Q-Q plots of genome-wide two-point and multipoint LOD scores are presented in Figure 2. The straight diagonal line represents the expected LOD score based on the asymptotic null distribution. A LOD score of 1.5 is indicated on each plot by a vertical red line. For the two-point results, the observed LOD scores were lower than expected (Figure 2A); this conservative bias was most pronounced for SNP2. In contrast, the SNP2 observed multipoint LOD scores, plotted every 5 cM, appear to fit the expected distribution better (Figure 2B).
