Quality scoring of Assemblies and Align to Reference alignments can be visualized directly on the sequence. Residues can be shaded according to their quality scores. These can be displayed anywhere quality values are available, including de novo and reference assemblies in Assembler and Align to Reference alignments.
The intensity of the shading of residues indicates the phred-based quality value of each residue.
- For individual reads, this ranges from 0 (deep red) through 20 (white) to 40 or above (deep green). The consensus scale is doubled and ranges from 0 (deep red) through 40 (white) to 80 or above (deep green).
- Gaps are always shown with a white background. You can “mouse-over” a residue to view the numerical information in a tooltip.
- Edited residues are always given a phred quality value of 99 and these residues are given a blue background.
Most assembly algorithms are quality score aware and better quality reads will take priority over lower quality sequences. However, edited residues will always override all other sequences/reads even if they are high quality. This also means that a single read with an edited sequence will take priority over many other reads with a different sequence and the edited residues in that single edited read will define the consensus. This is done as we assume that the user knows best!
