When the accuracy is high (R2>0.9), using the best-guess genotype from the imputation procedure results in little loss of power. The gain from using a dosage or mixture model is greatest at intermediate accuracies, since posterior probabilities are informative about the underlying genetic variation, even if they do not allow accurate “best-guess imputation” of genotypes. For all three strategies, at low imputation accuracies, the lines of the additive regression models converge, so do the lines of the dominant regression models.
