Read conflicts
When the mapping is created, 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 have a different
residue.
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.