Schema for refSeqAli
  Database: vicPac2    Primary Table: refSeqAli    Row Count: 17   Data last updated: 2016-01-21
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 604smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 811int(10) unsigned range Number of bases that match that aren't repeats
misMatches 7int(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 2int(10) unsigned range Number of bases inserted in query
tNumInsert 3int(10) unsigned range Number of inserts in target
tBaseInsert 5275int(10) unsigned range Number of bases inserted in target
strand +char(2) values + or - for strand. First character query, second target (optional)
qName NM_001287199varchar(255) values Query sequence name
qSize 881int(10) unsigned range Query sequence size
qStart 26int(10) unsigned range Alignment start position in query
qEnd 846int(10) unsigned range Alignment end position in query
tName KB632446varchar(255) values Target sequence name
tSize 17585923int(10) unsigned range Target sequence size
tStart 2560731int(10) unsigned range Alignment start position in target
tEnd 2566824int(10) unsigned range Alignment end position in target
blockCount 5int(10) unsigned range Number of blocks in alignment
blockSizes 184,108,180,42,304,longblob   Size of each block
qStarts 26,210,318,498,542,longblob   Start of each block in query.
tStarts 2560731,2561983,2564135,256...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)
      vicPac2.all_est.qName (via refSeqAli.qName)
      vicPac2.all_mrna.qName (via refSeqAli.qName)
      vicPac2.mrnaOrientInfo.name (via refSeqAli.qName)
      vicPac2.refFlat.name (via refSeqAli.qName)
      vicPac2.refGene.name (via refSeqAli.qName)
      vicPac2.xenoRefGene.name (via refSeqAli.qName)
      vicPac2.xenoRefSeqAli.qName (via refSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
6048117001235275+NM_00128719988126846KB63244617585923256073125668245184,108,180,42,304,26,210,318,498,542,2560731,2561983,2564135,2566478,2566520,
608804000004920-NM_0012871988141805KB63244916583958311157231132965295,162,117,161,69,9,304,466,583,744,3111572,3112143,3112491,3112823,3113227,
62387900000112942+NM_0012872008790879KB6325605281909505873950625601237,89,68,61,57,96,75,97,70,61,81,87,0,37,126,194,255,312,408,483,580,650,711,792,5058739,5059442,5059622,5059828,5059986,5060738,5060975,5061210,5061490,5062133,5062306,5062473,
590520300002227-NM_0012871975530523KB63260539313487707267714763166,173,184,30,196,369,770726,770973,771292,
6613441000023573-NM_0012878583450345KB6324681249494610005200100091183120,65,160,0,120,185,10005200,10007602,10008958,
73133070000611460+NM_001290071136201337KB63263730671072536122664097375,161,118,78,148,154,303,0,375,536,654,732,880,1034,253612,256887,258300,260041,260403,265455,266106,
614189400000410883-NM_001290156189401894KB63253266919403853797386657451239,86,176,158,235,0,1239,1325,1501,1659,3853797,3855274,3856145,3857564,3866339,
5958470000046286+NM_0012906478470847KB6327071788075138813713952705196,137,176,86,252,0,196,333,509,595,1388137,1392631,1393536,1394214,1395018,
62865840000016375-NM_001291337658506584KB63250680136745739149575210826362,222,1,6363,5739149,5751886,
62865840000016375-NM_001291338658506584KB63250680136745739149575210826362,222,1,6363,5739149,5751886,

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