Schema for xenoRefSeqAli
  Database: latCha1    Primary Table: xenoRefSeqAli    Row Count: 434,959   Data last updated: 2020-08-19
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 705int(10) unsigned range Number of bases that match that aren't repeats
misMatches 319int(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 20int(10) unsigned range Number of 'N' bases
qNumInsert 2int(10) unsigned range Number of inserts in query
qBaseInsert 201int(10) unsigned range Number of bases inserted in query
tNumInsert 2int(10) unsigned range Number of inserts in target
tBaseInsert 758int(10) unsigned range Number of bases inserted in target
strand +-char(2) values + or - for strand. First character query, second target (optional)
qName NM_001107522varchar(255) values Query sequence name
qSize 2608int(10) unsigned range Query sequence size
qStart 463int(10) unsigned range Alignment start position in query
qEnd 1708int(10) unsigned range Alignment end position in query
tName AFYH01266222varchar(255) values Target sequence name
tSize 36089int(10) unsigned range Target sequence size
tStart 33164int(10) unsigned range Alignment start position in target
tEnd 34966int(10) unsigned range Alignment end position in target
blockCount 4int(10) unsigned range Number of blocks in alignment
blockSizes 421,173,330,120,longblob   Size of each block
qStarts 463,884,1060,1588,longblob   Start of each block in query.
tStarts 1123,2104,2277,2805,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)
      latCha1.all_mrna.qName (via xenoRefSeqAli.qName)
      latCha1.xenoMrna.qName (via xenoRefSeqAli.qName)
      latCha1.xenoRefFlat.name (via xenoRefSeqAli.qName)
      latCha1.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
58570531902022012758+-NM_00110752226084631708AFYH012662223608933164349664421,173,330,120,463,884,1060,1588,1123,2104,2277,2805,
58568832702022163767+-NM_0011923321272211272AFYH012662223608933164349664421,164,330,120,21,442,618,1152,1123,2104,2277,2805,
58570730502022192770+-NM_02952926294551706AFYH012662223608933164349664421,173,330,108,455,876,1052,1598,1123,2104,2277,2817,
585189320015210837++NM_0011409671073223449AFYH01266594285671359324651330,40,151,223,258,298,13593,13631,24500,
58513524000000++NM_2001522271248407AFYH012665942856724493246521159,248,24493,
58514519000000++NM_0011704691621180344AFYH012665942856724494246581164,180,24494,
58514618000000++NM_0274908643181345AFYH012665942856724494246581164,181,24494,
585149260220000++NM_001078023741179376AFYH012665942856724494246911197,179,24494,
5856333000000++NM_0010145852690523619AFYH01266594285672449824594196,523,24498,
5856333000000++NM_001259847593414981594AFYH01266594285672449824594196,1498,24498,

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