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Database: gadMor1 Primary Table: xenoRefSeqAli Row Count: 656,045   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 | description |
bin | 585 | smallint(5) unsigned | Indexing field to speed chromosome range queries. |
matches | 186 | int(10) unsigned | Number of bases that match that aren't repeats |
misMatches | 66 | 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 | NM_001091911 | varchar(255) | Query sequence name |
qSize | 4026 | int(10) unsigned | Query sequence size |
qStart | 1154 | int(10) unsigned | Alignment start position in query |
qEnd | 1406 | int(10) unsigned | Alignment end position in query |
tName | CAEA01000002 | varchar(255) | Target sequence name |
tSize | 1070 | int(10) unsigned | Target sequence size |
tStart | 510 | int(10) unsigned | Alignment start position in target |
tEnd | 762 | int(10) unsigned | Alignment end position in target |
blockCount | 1 | int(10) unsigned | Number of blocks in alignment |
blockSizes | 252, | longblob | Size of each block |
qStarts | 1154, | longblob | Start of each block in query. |
tStarts | 308, | longblob | Start of each block in target. |
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Connected Tables and Joining Fields
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gadMor1.all_est.qName (via xenoRefSeqAli.qName)
gadMor1.all_mrna.qName (via xenoRefSeqAli.qName)
gadMor1.xenoRefFlat.name (via xenoRefSeqAli.qName)
gadMor1.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 | 186 | 66 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NM_001091911 | 4026 | 1154 | 1406 | CAEA01000002 | 1070 | 510 | 762 | 1 | 252, | 1154, | 308, |
585 | 208 | 44 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NM_001099034 | 4027 | 1251 | 1503 | CAEA01000002 | 1070 | 510 | 762 | 1 | 252, | 1251, | 308, |
585 | 172 | 80 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NM_001299447 | 4375 | 1383 | 1635 | CAEA01000002 | 1070 | 510 | 762 | 1 | 252, | 1383, | 308, |
585 | 172 | 80 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NM_001299448 | 4350 | 1358 | 1610 | CAEA01000002 | 1070 | 510 | 762 | 1 | 252, | 1358, | 308, |
585 | 186 | 66 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NM_001310540 | 4669 | 1238 | 1490 | CAEA01000002 | 1070 | 510 | 762 | 1 | 252, | 1238, | 308, |
585 | 186 | 66 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NM_009418 | 4708 | 1238 | 1490 | CAEA01000002 | 1070 | 510 | 762 | 1 | 252, | 1238, | 308, |
585 | 185 | 67 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NM_031137 | 4566 | 1156 | 1408 | CAEA01000002 | 1070 | 510 | 762 | 1 | 252, | 1156, | 308, |
585 | 172 | 80 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NM_057899 | 4287 | 1295 | 1547 | CAEA01000002 | 1070 | 510 | 762 | 1 | 252, | 1295, | 308, |
585 | 172 | 80 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NM_165966 | 4641 | 1649 | 1901 | CAEA01000002 | 1070 | 510 | 762 | 1 | 252, | 1649, | 308, |
585 | 103 | 71 | 0 | 0 | 0 | 0 | 0 | 0 | +- | NM_001020382 | 3959 | 1407 | 1581 | CAEA01000002 | 1070 | 513 | 687 | 1 | 174, | 1407, | 383, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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