There was also some difference in LOD scores between the Affymetrix and Illumina SNPs, with the Illumina SNPs giving higher scores at the main linkage peaks in these analyses. These differences may be due to the differing number of SNPs typed and their distribution on the chromosome. Though the overall information content for the Illumina and Affymetrix maps were similar, by chance it appears that the information content is lower in the Affymetrix map at these linkage peaks.
