The mean IC for each individual chromosome for the full SNP set, SNP subset, and microsatellites across 22 autosomal chromosomes when the erroneous genotypes were either excluded or included were summarized in Table 2. The IC for the full SNP set was significantly and uniformly higher than that for the microsatellites. When the erroneous genotypes were excluded, the mean genome-wide IC for the microsatellites was 0.783, with an inter-quartile range of 0.134, and was 0.950 for the SNPs with an inter-quartile range of 0.017. The mean IC for the SNP subset was 0.905 with an inter-quartile range of 0.044 when erroneous genotypes were excluded. When erroneous genotypes were included, the mean IC for the SNP subset was 0.910 with an inter-quartile range of 0.042. We noted that although genotyping errors were expected to reduce the values of IC slightly, their impact was quite small, which may be due to the small genotyping error rate.
