The current study provides evidence that false-positive rate is influenced by MAF. We report that common SNPs (MAF 25-50%) result in significantly fewer false positives than expected under the null χ2 distribution, suggesting that for common SNPs the current thresholds may be too conservative. Also, we report more false positives with 5% MAF SNPs than with common SNPs at the thresholds examined. In addition, under the null hypothesis, up to 5% randomly missing data did not impact our findings. Thus, under the null hypothesis, MAF but not proportion of missing data appears to affect the likelihood of a false positive result.
