Genome-wide scans for (a) mandible and (b) skull.

<p>This plot shows <i>p</i>-values for association with craniofacial phenotypes—22 skull shape PCs, 21 mandible shape PCs and centroid size—at 80,027 candidate SNPs. Since only the smallest <i>p</i>-values are visible from this plot, <i>p</i>-values for individual PCs are drawn in separate plots; see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005607#pgen.1005607.s014" target="_blank">S9</a> and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005607#pgen.1005607.s015" target="_blank">S10</a> Figs. The associated phenotype (PC or centroid size) is indicated for each QTL. The blue line represents an approximate genome-wide significance threshold, 1e-6 (-log(p) = 6); the actual threshold we used to determine significance of the p-values is different for each phenotype (average–log(p) = 6.05, min = 5.95, max = 6.16). *To improve visualization, the <i>p</i>-value shown in the Figure is larger than the actual p-value; the actual p-values are PC4* -log(p) = 26.6, PC3* -log(p) = 14.8.