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Database: chlSab2 Primary Table: xenoRefSeqAli Row Count: 265,464 Data last updated: 2020-08-18
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
| field | example | SQL type | info | description |
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| bin | 587 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
| matches | 1487 | int(10) unsigned | range | Number of bases that match that aren't repeats |
| misMatches | 41 | 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 | 8 | int(10) unsigned | range | Number of inserts in target |
| tBaseInsert | 13798 | 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_001204462 | varchar(255) | values | Query sequence name |
| qSize | 1550 | int(10) unsigned | range | Query sequence size |
| qStart | 22 | int(10) unsigned | range | Alignment start position in query |
| qEnd | 1550 | int(10) unsigned | range | Alignment end position in query |
| tName | chr5 | varchar(255) | values | Target sequence name |
| tSize | 75399963 | int(10) unsigned | range | Target sequence size |
| tStart | 342034 | int(10) unsigned | range | Alignment start position in target |
| tEnd | 357360 | int(10) unsigned | range | Alignment end position in target |
| blockCount | 9 | int(10) unsigned | range | Number of blocks in alignment |
| blockSizes | 173,69,52,136,125,94,105,21... | longblob | | Size of each block |
| qStarts | 22,195,264,316,452,577,671,... | longblob | | Start of each block in query. |
| tStarts | 342034,344988,346459,347521... | longblob | | Start of each block in target. |
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Connected Tables and Joining Fields
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chlSab2.all_est.qName (via xenoRefSeqAli.qName)
chlSab2.all_mrna.qName (via xenoRefSeqAli.qName)
chlSab2.xenoRefFlat.name (via xenoRefSeqAli.qName)
chlSab2.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 |
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| 587 | 1487 | 41 | 0 | 0 | 0 | 0 | 8 | 13798 | ++ | NM_001204462 | 1550 | 22 | 1550 | chr5 | 75399963 | 342034 | 357360 | 9 | 173,69,52,136,125,94,105,218,556, | 22,195,264,316,452,577,671,776,994, | 342034,344988,346459,347521,349792,350167,350442,356276,356804, |
| 585 | 349 | 3 | 0 | 0 | 0 | 0 | 2 | 1038 | ++ | NM_001193437 | 352 | 0 | 352 | chr1 | 126035930 | 3814 | 5204 | 3 | 69,200,83, | 0,69,269, | 3814,4413,5121, |
| 585 | 201 | 32 | 0 | 0 | 0 | 0 | 1 | 508 | ++ | NM_001206224 | 420 | 53 | 286 | chr1 | 126035930 | 4411 | 5152 | 2 | 202,31, | 53,255, | 4411,5121, |
| 585 | 161 | 43 | 0 | 0 | 0 | 0 | 0 | 0 | ++ | NM_001099742 | 451 | 66 | 270 | chr1 | 126035930 | 4412 | 4616 | 1 | 204, | 66, | 4412, |
| 585 | 167 | 37 | 0 | 0 | 0 | 0 | 0 | 0 | ++ | NM_001107561 | 459 | 84 | 288 | chr1 | 126035930 | 4412 | 4616 | 1 | 204, | 84, | 4412, |
| 107 | 5318 | 152 | 0 | 0 | 16 | 396 | 27 | 131222 | +- | NM_024529 | 5869 | 0 | 5866 | chr25 | 85787240 | 36166077 | 36302769 | 40 | 301,106,70,63,53,89,217,99,79,65,58,36,88,162,101,142,306,196,76,64,505,102,53,204,64,396,109,30,205,69,82,82,292,148,70,64,276, ... | 0,301,407,477,540,593,682,899,998,1077,1142,1200,1236,1324,1486,1587,1729,2038,2234,2314,2381,2894,2996,3053,3258,3327,3723,3832 ... | 49484471,49487492,49492238,49497437,49497599,49500133,49503898,49509411,49511893,49513982,49570253,49578458,49578786,49599567,49 ... |
| 585 | 728 | 95 | 0 | 0 | 0 | 0 | 5 | 2089 | ++ | NM_001080252 | 1580 | 517 | 1340 | chr1 | 126035930 | 7259 | 10171 | 6 | 162,197,106,122,141,95, | 517,679,876,982,1104,1245, | 7259,7558,8192,8599,9518,10076, |
| 585 | 721 | 90 | 0 | 0 | 1 | 85 | 6 | 2167 | ++ | NM_027019 | 924 | 20 | 916 | chr1 | 126035930 | 7302 | 10280 | 7 | 119,197,100,128,141,90,36, | 20,139,336,436,564,705,880, | 7302,7558,8192,8593,9518,10076,10244, |
| 585 | 743 | 101 | 0 | 0 | 1 | 93 | 6 | 2158 | ++ | NM_001108924 | 1141 | 129 | 1066 | chr1 | 126035930 | 7302 | 10304 | 7 | 119,197,100,134,141,93,60, | 129,248,445,545,679,820,1006, | 7302,7558,8192,8593,9518,10076,10244, |
| 585 | 2589 | 169 | 0 | 0 | 7 | 56 | 6 | 1753 | +- | NM_001098787 | 2830 | 1 | 2815 | chr1 | 126035930 | 13158 | 17669 | 13 | 119,92,57,720,268,238,44,319,327,176,86,64,248, | 1,120,212,269,1029,1298,1541,1585,1907,2235,2416,2502,2567, | 126018261,126019626,126020002,126020201,126020976,126021244,126021482,126021549,126021868,126022195,126022371,126022460,12602252 ... |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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US Server