QQ-plots comparing the null distribution of the test statistic of interest with a χ2(1) distribution. Each column corresponds to a different test statistic: (1) G-statistic computed using the true genotypes (True); (2) G-statistic computed using called genotypes without filtering (Call NF); (3) G-statistic computed using called genotypes with filtering (Call F); and (4) the likelihood ratio test statistic with unknown minor allele (LRT). Assuming 500 cases and 500 controls, under the null hypothesis, a set of 5,000 sites were simulated with a MAF of 5% with a sequencing depth of 2× (upper panels) and 5× (lower panels). The "Inflation" factor  is shown in the upper left corner of each figure.
Kim et al. BMC Bioinformatics 2011 12:231 doi:10.1186/1471-2105-12-231