diagonal line. We do not observe significant distortion, i.e., type I error, in both tests. On the other hand, the Q-Q plot of MH test lies above the diagonal line. As stated earlier, both Case-Control and the dTDT are not robust to the population stratification because of the dependence of allele frequencies in the populations. MH test is basically a combined statistic of these two tests. Though we have increased the sample size in the combined test, we have reason to believe that such sensitivity to population stratification has been inflated in the MH test. This is a tradeoff that we need to pay attention to in the future studies. However, this issue can be partially addressed by restricting accurate genotypes based on the imputation quality score (IQS) [86] (discussed below in Dealing with errors).
