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The simulated effect of European gene flow into Native American haplotypes on estimation accuracy. Different fractions of the 169 (CHB+CHD) reference haplotypes were replaced by TSI haplotypes along 10 different regions, each of length 5 Mb. The plot gives, for each fraction and for each region (in different colors), the maximal corrected deviation (see text for details) of the estimated average European ancestry from the true average european ancestry along the region.
