Schema for refSeqAli
  Database: aptMan1    Primary Table: refSeqAli    Row Count: 1   Data last updated: 2015-12-22
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 586smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 1553int(10) unsigned range Number of bases that match that aren't repeats
misMatches 6int(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 7int(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 7int(10) unsigned range Number of inserts in target
tBaseInsert 45805int(10) unsigned range Number of bases inserted in target
strand +char(2) values + or - for strand. First character query, second target (optional)
qName NM_001315498varchar(255) values Query sequence name
qSize 1566int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 1566int(10) unsigned range Alignment end position in query
tName NW_013989391v1varchar(255) values Target sequence name
tSize 307878int(10) unsigned range Target sequence size
tStart 205389int(10) unsigned range Alignment start position in target
tEnd 252760int(10) unsigned range Alignment end position in target
blockCount 8int(10) unsigned range Number of blocks in alignment
blockSizes 147,95,120,148,153,92,227,584,longblob   Size of each block
qStarts 0,147,242,362,510,663,755,982,longblob   Start of each block in query.
tStarts 205389,210620,213814,214713...longblob   Start of each block in target.

Connected Tables and Joining Fields
        aptMan1.all_mrna.qName (via refSeqAli.qName)
      aptMan1.mrnaOrientInfo.name (via refSeqAli.qName)
      aptMan1.refFlat.name (via refSeqAli.qName)
      aptMan1.refGene.name (via refSeqAli.qName)
      aptMan1.xenoRefGene.name (via refSeqAli.qName)
      aptMan1.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
586155360700745805+NM_001315498156601566NW_013989391v13078782053892527608147,95,120,148,153,92,227,584,0,147,242,362,510,663,755,982,205389,210620,213814,214713,219284,232189,242642,252176,

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