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Database: gorGor3 Primary Table: xenoRefSeqAli Row Count: 554,749 Data last updated: 2020-08-21
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
| field | example | SQL type | description |
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| bin | 585 | smallint(5) unsigned | Indexing field to speed chromosome range queries. |
| matches | 89 | int(10) unsigned | Number of bases that match that aren't repeats |
| misMatches | 2 | int(10) unsigned | Number of bases that don't match |
| repMatches | 0 | int(10) unsigned | Number of bases that match but are part of repeats |
| nCount | 0 | int(10) unsigned | Number of 'N' bases |
| qNumInsert | 0 | int(10) unsigned | Number of inserts in query |
| qBaseInsert | 0 | int(10) unsigned | Number of bases inserted in query |
| tNumInsert | 0 | int(10) unsigned | Number of inserts in target |
| tBaseInsert | 0 | int(10) unsigned | Number of bases inserted in target |
| strand | +- | char(2) | + or - for strand. First character query, second target (optional) |
| qName | NR_030386 | varchar(255) | Query sequence name |
| qSize | 93 | int(10) unsigned | Query sequence size |
| qStart | 0 | int(10) unsigned | Alignment start position in query |
| qEnd | 91 | int(10) unsigned | Alignment end position in query |
| tName | CABD02411070 | varchar(255) | Target sequence name |
| tSize | 551 | int(10) unsigned | Target sequence size |
| tStart | 96 | int(10) unsigned | Alignment start position in target |
| tEnd | 187 | int(10) unsigned | Alignment end position in target |
| blockCount | 1 | int(10) unsigned | Number of blocks in alignment |
| blockSizes | 91, | longblob | Size of each block |
| qStarts | 0, | longblob | Start of each block in query. |
| tStarts | 364, | longblob | Start of each block in target. |
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Connected Tables and Joining Fields
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gorGor3.all_mrna.qName (via xenoRefSeqAli.qName)
gorGor3.xenoMrna.qName (via xenoRefSeqAli.qName)
gorGor3.xenoRefFlat.name (via xenoRefSeqAli.qName)
gorGor3.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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| 585 | 89 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NR_030386 | 93 | 0 | 91 | CABD02411070 | 551 | 96 | 187 | 1 | 91, | 0, | 364, |
| 585 | 87 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NR_038473 | 90 | 0 | 90 | CABD02411070 | 551 | 97 | 187 | 1 | 90, | 0, | 364, |
| 585 | 89 | 55 | 0 | 0 | 0 | 0 | 1 | 72 | ++ | NM_001168456 | 501 | 85 | 229 | CABD02411459 | 595 | 378 | 594 | 2 | 58,86, | 85,143, | 378,508, |
| 124 | 196 | 19 | 0 | 0 | 3 | 1448 | 2 | 148144 | ++ | NM_001324230 | 6411 | 4156 | 5819 | chr19 | 56181278 | 53711540 | 53859899 | 4 | 50,45,52,68, | 4156,4215,5697,5751, | 53711540,53711600,53859779,53859831, |
| 585 | 280 | 106 | 0 | 0 | 2 | 393 | 2 | 435 | +- | NM_001038687 | 807 | 11 | 790 | CABD02412305 | 2145 | 1138 | 1959 | 3 | 301,22,63, | 11,318,727, | 186,490,944, |
| 585 | 689 | 214 | 0 | 0 | 0 | 0 | 0 | 0 | ++ | NM_001000366 | 912 | 0 | 903 | CABD02413273 | 2677 | 1537 | 2440 | 1 | 903, | 0, | 1537, |
| 585 | 682 | 221 | 0 | 0 | 0 | 0 | 0 | 0 | ++ | NM_146396 | 912 | 0 | 903 | CABD02413273 | 2677 | 1537 | 2440 | 1 | 903, | 0, | 1537, |
| 585 | 739 | 170 | 0 | 0 | 0 | 0 | 0 | 0 | ++ | NM_001011773 | 918 | 0 | 909 | CABD02413273 | 2677 | 1537 | 2446 | 1 | 909, | 0, | 1537, |
| 585 | 757 | 153 | 0 | 0 | 0 | 0 | 0 | 0 | ++ | NM_001000921 | 918 | 0 | 910 | CABD02413273 | 2677 | 1537 | 2447 | 1 | 910, | 0, | 1537, |
| 585 | 740 | 171 | 0 | 0 | 0 | 0 | 0 | 0 | ++ | NM_001000614 | 918 | 0 | 911 | CABD02413273 | 2677 | 1537 | 2448 | 1 | 911, | 0, | 1537, |
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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