Using the data about ancestral state from UCSC we calculate the fraction of sites that are different between Human and Chimp. We can see in below table that on average 14% of the sites are different between human and chimp. ChrX shows a much higher divergence at 23%, which is expected given its lower Ne.
|Chromosome||Number of sites that are different||Total number of sites||Percent difference|
When we look divergence in windows across chromsome 2 and chromosome X we see higher divergence at the centromere and telomere. (see figures below and note the difference in scale of y-axis).
The fraction of sites that are different between human and chimp in a window is correlated with the DAF's we looked at earlier. The correlation coefficient for chr2 is 0.4 and for chrX it is 0.2.