Read conflicts
After assembly or mapping, conflicts between the reads are
annotated on the consensus sequence. The definition of a conflict is
a position where at least one of the reads has a different
residue compared to the reference.
A conflict can be in two states:
- Conflict. Both the annotation and the corresponding
row in the Table (
) are colored red.
- Resolved. Both the annotation and the corresponding
row in the Table () are colored green.
The conflict can be resolved by correcting the deviating residues in the reads as described Editing a contig or read mapping.
A fast way of making all the reads reflect the consensus sequence is to select the position in the consensus, right-click the selection, and choose Transfer Selection to All Reads.
The opposite is also possible: make a selection on one of the reads,
right click, and Transfer Selection to Contig Sequence.