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 the 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.