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Database: equCab3 Primary Table: xenoRefSeqAli Row Count: 301,814   Data last updated: 2019-07-17
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 | 398 | int(10) unsigned | range | Number of bases that match that aren't repeats |
misMatches | 66 | 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 | 4 | int(10) unsigned | range | Number of inserts in query |
qBaseInsert | 328 | int(10) unsigned | range | Number of bases inserted in query |
tNumInsert | 7 | int(10) unsigned | range | Number of inserts in target |
tBaseInsert | 4252 | 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_001143765 | varchar(255) | values | Query sequence name |
qSize | 1462 | int(10) unsigned | range | Query sequence size |
qStart | 118 | int(10) unsigned | range | Alignment start position in query |
qEnd | 910 | int(10) unsigned | range | Alignment end position in query |
tName | chr1 | varchar(255) | values | Target sequence name |
tSize | 188260577 | int(10) unsigned | range | Target sequence size |
tStart | 10433 | int(10) unsigned | range | Alignment start position in target |
tEnd | 15149 | int(10) unsigned | range | Alignment end position in target |
blockCount | 8 | int(10) unsigned | range | Number of blocks in alignment |
blockSizes | 64,60,73,56,93,64,18,36, | longblob | | Size of each block |
qStarts | 118,182,242,364,420,577,657... | longblob | | Start of each block in query. |
tStarts | 10433,11144,11567,12534,133... | longblob | | Start of each block in target. |
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Connected Tables and Joining Fields
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equCab3.all_est.qName (via xenoRefSeqAli.qName)
equCab3.all_mrna.qName (via xenoRefSeqAli.qName)
equCab3.refGene.name (via xenoRefSeqAli.qName)
equCab3.refSeqAli.qName (via xenoRefSeqAli.qName)
equCab3.xenoRefFlat.name (via xenoRefSeqAli.qName)
equCab3.xenoRefGene.name (via xenoRefSeqAli.qName)
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)
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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 |
---|
585 | 398 | 66 | 0 | 0 | 4 | 328 | 7 | 4252 | ++ | NM_001143765 | 1462 | 118 | 910 | chr1 | 188260577 | 10433 | 15149 | 8 | 64,60,73,56,93,64,18,36, | 118,182,242,364,420,577,657,874, | 10433,11144,11567,12534,13318,14536,14698,15113, |
585 | 811 | 103 | 0 | 0 | 4 | 59 | 14 | 4218 | ++ | NM_001038149 | 1108 | 102 | 1075 | chr1 | 188260577 | 10433 | 15565 | 15 | 64,60,75,48,55,90,64,3,64,75,39,60,90,73,54, | 102,166,226,301,349,404,494,558,561,625,704,747,855,945,1021, | 10433,11144,11567,12236,12535,13318,13656,14095,14536,14682,14764,14877,15113,15433,15511, |
585 | 694 | 117 | 0 | 0 | 5 | 118 | 12 | 5089 | ++ | NM_001143763 | 1452 | 177 | 1106 | chr1 | 188260577 | 10433 | 16333 | 13 | 64,60,74,36,53,93,64,65,125,3,61,86,27, | 177,241,301,380,423,476,569,635,700,825,828,933,1079, | 10433,11144,11567,12240,12534,13315,13656,14535,14682,14873,14880,15113,16306, |
585 | 419 | 84 | 0 | 0 | 4 | 310 | 7 | 4234 | ++ | NM_001025058 | 1471 | 116 | 929 | chr1 | 188260577 | 10445 | 15182 | 8 | 52,60,75,56,93,64,34,69, | 116,168,228,350,406,563,639,860, | 10445,11144,11567,12534,13318,14536,14694,15113, |
585 | 678 | 117 | 0 | 0 | 3 | 56 | 12 | 4210 | ++ | NM_001280134 | 1392 | 190 | 1041 | chr1 | 188260577 | 10445 | 15450 | 13 | 52,60,74,36,53,93,64,67,125,3,61,89,18, | 190,242,302,381,424,477,570,634,701,826,829,934,1023, | 10445,11144,11567,12240,12534,13315,13656,14533,14682,14873,14880,15113,15432, |
585 | 685 | 114 | 0 | 0 | 5 | 118 | 12 | 5089 | ++ | NM_130784 | 1362 | 99 | 1016 | chr1 | 188260577 | 10445 | 16333 | 13 | 52,60,74,36,53,93,64,65,125,3,61,86,27, | 99,151,211,290,333,386,479,545,610,735,738,843,989, | 10445,11144,11567,12240,12534,13315,13656,14535,14682,14873,14880,15113,16306, |
585 | 620 | 122 | 0 | 0 | 3 | 121 | 9 | 3628 | ++ | NM_001283833 | 1317 | 196 | 1059 | chr1 | 188260577 | 11164 | 15534 | 10 | 40,73,36,56,90,64,67,125,89,102, | 196,236,315,358,414,504,568,635,868,957, | 11164,11567,12240,12534,13318,13656,14533,14682,15113,15432, |
585 | 446 | 202 | 0 | 0 | 2 | 199 | 3 | 36838 | +- | NM_001078916 | 2617 | 1139 | 1986 | chr1 | 188260577 | 28744 | 66230 | 4 | 437,127,60,24, | 1139,1576,1811,1962, | 188194347,188231066,188231298,188231809, |
585 | 376 | 222 | 0 | 0 | 1 | 83 | 3 | 36951 | +- | NM_001100925 | 1507 | 638 | 1319 | chr1 | 188260577 | 28744 | 66293 | 5 | 64,193,34,289,18, | 638,702,895,929,1301, | 188194284,188194684,188231324,188231526,188231815, |
585 | 398 | 206 | 0 | 0 | 6 | 597 | 5 | 36966 | +- | NM_001171529 | 2387 | 804 | 2005 | chr1 | 188260577 | 28744 | 66314 | 7 | 60,133,45,111,111,114,30, | 804,899,1065,1248,1482,1842,1975, | 188194263,188194526,188194692,188231076,188231475,188231586,188231803, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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