Table 1.
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Numerical differences in variant calling outcomes on chromosome 8 and the X chromosome between SCC-aware and default reference alignment.

CategoryChromDefaultSCC-aware% change (SCC/D)
Total SNPs8719,826719,824−0.0002%
Per-indiv. avg SNPs8178,885178,882−0.002%
Per-indiv. ref allele8540,938540,9390.0002%
Total SNPsX475,763498,2974.74%
Per-indiv. avg SNPsX98,877105,4136.61%
Per-indiv. ref alleleX376,884392,8824.07%
CategoryChromDefaultSCC-aware% change (SCC/D)
Total SNPs8719,826719,824−0.0002%
Per-indiv. avg SNPs8178,885178,882−0.002%
Per-indiv. ref allele8540,938540,9390.0002%
Total SNPsX475,763498,2974.74%
Per-indiv. avg SNPsX98,877105,4136.61%
Per-indiv. ref alleleX376,884392,8824.07%

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

Table 1.
Open in new tab

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

CategoryChromDefaultSCC-aware% change (SCC/D)
Total SNPs8719,826719,824−0.0002%
Per-indiv. avg SNPs8178,885178,882−0.002%
Per-indiv. ref allele8540,938540,9390.0002%
Total SNPsX475,763498,2974.74%
Per-indiv. avg SNPsX98,877105,4136.61%
Per-indiv. ref alleleX376,884392,8824.07%
CategoryChromDefaultSCC-aware% change (SCC/D)
Total SNPs8719,826719,824−0.0002%
Per-indiv. avg SNPs8178,885178,882−0.002%
Per-indiv. ref allele8540,938540,9390.0002%
Total SNPsX475,763498,2974.74%
Per-indiv. avg SNPsX98,877105,4136.61%
Per-indiv. ref alleleX376,884392,8824.07%

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

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