Table 1 Coverage statistics for two quartets used in validation experiments.
From: Joint genotype inference with germline and somatic mutations
Exome sequencing (AB SOLiD system) | |||||
|---|---|---|---|---|---|
Total | Normal | Tumor | Father | Mother | |
Quartet A (chromosome 12 only) | |||||
Sites: | 11 458 426 | ||||
Reads: | 5 530 702 | 1 454 529 | 1 396 361 | 1 117 647 | 1 562 165 |
Depth: | 23.0 | 6.0 | 5.8 | 4.6 | 6.6 |
Experimental tumor purity: | 0.63 | ||||
QUAD GT's purity estimate: | 0.41 | ||||
Quartet B (all chromosomes) | |||||
Sites: | 425 344 130 | ||||
Reads: | 134 574 732 | 38 156 404 | 34 580 382 | 29 997 426 | 31 840 520 |
Depth: | 23.0 | 5.4 | 5.1 | 6.5 | 5.9 |
Experimental tumor purity: | 0.97 | ||||
QUAD GT's purity estimate: | 0.44 | ||||
Whole-genome sequencing (Illumina HiSeq 2000) | |||||
Quartet B (whole genome) | |||||
Total | Normal | Tumor | |||
Depth: | 123.8 | 48.6 | 75.2 | ||
Illumina's purity estimate: | 0.46 | ||||