Insertions
If a single read contains an insertion compared to the reference sequence, this will be indicated by a purple line within the read. When hovering over, the inserted nucleotide will be shown.
When a large proportion of the reads have an insertion at the same location, NGSengine determines whether this is a new insertion, and will subsequently report this by a triangle and a purple highlight on the insert position.
The insertion may be present in only one of the two alleles but the purple highlight will always be shown in both reference alleles. The purple background for an insertion will only be visible if the insertion has never been described before (no alleles with the insertion at that position submitted in the IMGT database).
New insertions are also represented in the Overview screen and the Insertions plot of the Statistics tab. Insertions will be indicated as mismatch and have to be inspected by the user.