SNPs with genotyped SNPs without other quality control is problematic (Fig. 2B). Therefore, the observed distortion was due to imputation error and the statistically skewed SNPs (Fig. 2B) are false positives. We then filtered the imputed data by removing all SNPs with IQS≤0.9, retaining 76% of the imputed SNPs, and dramatically improving the Q-Q Plot (λ = 1.04) (Fig. 2C). The Q-Q plot remained grossly distorted even when the filter was changed to an imputation accuracy of >99%, retaining 72% of the SNPs, although λ improved to 1.05 (Fig. 2D). Although this is a very strict value for imputation accuracy, the Q-Q plot clearly shows there is significant type I error.
