We tested the 2,108,983 variants identified in at least six individuals from the 269,171 predominantly unrelated European ancestry UKB exomes. Variants were required to pass the following quality control criteria: minimum coverage 10X; percent of alternate reads in heterozygous variants ≥ 0.2; binomial test of alternate allele proportion departure from 50% in heterozygous state P > 1 × 10−6; genotype quality score (GQ) ≥ 20; Fisher’s strand bias score (FS) ≤ 200 (indels) ≤ 60 (SNVs); mapping quality score (MQ) ≥ 40; quality score (QUAL) ≥ 30; read position rank sum score (RPRS) ≥ −2; mapping quality rank sum score (MQRS) ≥ −8; DRAGEN variant status = PASS; variant site is not missing (that is, less than 10X coverage) in 10% or more of sequences; the variant did not fail any of the aforementioned quality control in 5% or more of sequences; the variant site achieved tenfold coverage in 30% or more of gnomAD exomes, and if the variant was observed in gnomAD exomes, 50% or more of the time those variant calls passed the gnomAD quality control filters (gnomAD exome AC/AC_raw ≥ 50%).
