PSL format and other UCSC tools.
Here are the columns as taken from the UCSC documentation.
- matches - Number of bases that match that aren’t repeats
- misMatches - Number of bases that don’t match
- repMatches - Number of bases that match but are part of repeats
- nCount - Number of ‘N’ bases
- qNumInsert - Number of inserts in query
- qBaseInsert - Number of bases inserted in query
- tNumInsert - Number of inserts in target
- tBaseInsert - Number of bases inserted in target
- strand - ‘+’ or ‘-‘ for query strand. In mouse, second ‘+’or ‘-‘ is for genomic strand
- qName - Query sequence name
- qSize - Query sequence size
- qStart - Alignment start position in query
- qEnd - Alignment end position in query
- tName - Target sequence name
- tSize - Target sequence size
- tStart - Alignment start position in target
- tEnd - Alignment end position in target
- blockCount - Number of blocks in the alignment
- blockSizes - Comma-separated list of sizes of each block
- qStarts - Comma-separated list of starting positions of each block in query
- tStarts - Comma-separated list of starting positions of each block in target