Angela
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I have run La Brana and several other higher coverage WHG through on the calculator, they all get lighter skin predictions when you swap the blue eye associated variants for the ancestral brown eye alleles. I cannot post screenshots but if you want to put the data through yourself here is the number of alleles to input for each snp for La Brana for the darker prediction range suggested in the original study:
12: 2
13: 2
16: 1
19: 1
27: 2
29: 1
35: 2
39: 1
Then see how the skin prediction changes when you plug in 2 alleles for snps:
20, 31 & 32
You will notice that whilst the blue eyes are totally gone, the skin prediction changes to dark from dark to black.
So, academics putting out a major paper just decided not to input the snps for eye color???