Schema for refSeqAli
  Database: ce2    Primary Table: refSeqAli    Row Count: 51,856   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 594smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 78int(10) unsigned range Number of bases that match that aren't repeats
misMatches 0int(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 0int(10) unsigned range Number of inserts in query
qBaseInsert 0int(10) unsigned range Number of bases inserted in query
tNumInsert 0int(10) unsigned range Number of inserts in target
tBaseInsert 0int(10) unsigned range Number of bases inserted in target
strand +char(2) values + or - for strand. First character query, second target (optional)
qName NR_050829varchar(255) values Query sequence name
qSize 78int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 78int(10) unsigned range Alignment end position in query
tName chrIIvarchar(255) values Target sequence name
tSize 15279308int(10) unsigned range Target sequence size
tStart 1246972int(10) unsigned range Alignment start position in target
tEnd 1247050int(10) unsigned range Alignment end position in target
blockCount 1int(10) unsigned range Number of blocks in alignment
blockSizes 78,longblob   Size of each block
qStarts 0,longblob   Start of each block in query.
tStarts 1246972,longblob   Start of each block in target.

Connected Tables and Joining Fields
        ce2.all_est.qName (via refSeqAli.qName)
      ce2.all_mrna.qName (via refSeqAli.qName)
      ce2.mrnaOrientInfo.name (via refSeqAli.qName)
      ce2.refFlat.name (via refSeqAli.qName)
      ce2.refGene.name (via refSeqAli.qName)
      ce2.xenoRefGene.name (via refSeqAli.qName)
      ce2.xenoRefSeqAli.qName (via refSeqAli.qName)
      hgFixed.gbCdnaInfo.acc (via refSeqAli.qName)
      hgFixed.gbMiscDiff.acc (via refSeqAli.qName)
      hgFixed.gbSeq.acc (via refSeqAli.qName)
      hgFixed.gbWarn.acc (via refSeqAli.qName)
      hgFixed.imageClone.acc (via refSeqAli.qName)
      hgFixed.refLink.mrnaAcc (via refSeqAli.qName)
      hgFixed.refSeqStatus.mrnaAcc (via refSeqAli.qName)
      hgFixed.refSeqSummary.mrnaAcc (via refSeqAli.qName)
      knownGeneV39.kgXref.refseq (via refSeqAli.qName)
      knownGeneV39.knownToRefSeq.value (via refSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
594780000000+NR_05082978078chrII1527930812469721247050178,0,1246972,
5941430000000-NR_0508301430143chrII15279308124701512471581143,0,1247015,
603990000000+NR_00091899099chrII1527930824528372452936199,0,2452837,
603610000000+NR_13140561061chrII1527930824640272464088161,0,2464027,
6041470000000-NR_1314761470147chrII15279308261510526152521147,0,2615105,
59411610000061214-NM_061535116101161chrII1527930812695441271919757,166,123,113,124,279,299,0,57,223,346,459,583,862,1269544,1269741,1269955,1270347,1270511,1270759,1271620,
691744000006468+NM_0013731507440744chrV209222311396655913967771776,128,120,153,63,132,72,0,76,204,324,477,540,672,13966559,13966684,13966861,13967033,13967346,13967525,13967699,
61922010000091342+NM_065524220202201chrIII137833134562702456624510135,59,124,344,221,213,152,130,269,554,0,135,194,318,662,883,1096,1248,1378,1647,4562702,4562905,4563020,4563246,4563641,4564198,4564459,4564660,4565365,4565691,
6191262000004729+NM_065523126201262chrIII13783313456425745662485154,152,130,269,557,0,154,306,436,705,4564257,4564459,4564660,4565365,4565691,
61927900000157+NM_0013066932790279chrIII13783313456550845658442126,153,0,126,4565508,4565691,

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