Quality filtering
Once an alignment has been found, it is examined by the quality filter. If it fails to meet the criteria enforced by the filter, it is discarded. If all alignments of a particular read fail to meet the criteria, the read is reported as unmapped.
The quality filter has two parameters: -s/--similarity and -l/--lengthfraction. They interact and must be understood together.
For example, the default setting (similarity=0.8, length fraction=0.5) means that a read will be reported as unmapped, if none of its alignments feature a stretch, at least 50% of the total alignment length4.4, consisting of at least 80% matches.
If you want to see all alignments found, you can disable the filter altogether by specifying -s 0.
Footnotes
- ... length4.4
- By total alignment length we mean the combined length of all matches, mismatches, insertions, and deletions.