For Sample 1 (GSA), 991 Thai subjects were phenotyped initially. Some DNA was available for 863 of these. Two hundred fifty-seven subjects were removed due to low genotype call rate (< 0.9). (A quality control (QC) call rate of 0.95 is preferred, but the quantity and quality of DNA from Sample 1 was poor, so we used a lesser standard; had we used a threshold of 0.95, more than 100 additional subjects would have been removed.) Two subjects were removed due to mismatched genotype and phenotypic sex; six subjects were removed due to high heterozygosity rate; seven were removed because they were duplicates; and ten were removed because the same subjects were also present in the Sample 2, for which better-quality DNA was available. 581 subjects remained for analysis. Only autosomal SNPs were retained. SNPs with low genotype call rate (< 0.95), MAF < 0.01, or HWE p < 10−6 were removed. 334,631 SNPs remained for imputation.
