SNP Highlighter

The "SNP Highlighter" graph type is an extension of the default region track graph type that also allows mismatches and similarities between the regions and a reference DNA track to be highlighted. In order to compare the regions to the reference track, the regions must have "sequence" properties (with correct lengths). The reference DNA track is the first DNA track above the region track (or first track below). This applies even if this DNA track is hidden.

If the region height is at least 15 and the zoom scale is 1000% or closer, the (mis)matches will be displayed as colored letters superimposed on the region, as shown in the first sequence in the image below. The letter indicates the DNA base in the region at that position, which can be either different from or the same as the reference track, depending on the chosen mode. If the region height is smaller than 15 or the zoom scale is less than 1000%, the (mis)matches will be shown as colored boxes on top of the regions with the color indicating the base, as shown in the second sequence below.

To change the highlight mode, right-click on the track in the Features Panel and go to "Graph Settings" in the context menu and then "Highlight". The four possible modes are: Mismatches, Matches, Full sequence and None. In mismatches mode, the differences between the regions and the reference track will be highlighted (i.e. SNPs in the regions). In matches mode, the similarities will be highlighted instead. With full sequence, the full sequence of the regions will be shown with letters or colored boxes. If either of these three modes are selected, the region labels will not be displayed and neither will motif match logos for TFBS regions. If the none mode is selected, nothing will be highlighted, and the regions will be displayed exactly as they would be with the default graph type.