Peaks with high cross-population homozygosity and high Fst/θ identify genomic regions with dissimilar haplotype structure. Outlier peaks for each base population were chosen, filtered to include those with high ranking extAUC across all four populations, and sorted based on average Fst/θ between the base population and the other three populations (or with YRI and CEU if the base population was CHB or JPT). Phased haplotypes were plotted for an example peak for YRI with high differentiation (mean Fst/θ = 0.83).
Johnson et al. Genome Biology 2011 12:R21 doi:10.1186/gb-2011-12-3-r21