIE+BLAT;BOWTIE+STAR	CDS(truncated)/intronic	0	12	3	21	13	52439098	-	13	48391561	-	5.4698	0.7069	FALSE	FALSE	FALSE	FALSE	TRUE	FALSE	FALSE	FALSE	protein_coding	protein_coding	FALSE	NA	TRUE	TRUE