Schema for all_mrna
  Database: mm39    Primary Table: all_mrna    Row Count: 2,039,934   Data last updated: 2020-08-18
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 608smallint(5) unsigned Indexing field to speed chromosome range queries.
matches 27int(10) unsigned Number of bases that match that aren't repeats
misMatches 0int(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 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 AB351640varchar(255) Query sequence name
qSize 27int(10) unsigned Query sequence size
qStart 0int(10) unsigned Alignment start position in query
qEnd 27int(10) unsigned Alignment end position in query
tName chr1varchar(255) Target sequence name
tSize 195154279int(10) unsigned Target sequence size
tStart 3056357int(10) unsigned Alignment start position in target
tEnd 3056384int(10) unsigned Alignment end position in target
blockCount 1int(10) unsigned Number of blocks in alignment
blockSizes 27,longblob Size of each block
qStarts 0,longblob Start of each block in query.
tStarts 3056357,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)
      mm39.all_est.qName (via all_mrna.qName)
      mm39.mrnaOrientInfo.name (via all_mrna.qName)
      mm39.refGene.name (via all_mrna.qName)
      mm39.refSeqAli.qName (via all_mrna.qName)
      mm39.xenoMrna.qName (via all_mrna.qName)
      mm39.xenoRefGene.name (via all_mrna.qName)
      mm39.xenoRefSeqAli.qName (via all_mrna.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
608270000000-AB35164027027chr119515427930563573056384127,0,3056357,
608250000000-AB35015425025chr119515427930563593056384125,0,3056359,
608240000000-AB35293824024chr119515427930563603056384124,0,3056360,
60845000001428+LF28848245045chr119515427930563623056835221,24,0,21,3056362,3056811,
60845000001428+MA52405945045chr119515427930563623056835221,24,0,21,3056362,3056811,
608300000000-DQ68552830030chr119515427930567573056787130,0,3056757,
608260000000+DQ70672728026chr119515427930567583056784126,0,3056758,
608290000011+DQ54017729029chr11951542793056760305679026,23,0,6,3056760,3056767,
608280000000-AB35105828028chr119515427930567643056792128,0,3056764,
608260000000+DQ56745627026chr119515427930568023056828126,0,3056802,

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