Sample ID
C828.TCGA-EE-A29B-06A-11D-A197-08.2.mutect.tcga_filtered.reheadered

Sample VCF File
C828.TCGA-EE-A29B-06A-11D-A197-08.2.mutect.tcga_filtered.reheadered.vcf

Sample VCF Genome
hg19

Sample VCF Total Point Mutations
107,372

FIREVAT Execution Start Datetime
2019-10-16 05:47:09

FIREVAT Execution End Datetime
2019-10-16 10:33:15


FIREVAT Genetic Algorithm (GA) Parameters
GA Population Size 200
GA Maximum Iteration 100
GA Run 100
GA Mutation Probability 0.100

1. Refinement Optimization

Filter Variable Filter Direction Optimized Cutoff
PrimaryBQ >= 16
NormalADRef >= 16
NormalADAlt <= 1
PrimaryADRef >= 16
PrimaryADAlt >= 9
TumorVAF >= 5
Objective Value C.refined W.refined C.artifact W.artifact
0.297 0.998 0.0339 0.993 0.31

2. Optimzed Mutational Signature Identification


2.1. Identified Signatures


2.2. Trinucleotide Spectrums

Original VCF Refined VCF Artifactual VCF
Mutations Count (%) 107,372 (100%) 816 (0.76%) 106,556 (99.24%)
Cosine Similarity Score 0.978 0.997 0.978
Residual Sum of Squares (RSS) 0.000819 0.000704 0.000809
2.2.1. Observed Spectrum

2.2.2. Maximum-likelihood Estimation (MLE) Reconstructed Spectrum

2.2.3. Residual Spectrum


2.3. Nucleotide Substitution Types

3. Optimized VCF Statistics

4. Variants with Strand Bias


4.1. Refined VCF

## None to display.


4.2. Artifactual VCF

## None to display.

5. VCF Annotation (ClinVar)


5.1. Refined VCF

CHROM POS REF ALT GENEINFO CLNSIG
chr2 209,113,113 G A IDH1:3417 Pathogenic/Likely_pathogenic
chr15 35,083,353 C T ACTC1:70|LOC101928174:101928174 Likely_pathogenic


5.2. Artifactual VCF

CHROM POS REF ALT GENEINFO CLNSIG
chr1 151,338,921 C A SELENBP1:8991 Likely_pathogenic
chr3 70,008,546 A G MITF:4286 Likely_pathogenic
chr3 165,548,529 T C BCHE:590 Pathogenic/Likely_pathogenic
chr5 39,342,214 G T C9:735 Pathogenic/Likely_pathogenic
chr4 187,158,034 G A KLKB1:3818 Pathogenic
chr7 44,192,981 G T GCK:2645 Likely_pathogenic
chr7 142,458,451 A T PRSS1:5644|TRB:6957 Pathogenic
chr8 11,606,312 T C GATA4:2626 Pathogenic
chr8 11,615,695 A G GATA4:2626 Pathogenic
chr11 18,290,859 C T SAA1:6288 Pathogenic
chr11 46,761,055 G A F2:2147 Pathogenic
chr11 111,635,566 C T PPP2R1B:5519 Pathogenic
chr10 70,645,376 A C STOX1:219736 Pathogenic
chr12 25,380,276 T C KRAS:3845 Pathogenic
chr15 43,552,349 C A TGM5:9333 Pathogenic
chr14 73,685,900 C A PSEN1:5663 Pathogenic
chr14 74,060,517 A G ACOT4:122970 Likely_pathogenic
chr16 16,244,584 C T ABCC6:368 Pathogenic
chrM 14,766 C T MT-CYB:4519 Likely_pathogenic