Schema for all_mrna
  Database: mm10    Primary Table: all_mrna    Row Count: 881,044   Data last updated: 2020-08-18
Format description: Summary info about a patSpace alignment
fieldexampleSQL type description
bin 608smallint(5) unsigned Indexing field to speed chromosome range queries.
matches 867int(10) unsigned Number of bases that match that aren't repeats
misMatches 1int(10) unsigned Number of bases that don't match
repMatches 202int(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 0int(10) unsigned Number of inserts in target
tBaseInsert 0int(10) unsigned Number of bases inserted in target
strand +char(2) + or - for strand. First character query, second target (optional)
qName AK016604varchar(255) Query sequence name
qSize 1070int(10) unsigned Query sequence size
qStart 0int(10) unsigned Alignment start position in query
qEnd 1070int(10) unsigned Alignment end position in query
tName chr1varchar(255) Target sequence name
tSize 195471971int(10) unsigned Target sequence size
tStart 3073252int(10) unsigned Alignment start position in target
tEnd 3074322int(10) unsigned Alignment end position in target
blockCount 1int(10) unsigned Number of blocks in alignment
blockSizes 1070,longblob Size of each block
qStarts 0,longblob Start of each block in query.
tStarts 3073252,longblob Start of each block in target.

Connected Tables and Joining Fields
        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)
      mm10.all_est.qName (via all_mrna.qName)
      mm10.mgcFullMrna.qName (via all_mrna.qName)
      mm10.mgcGenes.name (via all_mrna.qName)
      mm10.mrnaOrientInfo.name (via all_mrna.qName)
      mm10.orfeomeGenes.name (via all_mrna.qName)
      mm10.orfeomeMrna.qName (via all_mrna.qName)
      mm10.refGene.name (via all_mrna.qName)
      mm10.refSeqAli.qName (via all_mrna.qName)
      mm10.xenoMrna.qName (via all_mrna.qName)
      mm10.xenoRefGene.name (via all_mrna.qName)
      mm10.xenoRefSeqAli.qName (via all_mrna.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
608867120200000+AK016604107001070chr11954719713073252307432211070,0,3073252,
608380000000-LF22075245038chr119547197131026813102719138,7,3102681,
608400000000-LF22233945545chr119547197131372023137242140,0,3137202,
7638000001107858-LF30495246240chr119547197131744443282340218,20,6,24,3174444,3282320,
60945000001424+LF28848245045chr119547197131755233175992221,24,0,21,3175523,3175968,
6093959119001116291-AK220428416004151chr1195471971320590332163443462,952,2736,9,472,1424,3205903,3206365,3213608,
6092817117000026122-AK135172298802988chr1195471971320652232156323795,585,1608,0,795,1380,3206522,3213438,3214024,
76320504290002453383-AY534250365203634chr11954719713214481367149832487,200,947,18,2505,2705,3214481,3421701,3670551,
6098600000000-BC16929492711871chr1195471971321602232168821860,56,3216022,
7696001290002453383-BC1692931160611150chr119547197132168773671349391,200,798,10,101,301,3216877,3421701,3670551,

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