The distribution of information content in the SNPs is shown in Figure 2. We performed regression of information content on percent heterozygotes for the Affymetrix and the Illumina SNPs in Figure 2. The slopes of these lines are not significantly different from 0 and the intercepts are 0.053 and 0.051 for Affymetrix and Illumina, respectively. Although nearly all of the Illumina SNPs have between 40 and 50% heterozygotes, and the Affymetrix panel includes a large number of SNPs with low heterozygosity, it appears that by this measure a SNP chosen at random from either dataset would have approximately the same degree of informativeness.
