Peaks with high cross-population homozygosity and low Fst/θ identify genomic regions with similar 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). The structure of phased haplotypes is plotted for an example peak for JPT with low differentiation (mean Fst/θ = 0.0235).
Johnson et al. Genome Biology 2011 12:R21 doi:10.1186/gb-2011-12-3-r21