Schema for refSeqAli
  Database: hg18    Primary Table: refSeqAli    Row Count: 79,204   Data last updated: 2020-08-21
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 1732int(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 37int(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 10int(10) unsigned range Number of inserts in target
tBaseInsert 13240int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName NR_024540varchar(255) values Query sequence name
qSize 1786int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 1769int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 247249719int(10) unsigned range Target sequence size
tStart 4224int(10) unsigned range Alignment start position in target
tEnd 19233int(10) unsigned range Alignment end position in target
blockCount 11int(10) unsigned range Number of blocks in alignment
blockSizes 468,69,152,159,198,136,137,...longblob   Size of each block
qStarts 17,485,554,706,865,1063,119...longblob   Start of each block in query.
tStarts 4224,4832,5658,6469,6720,70...longblob   Start of each block in target.

Connected Tables and Joining Fields
        hg18.all_est.qName (via refSeqAli.qName)
      hg18.all_mrna.qName (via refSeqAli.qName)
      hg18.ccdsInfo.mrnaAcc (via refSeqAli.qName)
      hg18.kgXref.refseq (via refSeqAli.qName)
      hg18.knownToRefSeq.value (via refSeqAli.qName)
      hg18.mrnaOrientInfo.name (via refSeqAli.qName)
      hg18.mrnaRefseq.refseq (via refSeqAli.qName)
      hg18.refFlat.name (via refSeqAli.qName)
      hg18.refGene.name (via refSeqAli.qName)
      hg18.xenoEst.qName (via refSeqAli.qName)
      hg18.xenoMrna.qName (via refSeqAli.qName)
      hg18.xenoRefGene.name (via refSeqAli.qName)
      hg18.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
58517320370001013240-NR_024540178601769chr124724971942241923311468,69,152,159,198,136,137,147,99,154,50,17,485,554,706,865,1063,1199,1336,1483,1582,1736,4224,4832,5658,6469,6720,7095,7468,7777,8130,14600,19183,
58559805320002341-NR_026818113001130chr124724971924473259443564,205,361,0,564,769,24473,25139,25583,
58559805320002341-NR_026820113001130chr124724971924473259443564,205,361,0,564,769,24473,25139,25583,
5859180000000+NM_0010054849180918chr124724971958953598711918,0,58953,
587425901110002320+NR_028322437004370chr12472497193137543184443169,58,4143,0,169,227,313754,314150,314301,
587425541110002320+NR_028325437004370chr12472497193137543184443169,58,4143,0,169,227,313754,314150,314301,
5879390000000+NM_0010052219390939chr12472497193575213584601939,0,357521,
5879390000000+NM_0010052249390939chr12472497193575213584601939,0,357521,
5879390000000+NM_0010052779390939chr12472497193575213584601939,0,357521,
5899390000000-NM_0010052219390939chr12472497196109586118971939,0,610958,

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