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Database: ornAna2 Primary Table: refSeqAli Row Count: 705   Data last updated: 2020-02-05
Format description: Summary info about a patSpace alignment On download server: MariaDB table dump directory
field | example | SQL type | info | description |
bin | 641 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
matches | 87 | int(10) unsigned | range | Number of bases that match that aren't repeats |
misMatches | 0 | 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_034618 | varchar(255) | values | Query sequence name |
qSize | 87 | int(10) unsigned | range | Query sequence size |
qStart | 0 | int(10) unsigned | range | Alignment start position in query |
qEnd | 87 | int(10) unsigned | range | Alignment end position in query |
tName | chr1 | varchar(255) | values | Target sequence name |
tSize | 47594283 | int(10) unsigned | range | Target sequence size |
tStart | 7455188 | int(10) unsigned | range | Alignment start position in target |
tEnd | 7455275 | int(10) unsigned | range | Alignment end position in target |
blockCount | 1 | int(10) unsigned | range | Number of blocks in alignment |
blockSizes | 87, | longblob | | Size of each block |
qStarts | 0, | longblob | | Start of each block in query. |
tStarts | 7455188, | longblob | | Start of each block in target. |
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Connected Tables and Joining Fields
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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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641 | 87 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | - | NR_034618 | 87 | 0 | 87 | chr1 | 47594283 | 7455188 | 7455275 | 1 | 87, | 0, | 7455188, |
711 | 120 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | - | NR_034619 | 120 | 0 | 120 | chr1 | 47594283 | 16589755 | 16589875 | 1 | 120, | 0, | 16589755, |
713 | 126 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | - | NR_034620 | 129 | 0 | 127 | chr1 | 47594283 | 16822265 | 16822392 | 1 | 127, | 2, | 16822265, |
745 | 145 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | + | NR_034621 | 145 | 0 | 145 | chr1 | 47594283 | 21080347 | 21080492 | 1 | 145, | 0, | 21080347, |
805 | 126 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | - | NR_034622 | 126 | 0 | 126 | chr1 | 47594283 | 28887188 | 28887314 | 1 | 126, | 0, | 28887188, |
808 | 94 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | + | NR_034623 | 94 | 0 | 94 | chr1 | 47594283 | 29293792 | 29293886 | 1 | 94, | 0, | 29293792, |
613 | 128 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | + | NR_034624 | 128 | 0 | 128 | chr10 | 11243762 | 3704099 | 3704227 | 1 | 128, | 0, | 3704099, |
619 | 100 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | - | NR_034950 | 100 | 0 | 100 | chr10 | 11243762 | 4559451 | 4559551 | 1 | 100, | 0, | 4559451, |
619 | 109 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | - | NR_034625 | 109 | 0 | 109 | chr10 | 11243762 | 4568762 | 4568871 | 1 | 109, | 0, | 4568762, |
619 | 131 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | - | NR_034626 | 131 | 0 | 131 | chr10 | 11243762 | 4569066 | 4569197 | 1 | 131, | 0, | 4569066, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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