Table 1.

Numerical differences in variant calling outcomes on chromosome 8 and the X chromosome between SCC-aware and default reference alignment.

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%

Numbers are quality-filtered biallelic SNPs for chromosome 8 (top) and the X chromosome (bottom).