Imputation accuracy characterized by minor allele*.

*Genetic markers were classified into three categories based on Minor Allele Frequency (MAF). The cutoffs of MAF were 5% and 25%. Known genotypes were masked as missing at three different rates: 60%, 70% and 80%. Three imputation methods (BEAGLE, fastPHASE and iBLUP) were used to impute the masked genotypes. Accuracy was calculated as Pearson correlation coefficient between known genotype and imputed. Three subset of genotypes were examined: 1) Genotypes with major allele (Major), including homozygous of major allele and heterozygous; 2) Genotypes with minor allele (Minor), including homozygous of minor allele and heterozygous; 3) Genotypes of two homozygous and heterozygous (All).