The imputation results are given in Table 2. The mean IQS is lower than the mean accuracy in both EA and AA. There are cases where IQS is negative, indicating that imputation did worse than chance in assigning genotypes. In this situation, 95% of the minor allele frequencies lie between 0 and 0.058, 95% of the chance agreement rates lie between 0.78 and 1, and the imputation accuracy is below chance agreement with 95% of the values between 0.81 and 1. These are strong examples of how imputation accuracy can be misleading when “chance” contributes so strongly to the proportion of agreement.
