When using multi-sample data, an enhanced version of the Alignment View is displayed.
The enhanced Alignment View displays all reference sequences and data reads in a single alignment, sorted by sample. Each sample is displayed in a two-tiered hierarchy:
•As a “faux” consensus sequence, displayed with a goldenrod background. In this sequence, all called variants are included in red lettering for ease of evaluation.
•In expanded form, with the associated reads shown under the "faux" consensus. Click on the expansion arrows to the left of each "faux" consensus to toggle between showing or hiding these reads.
In the enhanced Alignment View, click any expand arrow to the left of a group name (circled in red, below) to toggle between showing all sequences in the group or showing only the consensus. To collapse or expand all multi-sample data simultaneously, hold down the Alt key while clicking any expand arrow.
