Schema for all_mrna
  Database: hg19    Primary Table: all_mrna    Row Count: 9,811,564   Data last updated: 2020-08-17
Format description: Summary info about a patSpace alignment
fieldexampleSQL type description
bin 585smallint(5) unsigned Indexing field to speed chromosome range queries.
matches 1579int(10) unsigned Number of bases that match that aren't repeats
misMatches 25int(10) unsigned Number of bases that don't match
repMatches 0int(10) unsigned Number of bases that match but are part of repeats
nCount 0int(10) unsigned Number of 'N' bases
qNumInsert 0int(10) unsigned Number of inserts in query
qBaseInsert 0int(10) unsigned Number of bases inserted in query
tNumInsert 2int(10) unsigned Number of inserts in target
tBaseInsert 884int(10) unsigned Number of bases inserted in target
strand +char(2) + or - for strand. First character query, second target (optional)
qName AM992877varchar(255) Query sequence name
qSize 1604int(10) unsigned Query sequence size
qStart 0int(10) unsigned Alignment start position in query
qEnd 1604int(10) unsigned Alignment end position in query
tName chr1varchar(255) Target sequence name
tSize 249250621int(10) unsigned Target sequence size
tStart 11873int(10) unsigned Alignment start position in target
tEnd 14361int(10) unsigned Alignment end position in target
blockCount 3int(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.

Connected Tables and Joining Fields
        hg19.all_est.qName (via all_mrna.qName)
      hg19.mgcFullMrna.qName (via all_mrna.qName)
      hg19.mgcGenes.name (via all_mrna.qName)
      hg19.mrnaOrientInfo.name (via all_mrna.qName)
      hg19.orfeomeGenes.name (via all_mrna.qName)
      hg19.orfeomeMrna.qName (via all_mrna.qName)
      hg19.refGene.name (via all_mrna.qName)
      hg19.refSeqAli.qName (via all_mrna.qName)
      hg19.xenoEst.qName (via all_mrna.qName)
      hg19.xenoMrna.qName (via all_mrna.qName)
      hg19.xenoRefGene.name (via all_mrna.qName)
      hg19.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
58515792500002884+AM992877160401604chr124925062111873143613354,109,1141,0,354,463,11873,12612,13220,
585141921000021048+AM992881144001440chr124925062111873143613354,127,959,0,354,481,11873,12594,13402,
58515331200004944+AM992878154501545chr124925062111873143625354,52,436,299,404,0,354,406,842,1141,11873,12645,13220,13658,13958,
58515782700002884+AM992879160501605chr124925062111873143623354,109,1142,0,354,463,11873,12612,13220,
5851652000002884+AM992871165201652chr124925062111873144093354,109,1189,0,354,463,11873,12612,13220,
5851650200002884+AM992872165201652chr124925062111873144093354,109,1189,0,354,463,11873,12612,13220,
5851648400002884+AM992875165201652chr124925062111873144093354,109,1189,0,354,463,11873,12612,13220,
58514853000021048+AM992880148801488chr124925062111873144093354,127,1007,0,354,481,11873,12594,13402,
5851631800004897+BC032353167301639chr124925062111873144095354,109,737,300,139,0,354,463,1200,1500,11873,12612,13220,13958,14270,
5851736400003796+LP896001174001740chr124925062111873144094354,127,70,1189,0,354,481,551,11873,12594,12974,13220,

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