Schema for all_mrna
  Database: susScr3    Primary Table: all_mrna    Row Count: 49,242   Data last updated: 2020-09-01
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 100int(10) unsigned range Number of bases that match that aren't repeats
misMatches 0int(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 AK232581varchar(255) values Query sequence name
qSize 1759int(10) unsigned range Query sequence size
qStart 1120int(10) unsigned range Alignment start position in query
qEnd 1220int(10) unsigned range Alignment end position in query
tName GL892100-1varchar(255) values Target sequence name
tSize 100int(10) unsigned range Target sequence size
tStart 0int(10) unsigned range Alignment start position in target
tEnd 100int(10) unsigned range Alignment end position in target
blockCount 1int(10) unsigned range Number of blocks in alignment
blockSizes 100,longblob   Size of each block
qStarts 1120,longblob   Start of each block in query.
tStarts 0,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)
      susScr3.all_est.qName (via all_mrna.qName)
      susScr3.mrnaOrientInfo.name (via all_mrna.qName)
      susScr3.refGene.name (via all_mrna.qName)
      susScr3.refSeqAli.qName (via all_mrna.qName)
      susScr3.xenoMrna.qName (via all_mrna.qName)
      susScr3.xenoRefGene.name (via all_mrna.qName)
      susScr3.xenoRefSeqAli.qName (via all_mrna.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
5851000000000+AK232581175911201220GL892100-110001001100,1120,0,
585970000000-AK3461452827521618GL892101-1101097197,2209,0,
585970000000-AK3942771959522619GL892101-1101097197,1340,0,
585990000000-AK2328631900462561GL892101-1101099199,1339,0,
585990000000-AK2329892082642741GL892101-1101099199,1341,0,
585990000000-AK3931432111679778GL892101-1101099199,1333,0,
585990000000-AK3931992965822921GL892101-1101099199,2044,0,
585990000000-AK3942641961526625GL892101-1101099199,1336,0,
585981000000-AK3943661903465564GL892101-1101099199,1339,0,
585990000000-AK4005152256826925GL892101-1101099199,1331,0,

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