Top twenty regions of shared human/chimpanzee haplotypes by estimated TMRCA.

a<p>Genomic coordinates in hg19 assembly.</p>b<p>Posterior expected TMRCA in generations, averaged across unfiltered genomic positions in region.</p>c<p>Number of polymorphisms in Complete Genomics dataset in region per kilobase of unfiltered sequence.</p>d<p>Normalized polymorphism rate: number of polymorphisms per unfiltered kilobase divided first by the local mutation rate (as estimated from divergence to nonhuman primate outgroup genomes) then by the average of the same polymorphism/divergence ratio in designated neutral regions (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004342#s4" target="_blank">Methods</a>). The resulting value can be interpreted as a fold increase in the mutation-normalized polymorphism rate compared with the expectation under neutrality.</p>e<p>Possible copy number variant (CNV), based on Complete Genomics “hypervariable” or “invariant” labels (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004342#s4" target="_blank">Methods</a>). Polymorphism rates in these regions may be inflated. Few of these regions were identified in the Leffler et al. data set, probably because the authors were careful to filter out duplicated regions from their analysis <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004342#pgen.1004342-Leffler1" target="_blank">[77]</a>.