Schema for refSeqAli
  Database: hg19    Primary Table: refSeqAli    Row Count: 81,407   Data last updated: 2020-08-18
Format description: Summary info about a patSpace alignment
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 1603int(10) unsigned range Number of bases that match that aren't repeats
misMatches 4int(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 4int(10) unsigned range Number of inserts in target
tBaseInsert 887int(10) unsigned range Number of bases inserted in target
strand +char(2) values + or - for strand. First character query, second target (optional)
qName NR_148357varchar(255) values Query sequence name
qSize 1607int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 1607int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 249250621int(10) unsigned range Target sequence size
tStart 11868int(10) unsigned range Alignment start position in target
tEnd 14362int(10) unsigned range Alignment end position in target
blockCount 5int(10) unsigned range Number of blocks in alignment
blockSizes 359,109,436,299,404,longblob   Size of each block
qStarts 0,359,468,904,1203,longblob   Start of each block in query.
tStarts 11868,12612,13220,13658,13958,longblob   Start of each block in target.

Connected Tables and Joining Fields
        hg19.all_est.qName (via refSeqAli.qName)
      hg19.all_mrna.qName (via refSeqAli.qName)
      hg19.ccdsInfo.mrnaAcc (via refSeqAli.qName)
      hg19.kgXref.refseq (via refSeqAli.qName)
      hg19.knownToRefSeq.value (via refSeqAli.qName)
      hg19.mrnaOrientInfo.name (via refSeqAli.qName)
      hg19.refFlat.name (via refSeqAli.qName)
      hg19.refGene.name (via refSeqAli.qName)
      hg19.xenoEst.qName (via refSeqAli.qName)
      hg19.xenoMrna.qName (via refSeqAli.qName)
      hg19.xenoRefGene.name (via refSeqAli.qName)
      hg19.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)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
5851603400004887+NR_148357160701607chr124925062111868143625359,109,436,299,404,0,359,468,904,1203,11868,12612,13220,13658,13958,
5851652000002884+NR_046018165201652chr124925062111873144093354,109,1189,0,354,463,11873,12612,13220,
5851769000001013240-NR_024540178601769chr1249250621143612937011468,69,152,159,198,136,137,147,99,154,50,17,485,554,706,865,1063,1199,1336,1483,1582,1736,14361,14969,15795,16606,16857,17232,17605,17914,18267,24737,29320,
585680000000-NR_10691868068chr12492506211736817436168,0,17368,
585680000000-NR_10706268068chr12492506211736817436168,0,17368,
585680000000-NR_10706368068chr12492506211736817436168,0,17368,
585680000000-NR_12872068068chr12492506211736817436168,0,17368,
5851380000000+NR_0360511380138chr124925062130365305031138,0,30365,
5851380000000+NR_0362661380138chr124925062130365305031138,0,30365,
5851380000000+NR_0362671380138chr124925062130365305031138,0,30365,

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