Friday, December 12, 2014

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. 

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