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Database: hg38 Primary Table: all_mrna Row Count: 10,489,979   Data last updated: 2020-08-17
Format description: Summary info about a patSpace alignment On download server: MariaDB table dump directory
field | example | SQL type | description |
bin | 585 | smallint(5) unsigned | Indexing field to speed chromosome range queries. |
matches | 1579 | int(10) unsigned | Number of bases that match that aren't repeats |
misMatches | 25 | int(10) unsigned | Number of bases that don't match |
repMatches | 0 | int(10) unsigned | Number of bases that match but are part of repeats |
nCount | 0 | int(10) unsigned | Number of 'N' bases |
qNumInsert | 0 | int(10) unsigned | Number of inserts in query |
qBaseInsert | 0 | int(10) unsigned | Number of bases inserted in query |
tNumInsert | 2 | int(10) unsigned | Number of inserts in target |
tBaseInsert | 884 | int(10) unsigned | Number of bases inserted in target |
strand | + | char(2) | + or - for strand. First character query, second target (optional) |
qName | AM992877 | varchar(255) | Query sequence name |
qSize | 1604 | int(10) unsigned | Query sequence size |
qStart | 0 | int(10) unsigned | Alignment start position in query |
qEnd | 1604 | int(10) unsigned | Alignment end position in query |
tName | chr1 | varchar(255) | Target sequence name |
tSize | 248956422 | int(10) unsigned | Target sequence size |
tStart | 11873 | int(10) unsigned | Alignment start position in target |
tEnd | 14361 | int(10) unsigned | Alignment end position in target |
blockCount | 3 | int(10) unsigned | Number of blocks in alignment |
blockSizes | 354,109,1141, | longblob | Size of each block |
qStarts | 0,354,463, | longblob | Start of each block in query. |
tStarts | 11873,12612,13220, | 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 | 1579 | 25 | 0 | 0 | 0 | 0 | 2 | 884 | + | AM992877 | 1604 | 0 | 1604 | chr1 | 248956422 | 11873 | 14361 | 3 | 354,109,1141, | 0,354,463, | 11873,12612,13220, |
585 | 1419 | 21 | 0 | 0 | 0 | 0 | 2 | 1048 | + | AM992881 | 1440 | 0 | 1440 | chr1 | 248956422 | 11873 | 14361 | 3 | 354,127,959, | 0,354,481, | 11873,12594,13402, |
585 | 1533 | 12 | 0 | 0 | 0 | 0 | 4 | 944 | + | AM992878 | 1545 | 0 | 1545 | chr1 | 248956422 | 11873 | 14362 | 5 | 354,52,436,299,404, | 0,354,406,842,1141, | 11873,12645,13220,13658,13958, |
585 | 1578 | 27 | 0 | 0 | 0 | 0 | 2 | 884 | + | AM992879 | 1605 | 0 | 1605 | chr1 | 248956422 | 11873 | 14362 | 3 | 354,109,1142, | 0,354,463, | 11873,12612,13220, |
585 | 1652 | 0 | 0 | 0 | 0 | 0 | 2 | 884 | + | AM992871 | 1652 | 0 | 1652 | chr1 | 248956422 | 11873 | 14409 | 3 | 354,109,1189, | 0,354,463, | 11873,12612,13220, |
585 | 1650 | 2 | 0 | 0 | 0 | 0 | 2 | 884 | + | AM992872 | 1652 | 0 | 1652 | chr1 | 248956422 | 11873 | 14409 | 3 | 354,109,1189, | 0,354,463, | 11873,12612,13220, |
585 | 1648 | 4 | 0 | 0 | 0 | 0 | 2 | 884 | + | AM992875 | 1652 | 0 | 1652 | chr1 | 248956422 | 11873 | 14409 | 3 | 354,109,1189, | 0,354,463, | 11873,12612,13220, |
585 | 1485 | 3 | 0 | 0 | 0 | 0 | 2 | 1048 | + | AM992880 | 1488 | 0 | 1488 | chr1 | 248956422 | 11873 | 14409 | 3 | 354,127,1007, | 0,354,481, | 11873,12594,13402, |
585 | 1631 | 8 | 0 | 0 | 0 | 0 | 4 | 897 | + | BC032353 | 1673 | 0 | 1639 | chr1 | 248956422 | 11873 | 14409 | 5 | 354,109,737,300,139, | 0,354,463,1200,1500, | 11873,12612,13220,13958,14270, |
585 | 1736 | 4 | 0 | 0 | 0 | 0 | 3 | 796 | + | LP896001 | 1740 | 0 | 1740 | chr1 | 248956422 | 11873 | 14409 | 4 | 354,127,70,1189, | 0,354,481,551, | 11873,12594,12974,13220, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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