plot for the SNP, can be used to screen for a technical origin of the HWE deviation: null alleles can produce multimodal genotype clusters in the heterozygote clusters and one of the homozygote clusters (Figure 8) or can produce an unexpected number of samples with no signal (Figure 9), and SNPs within CNVs or segmental duplications can produce clusters of genotypes intermediate between the three expected clusters of genotype (Figure 10) [48]. In the loci depicted in figures 8, 9 and 10, chi-square tests for HWE are rejected at P-values less than 10−80, so these represent the most egregious examples of the aforementioned behavior. If no technical errors are detected then a number of biologically plausible explanations exist for HWE deviations toward an excess of homozygotes: population stratification, assortative mating and inbreeding, to name a few.
