Figure 13. Genome-wide distribution of QTLs. Each point represents a single probe set. The x-axis gives the position of the QTLs (the single best QTL for those probe sets at a false discovery rate of 0.2), whereas the y-axis gives the position of the gene or probe set target itself. Positions are measured in genome-wide Mb (GMb) from Chr 1 through to the Chr Y (2600 GMb). The gray lines mark chromosome boundaries, and the significance level of individual QTLs are color-coded. High LRS values (low genome-wide P values) are represented by red, intermediate LRS values by green, and low values by blue. A large number of highly significant cis QTLs form a diagonal (red) line. Vertical bands such as that at 610 GMb (Chr 4 at 80 Mb) represent groups of transcripts that have trans QTLs at the same location. The major trans-acting band at 610 GMb corresponds to the Tyrp1 locus. How to perform a genome-wide scan by examining all of the QTLs in the HEIMED: Step 1. Link to GeneNetwork and select GenomeGraph from the “Search” pull-down menu at the top left of the page. Step 2. Configure the pull-down menus to read “Choose Species=Mouse, Group=BXD, Type=Eye mRNA, Database=Eye M430v2 (Sep08) RMA.” Step 3. Select the 'Mapping' button. This will generate the Whole Transcriptome Mapping page. You may adjust the false discovery rate (FDR). In our studies, we chose an FDR of 0.2. The entire data set of values used to construct this type of graph can be downloaded at GeneNetwork.