Schema for refSeqAli
  Database: dm6    Primary Table: refSeqAli    Row Count: 36,533   Data last updated: 2020-08-18
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 621smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 2905int(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 1int(10) unsigned range Number of inserts in target
tBaseInsert 9806int(10) unsigned range Number of bases inserted in target
strand +char(2) values + or - for strand. First character query, second target (optional)
qName NR_167863varchar(255) values Query sequence name
qSize 2905int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 2905int(10) unsigned range Alignment end position in query
tName chr2Rvarchar(255) values Target sequence name
tSize 25286936int(10) unsigned range Target sequence size
tStart 4802419int(10) unsigned range Alignment start position in target
tEnd 4815130int(10) unsigned range Alignment end position in target
blockCount 2int(10) unsigned range Number of blocks in alignment
blockSizes 2791,114,longblob   Size of each block
qStarts 0,2791,longblob   Start of each block in query.
tStarts 4802419,4815016,longblob   Start of each block in target.

Connected Tables and Joining Fields
        dm6.all_est.qName (via refSeqAli.qName)
      dm6.all_mrna.qName (via refSeqAli.qName)
      dm6.mrnaOrientInfo.name (via refSeqAli.qName)
      dm6.refFlat.name (via refSeqAli.qName)
      dm6.refGene.name (via refSeqAli.qName)
      dm6.xenoMrna.qName (via refSeqAli.qName)
      dm6.xenoRefGene.name (via refSeqAli.qName)
      dm6.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
62129050000019806+NR_167863290502905chr2R252869364802419481513022791,114,0,2791,4802419,4815016,
60637040000000+NR_167869370403704chr2R252869362862766286647013704,0,2862766,
6758750000000+NM_1443098750875chr2L2351371211843137118440121875,0,11843137,
58552480000083484-NM_078715524805248chr2L2351371298381857091506,109,443,643,106,1192,779,160,310,0,1506,1615,2058,2701,2807,3999,4778,4938,9838,11409,11778,12285,13519,13682,14932,17052,18260,
58553910000093341-NM_164349539105391chr2L23513712983818570101506,109,443,643,106,1192,779,160,143,310,0,1506,1615,2058,2701,2807,3999,4778,4938,5081,9838,11409,11778,12285,13519,13682,14932,17052,18025,18260,
58553150000096223-NM_001258872531505315chr2L23513712983821376101506,109,443,643,106,1192,779,160,136,241,0,1506,1615,2058,2701,2807,3999,4778,4938,5074,9838,11409,11778,12285,13519,13682,14932,17052,19879,21135,
58551790000086359-NM_001258873517905179chr2L2351371298382137691506,109,443,643,106,1192,779,160,241,0,1506,1615,2058,2701,2807,3999,4778,4938,9838,11409,11778,12285,13519,13682,14932,17052,21135,
58553900000096148-NM_001258874539005390chr2L23513712983821376101506,109,443,643,106,1192,779,160,141,311,0,1506,1615,2058,2701,2807,3999,4778,4938,5079,9838,11409,11778,12285,13519,13682,14932,17052,19879,21065,
585552800000106010-NM_001258875552805528chr2L23513712983821376111506,109,443,643,106,1192,779,160,136,143,311,0,1506,1615,2058,2701,2807,3999,4778,4938,5074,5217,9838,11409,11778,12285,13519,13682,14932,17052,19879,20830,21065,
58552810000086257-NM_001272858528105281chr2L2351371298382137691506,443,643,106,1192,779,160,141,311,0,1506,1949,2592,2698,3890,4669,4829,4970,9838,11778,12285,13519,13682,14932,17052,19879,21065,

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