The mapped reads are colored by default according to the following color code (see figure 28.12 for a simplified illustration of the color scheme):
- Single reads mapping in their forward direction are green.
- Single reads mapping in their reverse direction are red.
- Paired reads are blue. Reverse paired reads are light blue (always in stand-alone read mapping, and only if the option "Highlight reverse paired reads" is checked, as it is by default, in reads tracks). The thick line represents the read itself; the thin line represents the distance between each read in the pair.
- Reads from broken pairs are colored as single reads, i.e., according to their forward/reverse orientation or as a non-specific match. In stand-alone read mappings, reads that are members of a broken pair are highlighted in darker shades of the read color, unless the Read layout is set to "Packed". Broken pairs and Single reads cannot be differentiated in tracks.
- Non-specific matches are yellow. When a read would have matched equally well another place in the mapping, it is considered a non-specific match. This color will "overrule" the other colors. Note that when mapping to several reference sequences, i.e. chromosomes, a read is considered a double match when it matches more than once across all the chromosomes.
- Unaligned ends, that is the part of the reads that is not mapped to the reference (also known as soft-clipped read ends) will be shown with a faded color, e.g., light green, light red, light blue or light yellow, depending on the color of the read.
- Deletions are shown as dashed lines (figure 28.13). Insertions with a frequency lower than 1% are shown with a black vertical line.
- Mismatches between the read and reference are shown as narrow vertical lines on the reads (or black letters on a colored background at the nucleotide level) following the Rasmol color scheme: A in red, T in green, C in blue, G in yellow (figure 28.14). Ambiguous bases are in gray.
These default colors can be changed using the side panel as shown in figure 28.15.
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.