Table 3. Variant-level quality metrics of high-quality variants in the PSP dataset processed by four different methods.
| Metric | No QC | ABHet | VQSR | ForestQC |
|---|---|---|---|---|
| Total SNVs | 33273111 | 29771182 | 31281620 | 29352329 |
| Known SNVs | 25960464 | 24142744 | 24910728 | 23514257 |
| Known SNVs (%) | 78.02% | 81.09% | 79.63% | 80.11% |
| Total indels | 5093443 | 3311136 | 3682319 | 3418242 |
| Known indels | 3679990 | 2532899 | 3012662 | 2567879 |
| Known indels (%) | 72.25% | 76.50% | 81.81% | 75.12% |
| Multi-allelic SNVs | 250418 | 6685 | 188180 | 146247 |
| Multi-allelic SNVs (%) | 0.75% | 0.02% | 0.60% | 0.50% |
Four methods are compared, including no QC applied, ABHet approach, VQSR and ForestQC. “Known” stands for variants found in dbSNP. The version of dbSNP is 150.