Strong selective sweeps on the X chromosome in the human-chimpanzee ancestor explain its low divergence

* CoalHMM estimates in 1Mb chunks

ILS09_gamma_aln_coord_clean_fixscale.csv

Estimates for the full genome alignment obtained as described in Nature. 2012 Mar 7;483(7388):169-75. doi: 10.1038/nature10842.

* Alignment statistics for the X chromosome

chrX.statistics.csv

This file has been generated by MafFilter on the the human, chimpanzee, gorilla and orangutan alignment. It contains counts on the various parsimony-informative sites.

* ILS in 100 kb windows along the genome alignment.

full_scan_100k.csv

ILS computed by window scanning along the posterior decoding from the CoalHMM method.

* Divergence ratios computed along the X chromosome.

Compara.epo_6_primates_hsap-projected.chrXnew.subset.nogap.cleaned_aln.statistics.csv

This file was generated by MafFilter on the X chromosome alignment. It contains the divergence estimates between human, chimpanzee, gorilla and orangutan in 100 kb windows.

* Nucleotide diversity for the X chromosome in 14 human populations

piX_100kb_regions.csv

This file was generated from the 1000 Human Genomes Project data.

* Genome coordinates of the 8 low-ILS regions

PNILSR_1Mb_10pc_edited.csv

Coordinates are according to human hg19.

* Coordinates of regions devoid of neanderthal introgression (Asian population)
Neanderthal_ASN.csv

Coordinates are according to human hg19.

* Coordinates of regions devoid of neanderthal introgression (European population)
Neanderthal_EUR.csv

Coordinates are according to human hg19.

* Ampliconic regions
AmpliconicRegions_hg19.csv

Ampliconic regions in hg19 coordinates. The two last column describe is the region was included in our genome alignment, and if it was comprised in a low-ILS region.