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Database: panTro2 Primary Table: xenoRefSeqAli Row Count: 340,768   Data last updated: 2020-08-22
Format description: Summary info about a patSpace alignment On download server: MariaDB table dump directory
field | example | SQL type | info | description |
bin | 73 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
matches | 712 | int(10) unsigned | range | Number of bases that match that aren't repeats |
misMatches | 11 | int(10) unsigned | range | Number of bases that don't match |
repMatches | 0 | int(10) unsigned | range | Number of bases that match but are part of repeats |
nCount | 0 | int(10) unsigned | range | Number of 'N' bases |
qNumInsert | 0 | int(10) unsigned | range | Number of inserts in query |
qBaseInsert | 0 | int(10) unsigned | range | Number of bases inserted in query |
tNumInsert | 3 | int(10) unsigned | range | Number of inserts in target |
tBaseInsert | 14526 | int(10) unsigned | range | Number of bases inserted in target |
strand | +- | char(2) | values | + or - for strand. First character query, second target (optional) |
qName | NR_040415 | varchar(255) | values | Query sequence name |
qSize | 723 | int(10) unsigned | range | Query sequence size |
qStart | 0 | int(10) unsigned | range | Alignment start position in query |
qEnd | 723 | int(10) unsigned | range | Alignment end position in query |
tName | chr1 | varchar(255) | values | Target sequence name |
tSize | 229974691 | int(10) unsigned | range | Target sequence size |
tStart | 257501 | int(10) unsigned | range | Alignment start position in target |
tEnd | 272750 | int(10) unsigned | range | Alignment end position in target |
blockCount | 4 | int(10) unsigned | range | Number of blocks in alignment |
blockSizes | 350,169,58,146, | longblob | | Size of each block |
qStarts | 0,350,519,577, | longblob | | Start of each block in query. |
tStarts | 229701941,229706463,2297169... | longblob | | Start of each block in target. |
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Connected Tables and Joining Fields
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hgFixed.gbCdnaInfo.acc (via xenoRefSeqAli.qName)
hgFixed.gbMiscDiff.acc (via xenoRefSeqAli.qName)
hgFixed.gbSeq.acc (via xenoRefSeqAli.qName)
hgFixed.gbWarn.acc (via xenoRefSeqAli.qName)
hgFixed.imageClone.acc (via xenoRefSeqAli.qName)
panTro2.all_est.qName (via xenoRefSeqAli.qName)
panTro2.all_mrna.qName (via xenoRefSeqAli.qName)
panTro2.refGene.name (via xenoRefSeqAli.qName)
panTro2.refSeqAli.qName (via xenoRefSeqAli.qName)
panTro2.xenoMrna.qName (via xenoRefSeqAli.qName)
panTro2.xenoRefFlat.name (via xenoRefSeqAli.qName)
panTro2.xenoRefGene.name (via xenoRefSeqAli.qName)
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Sample Rows
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bin | matches | misMatches | repMatches | nCount | qNumInsert | qBaseInsert | tNumInsert | tBaseInsert | strand | qName | qSize | qStart | qEnd | tName | tSize | tStart | tEnd | blockCount | blockSizes | qStarts | tStarts |
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73 | 712 | 11 | 0 | 0 | 0 | 0 | 3 | 14526 | +- | NR_040415 | 723 | 0 | 723 | chr1 | 229974691 | 257501 | 272750 | 4 | 350,169,58,146, | 0,350,519,577, | 229701941,229706463,229716982,229717044, |
118 | 2207 | 15 | 0 | 0 | 2 | 3 | 14 | 25991 | ++ | NM_178033 | 2256 | 0 | 2225 | chr1 | 229974691 | 47821188 | 47849401 | 16 | 320,4,144,45,128,128,155,107,191,134,65,83,206,99,35,378, | 0,320,324,468,513,641,769,924,1031,1222,1356,1421,1504,1712,1812,1847, | 47821188,47821578,47827502,47828950,47830754,47833320,47833531,47837319,47838001,47845126,47847239,47848096,47848674,47848880,47 ... |
73 | 357 | 8 | 0 | 0 | 0 | 0 | 3 | 433437 | +- | NR_130699 | 1494 | 311 | 676 | chr1 | 229974691 | 268058 | 701860 | 4 | 64,38,93,170, | 311,375,413,506, | 229272831,229272896,229277108,229706463, |
73 | 406 | 9 | 0 | 0 | 0 | 0 | 4 | 433387 | +- | NR_130701 | 1419 | 311 | 726 | chr1 | 229974691 | 268058 | 701860 | 5 | 64,38,50,93,170, | 311,375,413,463,556, | 229272831,229272896,229274377,229277108,229706463, |
73 | 146 | 5 | 0 | 0 | 0 | 0 | 2 | 361991 | +- | NR_109817 | 442 | 291 | 442 | chr1 | 229974691 | 268112 | 630254 | 3 | 31,4,116, | 291,322,326, | 229344437,229376201,229706463, |
73 | 4682 | 156 | 0 | 0 | 9 | 2968 | 7 | 355403 | +- | NR_024368 | 10263 | 360 | 8166 | chr1 | 229974691 | 270013 | 630254 | 12 | 30,423,778,54,442,49,166,1069,1584,114,63,66, | 360,452,2040,2898,4285,4727,5083,5250,6319,7913,8036,8100, | 229344437,229698873,229699296,229700109,229700789,229701232,229701600,229701766,229702842,229704435,229704549,229704612, |
73 | 1248 | 104 | 0 | 0 | 4 | 3080 | 5 | 355094 | +- | NR_024497 | 5270 | 821 | 5253 | chr1 | 229974691 | 273808 | 630254 | 6 | 31,478,24,591,134,94, | 821,913,1571,1718,2309,5159, | 229344437,229698873,229699403,229699458,229700050,229700789, |
73 | 1079 | 74 | 0 | 0 | 8 | 1391 | 9 | 390722 | +- | NR_132119 | 2947 | 403 | 2947 | chr1 | 229974691 | 273808 | 665683 | 12 | 112,71,32,52,97,31,4,126,382,96,56,94, | 403,515,651,684,1072,1625,1656,1660,1920,2582,2679,2853, | 229309008,229314695,229318066,229318098,229318480,229344437,229376247,229698297,229698873,229699255,229699356,229700789, |
590 | 1328 | 24 | 0 | 0 | 4 | 478 | 2 | 3677 | ++ | NR_103536 | 1944 | 0 | 1830 | chr1 | 229974691 | 712073 | 717102 | 5 | 16,651,99,169,417, | 0,18,905,1006,1413, | 712073,712089,713496,713595,716685, |
590 | 1277 | 39 | 0 | 0 | 1 | 1 | 2 | 294 | +- | NR_024321 | 1317 | 0 | 1317 | chr1 | 229974691 | 725829 | 727439 | 4 | 70,273,601,372, | 0,70,344,945, | 229247252,229247615,229247888,229248490, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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