We estimated the accuracy of the imputation process using fivefold cross-validation in the reference panel samples. For samples of European ancestry, the estimated four-digit accuracy for the maximum posterior probability genotype is above 93.9% for all 11 loci (Supplementary Table 7). This accuracy improved to above 96.1% for all 11 loci after restricting to HLA allelic variant calls with a posterior probability greater than 0.70. This resulted in call rates above 95.1% for all loci (Supplementary Table 8).
