Download Bioinformatics Toolbox User's Guide

Visualize and Investigate Short-Read Alignments
Flag Reads with Low Mapping Quality
Set the Mapping quality threshold in the Alignment Pileup section to flag low-quality
reads. Reads with a mapping quality below this level appear in a lighter shade of gray.
Flag Duplicate Reads
Select Flag duplicate reads and select an outline color.
Flag Reads with Unmapped Pairs
Select Flag reads with unmapped pair and select an outline color.
Evaluate and Flag Mismatches
Mismatches display as colored blocks or letters, depending on the zoom level.
Zoomed out view of read — Mismatches display as bars
Zoomed in view of read — Mismatches display as letters
In addition to the base Phred quality information that displays in the tooltip, you can
visualize quality differences by using the Shade mismatch bases by Phred quality
settings.
The mismatch blocks or letters display in:
• Light shade — Mismatch bases with Phred scores below the minimum
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