It is important to note that the traditional genome inflation factor λ is not an ideal indicator of potential problems related to imputation quality. In our studies, we noticed that λ is not dramatically different from 1, in contrast to the extent that the Q-Q plot is distorted (Fig. 2B D). The reason is that λ reflects systematic inflation on all SNPs while the distortion of the Q-Q plot in our studies is due to a small number of poorly-imputed SNPs. However, problems with this limited number of SNPs (less than 0.5% of total SNPs) can be dramatic and lead to pronounced false positive P values that exceed genome wide significance.
