Figure 3.

(a and b) Pure likelihood plot of association evidence in discovery set (a, top) and in joint analysis of data sets (b, bottom). This pure likelihood analysis plots odds ratio (OR) on the y axis and base-pair position on the x axis. Each vertical line represents a likelihood interval (LI) for the OR at a given SNP. The OR=1 line is plotted as a solid black horizontal line, for reference. LIs in color are denoted as SNPs of interest, whereas a gray line indicates that the SNP is not of interest because the 1/32 LI for that SNP covers the OR=1 line. The small horizontal tick on each LI is the maximum likelihood estimator for the OR. The portion of the colored LI that covers the OR=1 horizontal line indicates the strength of the association information at that SNP. In particular, if the navy blue portion is above the OR=1 line while the yellow portion of the LI covers the OR=1 line, then the LOD evidence at that SNP is between 1.5 and 2 (ie, the 1/32 LI does not include the OR=1 value, but the 1/100 LI does); similarly, if both the yellow and navy blue portions are above the OR=1 line but the turquoise portion covers the line, then the LOD evidence is between 2 and 3 (ie, the 1/100 LI does not include OR=1 as a plausible value but the 1/1000 LI does). The further the colored line is above the OR=1 line, the stronger the association evidence. The max LR for each SNP in color is also provided as text in the plot, providing evidence not only of whether the LOD evidence is between 2 and 3, but also the exact value of the max LR.