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PSL File Format - Definition and supported options

PSL lines represent alignments, and are typically generated by BLAT. Each line consists of 21 required fields, and track lines may optionally be used to provide more information.

Fields

Fields are space-separated, and all 21 are required.

  1. matches - Number of matching bases that aren't repeats.
  2. misMatches - Number of bases that don't match.
  3. repMatches - Number of matching bases that are part of repeats.
  4. nCount - Number of 'N' bases.
  5. qNumInsert - Number of inserts in query.
  6. qBaseInsert - Number of bases inserted into query.
  7. tNumInsert - Number of inserts in target.
  8. tBaseInsert - Number of bases inserted into target.
  9. strand - defined as + (forward) or - (reverse) for query strand. In mouse, a second '+' or '-' indecates genomic strand.
  10. qName - Query sequence name.
  11. qSize - Query sequence size.
  12. qStart - Alignment start position in query.
  13. qEnd - Alignment end position in query.
  14. tName - Target sequence name.
  15. tSize - Target sequence size.
  16. tStart - Alignment start position in query.
  17. tEnd - Alignment end position in query.
  18. blockCount - Number of blocks in the alignment.
  19. blockSizes - Comma-separated list of sizes of each block.
  20. qStarts - Comma-separated list of start position of each block in query.
  21. tStarts - Comma-separated list of start position of each block in target.
browser position chr19:7117069-7293902
track name="INSR PSL" description="BLAT results for INSR_HUMAN" useScore=1 color=darkgreen
1366  2 0 0 4 14  20  172729  +-  INSR_HUMAN  1382  0 1382  chr19 59128983  7117069 7293902 21  33,184,107,49,48,72,42,82,57,68,92,47,53,33,23,82,37,53,44,45,117,  0,33,217,325,375,423,495,537,619,676,755,847,894,948,981,1004,1086,1123,1176,1220,1265, 51835081,51861075,51944334,51954242,51956540,51958222,51960880,51962569,51965769,51976044,51985880,51987155,51996655,52000020,52002319,52003444,52005983,52006199,52008222,52009390,52011563,
415 120 0 0 5 727 9 247989  ++  INSR_HUMAN  1382  70  1332  chr15 102531392 99250897  99500491  10  106,47,73,77,37,53,44,42,19,37, 70,327,423,1009,1086,1123,1176,1220,1267,1295,  99250897,99439992,99451914,99478051,99478544,99482429,99486150,99491803,99500296,99500380,
325 80  0 0 5 817 9 11667 +-  INSR_HUMAN  1382  33  1255  chr1  249250621 156811214 156824096 10  95,20,9,13,22,77,37,53,44,35, 33,140,207,889,915,1009,1086,1123,1176,1220,  92426525,92426846,92427047,92436193,92436271,92437595,92438321,92438558,92439034,92439302,
38  10  0 0 0 0 0 0 +-  INSR_HUMAN  1382  1172  1220  chr6  171115067 117631242 117631386 1 48, 1172, 53483681,
55  27  0 0 2 18  2 54  ++  INSR_HUMAN  1382  1142  1242  chr1  249250621 64643518  64643818  3 22,34,26, 1142,1172,1216, 64643518,64643608,64643740,
54  34  0 0 1 8 1 24  ++  INSR_HUMAN  1382  1143  1239  chr9  141213431 113562785 113563073 2 47,41,  1143,1198,  113562785,113562950,
33  15  0 0 0 0 0 0 ++  INSR_HUMAN  1382  1143  1191  chr1  249250621 156849010 156849154 1 48, 1143, 156849010,
33  16  0 0 0 0 0 0 +-  INSR_HUMAN  1382  1142  1191  chr15 102531392 88472421  88472568  1 49, 1142, 14058824,
33  16  0 0 0 0 0 0 ++  INSR_HUMAN  1382  1142  1191  chr9  141213431 87570285  87570432  1 49, 1142, 87570285,
19  4 0 0 0 0 0 0 ++  INSR_HUMAN  1382  1143  1166  chr7  159138663 116422083 116422152 1 23, 1143, 116422083,
41  26  0 0 0 0 0 0 ++  INSR_HUMAN  1382  1139  1206  chr6  171115067 30865871  30866072  1 67, 1139, 30865871,
16  4 0 0 0 0 0 0 +-  INSR_HUMAN  1382  1146  1166  chr3  198022430 49928628  49928688  1 20, 1146, 148093742,
23  13  0 0 0 0 0 0 +-  INSR_HUMAN  1382  1143  1179  chr3  198022430 195608992 195609100 1 36, 1143, 2413330,
22  12  0 0 0 0 0 0 +-  INSR_HUMAN  1382  1145  1179  chr19 59128983  10463672  10463774  1 34, 1145, 48665209,

Track lines

Although not part of the formal PSL specification, Ensembl will use track lines to further configure sets of features. Track lines should be placed at the beginning of the list of features they are to affect.

The track line consists of the word 'track' followed by space-separated key=value pairs - see the example above. Valid parameters used by Ensembl are:

  • name - unique name to identify this track when parsing the file
  • description - Label to be displayed under the track in Region in Detail
  • priority - integer defining the order in which to display tracks, if multiple tracks are defined.