How many of the human reference sequence alleles are derived alleles?

Question

[humanevo1]

What percentage of the human reference sequence is thought to be identical to what we believe the ancestral human sequence looked like? To put it another way, if I'm looking at a SNP in an individual, and they differ from the human reference sequence at that site, how likely is it that the SNP in the individual is the derived allele?

I'm thinking someone should have calculated this somewhere using primate outgroups to do the portions of the genome with high primate homology, but I can't find any papers that mention this.

Answer 1

[Katie D'Aco]

Check out the paper Initial sequence of the chimpanzee genome and comparison with the human genome it might have what you're looking for. From the first page:

Single-nucleotide substitutions occur at a mean rate of 1.23% between copies of the human and chimpanzee genome, with 1.06% or less corresponding to fixed divergence between the species.