Using a threshold of α = 0.05 in the stratification test described above, we found that 21 of the 395 SNPs showed evidence of population stratification. We had restricted our analysis to a single ethnic group in order to minimize the effects of population substructure, and this proportion (5.2%) of the total number of SNPs might have been expected to generate a significant test statistic purely by chance. Nevertheless, these SNPs were omitted from the QTLD portion of the test procedure.
