Schema for refSeqAli
  Database: dm2    Primary Table: refSeqAli    Row Count: 35,517   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 717smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 1791int(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 3int(10) unsigned range Number of inserts in target
tBaseInsert 174int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName NM_168723varchar(255) values Query sequence name
qSize 1791int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 1791int(10) unsigned range Alignment end position in query
tName chr3Lvarchar(255) values Target sequence name
tSize 23771897int(10) unsigned range Target sequence size
tStart 17302430int(10) unsigned range Alignment start position in target
tEnd 17304395int(10) unsigned range Alignment end position in target
blockCount 4int(10) unsigned range Number of blocks in alignment
blockSizes 512,330,608,341,longblob   Size of each block
qStarts 0,512,842,1450,longblob   Start of each block in query.
tStarts 17302430,17303001,17303387,...longblob   Start of each block in target.

Connected Tables and Joining Fields
        dm2.all_est.qName (via refSeqAli.qName)
      dm2.all_mrna.qName (via refSeqAli.qName)
      dm2.flyBaseToRefSeq.value (via refSeqAli.qName)
      dm2.mrnaOrientInfo.name (via refSeqAli.qName)
      dm2.refFlat.name (via refSeqAli.qName)
      dm2.refGene.name (via refSeqAli.qName)
      dm2.xenoMrna.qName (via refSeqAli.qName)
      dm2.xenoRefGene.name (via refSeqAli.qName)
      dm2.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
7171791000003174-NM_168723179101791chr3L2377189717302430173043954512,330,608,341,0,512,842,1450,17302430,17303001,17303387,17304054,
59717650000032377+NM_169109176501765chr3R27905053164040016445424605,552,36,572,0,605,1157,1193,1640400,1643237,1643873,1643970,
6854330000000-NR_1249184330433chr3L2377189713189213131896461433,0,13189213,
6725570000000+NR_1248915570557chr3L2377189711409596114101531557,0,11409596,
60940600000165+NM_1349124060406chr2L22407834317397131744422267,139,0,267,3173971,3174303,
677469000002124+NM_1402944690469chr3L2377189712110913121115063125,137,207,0,125,262,12110913,12111105,12111299,
6778680200003201-NM_1437858880888chr3L2377189712111442121125314283,107,230,268,0,283,390,620,12111442,12111784,12111962,12112263,
625143900000158+NM_136677143901439chr2R20766785534879753502942447,992,0,447,5348797,5349302,
6272266000003220+NM_141684226602266chr3R27905053558937155918574286,586,867,527,0,286,872,1739,5589371,5589762,5590402,5591330,
759381502500051227-NM_168975384003840chr3L2377189722807542228126096998,1267,932,426,82,135,0,998,2265,3197,3623,3705,22807542,22808964,22810297,22811290,22811777,22812474,

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