Schema for refSeqAli
  Database: ce6    Primary Table: refSeqAli    Row Count: 53,463   Data last updated: 2020-08-20
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 163int(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 NR_001477varchar(255) values Query sequence name
qSize 163int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 163int(10) unsigned range Alignment end position in query
tName chrIvarchar(255) values Target sequence name
tSize 15072421int(10) unsigned range Target sequence size
tStart 3746int(10) unsigned range Alignment start position in target
tEnd 3909int(10) unsigned range Alignment end position in target
blockCount 1int(10) unsigned range Number of blocks in alignment
blockSizes 163,longblob   Size of each block
qStarts 0,longblob   Start of each block in query.
tStarts 3746,longblob   Start of each block in target.

Connected Tables and Joining Fields
        ce6.all_est.qName (via refSeqAli.qName)
      ce6.all_mrna.qName (via refSeqAli.qName)
      ce6.mrnaOrientInfo.name (via refSeqAli.qName)
      ce6.refFlat.name (via refSeqAli.qName)
      ce6.refGene.name (via refSeqAli.qName)
      ce6.xenoMrna.qName (via refSeqAli.qName)
      ce6.xenoRefGene.name (via refSeqAli.qName)
      ce6.xenoRefSeqAli.qName (via refSeqAli.qName)
      hgFixed.gbCdnaInfo.acc (via refSeqAli.qName)
      hgFixed.gbMiscDiff.acc (via refSeqAli.qName)
      hgFixed.gbSeq.acc (via refSeqAli.qName)
      hgFixed.gbWarn.acc (via refSeqAli.qName)
      hgFixed.imageClone.acc (via refSeqAli.qName)
      hgFixed.refLink.mrnaAcc (via refSeqAli.qName)
      hgFixed.refSeqStatus.mrnaAcc (via refSeqAli.qName)
      hgFixed.refSeqSummary.mrnaAcc (via refSeqAli.qName)
      knownGeneV39.kgXref.refseq (via refSeqAli.qName)
      knownGeneV39.knownToRefSeq.value (via refSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
5851630000000-NR_0014771630163chrI15072421374639091163,0,3746,
6381140000000-NR_0560811140114chrIV17493785699488869950021114,0,6994888,
638210000000+NR_05608221021chrIV1749378569948976994918121,0,6994897,
638210000000+NR_05608021021chrIV1749378569945426994563121,0,6994542,
638210000000-NR_05607621021chrIV1749378569939146993935121,0,6993914,
638210000000+NR_05607721021chrIV1749378569941206994141121,0,6994120,
638210000000+NR_05607321021chrIV1749378569924876992508121,0,6992487,
638920000000-NR_05607492092chrIV1749378569928606992952192,0,6992860,
638210000000-NR_05607521021chrIV1749378569935666993587121,0,6993566,
638210000000-NR_05607221021chrIV1749378569923626992383121,0,6992362,

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