Schema for refSeqAli
  Database: taeGut2    Primary Table: refSeqAli    Row Count: 1,263   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 601smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 1090int(10) unsigned range Number of bases that match that aren't repeats
misMatches 9int(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 1int(10) unsigned range Number of inserts in query
qBaseInsert 8int(10) unsigned range Number of bases inserted in query
tNumInsert 4int(10) unsigned range Number of inserts in target
tBaseInsert 3028int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName NM_001245232varchar(255) values Query sequence name
qSize 1275int(10) unsigned range Query sequence size
qStart 151int(10) unsigned range Alignment start position in query
qEnd 1258int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 118548696int(10) unsigned range Target sequence size
tStart 2132708int(10) unsigned range Alignment start position in target
tEnd 2136835int(10) unsigned range Alignment end position in target
blockCount 6int(10) unsigned range Number of blocks in alignment
blockSizes 109,564,211,132,51,32,longblob   Size of each block
qStarts 17,126,698,909,1041,1092,longblob   Start of each block in query.
tStarts 2132708,2132819,2133383,213...longblob   Start of each block in target.

Connected Tables and Joining Fields
        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)
      taeGut2.all_est.qName (via refSeqAli.qName)
      taeGut2.all_mrna.qName (via refSeqAli.qName)
      taeGut2.mrnaOrientInfo.name (via refSeqAli.qName)
      taeGut2.refFlat.name (via refSeqAli.qName)
      taeGut2.refGene.name (via refSeqAli.qName)
      taeGut2.xenoRefGene.name (via refSeqAli.qName)
      taeGut2.xenoRefSeqAli.qName (via refSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
60110909001843028-NM_00124523212751511258chr1118548696213270821368356109,564,211,132,51,32,17,126,698,909,1041,1092,2132708,2132819,2133383,2134850,2136669,2136803,
75870450000257687+NM_0012452689591916chr111854869623229802381582356,52,807,1,57,109,2322980,2340930,2380775,
7591940000257687+NM_0011972589350923chr111854869623229822381592354,52,817,0,54,106,2322982,2340930,2380775,
6177961243000713539-NM_0012452418660851chr1118548696426664242810328256,93,134,99,50,67,88,64,15,271,364,498,597,647,714,802,4266642,4268572,4268959,4270786,4271463,4275648,4278610,4280968,
625740000000+NR_04902274074chr111854869652607245260798174,0,5260724,
625730000000+NR_04901973073chr111854869652612355261308173,0,5261235,
6358806000052797+NM_00124541396260946chr111854869666550816658764665,144,142,219,116,200,60,125,269,411,630,746,6655081,6655309,6656828,6657208,6658207,6658564,
642953201002212-NM_00124539412461731230chr1118548696751250775135643372,549,134,16,389,939,7512507,7512879,7513430,
681120140000728874+NM_0012453371276581263chr111854869612677190127072698115,100,117,152,79,143,189,310,58,173,273,390,542,621,764,953,12677190,12690011,12692170,12695422,12696489,12699628,12701962,12706959,
6849930000051696-NM_0012706631094861079chr111854869612978403129810926593,41,102,84,52,121,15,608,649,751,835,887,12978403,12979212,12979339,12980631,12980799,12980971,

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