How to increase alignment quality

[ardy20]

Hello Developers

We used scanPav to compare genome A with B. We filtered them for more than 10 KB fragments which are present in A but absent in B.
However, when we aligned the result to genome B they still show presence while there should be no match.

So, the question what is the criteria for mapping and how to get the present variation (in A genome) that is absolutely absent in the second species (B)?

Is there any criteria to increase the mapping quality?

Regards