Schema for refSeqAli
  Database: monDom4    Primary Table: refSeqAli    Row Count: 1,242   Data last updated: 2020-08-22
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 611smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 54int(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_127441varchar(255) values Query sequence name
qSize 54int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 54int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 748055161int(10) unsigned range Target sequence size
tStart 3445802int(10) unsigned range Alignment start position in target
tEnd 3445856int(10) unsigned range Alignment end position in target
blockCount 1int(10) unsigned range Number of blocks in alignment
blockSizes 54,longblob   Size of each block
qStarts 0,longblob   Start of each block in query.
tStarts 3445802,longblob   Start of each block in target.

Connected Tables and Joining Fields
        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)
      monDom4.all_est.qName (via refSeqAli.qName)
      monDom4.all_mrna.qName (via refSeqAli.qName)
      monDom4.mrnaOrientInfo.name (via refSeqAli.qName)
      monDom4.refFlat.name (via refSeqAli.qName)
      monDom4.refGene.name (via refSeqAli.qName)
      monDom4.xenoMrna.qName (via refSeqAli.qName)
      monDom4.xenoRefGene.name (via refSeqAli.qName)
      monDom4.xenoRefSeqAli.qName (via refSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
611540000000+NR_12744154054chr174805516134458023445856154,0,3445802,
624640000000+NR_12747164064chr174805516152091145209178164,0,5209114,
678590000000-NR_12744459059chr17480551611225848712258546159,0,12258487,
752550000000+NR_12743255055chr17480551612193212221932177155,0,21932122,
1103440000000+NR_12744044044chr17480551616794068367940727144,0,67940683,
11391010000000+NR_0349581010101chr174805516172640993726410941101,0,72640993,
1441964500001131143-NM_001032979197891978chr1748055161750867897511990112300,164,84,264,109,133,124,72,171,135,175,238,0,300,464,548,812,921,1054,1178,1250,1421,1556,1731,75086789,75087090,75087938,75094834,75099000,75101399,75102809,75103522,75106179,75110035,75112614,75119663,
1210840000000+NR_03216284084chr17480551618198110581981189184,0,81981105,
1421680000000-NR_03497868068chr1748055161109630335109630403168,0,109630335,
1421620000000+NR_12756962062chr1748055161109663247109663309162,0,109663247,

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