The Sanger reads mapping algorithm in UGENE has two steps:
- Finding of results with BLAST.
- Adjustment of the result with the Smith-Waterman algorithm.
In version 1.28 the value of the "Mapping min identity" parameter in the "Map Sanger Reads to Reference" dialog applies to the first step of the algorithm only. The identity should be checked after the two steps instead.
Note also, that the parameter shouldn't be misinterpreted with the "Identity" value of a BLAST result. The latter one is the identity between the found part of a read with the reference. The "Mapping min identity" parameter specifies required identity between and the reference.