The information content results for microsatellites show substantial dips between markers. Both the Affymetrix and Illumina map provide a higher and much more uniform level of information. There are several sharp dips in the Affymetrix map, but this may be due to the IBD generation failing to converge; the locations of reduced information correspond to the locations of higher variance in Figures 1 and 2. Although the Affymetrix map has more than twice as many SNPs as the Illumina map, information is not significantly higher (p = 0.3). We also note that the "sparse" Illumina map (with an average intermarker spacing of 1.1 cM) contains substantially more information for sibships than the microsatellites and nearly as much information as the full Illumina map (with an average intermarker spacing of 0.69 cM). The information for relative pairs is uniformly lower than sibling pairs for all four map sets (results not shown). This may be due to the greater number of missing founders when considering the extended pedigrees as opposed to sibships.
