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So what about the autosomal differences in the Science publication what I quoted? Where does that fit into the mix? I presume there are negligible autosomal differences between any two humans?

I am assuming you are referring to this statement "...Mean autosomal divergence is 1.27 ± 0.20% (human-chimpanzee), 1.61 ± 0.21% (human-gorilla), and 3.12 ± 0.33% (human-orangutan)."

These frequencies refer to SNP frequencies (the Science article refers to these as SNVs, same thing). I said SNP difference between humans and chimps was between 1-4% (I was going by memory). Pretty close.

The autosomal SNP difference between two unrelated humans is about 0.1%.

Again, higher levels of variation are observed with copy number variants, both between humans as well as between humans and other species. https://www.sciencedaily.com/releases/2006/11/061123115741.h...
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