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Database: sacCer1 Primary Table: all_mrna Row Count: 1,655 Data last updated: 2020-05-08
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 | 2873 | int(10) unsigned | range | Number of bases that match that aren't repeats |
| misMatches | 4 | 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 | 5 | int(10) unsigned | range | Number of inserts in query |
| qBaseInsert | 8 | int(10) unsigned | range | Number of bases inserted in query |
| tNumInsert | 3 | int(10) unsigned | range | Number of inserts in target |
| tBaseInsert | 7 | int(10) unsigned | range | Number of bases inserted in target |
| strand | + | char(2) | values | + or - for strand. First character query, second target (optional) |
| qName | E00249 | varchar(255) | values | Query sequence name |
| qSize | 2885 | int(10) unsigned | range | Query sequence size |
| qStart | 0 | int(10) unsigned | range | Alignment start position in query |
| qEnd | 2885 | int(10) unsigned | range | Alignment end position in query |
| tName | chr1 | varchar(255) | values | Target sequence name |
| tSize | 230208 | int(10) unsigned | range | Target sequence size |
| tStart | 70879 | int(10) unsigned | range | Alignment start position in target |
| tEnd | 73763 | int(10) unsigned | range | Alignment end position in target |
| blockCount | 7 | int(10) unsigned | range | Number of blocks in alignment |
| blockSizes | 77,53,545,1374,12,494,322, | longblob | | Size of each block |
| qStarts | 0,78,132,678,2052,2065,2563, | longblob | | Start of each block in query. |
| tStarts | 70879,70956,71009,71554,729... | 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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| 585 | 2873 | 4 | 0 | 0 | 5 | 8 | 3 | 7 | + | E00249 | 2885 | 0 | 2885 | chr1 | 230208 | 70879 | 73763 | 7 | 77,53,545,1374,12,494,322, | 0,78,132,678,2052,2065,2563, | 70879,70956,71009,71554,72929,72944,73441, |
| 586 | 72 | 0 | 0 | 0 | 0 | 0 | 1 | 31 | + | M26096 | 75 | 0 | 72 | chr1 | 230208 | 139153 | 139256 | 2 | 36,36, | 0,36, | 139153,139220, |
| 586 | 1733 | 6 | 0 | 0 | 0 | 0 | 0 | 0 | - | GQ871187 | 1739 | 0 | 1739 | chr1 | 230208 | 139679 | 141418 | 1 | 1739, | 0, | 139679, |
| 586 | 102 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | + | U12981 | 102 | 0 | 102 | chr1 | 230208 | 142368 | 142470 | 1 | 102, | 0, | 142368, |
| 586 | 127 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | - | K00948 | 127 | 0 | 127 | chr1 | 230208 | 160274 | 160401 | 1 | 127, | 0, | 160274, |
| 586 | 125 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | - | K00952 | 125 | 0 | 125 | chr1 | 230208 | 160276 | 160401 | 1 | 125, | 0, | 160276, |
| 586 | 127 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | - | K00948 | 127 | 0 | 127 | chr1 | 230208 | 165862 | 165989 | 1 | 127, | 0, | 165862, |
| 586 | 125 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | - | K00952 | 125 | 0 | 125 | chr1 | 230208 | 165864 | 165989 | 1 | 125, | 0, | 165864, |
| 586 | 82 | 0 | 0 | 0 | 0 | 0 | 1 | 32 | + | K00228 | 85 | 0 | 82 | chr1 | 230208 | 181134 | 181248 | 2 | 38,44, | 0,38, | 181134,181204, |
| 586 | 80 | 2 | 0 | 0 | 0 | 0 | 1 | 32 | + | M10805 | 85 | 0 | 82 | chr1 | 230208 | 181134 | 181248 | 2 | 38,44, | 0,38, | 181134,181204, |
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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