The Affymetrix map contains regions of reduced information, corresponding to the same locations where variance of phi2 is high. We examined the Affymetrix SNPs around the largest peak (at 15 Mb) and found that they were not significantly different from other Affymetrix SNPs on chromosome 7 in terms of density, heterozygosity, LD, or missing data rate. Other possible explanations include an increase in Mendelian-compatible genotyping errors or incorrect maps (either spacing or marker order). These possibilities could be tested in additional datasets to see if convergence problems existed at the same location.
