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Table 4 Exome somatic calls supported by whole-genome data.

From: Joint genotype inference with germline and somatic mutations

  Locus Whole-genome      Exome    
   mutation score Quality score Rank   Base calls (A:C:G:T)  
     qGT GATK qGT GATK Normal Tumor Father Mother
1 chr20:577556 GG > AG 61 282 99,99 1 1 0:0:90:0 27:0:64:0 1:0:104:0 1:0:90:0
2 chr18:26965596 AA > GA 87 282 99,99 1 1 77:0:1:2 63:1:20:0 106:0:0:0 84:0:0:0
3 chr9:139897201 GG > AG 59 91 66,99 16 73 0:0:23:0 6:0:18:0 0:0:24:0 0:0:21:0
4 chr2:88942555 GG > TG 93 53 - 84 - 0:0:29:0 0:0:5:3 0:0:36:0 0:0:26:0
5 chr2:88942554 AA > CA 93 52 - 86 - 30:0:0:0 0:0:6:3 0:0:36:0 0:0:26:0
6 chr7:150399212 CC > TC 93 48 60,99 98 104 0:20:0:0 1:6:0:9 0:14:0:0 0:13:0:0
7 chrX:129017457 CC > AC 41 46 45,99 109 221 0:15:0:0 5:6:0:0 0:16:0:0 0:12:0:0
8 chr16:3681082 CC > TC 89 44 30,82 118 629 0:10:0:0 0:10:0:4 0:19:0:0 0:11:0:0
9 chr10:107013067 CC > AC 30 36 - 186 - 0:52:0:0 5:57:0:1 0:74:0:0 0:72:1:0
10 chr8:72396806 TT > CT 59 24 - 398 - 0:0:0:6 0:3:0:13 0:0:0:20 0:0:0:11
11 chrX:21779651 GG > TG 89 21 36,99 483 412 2:0:13:0 0:0:7:8 0:0:9:0 0:0:14:0
12 chr5:125673987 CC > TC 97 14 6,70 790 7393 0:2:0:0 0:7:0:3 0:6:0:0 0:5:0:0
13 chr12:10156011 GG > AG 89 8 - - - 0:0:16:0 3:0:8:0 0:0:28:0 0:0:9:0
14 chr19:43602412 GG > AG 32 5 - - - 0:0:10:0 2:0:10:0 0:1:17:0 0:0:10:0
15 chr6:112619582 GG > AG 68 3 - - - 0:0:5:0 2:1:5:0 0:0:6:0 0:0:5:0
  1. Somatic mutation calls of QUAD GT (qGT columns) and the Genome Analysis Toolkit (GATK columns) were ranked by quality score (smaller of normal and tumor genotype call qualities in GATK's VCF output, and score of somatic call in QUAD GT's VCF output that is q = - 10 log10(1 - p) for a mutation with posterior probability p).
  2. Rank is "-" at loci where no somatic mutations were inferred by QUAD GT or GATK. Genome coordinates refer to NCBI 36.1/hg18 genome build.
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