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Table 3 Whole-genome somatic loci and exome genotyping on Quartet B.

From: Joint genotype inference with germline and somatic mutations

Locus WG genotyping Exome base calls (A:C:G:T)   QuadGT call  
  mutation quality N T F M N T F M
chr4:85818319 GG > AG 68 0:0:8:0 2:0:6:0 0:0:9:0 0:0:9:0 0/0 0/0 0/0 0/0
chr6:29965983 TT > CT 17 0:1:0:27 0:1:0:25 0:3:0:0 0:0:0:43 0/0 0/0 0/1 0/0
chr8:10078796 GG > CG 15 0:2:1:0 0:2:3:0 0:5:2:0 0:2:4:0 0/1 0/1 0/1 0/1
chr12:25289551 CC > TC 29 0:37:0:1 0:31:0:2 0:57:0:0 1:45:0:0 0/0 0/0 0/0 0/0
  1. Genome coordinates refer to NCBI 36.1/hg18 genome build.
  2. a. WG somatic loci in exome reads: 274
  3. b. exome coverage ≥ 10: 40
  4. c. only ref base calls in normal and tumor: 12
  5. d. at least one non-ref base call in normal and tumor: 28 (= c - d)
  6. e. exactly 1 non-ref base call in normal and tumor: 4
  7. f. at least 2 non-ref base call in normal and tumor: 24 (= e - f)
  8. g. within misaligned region chr19:4463156-4463205: 5
  9. h. strong disagreement between exome and WG reads: 4
  10. i. QUAD GT calls SOMATIC: 15 (= f - (g + h)) -- see Table 4
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