We evaluated imputation accuracy in several ways. First, we compared minimac RSQ values between imputation results with MTFS sequences and 1000 Genomes sequences. Minimac RSQ is an estimate of the true squared correlation between the imputed allele dosage and the true allele dosage, based on the hidden Markov model in minimac (Li et al., 2010). RSQ > .3 is a conventional cutoff to conclude a variant has been imputed with sufficient accuracy. For instance, variants with RSQ ≤ .3 are commonly excluded in association studies.
