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 |