using SHAPEIT2 [48] and then Minimac3 [49]. Imputed SNPs with information (INFO) scores < 0.30 or individual genotype probability scores < 0.90 were excluded, as were palindromic SNPs (A/T or C/G), monomorphic SNPs, SNPs with a genotyping rate of < 95%, SNPs that were not in HWE (p < 1 × 10−6), and SNPs with a minor allele frequency less than 0.05%. In total, 6,881,872 SNPs passed quality control and were available for analysis.
