Diagram of the method for comparing the extent and frequency of homozygous segments with haplotypes underlying extAUC peaks. From a consensus set of genotypes, homozygous segments were detected, extAUC calculated and smooth spline interpolation performed, and peaks detected. Complementary quantiles (Pr(X >Extent) = (1 - Pr(X ≤ Extent)) = (1 - Percentile/100)) were calculated from each ISLV's percentile values underlying a particular peak. Values of Extent and Pr(X >Extent) that maximized the value of Extent × Pr(X >Extent) were extracted as parameters Extentmin and pmax, segments with length greater than Extentmin selected, and the maximum founder haplotype frequency (Freqhap-max) obtained across those segments. The expected haplotype frequency (Freqhap-exp) was calculated as the square-root of pmax.
Johnson et al. Genome Biology 2011 12:R21 doi:10.1186/gb-2011-12-3-r21