After correcting for multiple tests (p-value = 0.05/19 = 0.0026), SNP rs4903712 on chromosome 14 remained significant. This was the seventh most significant SNP from the MH test. As discussed above, there are several issues affecting the dependability of our test results. As we saw from the Q-Q plots, signals from MH test have been inflated because of double counting of the population stratification factor. On the other hand, the genotyping and imputation accuracy may be taken into account as well. To address these issues, we compute the IQS for the listed top SNP markers on Table 8 with and without setting a 0.8 threshold on the dosage probabilities. We report the number of individuals who meet such 0.8 threshold (in the last column, the numbers in the brackets next to IQS with dosage probabilities >0.8). According to the IQS, when we exclude the dosage probabilities that are below 0.8, the inference program performs very well and provides above ∼0.90 IQS on average. The reason is that for dosage probabilities that are lower than 0.8, there is too much uncertainty
