Table 1.

JPN_UNION: The combined autosomal variant dataset of Japanese populations collected in TogoVar.

Dataset	Sample size	Platform	The number of autosomal variants
GEM-J WGA	7609	WGS	92,311,243
JGA-NGS	125	WES	4,561,009
JGA-SNP	183,884	SNP array	1,236,461
ToMMo 8.3KJPN	8380	WGS	91,462,814
HGVD v2.3	1208	WES	539,980
JPN_UNION	201,206		116,006,352

JPN_UNION included no duplicates in the number of autosomal variants, while it included duplicates in the sample size. More than half of the GEM-J WGA samples overlapped with ToMMo 8.3KJPN. Quality filters for variant calling defined for each dataset were not considered (i.e., all detected variants were counted). Additionally, multiallelic variants were decomposed into two or more monoallelic variants and considered as separate variants.