Genome-wide two-point results from the three marker maps appeared to be comparable. However, the observed SNP-based LODs were lower than expected under the asymptotic null, which is probably due to the decreased information content of SNPs on an individual basis. For the multipoint results, the densest SNP map appeared to fit better, likely reflecting the increased information content provided by the larger number of markers or finer spacing. The asymptotic null distribution assumes independence across the genome, but LOD scores are correlated along a chromosome, even under the null hypothesis of no linkage. Our Q-Q plot comparisons may be affected by correlation among LOD scores. However, we would expect such correlation to cause greater deviations from the asymptotic null for the multipoint results rather than the two-point results as we observed.
