The ratio of the observed dosage variance to the expected binomial variance, the dosage-variance ratio, has proved to be useful metric of imputation quality. To assess accuracy of imputed genotypes, cohorts compared the imputation output to SNPs that had been previously genotyped on other platforms and that had not been used in the imputation process. In an internal analysis that compared the imputed SNPs to the actually genotyped SNPs in the RS, the mean concordance (number of concordant individuals/total number of individuals) between the imputed and the genotyped SNPs was 0.989 for imputed SNPs with a dosage-variance ratio >= 0.9. For ratios between 0.5 and 0.9, the concordance was 0.937; and for ratios <= 0.5, it was 0.889. Validation efforts produced similar results in other cohorts.
