To further explore the distribution of maximum LOD scores for each marker map, we simulated chromosome 1 data, where we obtained our highest genome-wide LOD scores, under the null hypothesis of no linkage. We generated 500 replicates for the microsatellite and SNP1 maps, and 200 replicates for the SNP2 map. The empirical LOD score cutpoints were consistently higher for the SNP maps than for the microsatellite map (Table 2). Our observed chromosome 1 LOD scores of 2.02 for SNP1 and 2.10 for SNP2 fall between the P = 0.05 and P = 0.01 cutpoints, whereas the microsatellite LOD of 1.26 corresponds to an empirical P > 0.10. A chromosome 1 P-value of 0.004 corresponds to a genomewide P-value of 0.05 . None of our LOD scores reached genome-wide level of significance.
