Additional file 2. Validated fusions in TCGA BRCA and GBM samples.
Cancer type	Sample	5' symbol	3' symbols	Predicted effect	N junction supporting read pairs	Fusion_sequence	5' chromosome	5' strand	5' junction hg38	3' chromosome	3' strand	3' junction hg38	N discordant read pair support	Manta support	Breakdancer support	Manta read pair support	Breakdancer read pair support	breakpoint_identified
BRCA	TCGA-A7-A0CE-01	RNF121	CYSLTR2	CDS(complete)/UTR	31	GGTGCAGTGGAAGCAGAGGCACCCACGCTCCTACAAT*CATGGAGAGAAAATTTATGTCCTTGCAACCATCCATC	11	+	71960891	13	+	48706817	5	TRUE	TRUE	3	1	TRUE
BRCA	TCGA-A7-A0CE-01	LPCAT1	CLPTM1L	in-frame	24	GCACGAGCTGCGCCTCAGCGCCCTGCAGAAGGCCCAG*CTTCTCTTTGATTTCCTGGCCTTTAAAAATGACATCA	5	-	1523710	5	-	1331883	8	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-A7-A0CE-01	UBL3	MTIF3	CDS(truncated)/UTR	24	AAACGGCAAGATGTCCAGTAATGTCCCGGCGGATATG*CTGTCATTCTTCTCTACAGAAGAGCTTCTCCTCATCA	13	-	29849512	13	-	27445156	6	FALSE	TRUE	NA	3	TRUE
BRCA	TCGA-A7-A0CE-01	PTK2	SLC45A4	CDS(truncated)/UTR	18	CTGGGACTCCGGAGGGTCTGATGAAGCACCGCCCAAG*ATCATCCAGTCACTCGATGGGGATTACCAGCGGACCA	8	-	140717598	8	-	141254629	4	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-A8-A07I-01	RNF43	CACNA1G-AS1	CDS(truncated)/exonic(no-known-CDS)	71	ACGGGCCCCCCGCCCCTGCCTGTCACTGGCTAGCAAG*AATCCCATCATCGCGTGCACATCTCATCCCAGGAGGG	17	-	58370911	17	-	50557458	23	FALSE	TRUE	NA	9.5	TRUE
BRCA	TCGA-A8-A07I-01	SLFN5	SYNRG	UTR/CDS(truncated)	20	CCCGGAGGGAGACGCGCTGCCGAGGAGAACCCAGCGG*GAGAAAGCTTTGCAGAATTCAGATCTGCAGGAACTGA	17	+	35243143	17	-	37554059	7	TRUE	TRUE	7	3	TRUE
BRCA	TCGA-A8-A07I-01	ACSF2	SPAG9	in-frame	19	GGCAGGAAGCCAGGTTGCAGGGTGTCCGCTTCCTCAG*CACTCCCACCAAAGGCATAGAGAACAAAGCTTTTGAT	17	+	50426389	17	-	51014353	35	TRUE	TRUE	35	17	TRUE
BRCA	TCGA-A8-A07I-01	CDK8	IKZF3	out-of-frame	15	CTTATGGTCACGTCTACAAAGCCAAGAGGAAAGATGG*ATATACAAACAAATGCGGAACTGAAAAGCACTCAGGA	13	+	26254769	17	-	39832151	29	TRUE	TRUE	29	14	TRUE
BRCA	TCGA-A8-A07I-01	ADCK2	DPP6	in-frame	9	TCTCTCTAGTGTCTTTAAGTTGCTGATGACTCACAAG*ATATATCAACACTCGTATACTGGATATTACGTCCTGA	7	+	140690813	7	+	154637821	5	FALSE	TRUE	NA	1.5	TRUE
BRCA	TCGA-A8-A07I-01	AKAP1	ANKFN1	UTR/CDS(truncated)	3	CTCCGCATCCCGCACCCCGATGGTAGCCGAGGAGCTG*GAATTGTCGTGTGAAAATGACGCAACAAATGCAAAAT	17	+	57085398	17	+	56350766	17	FALSE	TRUE	NA	8	TRUE
BRCA	TCGA-A2-A0D4-01	CNIH1	AP001107.9	CDS(truncated)/exonic(no-known-CDS)	9	GCTCACTGCCGCGCTCATCTTCTTCGCCATTTGGCAC*ATTGAAGGTGGCGGGTTCCTGTAGTCCCAGCTACTCA	14	-	54441247	11	+	66353455	1	FALSE	FALSE	NA	NA	NA
BRCA	TCGA-A2-A0D4-01	RB1	CDADC1	out-of-frame	5	AACAGCATACAAGGATCTTCCTCATGCTGTTCAGGAG*AGGATCATAAAACAGGAGTTGGGGCAGTCATTTGGGC	13	+	48463835	13	+	49274291	10	FALSE	TRUE	NA	2	TRUE
BRCA	TCGA-A2-A04P-01	IPO8	CDH13	out-of-frame	55	CGGATCATTGATCTTGTTCTGCAGAAACATGTAATTG*AGAACCCACAATCCTATTAACAGCGAACTTCTCTTGA	12	-	30656684	16	+	83180870	8	TRUE	TRUE	8	3.5	TRUE
BRCA	TCGA-A2-A04P-01	PDE7A	TRIM55	in-frame	51	TCTCTTCGGCTGCCCCAATCCCCGGCAGCTCTCTCAG*GAATGTTGCAGAAAACAGAAACAAGAGCTTTGTGAGA	8	-	65841371	8	+	66149645	11	TRUE	TRUE	6	3	TRUE
BRCA	TCGA-A2-A04P-01	LINC02015	KCNMB2-AS1	exonic(no-known-CDS)/exonic(no-known-CDS)	42	ATTAGAGCGTCATCCATTAATGCTTTGGCTAGGAGGG*GCATTCTAATATATGCATTCTTCATAACAACTGTGTG	3	+	177827830	3	-	178749236	52	FALSE	TRUE	NA	70.5	TRUE
BRCA	TCGA-A2-A04P-01	LINC02015	KCNMB2-AS1	exonic(no-known-CDS)/exonic(no-known-CDS)	42	AAAATTGTAGGAAAAGAGAGCACTTTGGCACGGAAGG*GCATTCTAATATATGCATTCTTCATAACAACTGTGTG	3	+	177816996	3	-	178749236	54	FALSE	TRUE	NA	70.5	TRUE
BRCA	TCGA-A2-A04P-01	LINC02015	KCNMB2-AS1	intronic/exonic(no-known-CDS)	42	AGTGCTGGGAAGTCATGCAGGGATTGGAAACCACAAAGATTCTACAGAAA*GCATTCTAATATATGCATTCTTCATAACAACTGTGTGAAACATATTAATA	3	+	177820889	3	-	178749236	54	FALSE	TRUE	NA	70.5	TRUE
BRCA	TCGA-A2-A04P-01	ZMAT3	LINC01014	UTR/exonic(no-known-CDS)	14	GCGGCGCGGAGACTGCCGGCGCGTCCCGGGGGTTCCG*GTGGGAAACTACATGTGCGTGCTTGACACAACTTGAA	3	-	179071595	3	+	178456614	1	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-A2-A04P-01	ZMAT3	LINC01014	UTR/exonic(no-known-CDS)	14	ATTCCATCCTTCGTGATGGCATCCATACCGGGTTGAG*GTGGGAAACTACATGTGCGTGCTTGACACAACTTGAA	3	-	179071327	3	+	178456614	1	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-A2-A04P-01	RUNX1	LINC01695	CDS(truncated)/exonic(no-known-CDS)	12	ATCAAAATCACAGTGGATGGGCCCCGAGAACCTCGAA*TAGGCCCACAGCCAAGCCATTGAGAGACAAGTCCATG	21	-	34859474	21	-	28212351	11	FALSE	TRUE	NA	1.5	TRUE
BRCA	TCGA-A2-A04P-01	CYB561	AC097478.1	UTR/exonic(no-known-CDS)	3	GGCGCGGGGAGGCTGAAGGGACGCTCGGGTAGGCAAG*GTAGTCGTACAGTGTCCAGAAGGCAAAAGGACAAGTA	17	-	63446245	4	+	89719826	9	TRUE	TRUE	9	4	TRUE
BRCA	TCGA-A2-A04P-01	CYB561	AC097478.1	UTR/exonic(no-known-CDS)	3	GGCGCGGGGAGGCTGAAGGGACGCTCGGGTAGGCAAG*GTGGGTGTCATTGTGACTGGCTGCTACCTCCCCATGA	17	-	63446245	4	+	89691285	9	TRUE	TRUE	9	4	TRUE
BRCA	TCGA-A2-A04P-01	CYB561	AC097478.1	UTR/exonic(no-known-CDS)	3	TTTGGATCTTTGCTCCTGCGCCGCGTTCTAGAGCAAG*GTAGTCGTACAGTGTCCAGAAGGCAAAAGGACAAGTA	17	-	63445898	4	+	89719826	9	TRUE	TRUE	9	4	TRUE
BRCA	TCGA-A2-A259-01	NUTM2A-AS1	SYT15	exonic(no-known-CDS)/UTR	5	CCGCCTGCCTCAGCCTCCAAAGTAGCTGAGACTACAG*CAGTTTAAGTATAGTGTGCCTGGGTTGGGTGCGGTGG	10	-	87246115	10	+	46593287	1	FALSE	FALSE	NA	NA	NA
BRCA	TCGA-A2-A04T-01	ZNF462	DNAJC1	UTR/CDS(truncated)	27	AACCCGAAGCACCTCCCGGCGCCGGGACGCTTCTTCT*GCACCTGAATGGACAGAAGAGGACCTCAGCCAACTGA	9	+	106863355	10	-	21806099	7	TRUE	TRUE	7	3.5	TRUE
BRCA	TCGA-A2-A04T-01	TCF12	TEX9	out-of-frame	13	CCAACTACACTGGGAAGCAGTCAATTCAGTGGATCAG*GCGTTTAAATGCAGAATTGCAGGCAAAAACAGCTGAC	15	+	56921098	15	+	56373441	10	FALSE	TRUE	NA	3	TRUE
BRCA	TCGA-A2-A04T-01	MKL2	SNX29	in-frame	12	ACTACAACTACCAGACCATCCTGCCTGCACCATTCAA*GGTCACCTGTCTGTGTGCCCAGTTTGAAGCCGTCCTG	16	+	14240484	16	+	12027320	5	FALSE	TRUE	NA	2.5	TRUE
BRCA	TCGA-A2-A04T-01	AC009163.5	TMEM170A	exonic(no-known-CDS)/CDS(truncated)	4	CCCAGGGATTTTCCTGGACGGGATTGTGAAGTAGCGG*AGATGTGGTATGGTGTATTCCTGTGGGCACTGGTGTC	16	-	75516203	16	-	75451839	1	FALSE	FALSE	NA	NA	NA
BRCA	TCGA-A2-A04X-01	SNX27	ADAR	in-frame	25	ATACAAACATGTGGAGCAGAATGGTGAGAAGTTTGTG*GGGTATTCCCTCAGCGGATACTACACCCATCCATTTC	1	+	151639119	1	-	154602626	32	TRUE	TRUE	32	14	TRUE
BRCA	TCGA-A2-A04X-01	AC010522.1	ZSCAN4	CDS(no-known-start-or-end)/UTR	15	TCCGATGGCTGCGGCTGCGCCGAGGCGCCCTACTCAG*CTTGCAGTTTTAAAGAATCCACCAACTGTTGAAACAA	19	+	57819945	19	+	57676041	11	FALSE	TRUE	NA	3	TRUE
BRCA	TCGA-A2-A04X-01	ZNF587	ZSCAN4	CDS(truncated)/UTR	13	TCCGATGGCAGCGGCTGTGCCGAGGCGCCCAACTCAG*CTTGCAGTTTTAAAGAATCCACCAACTGTTGAAACAA	19	+	57850071	19	+	57676041	11	FALSE	TRUE	NA	3	TRUE
BRCA	TCGA-A2-A04X-01	MYO1D	SSH2	in-frame	4	ATACATGAATGTCCTCTTTTCCTGTCACGTCCGTAAG*AGCTCTCATTTGGAAGACAGTGAATCAGCAGCATTAC	17	-	32653843	17	-	29848929	8	FALSE	TRUE	NA	1	TRUE
BRCA	TCGA-A7-A26G-01	DCAF6	MPZL1	in-frame	149	GTTGAGGCATCTGGACACCACACACATCATCAGTCTG*TGACAGCTGGAGTATCAGCCTTGGAAGTATATACGCC	1	+	168004793	1	+	167765583	2	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-A7-A26G-01	MSH2	TTC7A	in-frame	36	GGATATTGCAGCAGTCAGAGCCCTTAACCTTTTTCAG*GCAACTCGAGATGTGGTGCTGAGCCGGGTGCCGGAGC	2	+	47414418	2	+	47005922	6	FALSE	TRUE	NA	1.5	TRUE
BRCA	TCGA-A7-A26G-01	NSD1	ZNF346	out-of-frame	34	AACTTCATCATCATCTACTTCACAGGAATTGCCATTT*TGGAGCACATGATCCAGAAGAACCAATGTCTCTTCAC	5	+	177136030	5	+	177041126	3	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-A7-A26G-01	ASH1L	ARHGEF2	in-frame	24	CATTACCAGAGGAAGAAGAGCAAGAGAATAATAAAAG*CTGCAGCCAGCTGGAAGGACATTCAGGTACCCGGGTA	1	-	155438327	1	-	155983200	3	FALSE	FALSE	NA	NA	NA
BRCA	TCGA-A7-A26G-01	RNF13	TM4SF4	UTR/CDS(truncated)	13	GGCAAGACTGTTTGTGTTGCGGGGGCCGGACTTCAAG*GGATTATCTCAATGATGAGGCCTTATGGAACAAGTGC	3	+	149813353	3	+	149498722	3	FALSE	TRUE	NA	1.5	TRUE
BRCA	TCGA-A7-A26G-01	SMAD3	DIS3L	out-of-frame	13	CGCAGAACGTCAACACCAAGTGCATCACCATCCCCAG*AATTACCTGGACAATTTCTGGCCTGATTTAAAAGCTG	15	+	67066360	15	+	66311724	9	FALSE	TRUE	NA	3.5	TRUE
BRCA	TCGA-A7-A26G-01	SMAD3	DIS3L	out-of-frame	13	CGCAGAACGTCAACACCAAGTGCATCACCATCCCCAG*GGAATTCTGAATGTCAACAAACACAGAGCCCAAATAG	15	+	67066360	15	+	66314039	9	FALSE	TRUE	NA	3.5	TRUE
BRCA	TCGA-A7-A26G-01	LIFR	C9	out-of-frame	9	GTTCCCTCAAACAGCACTGAAACTGTAATAGAATCTG*ACCAAAGGCGAGAAAAATTTCAGAACCGAACATTACG	5	-	38493606	5	-	39316029	1	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-A7-A26G-01	TP53BP1	DMXL2	in-frame	9	TGCTCCTGGGGATGATACAGAGTCGCTCCATAGCCAG*AAACTTATTGGAGAAGTGTTTAATATTGTGAGCCAAC	15	-	43432194	15	-	51517167	6	FALSE	TRUE	NA	1.5	TRUE
BRCA	TCGA-A7-A26G-01	DGCR2	CLTCL1	out-of-frame	7	ACTTGCGAGGATGAGAGCGACGAAGCCAACTGTCCAG*CTCCAAAACCTTGGAATTAATCCAGCTAACATTGGAT	22	-	19089368	22	-	19275830	8	FALSE	TRUE	NA	2	TRUE
BRCA	TCGA-A7-A26G-01	ENOX1	FNDC3A	UTR/CDS(truncated)	7	ATGATGTCGTATTTATAATATGTGGAGGAGAGAGAGCTCACCATGCTCAG*GTTATTCTGGTACAAGTTAACCCAGGAGAAGCATTTACAATAAGAAGAGA	13	-	43667479	13	+	49075289	11	TRUE	TRUE	11	3.5	TRUE
BRCA	TCGA-A7-A26G-01	ICMT	ACOT7	out-of-frame	7	TAAGTTTTAGCCAGTCTTCTTGGAGTCACTTTGGCTG*AGCCGAACACTGTCAGCTACAGCCAGTCCAGCTTGAT	1	-	6234886	1	-	6318578	3	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-A7-A26G-01	PBRM1	TKT	in-frame	7	CATTAGCGAACTTTTTCAGAAACTGCCTTCTAAAGTG*CCACCCCACGTCATGCTGCAGCGCCGCAGAGATCATG	3	-	52658199	3	-	53242242	5	FALSE	TRUE	NA	1.5	TRUE
BRCA	TCGA-A7-A26G-01	SDHD	CUL5	in-frame	7	ATTCCCTGGCTGCAGCCCTCACTCTTCATGGTCACTG*AATTACATTTAATGTTTTCATTGATGGACAAAGTTCC	11	+	112089011	11	+	108072332	5	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-A7-A26G-01	MTF2	BRDT	out-of-frame	6	TATGAAGCGGTTGGCACCACTGAAGTGACCGAATGAG*GATATAAAGATTAAGAATGCAGATTCATGGAAAAGTT	1	+	93079531	1	+	92004414	2	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-A7-A26G-01	DIP2B	ATF1	in-frame	5	TTTGTCCGCCGGACCGAGCTCACAGCGGCCACTGGAG*GTATCATCTTTATCAGAAAGTGAGGAGTCCCAGGACT	12	+	50739586	12	+	50795909	2	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-A7-A26G-01	ILKAP	PER2	in-frame	4	AGCGGATGAGGATACAGAAGGCTGGAGGAAACGTCAG*AAATTTAGAAGCGGTTTTGAAGGAGGACAGAGAGAAG	2	-	238182065	2	-	238249212	9	FALSE	TRUE	NA	2.5	TRUE
BRCA	TCGA-A7-A26G-01	MCU	CDH23	in-frame	3	CGTCAGCCGCCACCGGCAGCAGCAGCACCACCGGACG*GCAACTGACAATGATGCAGGCACCTTTGGGGAAGTCA	10	+	72692301	10	+	71675112	5	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-A8-A08B-01	RARA	PGAP3	UTR/CDS(truncated)	15	GCTGGCACCCCGAACGGGTTGCTTCCCCCGCTGCGAG*GCTGGACCTGTCGGGACGACTGTAAGTATGAGTGTAT	17	+	40318448	17	-	39686019	4	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-BH-A0B9-01	YARS	ADM5	CDS(truncated)/UTR	178	TCCCATCCCGGCTGGATATCCGTGTGGGGAAAATCATCACTGTGGAGAAG*ACTTTTGGCCTCAGTGTTCCCCGCCTGGGAAGTGGGGACTGGCCCTGGTA	1	-	32781048	19	+	49689688	2	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-BH-A0B9-01	YARS	ADM5	intronic/UTR	178	GCTGGATATCCGTGTGGGGAAAATCATCACTGTGGAGAAGGTACTCATTT*TTCCCCACGCTTTGAAGGGGGCGAGTCTCCACAGACCTCCTAGGGGGATA	1	-	32781038	19	+	49689523	2	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-BH-A0B9-01	YARS	ADM5	out-of-frame	178	TCCCATCCCGGCTGGATATCCGTGTGGGGAAAATCATCACTGTGGAGAAG*GGGACCTGGACACTGCAGCCAGGTGAGAAACCCGGGTGGCAGCAGGGACA	1	-	32781048	19	+	49689890	2	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-BH-A0B9-01	YARS	ADM5	in-frame	178	ATATCCGTGTGGGGAAAATCATCACTGTGGAGAAG*GCGAGGCCAGCACCAGGTCCCCCAGCACCGCGGGC	1	-	32781048	19	+	49690106	2	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-BH-A0B9-01	SENP3	ACADVL	UTR/CDS(truncated)	118	GCATGCATGAGTCAACTGTGTGCATCCCATTGTGCTTTCCCCAGGCCAGT*CCGGAGTTGAGTCGGAGTGGCGAGCTGGTAAGTGGCCAGGGGTCCAGGAG	17	+	7564590	17	+	7224367	7	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-BH-A0B9-01	AARS	COG4	in-frame	112	CCACTTTGCTCTTTGCCAATGCAGGCATGAACCAG*AAAGTGGTGGAGAGAGAGCTGGATGCTCTTTTGGA	16	-	70282620	16	-	70519731	6	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-BH-A0B9-01	RANBP17	KCNIP1	in-frame	101	TTCTGGTGTAACTGTGGACATCACCATTCAGGAAG*ATAAGATTGAAGATGAGCTGGAGATGACCATGGTT	5	+	170924550	5	+	170718758	3	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-BH-A0B9-01	CDV3	TMEM108	in-frame	100	TACAGCGGCCTCAGGGTTCAGGCAATGCAAATAAG*GTTTCCTGCTGATCTTGGCACTGACCGAAGCGCTG	3	+	133575115	3	+	133379752	6	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-BH-A0B9-01	ACTN4	CAPZB	in-frame	96	CCGCCTTCATGCCCTCCGAGGGCAAGATGGTCTCG*GTCCCCAGTCTATGTGAGGATCTCCTGTCTTCTGT	19	+	38717316	1	-	19385626	1	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-BH-A0B9-01	SENP3-EIF4A1	ACADVL	intronic/CDS(truncated)	80	GCATGCATGAGTCAACTGTGTGCATCCCATTGTGCTTTCCCCAGGCCAGT*CCGGAGTTGAGTCGGAGTGGCGAGCTGGTAAGTGGCCAGGGGTCCAGGAG	17	+	7564590	17	+	7224367	7	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-BH-A0B9-01	AARS	ST3GAL2	out-of-frame	76	GCTGATGGTGGCCGGCCTGACAACACAGGGCGTGG*GTGAACGTGTACGGGTTCGGGGCCGACAGCCGGGG	16	-	70269618	16	-	70381862	8	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-BH-A0B9-01	AL355315.1	ZDHHC16	in-frame	49	AGCGAGTCCTACACACAGAGCTTTCAGAGCCGGAAGCCCTTCTTTTCATG*CTATGGAAGTTGGGACCTTTTCCGGGAGGCTTATGCTGCCATTGAGGTGA	10	+	97673735	10	+	97453618	4	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-BH-A0B9-01	NUTM2A-AS1	SYT15	exonic(no-known-CDS)/UTR	31	GGAGCTTCTCAGAAGACAGAGGGTTTTCTTTTGAG*CAGTTTAAGTATAGTGTGCCTGGGTTGGGTGCGGT	10	-	87288442	10	+	46593287	12	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-BH-A0B9-01	NUTM2A-AS1	SYT15	exonic(no-known-CDS)/UTR	31	GCCTGCCTCAGCCTCCAAAGTAGCTGAGACTACAG*CAGTTTAAGTATAGTGTGCCTGGGTTGGGTGCGGT	10	-	87246115	10	+	46593287	12	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-BH-A0B9-01	NUTM2A-AS1	SYT15	exonic(no-known-CDS)/UTR	31	GGAGCTTCTCAGAAGACAGAGGGTTTTCTTTTGAG*ATTCCAGTTCTTTGATGAAAGTCTCTATTCCACCC	10	-	87288442	10	+	46593989	13	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-BH-A0B9-01	NUTM2A-AS1	SYT15	exonic(no-known-CDS)/UTR	31	GCCTGCCTCAGCCTCCAAAGTAGCTGAGACTACAG*ATTCCAGTTCTTTGATGAAAGTCTCTATTCCACCC	10	-	87246115	10	+	46593989	13	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-BH-A0B9-01	STUB1	RAB11FIP3	UTR/CDS(truncated)	29	ATCGCTTTTGCTGGGCCGTGATCGTCCCCCTTTGTGGGCTGGAAAAGCAG*GTTGTCTTCCTGGAAAGGCGTGTGCTGGAGCTGGAAAAGGACACGGCAGC	16	+	682682	16	+	505524	3	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-BH-A0B9-01	PYGB	ENTPD6	in-frame	23	AGGAACATCGCCTGCTCGGGCAAGTTCTCCAGTGACCGGACCATCACGGA*AGCGCTCAGGGAATCCGGGAACTACTGGATGTTGCTAAACAGGACATTCC	20	+	25296449	20	+	25213263	6	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-BH-A0B9-01	PYGB	ENTPD6	out-of-frame	23	GAACCCCAAGGAGTGGACCAAGAAGGTCATCAGGAACATCGCCTGCTCGG*AGCGCTCAGGGAATCCGGGAACTACTGGATGTTGCTAAACAGGACATTCC	20	+	25296418	20	+	25213263	6	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-BH-A0B9-01	ZNF607	CAPN12	in-frame	23	GATTGTGAGGGAAGAAACAAGAGGAGAGTGTACAG*GTAACTGCTGGTTCCTTGCAGCTGCCGCCTCCCTT	19	-	37707914	19	-	38742528	2	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-BH-A0B9-01	HDAC1	KPNA6	in-frame	19	TGAGTTCTGTCAGTTGTCTACTGGTGGTTCTGTGG*AGACCATGGCGAGCCCAGGGAAAGACAATTATCGA	1	+	32324553	1	+	32154588	5	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-BH-A0B9-01	ARFGAP2	CELF1	out-of-frame	15	CACCGCTCCCTGGGCGTCCATCTGAGCTTCATCAG*GGTGCTGTTTTGTTACATTTTACACCCGTAAAGCT	11	-	47176516	11	-	47487241	2	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-BH-A0B9-01	GSE1	USP10	CDS(no-known-start-or-end)/CDS(truncated)	11	TGAGCTGGAGCTCCCCGGTGGCAGCAGCGACGAAG*TATATTTTTGGAGATTTTAGCCCTGATGAATTCAA	16	+	85171807	16	+	84733435	2	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-A7-A0D9-01	KAT6A	ADAM5	UTR/exonic(no-known-CDS)	700	GGTGCTATTGAGAAATTCATTGGGAAGTTGGAAGACATTTCAATCAACAG*AGAGAAGTTACATGGAGGAGGGAAGATAGGCCACTTTTCAAAAACAACGG	8	-	42049170	8	+	39401333	8	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-A7-A0D9-01	KAT6A	ADAM5	CDS(truncated)/exonic(no-known-CDS)	700	ACCTCCAGTGTCCCTTCTTCCACATGAAAAGGATAAG*AGAGAAGTTACATGGAGGAGGGAAGATAGGCCACTTT	8	-	42048378	8	+	39401333	8	FALSE	FALSE	NA	NA	TRUE
BRCA	TCGA-A7-A0D9-01	NSD3	RAB11FIP1	in-frame	246	ACAAGCAGATTGTTTGGGTCAAATTGGGAAATTACAG*GTGGTATAAGTTGAAATCCAAACCAGGAAAGAAGGAC	8	-	38295796	8	-	37877551	5	FALSE	TRUE	NA	2	TRUE
GBM	TCGA-19-2624-01	PPM1H	RAP1B	CDS(truncated)/UTR	511	ATTTGCCTTTTGGGGAAGCTGTATGTTGCAAATGCTGGGGATAGCAG*GTACTAGGTTTTGACAAGCTTGCATCATGCGTGAGTATAAGCTAGTC	12	-	62788226	12	+	68648699	1	FALSE	FALSE	NA	NA	NA
GBM	TCGA-19-2624-01	PPM1H	RAP1B	out-of-frame	511	ATTTGCCTTTTGGGGAAGCTGTATGTTGCAAATGCTGGGGATAGCAG*ACTGTACAATTTGTTCAAGGAATTTTTGTAGAAAAATACGATCCTAC	12	-	62788226	12	+	68650400	1	FALSE	FALSE	NA	NA	NA
GBM	TCGA-19-2624-01	PPM1H	RAP1B	CDS(truncated)/UTR	511	ATTTGCCTTTTGGGGAAGCTGTATGTTGCAAATGCTGGGGATAGCAG*GTTTTGACAAGCTTGCATCATGCGTGAGTATAAGCTAGTCGTTCTTG	12	-	62788226	12	+	68648706	1	FALSE	FALSE	NA	NA	NA
GBM	TCGA-19-2624-01	PPM1H	RAP1B	CDS(truncated)/UTR	511	ATGAGTGCCTGGTCATCGGAGCGCTTGAAAGTGCATTCAAGGAAATG*GTACTAGGTTTTGACAAGCTTGCATCATGCGTGAGTATAAGCTAGTC	12	-	62801816	12	+	68648699	1	FALSE	FALSE	NA	NA	NA
GBM	TCGA-19-2624-01	LINC02231	MDM2	intronic/UTR	146	AAAAAAGATCATGGCTTCTGTCTTAGTCTCTCTCTCTCTCTGTCTCTCTC*AATAAAATCAACTGAACTGTAAGCTTAGAATAGGACTGAGGTAATTCTGC	12	-	64944844	12	+	68843612	4	FALSE	FALSE	NA	NA	TRUE
GBM	TCGA-19-2624-01	MDM2	LINC02231	CDS(truncated)/exonic(no-known-CDS)	146	TATTAAAGTCTGTTGGTGCACAAAAAGACACTTATACTATGAAAGAG*AGAATCATGGGAACCATTATAACAAAGAAGTCAAGAGTGTTGGTGTG	12	+	68813628	12	-	64921070	4	FALSE	FALSE	NA	NA	TRUE
GBM	TCGA-19-2624-01	MDM2	LINC02231	CDS(truncated)/exonic(no-known-CDS)	146	CTAGGAGATTTGTTTGGCGTGCCAAGCTTCTCTGTGAAAGAGCACAG*AGAATCATGGGAACCATTATAACAAAGAAGTCAAGAGTGTTGGTGTG	12	+	68816945	12	-	64921070	3	FALSE	FALSE	NA	NA	TRUE
GBM	TCGA-19-2624-01	MDM2	LINC02231	CDS(truncated)/intronic	146	AGTTATTAAAGTCTGTTGGTGCACAAAAAGACACTTATACTATGAAAGAG*GAGCCCACTTGGATCTCTTCCAAGGGATCTTTCTTTCTTCTCTTATTAAG	12	+	68813628	12	-	64921666	3	FALSE	FALSE	NA	NA	TRUE
GBM	TCGA-19-2624-01	TSFM	NUP107	out-of-frame	131	GCCTGACAGAGAAGGCTCACTCAAGGATCAGTTGGCTTTAGCAATTG*GCTGTTAATGCCAGTGAAAAAACAGTTGTGGAAGCGTTATTTCAGAG	12	+	57793073	12	+	68709238	54	FALSE	TRUE	NA	22	TRUE
GBM	TCGA-19-2624-01	TSFM	NUP107	in-frame	131	TGATGCATTGTCAGACCCTAAAGGATCAACCCTCTGCATACAGTAAA*GCTGTTAATGCCAGTGAAAAAACAGTTGTGGAAGCGTTATTTCAGAG	12	+	57787162	12	+	68709238	56	FALSE	TRUE	NA	22	TRUE
GBM	TCGA-19-2624-01	TSFM	NUP107	UTR/CDS(truncated)	131	TACAGGCTAAATAGATTTTAGAAATAATCATCTTAAAATTGAAAACAAAG*GCTGTTAATGCCAGTGAAAAAACAGTTGTGGAAGCGTTATTTCAGAGGGA	12	+	57797533	12	+	68709238	53	FALSE	TRUE	NA	22	TRUE
GBM	TCGA-19-2624-01	TSFM	NUP107	UTR/CDS(truncated)	131	CATTACAAAAAGGAATATTTCCCAAACCTCTTCAGACCGAGAATGCATGG*GCTGTTAATGCCAGTGAAAAAACAGTTGTGGAAGCGTTATTTCAGAGGGA	12	+	57796684	12	+	68709238	53	FALSE	TRUE	NA	22	TRUE
GBM	TCGA-19-2624-01	EGFR	PPM1H	out-of-frame	94	GCTGGCTGCGCTCTGCCCGGCGAGTCGGGCTCTGGAGGAAAAGAAAG*GAATCCGAGGGTGTTTCCTGCCACTATTGGTCGCTGTTTGACGGGCA	7	+	55019365	12	-	62802160	16	FALSE	FALSE	NA	NA	TRUE
GBM	TCGA-19-2624-01	MDM2	PPM1H	in-frame	35	AGAGTGATACAGATTCATTTGAAGAAGATCCTGAAATTTCCTTAGCT*GAATCCGAGGGTGTTTCCTGCCACTATTGGTCGCTGTTTGACGGGCA	12	+	68836749	12	-	62802160	59	FALSE	TRUE	NA	27.5	TRUE
GBM	TCGA-19-2624-01	MDM2	PPM1H	UTR/intronic	35	GAGGTAATTCTGCACAGCAACTTTACTAATGGTACATTGTTGCTTCAAAA*CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTAGCTCAAGGTCATG	12	+	68843698	12	-	62702578	2	FALSE	TRUE	NA	27.5	TRUE
GBM	TCGA-19-2624-01	PPM1H	MDM2	intronic/UTR	35	TTATTTCTCTCGCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTCT*CAATAAAATCAACTGAACTGTAAGCTTAGAATAGGACTGAGGTAATTCTG	12	-	62840048	12	+	68843611	73	FALSE	FALSE	NA	NA	TRUE
GBM	TCGA-19-2624-01	PPM1H	MDM2	intronic/UTR	35	TGGGAGGCCCAGGTGGGCAGATCACTTGAGGCCAGGAGTTCGAGACCAGC*CTGGGCAACATGGTGCAACCCTGTCTTAACTAAAAATACAAAAATTAGCC	12	-	62795940	12	+	68850092	10	FALSE	FALSE	NA	NA	TRUE
GBM	TCGA-19-2624-01	PPM1H	MDM2	intronic/UTR	35	CGCCACCATGCCTGGCTAATTTTTTGTATTTTTAGTAGAGACAGGGTTTC*CATGCTAGCCTTGAACTCCTGACCTTGTGATCTGCCTGCCTCGGCCTC	12	-	62768475	12	+	68849609	1	FALSE	FALSE	NA	NA	NA
GBM	TCGA-19-2624-01	HOXC9	PYM1	UTR/CDS(truncated)	26	ACAGAGTCTTCTGGGTCTCTCTGCCTGAGGCCCTGGAGGGAGAGAAG*GCAAGTATATCGCGTCAACACAGCGACCTGACGGGACCTGGCGCAAG	12	+	53995016	12	-	55903480	9	TRUE	TRUE	7	4	TRUE
GBM	TCGA-19-2624-01	NUP107	CYP27B1	out-of-frame	11	ACGTCTTGTTGTTTGTTGATGGAGGGTGGATGGTGGATGTTAGAGAG*ACTGTACCCTGTGGTACCTGGAAATTCTCGTGTCCCAGACAAAGACA	12	+	68735344	12	-	57764176	23	FALSE	FALSE	NA	NA	TRUE
GBM	TCGA-19-2624-01	NUP107	CYP27B1	CDS(truncated)/intronic	11	TATAACGTCTTGTTGTTTGTTGATGGAGGGTGGATGGTGGATGTTAGAGA*GGGCTGCAGCCCCTAGCCTCATCTTGTTGTCTCCATTTTGTGCTTTGCAA	12	+	68735343	12	-	57764231	23	FALSE	FALSE	NA	NA	TRUE
GBM	TCGA-19-2624-01	MDM2	VOPP1	UTR/intronic	10	AAAAGTACTAATCCCTTTGGCCATTTATTGAGAGAGAGAGAGAGAGAGAG*AGTAGGGTGACTATAGTTAATAATATATTTTATAATAGCTAGAAGAGAAT	12	+	68843316	7	-	55457001	3	FALSE	FALSE	NA	NA	TRUE
GBM	TCGA-19-2624-01	VOPP1	MDM2	in-frame	10	GCCAGCCTGCGAAGGTGGCGGCGCTGCTGCTCGGGCTGCTCTTGGAG*AATCATCGGACTCAGGTACATCTGTGAGTGAGAACAGGTGTCACCTT	7	-	55572271	12	+	68824363	79	FALSE	FALSE	NA	NA	TRUE
GBM	TCGA-19-2624-01	VOPP1	MDM2	in-frame	10	GCCAGCCTGCGAAGGTGGCGGCGCTGCTGCTCGGGCTGCTCTTGGAG*GAAAATATATACCATGATCTACAGGAACTTGGTAGTAGTCAATCAGC	7	-	55572271	12	+	68820325	78	FALSE	FALSE	NA	NA	TRUE
GBM	TCGA-19-2624-01	HOXC6	PYM1	UTR/CDS(truncated)	9	AGCTAACAGAAACGCCAGGAGCAGCAGGAGGAGGAGGCAGCGACAAG*GCAAGTATATCGCGTCAACACAGCGACCTGACGGGACCTGGCGCAAG	12	+	53990814	12	-	55903480	9	TRUE	TRUE	7	4	TRUE
GBM	TCGA-19-2624-01	MELK	ZMIZ1-AS1	UTR/exonic(no-known-CDS)	8	CCTGTCCTTCTGTCGGGCGCCGCTCAGCCGTGCCCTCCGCCCCTCAG*GGAGCTCAGGAGGGGGAATTGCACTGAAGATTTGTCCCATCGTGAAG	9	+	36573007	10	-	78945989	15	TRUE	TRUE	13	6.5	TRUE
GBM	TCGA-19-2624-01	AC012531.3	PYM1	intronic/CDS(truncated)	7	GGGACAGAGTCTTCTGGGTCTCTCTGCCTGAGGCCCTGGAGGGAGAGAAG*GCAAGTATATCGCGTCAACACAGCGACCTGACGGGACCTGGCGCAAGCAG	12	+	53995016	12	-	55903480	9	TRUE	TRUE	7	4	TRUE
GBM	TCGA-19-2624-01	TBC1D30	PPM1H	in-frame	5	GAAATCATCCTAAGGGTGTCGCTGGCTATCTGGGCAAAATTAGGAGA*GGTTATCAATGCCGGGAAGAGCACACACAATGAAGACCAAGCCAGCT	12	+	64838851	12	-	62832279	8	FALSE	TRUE	NA	235	TRUE
GBM	TCGA-06-0125-02	ARID1A	RNF31	in-frame	25	TCTATCGCCTCTATGTGTCTGTGAAGGAGATTGGTGGATTGACTCAG*ATGCAGGCCCTGACTTCCTGTGAGTGCACCATCTGTCCTGACTGCTT	1	+	26767999	14	+	24155157	13	TRUE	TRUE	13	5.5	TRUE
GBM	TCGA-06-0125-02	FAM168A	SNX29	UTR/CDS(truncated)	10	CCGCCTCAGCCGCCGCCGCCGCCGTTTTCGCCTGCAGCTGCTCACCG*GTCTACATCCGGATAAAAGACGATGAATGGAATATTTATCGCCGGTA	11	-	73597923	16	+	12477719	42	TRUE	TRUE	40	10.5	TRUE
GBM	TCGA-06-0125-02	SNX29	FAM168A	CDS(truncated)/UTR	10	CAGTGTTTCTCCGGGGCAAAGCAGCAAATGCATTCCACGTGTATCAG*GATCCTCAGTCTTCCACAATGAACCCTGTTTACAGCCCCGTGCAGCC	16	+	12403529	11	-	73468492	42	TRUE	TRUE	40	10.5	TRUE
GBM	TCGA-06-0125-02	FDX1	SLC35E2B	out-of-frame	5	GATGAGGAGAATGACATGCTCGATCTGGCATATGGACTAACAGACAG*GACGTCCCAGTGATCGGGAGGAGTGGGAAGAGCTTCAGCTACAACCA	11	+	110457047	1	-	1668472	15	TRUE	TRUE	15	7.5	TRUE
GBM	TCGA-06-0125-02	AF111169.4	POMT2	exonic(no-known-CDS)/CDS(truncated)	4	GCATCCAGACCCGGAAAGGACCTAGTTTCAGCCTGGCACCTCCCAAG*GGGAACAGTGGCCTCAAACCCAAGGACAATGAGTTCACGTCCAAACC	14	-	76781400	14	-	77280463	24	FALSE	TRUE	NA	11.5	TRUE
GBM	TCGA-06-0211-02	SHB	LINGO2	CDS(truncated)/UTR	4	GAGTGCTGGCTACATGGAGCCCTATGAGGCACAGAGGATCATGACAG*ACCCGTGACCAAGGTGTAGACTAAGAAGTGGAGTCATGCTTCACACG	9	-	38016011	9	-	27950706	23	FALSE	TRUE	NA	10.5	TRUE
GBM	TCGA-06-0125-01	ARID1A	RNF31	in-frame	28	TCTATCGCCTCTATGTGTCTGTGAAGGAGATTGGTGGATTGACTCAG*ATGCAGGCCCTGACTTCCTGTGAGTGCACCATCTGTCCTGACTGCTT	1	+	26767999	14	+	24155157	19	TRUE	TRUE	19	9.5	TRUE
GBM	TCGA-06-0125-01	ARID1A	AL136295.5	in-frame	26	ACCTCTATCGCCTCTATGTGTCTGTGAAGGAGATTGGTGGATTGACTCAG*ATGCAGGCCCTGACTTCCTGTGAGTGCACCATCTGTCCTGACTGCTTCCG	1	+	26767999	14	+	24155157	19	TRUE	TRUE	19	9.5	TRUE
GBM	TCGA-06-0125-01	AF111169.4	POMT2	exonic(no-known-CDS)/CDS(truncated)	4	GCATCCAGACCCGGAAAGGACCTAGTTTCAGCCTGGCACCTCCCAAG*GGGAACAGTGGCCTCAAACCCAAGGACAATGAGTTCACGTCCAAACC	14	-	76781400	14	-	77280463	24	FALSE	TRUE	NA	12	NA
GBM	TCGA-06-0190-01	PGD	CAMTA1	out-of-frame	7	TCATGGGCCAGAACTTAATTCTGAACATGAATGACCACGGCTTTGTG*ACCACAGAATGGCTCAATGATACTCTACAACAGGAAGAAAGTGAAAT	1	+	10399704	1	+	7249491	14	FALSE	TRUE	NA	7	TRUE
GBM	TCGA-02-2485-01	R3HDM2	MARS	UTR/CDS(truncated)	10	GCGGCGGGCGGAGACGTGGGCGCCCTCCCCGCCAAGGCCCGTGCGAG*AAGCCTCAGTGTAAAGTCTGCCGATCATGCCCTGTGGTGCAGTCGAG	12	-	57430720	12	+	57504225	79	FALSE	TRUE	NA	32	TRUE
GBM	TCGA-02-2485-01	EEF1AKMT3	INHBE	in-frame	9	ACTGGGTGCGGGGACAGGCATCGTGGGGATCTTGGCAGCGCTGCAGG*ACTCCACTTCAGCCTACAGCTCCCTGCTCACTTTTCACCTGTCCACT	12	+	57773128	12	+	57456094	3	FALSE	TRUE	NA	32	NA
GBM	TCGA-02-2485-01	EEF1AKMT3	INHBE	out-of-frame	9	ACTGGGTGCGGGGACAGGCATCGTGGGGATCTTGGCAGCGCTGCAGG*GCAGCGCTGACCAGAGCCCTCCGGAGACTACAGCCAGGGAGTGTGGC	12	+	57773128	12	+	57455744	3	FALSE	TRUE	NA	32	NA
GBM	TCGA-14-1823-01	MTERF1	VOPP1	UTR/CDS(truncated)	27	CAGAGGCGGAAGTAAAAGCGAACTACAGTGGATGGGTGCAGTTCAGG*GAGCCCAGCAGCCGGGGCCGCCCTATTACACCGACCCAGGAGGACCG	7	-	91880657	7	-	55473045	2	FALSE	FALSE	NA	NA	TRUE
GBM	TCGA-14-1823-01	MTERF1	VOPP1	UTR/CDS(truncated)	27	ACTAGCAAGCCAACAGGTGAAGTTTCGACACACCTCCTTTAATAAAG*GAGCCCAGCAGCCGGGGCCGCCCTATTACACCGACCCAGGAGGACCG	7	-	91827415	7	-	55473045	2	FALSE	FALSE	NA	NA	TRUE
GBM	TCGA-14-1823-01	MTERF1	VOPP1	out-of-frame	27	TCCAGCCTTTCTGGAGGGATGCAGAGCCTTTCCTTAGGACAAACAAG*GAGCCCAGCAGCCGGGGCCGCCCTATTACACCGACCCAGGAGGACCG	7	-	91880055	7	-	55473045	2	FALSE	FALSE	NA	NA	TRUE
GBM	TCGA-14-1402-02	H2AFV	AC002429.2	in-frame	104	CCGTGGTGATGAAGAGTTGGATTCTCTTATCAAGGCTACCATAGCTGGGG*TTCAAATTCTGGATGAGAATTCGCTTCTGCAAATTAGAAGCAATTCATCT	7	-	44835532	7	-	95036781	39	FALSE	TRUE	NA	17.5	TRUE
GBM	TCGA-14-1402-02	H2AFV	AC002429.2	CDS(truncated)/UTR	104	TGATGAAGAGTTGGATTCTCTTATCAAGGCTACCATAGCTGGGGGTG*AGTACTTTAAAGCAAATCCCAGACAATATGCGAATACTTCAGTATGT	7	-	44835529	7	-	95037111	39	FALSE	TRUE	NA	17.5	TRUE
GBM	TCGA-14-1402-02	H2AFV	AC002429.2	in-frame	104	TGATGAAGAGTTGGATTCTCTTATCAAGGCTACCATAGCTGGGGGTG*TTCAAATTCTGGATGAGAATTCGCTTCTGCAAATTAGAAGCAATTCA	7	-	44835529	7	-	95036781	39	FALSE	TRUE	NA	17.5	TRUE
GBM	TCGA-14-1402-02	XRN1	SMYD3	in-frame	39	TCTCAGAGCGGTATCCCTGTCTCAGCGAAGTGGTGAAAGAGCATCAG*GTGATCTGCAACTCTTTCACCATCTGTAATGCGGAGATGCAGGAAGT	3	-	142447870	1	-	245929937	14	TRUE	TRUE	13	3	NA
GBM	TCGA-14-1402-02	FCGRT	BCAT2	in-frame	6	CCTGCGGGAGCACCTGGAGAGGGGCCGCGGAAACCTGGAGTGGAAGG*CTGTTTGAGGGCATGAAGGCGTTCAAAGGCAAAGACCAGCAGGTGCG	19	+	49514486	19	-	48800297	23	TRUE	TRUE	22	11	TRUE
GBM	TCGA-14-1402-02	SLC22A3	ZDHHC14	in-frame	4	CAGTTAGCCATCACGCTGCCCAGCTTTCTCTTCCTCCTTTATTACTG*CTGTCCGTACCTGGCGGTGAAAATCACCCCTGCCATCCCTGCAGTCG	6	+	160408921	6	+	157542585	21	FALSE	TRUE	NA	10	TRUE
GBM	TCGA-14-1402-02	PDE10A	ZNF670-ZNF695	CDS(truncated)/UTR	3	TAATGCGAGCTGCTTCCGAAGGCTGACCGAGTGCTTCCTGAGCCCCA*GGTCCAGTCGTCGACCATCGAGCTGCTTTGAAGACCCTGCGGAGGTT	6	-	165661947	1	-	246945827	33	TRUE	TRUE	33	16	NA
GBM	TCGA-06-0171-02	KIDINS220	C3ORF70	out-of-frame	7	TTCATCTTTTACTGCAAAATGGTGCTAAAGTCAACTGCTCTGATAAG*GCAAATACATGTATCAGCCTATGACCCCTGTGGAACAGCTTCCAAGC	2	-	8812395	3	-	185083563	12	TRUE	TRUE	11	6	TRUE
GBM	TCGA-06-0171-02	EEF1E1	AC034223.2	CDS(truncated)/exonic(no-known-CDS)	4	TGGGACTGAGTAAGGGGAATAAATACAGTGCTCAGGGCGAGCGACAG*GTCATTGTTGAGAGACAAAATGAGATCATGTCTGGGAAAATACTTCT	6	-	8102435	5	-	33011560	5	TRUE	TRUE	5	2.5	TRUE
GBM	TCGA-06-0171-02	EEF1E1	AC034223.2	CDS(no-known-start-or-end)/exonic(no-known-CDS)	4	TCAGTTTAAGTGTTACGACCCACAGTGAATGCGGGAAACATCACAAG*GTCATTGTTGAGAGACAAAATGAGATCATGTCTGGGAAAATACTTCT	6	-	8101765	5	-	33011560	5	TRUE	TRUE	5	2.5	TRUE
GBM	TCGA-06-0171-02	VPS8	MBOAT2	in-frame	3	AACCAGGTTTTGCTTTTCAAATTTTTGAGGAGTCTTCTTGACCCAAG*TTACTGCTTTGTGTTTGCTCTGGGATACCTCACAGTGTGCCAAGTTA	3	+	184940243	2	-	8908716	8	TRUE	TRUE	7	4	TRUE
GBM	TCGA-06-5411-01	NFASC	NTRK1	in-frame	438	GAAGGGCCCTGAGCCAGAGTCCGTCATCGGTTACTCCGGAGAAGATT*ACACTAACAGCACATCTGGAGACCCGGTGGAGAAGAAGGACGAAACA	1	+	204982020	1	+	156874571	454	FALSE	TRUE	NA	222.5	TRUE
GBM	TCGA-06-5411-01	NFASC	NTRK1	intronic/UTR	438	ATGGACATATATGCCTGGCTTCCCAGACGGTGGTGGCCTCTCTGTCCCCA*GCTGCAGTCTCCTTCTCGCCGGTGGGTGAGTAGCCCAAGGTGGAGGGCAG	1	+	204982697	1	+	156874376	454	FALSE	TRUE	NA	222.5	TRUE
GBM	TCGA-06-5411-01	ATP2B4	NFASC	UTR/UTR	7	AGGGAGAGTCCCGCCTGAAGAAACCTGGATCTTTGCTAGAAAGAGAG*GTTGATTGACTTATGTGCAATTTGGGACGCTGGAGTTTACCTTCCCT	1	+	203627219	1	+	204920632	10	FALSE	TRUE	NA	9.5	TRUE