Genome Graphs is a tool for displaying genome-wide data sets such as the results of genome-wide SNP association studies, linkage studies and homozygosity mapping. This section provides line-by-line descriptions of the controls on this page. For more detailed instructions, see the Genome Graphs User's Guide.

• clade: Specifies which clade the organism is in.
• genome: Specifies which organism data to use.
• assembly: Specifies which version of the organism's genome sequence to use.
• graph ... in ...: Selects which graph(s) to display in which color.
• upload: Takes you to a page where you can upload your own data.
• import: Takes you to a page where you can import database tables from this assembly.
• configure: Takes you to a page where you can control many aspects of the display including the overall size of the image, how many graphs can be drawn, and the chromosome layout.
• correlate: If more than one graph is selected, takes you to a page listing the Pearson's correlation coefficient for each pair of graphs.
• significance threshold: Values above this threshold will be considered significant. A light blue line will be drawn across the graphs at the significance threshold of the first graph. Regions above the threshold will be included in the region list you get with the browse regions button.
• browse regions: Takes you to a page with a list of all regions above the significance threshold on the left, and a Genome Browser on the right. Clicking on a region will move the browser's window to that region.
• sort genes: Opens the Gene Sorter with a filter to display only those genes in regions that are above the significance threshold. If the graph was uploaded using markers, then a custom Gene Sorter column with the same name as the graph will be created. This column will list all markers for each gene that contain values above the significance threshold.