Schema for xenoRefSeqAli
  Database: otoGar3    Primary Table: xenoRefSeqAli    Row Count: 530,019   Data last updated: 2020-08-19
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 585smallint(5) unsigned Indexing field to speed chromosome range queries.
matches 250int(10) unsigned Number of bases that match that aren't repeats
misMatches 48int(10) unsigned Number of bases that don't match
repMatches 0int(10) unsigned Number of bases that match but are part of repeats
nCount 0int(10) unsigned Number of 'N' bases
qNumInsert 7int(10) unsigned Number of inserts in query
qBaseInsert 1922int(10) unsigned Number of bases inserted in query
tNumInsert 7int(10) unsigned Number of inserts in target
tBaseInsert 3159int(10) unsigned Number of bases inserted in target
strand +-char(2) + or - for strand. First character query, second target (optional)
qName NR_156691varchar(255) Query sequence name
qSize 3533int(10) unsigned Query sequence size
qStart 476int(10) unsigned Alignment start position in query
qEnd 2696int(10) unsigned Alignment end position in query
tName AAQR03191384varchar(255) Target sequence name
tSize 22255int(10) unsigned Target sequence size
tStart 17900int(10) unsigned Alignment start position in target
tEnd 21357int(10) unsigned Alignment end position in target
blockCount 8int(10) unsigned Number of blocks in alignment
blockSizes 51,5,22,40,50,24,33,73,longblob Size of each block
qStarts 476,605,611,644,1085,2361,2...longblob Start of each block in query.
tStarts 898,1031,1038,1072,2847,402...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)
      otoGar3.all_mrna.qName (via xenoRefSeqAli.qName)
      otoGar3.xenoMrna.qName (via xenoRefSeqAli.qName)
      otoGar3.xenoRefFlat.name (via xenoRefSeqAli.qName)
      otoGar3.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
58525048007192273159+-NR_15669135334762696AAQR03191384222551790021357851,5,22,40,50,24,33,73,476,605,611,644,1085,2361,2474,2623,898,1031,1038,1072,2847,4022,4138,4282,
58515129003143131328+-NR_11195626447362347AAQR03191384222551790019408450,24,33,73,736,2012,2125,2274,2847,4022,4138,4282,
58532668009212293480+-NR_15669034824212937AAQR031913842225517483213571051,5,22,40,50,24,33,73,78,18,421,550,556,589,891,2167,2280,2429,2826,2919,898,1031,1038,1072,2847,4022,4138,4282,4671,4754,
5853736800127138+-NM_00101663680420488AAQR0319156818291329237712414,27,20,461,14520,14972,
5854014100130133+-NM_0012874161368117589AAQR0319156818291329337682412,30,117,559,14523,14968,
585407370014911513+-NM_00104087453441534AAQR0319156818291329452512417,27,41,507,13040,14970,
585325560012218999+-NM_001024398154348451AAQR03191568182913294126742354,27,48,424,5617,14970,
5853716800120134+-NM_001025171133145504AAQR0319156818291329537682411,28,45,476,14523,14968,
5853796100121133+-NM_001318003563101562AAQR0319156818291329537682416,24,101,538,14523,14972,
70013712150061331816672++NM_001376932173811720GL8735442197230815079650150979081942,123,157,105,141,64,60,93,180,56,122,6,76,28,56,80,41,63,93,1,66,189,346,451,592,656,716,809,989,1086,1208,1214,1299,1327,1383,1464,1519,1627,15079650,15081307,15082348,15084445,15084920,15086287,15087953,15089023,15089252,15091054,15092964,15093367,15093909,15095430,15 ...

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