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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