Figure 3.

Effect of Variant Quality Filters on Distribution of Synonymous Variants

(A) Effect of adding pass/fail filters for variant quality. QQ plot of burden testing results following filtering for sites that passed GATK quality filters in the case and control sequencing data.

(B) Burden testing using QD scores to filter for sites. Only top 95% of sites in gnomAD based on QD scores and top 85% of sites in the case cohort sequencing based on QD scores are used.

Only sites where more than 90% of samples had sequencing read depth >10× in both gnomAD and the case cohort sequencing were considered (same as Figure 2B). QQ plots show burden testing results for synonymous variants.