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Database: dm2 Primary Table: refSeqAli Row Count: 35,517   Data last updated: 2020-08-21
Format description: Summary info about a patSpace alignment On download server: MariaDB table dump directory
field | example | SQL type | info | description |
bin | 717 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
matches | 1791 | 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 | 3 | int(10) unsigned | range | Number of inserts in target |
tBaseInsert | 174 | int(10) unsigned | range | Number of bases inserted in target |
strand | - | char(2) | values | + or - for strand. First character query, second target (optional) |
qName | NM_168723 | varchar(255) | values | Query sequence name |
qSize | 1791 | int(10) unsigned | range | Query sequence size |
qStart | 0 | int(10) unsigned | range | Alignment start position in query |
qEnd | 1791 | int(10) unsigned | range | Alignment end position in query |
tName | chr3L | varchar(255) | values | Target sequence name |
tSize | 23771897 | int(10) unsigned | range | Target sequence size |
tStart | 17302430 | int(10) unsigned | range | Alignment start position in target |
tEnd | 17304395 | int(10) unsigned | range | Alignment end position in target |
blockCount | 4 | int(10) unsigned | range | Number of blocks in alignment |
blockSizes | 512,330,608,341, | longblob | | Size of each block |
qStarts | 0,512,842,1450, | longblob | | Start of each block in query. |
tStarts | 17302430,17303001,17303387,... | 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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717 | 1791 | 0 | 0 | 0 | 0 | 0 | 3 | 174 | - | NM_168723 | 1791 | 0 | 1791 | chr3L | 23771897 | 17302430 | 17304395 | 4 | 512,330,608,341, | 0,512,842,1450, | 17302430,17303001,17303387,17304054, |
597 | 1765 | 0 | 0 | 0 | 0 | 0 | 3 | 2377 | + | NM_169109 | 1765 | 0 | 1765 | chr3R | 27905053 | 1640400 | 1644542 | 4 | 605,552,36,572, | 0,605,1157,1193, | 1640400,1643237,1643873,1643970, |
685 | 433 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | - | NR_124918 | 433 | 0 | 433 | chr3L | 23771897 | 13189213 | 13189646 | 1 | 433, | 0, | 13189213, |
672 | 557 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | + | NR_124891 | 557 | 0 | 557 | chr3L | 23771897 | 11409596 | 11410153 | 1 | 557, | 0, | 11409596, |
609 | 406 | 0 | 0 | 0 | 0 | 0 | 1 | 65 | + | NM_134912 | 406 | 0 | 406 | chr2L | 22407834 | 3173971 | 3174442 | 2 | 267,139, | 0,267, | 3173971,3174303, |
677 | 469 | 0 | 0 | 0 | 0 | 0 | 2 | 124 | + | NM_140294 | 469 | 0 | 469 | chr3L | 23771897 | 12110913 | 12111506 | 3 | 125,137,207, | 0,125,262, | 12110913,12111105,12111299, |
677 | 868 | 0 | 20 | 0 | 0 | 0 | 3 | 201 | - | NM_143785 | 888 | 0 | 888 | chr3L | 23771897 | 12111442 | 12112531 | 4 | 283,107,230,268, | 0,283,390,620, | 12111442,12111784,12111962,12112263, |
625 | 1439 | 0 | 0 | 0 | 0 | 0 | 1 | 58 | + | NM_136677 | 1439 | 0 | 1439 | chr2R | 20766785 | 5348797 | 5350294 | 2 | 447,992, | 0,447, | 5348797,5349302, |
627 | 2266 | 0 | 0 | 0 | 0 | 0 | 3 | 220 | + | NM_141684 | 2266 | 0 | 2266 | chr3R | 27905053 | 5589371 | 5591857 | 4 | 286,586,867,527, | 0,286,872,1739, | 5589371,5589762,5590402,5591330, |
759 | 3815 | 0 | 25 | 0 | 0 | 0 | 5 | 1227 | - | NM_168975 | 3840 | 0 | 3840 | chr3L | 23771897 | 22807542 | 22812609 | 6 | 998,1267,932,426,82,135, | 0,998,2265,3197,3623,3705, | 22807542,22808964,22810297,22811290,22811777,22812474, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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