Figure 6

Imputation performance across the study populations.

The performance of imputing samples within each of the 12 study populations was measured by the discordance rate, defined as 1 – r², where r² corresponds to the correlation between the observed genotype and the imputed allele dosage at 400 SNPs that were masked out of 1,607 SNPs in the MHC. For each of seven Japanese populations (except JPT), the imputation was performed on 19 additional samples which were not part of the main study and was used to construct the population-specific reference panel. On the other hand, the imputation at CHB, CHS, GIH and JPT were performed on 19 samples from the same population data, which was used to construct the reference panel and was thus subject to overfitting. The annotations of the reference panels used are as follow: JPTPanel = JPT; HAP_SGVPPanel = combined panel using the CHB, CHS, JPT samples; FukuokaPanel = Fukuoka; EhimePanel = Ehime; ShimanePanel = Shimane; AmaPanel = Amagasaki; Kita-NagoyaPanel = Kita-nagoya; TokyoPanel = Tokyo; OkinawaPanel = Okinawa; CHBPanel = CHB; CHSPanel = CHS.