An important factor in overall power summaries, such as those in Tables II and III (below), is the allele frequency distribution of SNPs present in the reference panel, at which genotypes are being imputed in the study samples, since the tables are constructed with averages over all SNPs. In Figures 2C and 3C, where phenotypes were simulated from an additive genetic model, powers for all regression models increase substantially when minor allele frequencies are relatively low. This may reflect the relative difficulty of accurate imputation at SNPs with a lower MAF. (Under the correct additive model, power for the true genotypes is unaffected, since we attempted to make power independent of allele frequency for the purposes of aggregating results across SNPs for general comparisons among analysis strategies; see Methods.) For data simulated under a dominant genetic model, methods that assume the correct dominant model for analysis are superior at a greater range of allele frequencies.
