Table 3.
Statistics of phasing results for the two phasing strategies
| Trusted set of variants | Traditional SNP filtering | |||||||
|---|---|---|---|---|---|---|---|---|
| WGS-P1 | WGS-P2 | WGS-P1 | WGS-P2 | |||||
| Average | Median | Average | Median | Average | Median | Average | Median | |
| Proportion of phasing errors | ||||||||
| Per animal | 50.95% | 50.13% | 0.38% | 0.32% | 50.80% | 50.41% | 1.10% | 1.04% |
| Number of switches | ||||||||
| Per animal | 739.2 | 631.5 | 704.5 | 574 | 4521 | 4291 | 4387.7 | 4079 |
| Per animal and chromosome | 25.49 | 18.5 | 24.29 | 16.5 | 155.9 | 105.5 | 151.3 | 112 |
WGS-P1 phased with LD information only, WGS-P2 phased with both LD and familial information