Filters | Variants removed | Number of variants (% of unfiltered) | Ti/Tv | p-valuea | |||
---|---|---|---|---|---|---|---|
Novel | Known† | Truth‡ | All | ||||
None | 0 | 448,862 (100%) | 1.93 | 2.71 | 3.05 | 2.39 | N/A |
VQSR | 56,036 | 392,826 (87.5%) | 2.21 | 2.88 | 3.07 | 2.63 | <10-320 |
HWE | 11,855 | 437,007 (97.4%) | 1.93 | 2.73 | 3.06 | 2.40 | 1.42 × 10-21 |
Ave. GQ | 33,083 | 415,779 (92.6%) | 2.00 | 2.73 | 3.06 | 2.47 | 1.13 × 10-265 |
Call Rate | 51,117 | 397,745 (88.6%) | 2.09 | 2.78 | 3.08 | 2.51 | <10-320 |
Combined* | 59,952 | 388,910 (86.6%) | 2.09 | 2.80 | 3.09 | 2.52 | <10-320 |
Combined* + VQSR | 97,840 | 351,022 (78.2%) | 2.38 | 2.96 | 3.10 | 2.75 | <10-320 (3.72 × 10-106)b |
VQSR + Combined* | 92,091 | 356,771 (79.5%) | 2.34 | 2.94 | 3.10 | 2.72 | <10-320 |