Figure 5
Diagram of the method for comparing the extent and frequency of homozygous segments with haplotypes underlying ext AUC 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 Extent min and p max , segments with length greater than Extent min selected, and the maximum founder haplotype frequency (Freq hap-max ) obtained across those segments. The expected haplotype frequency (Freq hap-exp ) was calculated as the square-root of p max .