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Database: xenTro2 Primary Table: xenoRefSeqAli Row Count: 367,227 Data last updated: 2020-09-02
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 | 585 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
| matches | 72 | int(10) unsigned | range | Number of bases that match that aren't repeats |
| misMatches | 7 | 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 | 0 | int(10) unsigned | range | Number of inserts in target |
| tBaseInsert | 0 | 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_002755 | varchar(255) | values | Query sequence name |
| qSize | 100 | int(10) unsigned | range | Query sequence size |
| qStart | 1 | int(10) unsigned | range | Alignment start position in query |
| qEnd | 80 | int(10) unsigned | range | Alignment end position in query |
| tName | scaffold_1 | varchar(255) | values | Target sequence name |
| tSize | 7817814 | int(10) unsigned | range | Target sequence size |
| tStart | 66 | int(10) unsigned | range | Alignment start position in target |
| tEnd | 145 | int(10) unsigned | range | Alignment end position in target |
| blockCount | 1 | int(10) unsigned | range | Number of blocks in alignment |
| blockSizes | 79, | longblob | | Size of each block |
| qStarts | 1, | longblob | | Start of each block in query. |
| tStarts | 7817669, | 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)
xenTro2.all_est.qName (via xenoRefSeqAli.qName)
xenTro2.all_mrna.qName (via xenoRefSeqAli.qName)
xenTro2.refGene.name (via xenoRefSeqAli.qName)
xenTro2.refSeqAli.qName (via xenoRefSeqAli.qName)
xenTro2.xenoRefFlat.name (via xenoRefSeqAli.qName)
xenTro2.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 | 72 | 7 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NR_002755 | 100 | 1 | 80 | scaffold_1 | 7817814 | 66 | 145 | 1 | 79, | 1, | 7817669, |
| 585 | 71 | 6 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NR_002754 | 119 | 0 | 77 | scaffold_1 | 7817814 | 69 | 146 | 1 | 77, | 0, | 7817668, |
| 585 | 40 | 6 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NR_000351 | 122 | 21 | 67 | scaffold_1 | 7817814 | 83 | 129 | 1 | 46, | 21, | 7817685, |
| 585 | 40 | 6 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NR_000352 | 122 | 21 | 67 | scaffold_1 | 7817814 | 83 | 129 | 1 | 46, | 21, | 7817685, |
| 585 | 40 | 6 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NR_000374 | 122 | 21 | 67 | scaffold_1 | 7817814 | 83 | 129 | 1 | 46, | 21, | 7817685, |
| 585 | 40 | 6 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NR_000375 | 122 | 21 | 67 | scaffold_1 | 7817814 | 83 | 129 | 1 | 46, | 21, | 7817685, |
| 585 | 40 | 6 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NR_000376 | 122 | 21 | 67 | scaffold_1 | 7817814 | 83 | 129 | 1 | 46, | 21, | 7817685, |
| 585 | 40 | 6 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NR_000377 | 122 | 21 | 67 | scaffold_1 | 7817814 | 83 | 129 | 1 | 46, | 21, | 7817685, |
| 585 | 40 | 6 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NR_003382 | 123 | 22 | 68 | scaffold_1 | 7817814 | 83 | 129 | 1 | 46, | 22, | 7817685, |
| 585 | 40 | 6 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NR_003445 | 126 | 21 | 67 | scaffold_1 | 7817814 | 83 | 129 | 1 | 46, | 21, | 7817685, |
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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