Schema for all_mrna
  Database: galGal2    Primary Table: all_mrna    Row Count: 35,128   Data last updated: 2020-08-22
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 1052int(10) unsigned range Number of bases that match that aren't repeats
misMatches 1int(10) unsigned range Number of bases that don't match
repMatches 0int(10) unsigned range Number of bases that match but are part of repeats
nCount 0int(10) unsigned range Number of 'N' bases
qNumInsert 0int(10) unsigned range Number of inserts in query
qBaseInsert 0int(10) unsigned range Number of bases inserted in query
tNumInsert 0int(10) unsigned range Number of inserts in target
tBaseInsert 0int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName CR354117varchar(255) values Query sequence name
qSize 1053int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 1053int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 188239860int(10) unsigned range Target sequence size
tStart 21946int(10) unsigned range Alignment start position in target
tEnd 22999int(10) unsigned range Alignment end position in target
blockCount 1int(10) unsigned range Number of blocks in alignment
blockSizes 1053,longblob   Size of each block
qStarts 0,longblob   Start of each block in query.
tStarts 21946,longblob   Start of each block in target.

Connected Tables and Joining Fields
        galGal2.all_est.qName (via all_mrna.qName)
      galGal2.mrnaOrientInfo.name (via all_mrna.qName)
      galGal2.refGene.name (via all_mrna.qName)
      galGal2.refSeqAli.qName (via all_mrna.qName)
      galGal2.xenoMrna.qName (via all_mrna.qName)
      galGal2.xenoRefGene.name (via all_mrna.qName)
      galGal2.xenoRefSeqAli.qName (via all_mrna.qName)
      hgFixed.gbCdnaInfo.acc (via all_mrna.qName)
      hgFixed.gbMiscDiff.acc (via all_mrna.qName)
      hgFixed.gbSeq.acc (via all_mrna.qName)
      hgFixed.gbWarn.acc (via all_mrna.qName)
      hgFixed.imageClone.acc (via all_mrna.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
58510521000000-CR354117105301053chr1188239860219462299911053,0,21946,
5857943000011-BX9324647970797chr118823986035270360682665,132,0,665,35270,35936,
5857943000011-BX9325077970797chr118823986035270360682665,132,0,665,35270,35936,
5857482000046209-BX9307157500750chr11882398603711844077557,67,97,126,403,0,57,124,221,347,37118,37484,38187,38562,43674,
5857694001346209-BX9319277859785chr11882398603711844100657,67,97,126,366,60,0,57,124,221,347,716,37118,37484,38187,38562,43674,44040,
5857272000000-CR3860557323732chr118823986097050977791729,0,97050,
5851436100001110122-BX929968144891446chr11882398609820710976612275,73,99,77,152,142,57,95,167,117,141,42,2,277,350,449,526,678,820,877,972,1139,1256,1397,98207,98615,99184,99678,100437,102118,104479,105422,106580,107271,108736,109724,
5857981000069764-CR39082281010809chr1188239860982141087777268,73,68,65,167,117,41,1,269,342,410,475,642,759,98214,98615,99184,105455,106580,107271,108736,
586102510000415281+AF143806111101026chr11882398601397871560945214,186,108,237,281,0,214,400,508,745,139787,151742,152142,152838,155813,
586102510000415281+AY772091102701026chr11882398601397871560945214,186,108,237,281,0,214,400,508,745,139787,151742,152142,152838,155813,

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.