Fig. 4: Comparison among variant datasets.

a Comparison between JPN_UNION and gnomAD v2.1.1. gnomAD is a union set of the gnomAD exome and genome. b Comparison between GEM-J WGA and ToMMo 8.3KJPN. c Alternative allele frequency distribution of JPN_UNION. d Alternative allele frequency distribution of JPN_UNION and gnomAD non-Finnish European (NFE) variants limited to those with the following clinical significance in ClinVar: pathogenic, likely pathogenic, pathogenic/likely pathogenic, drug response, risk factor, association, affects, and protective. Variants outside the black line have a frequency ratio of 10 times or more. The number of alleles of NFE is the sum of those from the gnomAD exome and genome. The minimum frequency of JPN_UNION was 5.97 × 10⁻⁵ for a singleton variant in ToMMo 8.3KJPN (n = 8380, allele number = 16,760), the sample size of which was the second largest. JGA-SNP (n = 183,884, allele number = 367,768), with the largest sample size, targeted common variants and did not contain variants with a frequency of 0.01 or less.