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Database: susScr3 Primary Table: all_est Row Count: 1,695,261 Data last updated: 2015-04-04
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 | 354 | int(10) unsigned | Number of bases that match that aren't repeats |
| misMatches | 1 | int(10) unsigned | Number of bases that don't match |
| repMatches | 99 | int(10) unsigned | Number of bases that match but are part of repeats |
| nCount | 2 | int(10) unsigned | Number of 'N' bases |
| qNumInsert | 2 | int(10) unsigned | Number of inserts in query |
| qBaseInsert | 2 | 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 | AA056899 | varchar(255) | Query sequence name |
| qSize | 458 | int(10) unsigned | Query sequence size |
| qStart | 0 | int(10) unsigned | Alignment start position in query |
| qEnd | 458 | int(10) unsigned | Alignment end position in query |
| tName | GL892953-2 | varchar(255) | Target sequence name |
| tSize | 188381 | int(10) unsigned | Target sequence size |
| tStart | 105417 | int(10) unsigned | Alignment start position in target |
| tEnd | 105873 | int(10) unsigned | Alignment end position in target |
| blockCount | 3 | int(10) unsigned | Number of blocks in alignment |
| blockSizes | 25,35,396, | longblob | Size of each block |
| qStarts | 0,26,62, | longblob | Start of each block in query. |
| tStarts | 105417,105442,105477, | 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 | 354 | 1 | 99 | 2 | 2 | 2 | 0 | 0 | + | AA056899 | 458 | 0 | 458 | GL892953-2 | 188381 | 105417 | 105873 | 3 | 25,35,396, | 0,26,62, | 105417,105442,105477, |
| 585 | 329 | 2 | 0 | 1 | 0 | 0 | 1 | 2 | + | AA063667 | 348 | 16 | 348 | GL895031-2 | 39987 | 3720 | 4054 | 2 | 274,58, | 16,290, | 3720,3996, |
| 585 | 184 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | + | AA063655 | 403 | 29 | 214 | GL896052-2 | 65521 | 39156 | 39341 | 1 | 185, | 29, | 39156, |
| 585 | 162 | 6 | 0 | 1 | 0 | 0 | 0 | 0 | + | AA063649 | 322 | 41 | 210 | GL896358-1 | 8090 | 1924 | 2093 | 1 | 169, | 41, | 1924, |
| 585 | 284 | 2 | 0 | 4 | 2 | 89 | 1 | 100 | + | AA063661 | 402 | 23 | 402 | GL896532-1 | 2727 | 81 | 471 | 3 | 21,12,257, | 23,45,145, | 81,102,214, |
| 1291 | 351 | 2 | 0 | 8 | 0 | 0 | 0 | 0 | - | AA056886 | 377 | 16 | 377 | chr1 | 315321322 | 92581725 | 92582086 | 1 | 361, | 0, | 92581725, |
| 178 | 363 | 1 | 0 | 0 | 0 | 0 | 4 | 3761 | + | AA056913 | 364 | 0 | 364 | chr1 | 315321322 | 110359280 | 110363405 | 5 | 62,104,110,44,44, | 0,62,166,276,320, | 110359280,110359907,110363115,110363316,110363361, |
| 1427 | 412 | 5 | 0 | 0 | 1 | 1 | 0 | 0 | - | AA056914 | 418 | 0 | 418 | chr1 | 315321322 | 110410114 | 110410531 | 2 | 67,350, | 0,68, | 110410114,110410181, |
| 2768 | 232 | 6 | 0 | 19 | 3 | 4 | 1 | 3 | + | AA056891 | 306 | 45 | 306 | chr1 | 315321322 | 286250480 | 286250740 | 4 | 31,86,33,107, | 45,77,164,199, | 286250480,286250511,286250597,286250633, |
| 735 | 174 | 1 | 14 | 3 | 0 | 0 | 0 | 0 | + | AA063650 | 199 | 7 | 199 | chr10 | 79102373 | 19696206 | 19696398 | 1 | 192, | 7, | 19696206, |
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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