Coloring of mapped reads

The mapped reads are colored by default according to the following color code (see figure 25.12 for a simplified illustration of the color scheme):

Image standalonenotpacked
Figure 25.12: Default reads color in a stand-alone read mapping where the read layout is not set to "Packed": you can see that members of a broken pairs are in darker shades than the single reads.

These default colors can be changed using the side panel as shown in figure 25.15.

Image sidepanelmappingtrack
Figure 25.15: Coloring of mapped reads legends for read mappings (left) and reads track (right). Clicking on a color allows you to change it (except for read mappings at the Packed compactness level.

If your read mapping or track shows the message 'Too much data for rendering' on a gray background, simply zoom in to see your reads in more detail. This occurs when there are too many reads to be displayed clearly. More specifically, where there are more than 500,000 reads displayed in a reads track, more than 200,000 reads displayed in a read mapping, or when the region being viewed in a read mapping is longer than 200,000 bases. Paired reads count as one in these cases.