10.4.3 Deletion, insertion and structural variant discovery (DNA mapping)

Geneious can discover structural rearrangements, short insertions, and arbitrarily large deletions from paired or unpaired reads by analyzing how fragments of each read align to different regions of the reference sequence(s). To enable this option, check Find structural variants, short insertions and deletions of any size. If you only want to find deletions up to a specified size, check Find short insertions and large deletions up to...

For this operation, Geneious makes two passes during mapping. On the first pass each read mapped will generate candidate junctions (sites for structural variants) based on where fragments of the read align to different regions of the reference sequence(s). The more reads that support a candidate junction, the more likely it will be used during the second pass. The second pass involves mapping reads using the discovered junctions.

Insertions, where the ends of a read map to nearby locations but the center of the read doesn’t map, are also detected. Since discovered insertions must be less than the read length, only short insertions are generally discovered. Only the most common insertion at a each position will be annotated and have reads correctly aligned with it.

By default, at least 2 reads must support the discovery of a junction in order for it to be used during the next pass. This threshold can be adjusted under More Options by changing the Minimum support for structural variant discovery setting. Insertion discovery can also be disabled here by unchecking Include insertions in structural variants.

Junctions used during the second mapping pass are annotated on the reference sequence under a track named after the reads. Annotations are only created for variants which are at least 3 bp in size. Each junction annotation has the following properties:

Reads spanning junctions may be represented in one of three possible ways: