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:

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.