Schema for xenoRefSeqAli
  Database: echTel1    Primary Table: xenoRefSeqAli    Row Count: 888,272   Data last updated: 2020-08-21
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 81int(10) unsigned Number of bases that match that aren't repeats
misMatches 10int(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 0int(10) unsigned Number of inserts in query
qBaseInsert 0int(10) unsigned Number of bases inserted in query
tNumInsert 1int(10) unsigned Number of inserts in target
tBaseInsert 3int(10) unsigned Number of bases inserted in target
strand ++char(2) + or - for strand. First character query, second target (optional)
qName NM_001199334varchar(255) Query sequence name
qSize 570int(10) unsigned Query sequence size
qStart 21int(10) unsigned Alignment start position in query
qEnd 112int(10) unsigned Alignment end position in query
tName scaffold_100007varchar(255) Target sequence name
tSize 4408int(10) unsigned Target sequence size
tStart 3998int(10) unsigned Alignment start position in target
tEnd 4092int(10) unsigned Alignment end position in target
blockCount 2int(10) unsigned Number of blocks in alignment
blockSizes 38,53,longblob Size of each block
qStarts 21,59,longblob Start of each block in query.
tStarts 3998,4039,longblob Start of each block in target.

Connected Tables and Joining Fields
        echTel1.xenoRefFlat.name (via xenoRefSeqAli.qName)
      echTel1.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
5858110000013++NM_00119933457021112scaffold_100007440839984092238,53,21,59,3998,4039,
58570019600272272++NM_17588332251631131scaffold_17681811322743083983460,108,328,163,653,803,7430,7920,8070,
58512726000000++NM_0010039482667302455scaffold_1000084263337435271153,302,3374,
58510944000000++NM_0010135041935195348scaffold_1000084263337435271153,195,3374,
58511928000000+-NM_0010345671204131278scaffold_25970234313384851147,131,2946,
58512924000000++NM_00117352065427180scaffold_1000084263337435271153,27,3374,
58512231000000++NM_00117814465427180scaffold_1000084263337435271153,27,3374,
5851232402621363928+-NM_001204074812716325scaffold_10001052675511652411,54,79,29,16,27,216,296,3615,4357,4488,4687,
58518428026295175+-NM_001204053813650383scaffold_1000105267651964327,82,129,50,78,254,4303,4330,4487,
585217330263137288+-NM_175375825142455scaffold_10001052676511015439,27,82,128,42,92,120,327,4252,4303,4330,4488,

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