Table 2.
The deep targeted sequencing and WES datasets used in this study. Two region sizes are listed in this table. The “calling” regions are used for variant calling. “Comparison” regions inlcude the intersection regions of capture target regions and NA12878 high-confidence regions used for comparison tests.
| Name | Mean coverage (“Tumor”) | Mean coverage (“Normal”) | True variant counts in the comparison regions | Region sizes in bases | |||
|---|---|---|---|---|---|---|---|
| SNVs | INDELs | Calling | Comparison | ||||
| Deep Targeted Sequencing | NA12878 (1%) vs NA24385 | 1639.11 | 1533.77 | 632 | 76 | 2,674,426 | 2,328,046 |
| NA12878 (2%) vs NA24385 | 1642.12 | ||||||
| NA12878 (5%) vs NA24385 | 1654.03 | ||||||
| NA12878 (10%) vs NA24385 | 1632.73 | ||||||
| NA12878 (20%) vs NA24385 | 1693.44 | ||||||
| NA12878 (50%) vs NA24385 | 1697.64 | ||||||
| WES | NA12878 (0.5%—100%) vs NA11840 | 54.38 | 61.29 | 9,603 | 377 | 45,326,658 | 44,006,127 |