Sequence divergence between human and chimp

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
chr1	574730	4097311	14.03
chr2	571968	4337056	13.19
chr3	460826	3601819	12.79
chr4	483915	3522581	13.74
chr5	432399	3222413	13.42
chr6	430879	3147588	13.69
chr7	426619	2928175	14.57
chr8	380886	2786423	13.67
chr9	333171	2283198	14.59
chr10	351451	2471725	14.22
chr11	354062	2492733	14.20
chr12	326365	2396839	13.62
chr13	234420	1761333	13.31
chr14	228533	1645955	13.88
chr15	207061	1516600	13.65
chr16	244166	1680348	14.53
chr17	215074	1476349	14.57
chr18	190200	1397643	13.61
chr19	207813	1157902	17.95
chr20	164209	1207849	13.60
chr21	106186	719102	14.77
chr22	113969	721194	15.80
chrX	439833	1906519	23.07
			14.54

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.