Table 1:
Numerical differences in variant calling outcomes on chromosome 8 and the X chromosome between sex chromosome complement-aware (SCC-aware) and default reference alignment. Numbers are quality-filtered biallelic SNPs for chromosome 8 (top) and the X chromosome (bottom).
| Category | Chrom | Default | SCC-aware | % change (SCC/D) |
|---|---|---|---|---|
|
| ||||
| Total SNPs | 8 | 719,826 | 719,824 | −0.0002% |
| Per-indiv. Avg SNPs | 8 | 178,885 | 178,882 | −0.002% |
| Per-indiv. Ref allele | 8 | 540,938 | 540,939 | 0.0002% |
| Total SNPs | X | 475,763 | 498,297 | 4.74% |
| Per-indiv. Avg SNPs | X | 98,877 | 105,413 | 6.61% |
| Per-indiv. Ref allele | X | 376,884 | 392,882 | 4.07% |