Schema for xenoRefSeqAli
  Database: macEug2    Primary Table: xenoRefSeqAli    Row Count: 598,021   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 172int(10) unsigned Number of bases that match that aren't repeats
misMatches 27int(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 0int(10) unsigned Number of inserts in target
tBaseInsert 0int(10) unsigned Number of bases inserted in target
strand ++char(2) + or - for strand. First character query, second target (optional)
qName NM_001265899varchar(255) Query sequence name
qSize 2944int(10) unsigned Query sequence size
qStart 1851int(10) unsigned Alignment start position in query
qEnd 2050int(10) unsigned Alignment end position in query
tName ABQO010000375varchar(255) Target sequence name
tSize 938int(10) unsigned Target sequence size
tStart 551int(10) unsigned Alignment start position in target
tEnd 750int(10) unsigned Alignment end position in target
blockCount 1int(10) unsigned Number of blocks in alignment
blockSizes 199,longblob Size of each block
qStarts 1851,longblob Start of each block in query.
tStarts 551,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)
      macEug2.all_est.qName (via xenoRefSeqAli.qName)
      macEug2.all_mrna.qName (via xenoRefSeqAli.qName)
      macEug2.xenoMrna.qName (via xenoRefSeqAli.qName)
      macEug2.xenoRefFlat.name (via xenoRefSeqAli.qName)
      macEug2.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
58517227000000++NM_001265899294418512050ABQO0100003759385517501199,1851,551,
58517326000000++NM_001281520376919662165ABQO0100003759385517501199,1966,551,
58517326000000++NM_001281521383520322231ABQO0100003759385517501199,2032,551,
58517326000000++NM_001281522357417711970ABQO0100003759385517501199,1771,551,
58516534000000++NM_001293169336316321831ABQO0100003759385517501199,1632,551,
58510245000000++NM_0013206062032652799GL06157118791149922500691147,652,49922,
58517325000000++NM_001291054348118642062ABQO0100003759385527501198,1864,552,
58513365000000++NM_001337836251814141612ABQO0100003759385527501198,1414,552,
58513365000000++NM_001337837260614141612ABQO0100003759385527501198,1414,552,
58513365000000++NM_001337838254314481646ABQO0100003759385527501198,1448,552,

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