Schema for xenoRefSeqAli
  Database: ci1    Primary Table: xenoRefSeqAli    Row Count: 212,629   Data last updated: 2020-08-21
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 285int(10) unsigned range Number of bases that match that aren't repeats
misMatches 124int(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 2int(10) unsigned range Number of inserts in query
qBaseInsert 497int(10) unsigned range Number of bases inserted in query
tNumInsert 3int(10) unsigned range Number of inserts in target
tBaseInsert 3342int(10) unsigned range Number of bases inserted in target
strand ++char(2) values + or - for strand. First character query, second target (optional)
qName NM_001035282varchar(255) values Query sequence name
qSize 5063int(10) unsigned range Query sequence size
qStart 1847int(10) unsigned range Alignment start position in query
qEnd 2753int(10) unsigned range Alignment end position in query
tName Scaffold_1varchar(255) values Target sequence name
tSize 972361int(10) unsigned range Target sequence size
tStart 547int(10) unsigned range Alignment start position in target
tEnd 4298int(10) unsigned range Alignment end position in target
blockCount 4int(10) unsigned range Number of blocks in alignment
blockSizes 69,100,186,54,longblob   Size of each block
qStarts 1847,2305,2405,2699,longblob   Start of each block in query.
tStarts 547,3168,3690,4244,longblob   Start of each block in target.

Connected Tables and Joining Fields
        ci1.all_est.qName (via xenoRefSeqAli.qName)
      ci1.all_mrna.qName (via xenoRefSeqAli.qName)
      ci1.refGene.name (via xenoRefSeqAli.qName)
      ci1.refSeqAli.qName (via xenoRefSeqAli.qName)
      ci1.xenoMrna.qName (via xenoRefSeqAli.qName)
      ci1.xenoRefFlat.name (via xenoRefSeqAli.qName)
      ci1.xenoRefGene.name (via xenoRefSeqAli.qName)
      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)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
58528512400249733342++NM_001035282506318472753Scaffold_19723615474298469,100,186,54,1847,2305,2405,2699,547,3168,3690,4244,
58512325800033933775+-NM_00135466463229063111Scaffold_19548072783168090341146,201,201,264,906,2073,2307,2847,467169,468336,468594,469492,
5851646100001794++NM_0010944501230176401Scaffold_197236115071160902110,115,176,286,15071,15975,
585789336006426105733+-NM_000124900117043255Scaffold_30397787220332889111156,114,71,181,81,72,102,74,139,99,36,1704,1866,2091,2162,2343,2553,2667,2883,2957,3096,3219,68896,69815,70388,70866,71519,72331,72730,74257,74972,75586,75718,
5851656000001794++NM_0011018071135128353Scaffold_197236115071160902110,115,128,238,15071,15975,
5851146300119811422+-NM_0010821751884610985Scaffold_3408547418219198182114,63,610,922,65656,67192,
5851959900002872++NM_1455001527260554Scaffold_197236115080162463101,113,80,260,361,474,15080,15975,16166,
58519983001122884++NM_0010894012006392686Scaffold_197236115080162463101,115,66,392,493,620,15080,15975,16180,
5869756000000++NM_0011300099957592745Scaffold_284508931602451603981153,592,160245,
58542220200327042158++NM_00109580519973421236Scaffold_19723612102523807572,150,69,150,183,342,462,612,753,1053,21025,21599,22383,22785,23624,

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