Schema for xenoRefSeqAli
  Database: susScr3    Primary Table: xenoRefSeqAli    Row Count: 477,106   Data last updated: 2020-09-01
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 640smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 679int(10) unsigned range Number of bases that match that aren't repeats
misMatches 119int(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 3int(10) unsigned range Number of inserts in query
qBaseInsert 220int(10) unsigned range Number of bases inserted in query
tNumInsert 7int(10) unsigned range Number of inserts in target
tBaseInsert 5540int(10) unsigned range Number of bases inserted in target
strand ++char(2) values + or - for strand. First character query, second target (optional)
qName NM_001193895varchar(255) values Query sequence name
qSize 1252int(10) unsigned range Query sequence size
qStart 168int(10) unsigned range Alignment start position in query
qEnd 1186int(10) unsigned range Alignment end position in query
tName chr5varchar(255) values Target sequence name
tSize 111506441int(10) unsigned range Target sequence size
tStart 7316537int(10) unsigned range Alignment start position in target
tEnd 7322875int(10) unsigned range Alignment end position in target
blockCount 8int(10) unsigned range Number of blocks in alignment
blockSizes 109,63,182,132,101,85,72,54,longblob   Size of each block
qStarts 168,277,340,522,655,756,884...longblob   Start of each block in query.
tStarts 7316537,7317873,7320888,732...longblob   Start of each block in target.

Connected Tables and Joining Fields
        hgFixed.gbCdnaInfo.acc (via xenoRefSeqAli.qName)
      hgFixed.gbMiscDiff.acc (via xenoRefSeqAli.qName)
      hgFixed.gbSeq.acc (via xenoRefSeqAli.qName)
      hgFixed.gbWarn.acc (via xenoRefSeqAli.qName)
      hgFixed.imageClone.acc (via xenoRefSeqAli.qName)
      susScr3.all_est.qName (via xenoRefSeqAli.qName)
      susScr3.all_mrna.qName (via xenoRefSeqAli.qName)
      susScr3.refGene.name (via xenoRefSeqAli.qName)
      susScr3.refSeqAli.qName (via xenoRefSeqAli.qName)
      susScr3.xenoMrna.qName (via xenoRefSeqAli.qName)
      susScr3.xenoRefFlat.name (via xenoRefSeqAli.qName)
      susScr3.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
64067911900322075540++NM_00119389512521681186chr5111506441731653773228758109,63,182,132,101,85,72,54,168,277,340,522,655,756,884,1132,7316537,7317873,7320888,7321783,7322095,7322320,7322447,7322821,
585909000000+-NM_0010423782261636735GL892101-1101099199,636,2,
7486661050023551175+-NM_001313949121729835chr12635885712147680921478755657,62,157,153,120,222,29,106,168,325,493,613,42109816,42110410,42110764,42111067,42111324,42111540,
5857917000000+-NM_0130982293627723GL892101-1101197196,627,4,
585899000000+-NM_0010761242741625723GL892101-1101199198,625,2,
5851417001300+-NM_001007613250819552106GL892102-11480148272,76,1955,2030,0,72,
5851453000000+-NM_001133486372418952043GL892102-114801481148,1895,0,
5851453000000+-NM_001144834235318952043GL892102-114801481148,1895,0,
585295460024994774+-NM_00119447094191931GL892962-11737787249839537,27,43,95,139,91,148,654,697,792,7538,7679,7887,8065,8514,
5851453000000+-NM_001258162374319552103GL892102-114801481148,1955,0,

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