Table 2:
Dissection of differences in variant calling within regions of interest across the X chromosome. Numbers are quality-filtered biallelic SNPs across various regions on the X chromosome (top) and within genic regions only across various regions on the X chromosome (bottom).
| Category | Default | SCC-aware | % change (SCC/D) | Added (F−) | Lost (F+) |
|---|---|---|---|---|---|
|
| |||||
| Total SNPs | 475,763 | 498,297 | +4.74% | 23,279 | 745 |
| non-PAR/XTR | 453,822 | 453,882 | +0.01% | 150 | 90 |
| PARs | 2,790 | 23,161 | +730.14% | 20,931 | 560 |
| XTR | 19,151 | 21,254 | +10.98% | 2,198 | 95 |
| Genic SNPs | 162,989 | 171,351 | +5.13% | 8,600 | 238 |
| non-PAR/XTR | 157,957 | 157,979 | +0.01% | 45 | 23 |
| PARs | 1,390 | 9,235 | +564.39% | 8,042 | 197 |
| XTR | 3,642 | 4,137 | +13.59% | 513 | 18 |