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Database: melUnd1 Primary Table: xenoRefSeqAli Row Count: 401,532   Data last updated: 2020-08-19
Format description: Summary info about a patSpace alignment On download server: MariaDB table dump directory
field | example | SQL type | info | description |
bin | 585 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
matches | 183 | int(10) unsigned | range | Number of bases that match that aren't repeats |
misMatches | 102 | 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 | 18 | int(10) unsigned | range | Number of 'N' bases |
qNumInsert | 1 | int(10) unsigned | range | Number of inserts in query |
qBaseInsert | 114 | int(10) unsigned | range | Number of bases inserted in query |
tNumInsert | 1 | int(10) unsigned | range | Number of inserts in target |
tBaseInsert | 123 | int(10) unsigned | range | Number of bases inserted in target |
strand | +- | char(2) | values | + or - for strand. First character query, second target (optional) |
qName | NM_001201662 | varchar(255) | values | Query sequence name |
qSize | 3649 | int(10) unsigned | range | Query sequence size |
qStart | 1919 | int(10) unsigned | range | Alignment start position in query |
qEnd | 2336 | int(10) unsigned | range | Alignment end position in query |
tName | JH531454 | varchar(255) | values | Target sequence name |
tSize | 1752 | int(10) unsigned | range | Target sequence size |
tStart | 147 | int(10) unsigned | range | Alignment start position in target |
tEnd | 573 | int(10) unsigned | range | Alignment end position in target |
blockCount | 2 | int(10) unsigned | range | Number of blocks in alignment |
blockSizes | 171,132, | longblob | | Size of each block |
qStarts | 1919,2204, | longblob | | Start of each block in query. |
tStarts | 1179,1473, | 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)
melUnd1.all_mrna.qName (via xenoRefSeqAli.qName)
melUnd1.xenoRefFlat.name (via xenoRefSeqAli.qName)
melUnd1.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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585 | 183 | 102 | 0 | 18 | 1 | 114 | 1 | 123 | +- | NM_001201662 | 3649 | 1919 | 2336 | JH531454 | 1752 | 147 | 573 | 2 | 171,132, | 1919,2204, | 1179,1473, |
585 | 183 | 102 | 0 | 18 | 1 | 114 | 1 | 123 | +- | NM_001272627 | 3643 | 1913 | 2330 | JH531454 | 1752 | 147 | 573 | 2 | 171,132, | 1913,2198, | 1179,1473, |
585 | 183 | 102 | 0 | 18 | 1 | 114 | 1 | 123 | +- | NM_001272628 | 3670 | 1940 | 2357 | JH531454 | 1752 | 147 | 573 | 2 | 171,132, | 1940,2225, | 1179,1473, |
585 | 246 | 72 | 0 | 0 | 1 | 81 | 2 | 444 | ++ | NM_001128496 | 561 | 162 | 561 | JH531468 | 1425 | 390 | 1152 | 3 | 81,141,96, | 162,243,465, | 390,634,1056, |
585 | 238 | 63 | 0 | 0 | 1 | 78 | 2 | 441 | ++ | NM_001310792 | 558 | 179 | 558 | JH531468 | 1425 | 410 | 1152 | 3 | 58,147,96, | 179,237,462, | 410,631,1056, |
603 | 154 | 92 | 0 | 0 | 2 | 81 | 2 | 72118 | +- | NM_001355237 | 6177 | 1771 | 2098 | JH556484 | 2502921 | 2369473 | 2441837 | 3 | 102,48,96, | 1771,1906,2002, | 61084,63342,133352, |
585 | 71 | 22 | 0 | 0 | 0 | 0 | 0 | 0 | ++ | NM_001191450 | 4784 | 2940 | 3033 | JH531470 | 1306 | 372 | 465 | 1 | 93, | 2940, | 372, |
585 | 82 | 11 | 0 | 0 | 0 | 0 | 0 | 0 | ++ | NM_001197042 | 4805 | 3069 | 3162 | JH531470 | 1306 | 372 | 465 | 1 | 93, | 3069, | 372, |
585 | 219 | 75 | 0 | 0 | 1 | 1294 | 1 | 415 | +- | NM_001159371 | 15255 | 1136 | 2724 | JH531521 | 1179 | 136 | 845 | 2 | 78,216, | 1136,2508, | 334,827, |
585 | 76 | 44 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NM_131630 | 3525 | 328 | 448 | JH531537 | 3139 | 2159 | 2279 | 1 | 120, | 328, | 860, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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