Additional file 2.
QQ-plot comparing the null distribution of the Armitage trend test statistic with a χ2(1) distribution. QQ-plots comparing the null distribution of the test statistic of interest with a χ2(1) distribution. The first three columns correspond to the Armitage trend test statistic computed using the true genotypes (True), called genotypes without filtering (Call NF), and called genotypes with filtering (Call F), respectively. The fourth column corresponds to 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.
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Kim et al. BMC Bioinformatics 2011 12:231 doi:10.1186/1471-2105-12-231