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Database: rheMac3 Primary Table: all_est Row Count: 62,206   Data last updated: 2012-11-06
Format description: Summary info about a patSpace alignment On download server: MariaDB table dump directory
field | example | SQL type | info | description |
bin | 1111 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
matches | 301 | 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 | 13684 | int(10) unsigned | range | Number of bases inserted in target |
strand | + | char(2) | values | + or - for strand. First character query, second target (optional) |
qName | AB471888 | varchar(255) | values | Query sequence name |
qSize | 301 | int(10) unsigned | range | Query sequence size |
qStart | 0 | int(10) unsigned | range | Alignment start position in query |
qEnd | 301 | int(10) unsigned | range | Alignment end position in query |
tName | chr1 | varchar(255) | values | Target sequence name |
tSize | 229590362 | int(10) unsigned | range | Target sequence size |
tStart | 68986994 | int(10) unsigned | range | Alignment start position in target |
tEnd | 69000979 | int(10) unsigned | range | Alignment end position in target |
blockCount | 4 | int(10) unsigned | range | Number of blocks in alignment |
blockSizes | 46,106,76,73, | longblob | | Size of each block |
qStarts | 0,46,152,228, | longblob | | Start of each block in query. |
tStarts | 68986994,68988379,68989897,... | 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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1111 | 301 | 0 | 0 | 0 | 0 | 0 | 3 | 13684 | + | AB471888 | 301 | 0 | 301 | chr1 | 229590362 | 68986994 | 69000979 | 4 | 46,106,76,73, | 0,46,152,228, | 68986994,68988379,68989897,69000906, |
1111 | 301 | 1 | 92 | 0 | 0 | 0 | 4 | 13591 | + | AB471889 | 394 | 0 | 394 | chr1 | 229590362 | 68986994 | 69000979 | 5 | 46,106,76,93,73, | 0,46,152,228,321, | 68986994,68988379,68989897,68993762,69000906, |
1432 | 220 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | - | AF159450 | 222 | 0 | 222 | chr1 | 229590362 | 111031907 | 111032129 | 1 | 222, | 0, | 111031907, |
683 | 132 | 1 | 27 | 0 | 0 | 0 | 0 | 0 | + | AF075126 | 165 | 0 | 160 | chr11 | 134985053 | 12903799 | 12903959 | 1 | 160, | 0, | 12903799, |
778 | 257 | 1 | 21 | 0 | 0 | 0 | 0 | 0 | + | AF139027 | 279 | 0 | 279 | chr12 | 106825570 | 25309285 | 25309564 | 1 | 279, | 0, | 25309285, |
984 | 179 | 0 | 74 | 0 | 0 | 0 | 0 | 0 | + | AF148885 | 253 | 0 | 253 | chr12 | 106825570 | 52388493 | 52388746 | 1 | 253, | 0, | 52388493, |
984 | 365 | 3 | 14 | 0 | 0 | 0 | 2 | 186 | - | AF140287 | 382 | 0 | 382 | chr12 | 106825570 | 52422344 | 52422912 | 3 | 248,127,7, | 0,248,375, | 52422344,52422600,52422905, |
1254 | 480 | 2 | 0 | 0 | 1 | 1 | 0 | 0 | + | AF140292 | 483 | 0 | 483 | chr12 | 106825570 | 87747667 | 87748149 | 2 | 334,148, | 0,335, | 87747667,87748001, |
1530 | 196 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | - | AF159161 | 198 | 0 | 198 | chr14 | 135538710 | 123878552 | 123878750 | 1 | 198, | 0, | 123878552, |
860 | 29 | 5 | 352 | 0 | 0 | 0 | 0 | 0 | + | AF075123 | 386 | 0 | 386 | chr15 | 112192347 | 36162504 | 36162890 | 1 | 386, | 0, | 36162504, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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