Schema for refSeqAli
  Database: criGri1    Primary Table: refSeqAli    Row Count: 555   Data last updated: 2020-05-06
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 131int(10) unsigned range Number of bases that match that aren't repeats
misMatches 1int(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 NM_001246827varchar(255) values Query sequence name
qSize 1871int(10) unsigned range Query sequence size
qStart 281int(10) unsigned range Alignment start position in query
qEnd 413int(10) unsigned range Alignment end position in query
tName AMDS01167778varchar(255) values Target sequence name
tSize 213int(10) unsigned range Target sequence size
tStart 81int(10) unsigned range Alignment start position in target
tEnd 213int(10) unsigned range Alignment end position in target
blockCount 1int(10) unsigned range Number of blocks in alignment
blockSizes 132,longblob   Size of each block
qStarts 1458,longblob   Start of each block in query.
tStarts 81,longblob   Start of each block in target.

Connected Tables and Joining Fields
        criGri1.all_est.qName (via refSeqAli.qName)
      criGri1.all_mrna.qName (via refSeqAli.qName)
      criGri1.mrnaOrientInfo.name (via refSeqAli.qName)
      criGri1.refFlat.name (via refSeqAli.qName)
      criGri1.refGene.name (via refSeqAli.qName)
      criGri1.xenoMrna.qName (via refSeqAli.qName)
      criGri1.xenoRefGene.name (via refSeqAli.qName)
      criGri1.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
5851311000000-NM_0012468271871281413AMDS01167778213812131132,1458,81,
585903000011+NM_001246827187114107AMDS01171878227195235,58,14,49,1,37,
5851192000000-NM_0012468049640121AMDS011841403261552761121,843,155,
585880000000-NR_04513488088AMDS01189071451112200188,0,112,
585870000000+NR_04513587087AMDS01189430467146233187,0,146,
585192000001257+NM_0012440221746478670AMDS011921306470449231,161,478,509,0,288,
5854301000000+NM_001244022174613151746AMDS011925856972576881431,1315,257,
5851060000000-NM_0012440221746667773AMDS0119277270001061106,973,0,
58510792000000+NM_0012440881462481129AMDS0119471210810108111081,48,0,
585466000002967+NM_001244022174645511AMDS011956371448014333148,166,152,45,193,359,0,412,1281,

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