Fig 1 shows regional plots of iHS scores for the LCT, CHRNA5-A3-B4 nicotinic receptor gene region and CHRNA6-B3 nicotinic receptor gene region. Within each of these regions, we calculated the iHS score for all SNPs for which we could unambiguously determine the chimp ancestral allele. We then compared the number of SNPs within each region with iHS values above 2 or below -2, to the 10,000 equally sized permutated regions that were chosen at random.
