Distribution of significant GWAS hits.

<p>Horizontal violin plots depict the distribution of minor allele frequencies (MAF) of the most strongly associated single marker in a GWAS. Individual hits are plotted as translucent points and jittered to provide a sense of the total number and density of hits. Each panel contains simulated data pooled across model replicates for each value of <i>λ</i> with empirical data for comparison. Empirical data are described in Materials and Methods. In cases where more than one marker was tied for the lowest p-value, one was chosen at random. Shown here are the additive co-dominant (AC), gene-based (GBR), incomplete multiplicative recessive (Mult. recessive (<i>h</i> = 0.25); iMR) and complete multiplicative recessive (Mult. recessive (<i>h</i> = 0);cMR) models. All data shown are for models where <i>H</i>² ∼ 0.08, because single marker test power was too low under <i>H</i>² ∼ 0.04 to make informative density plots. To further increase the number simulated data points, we perfromed n = 1,250 replicates at each level for this figure. Simulated data were subjected to ascertainment sampling such that the MAF distribution of all markers on the simulated genotyping chip was uniform. Specific information regarding the empirical data can be obtained in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006573#pgen.1006573.s025" target="_blank">S1 Table</a>.