Schema for refSeqAli
  Database: sarHar1    Primary Table: refSeqAli    Row Count: 72   Data last updated: 2016-04-05
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 601smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 150int(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_105676varchar(255) values Query sequence name
qSize 150int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 150int(10) unsigned range Alignment end position in query
tName chr1_GL834484_randomvarchar(255) values Target sequence name
tSize 3839433int(10) unsigned range Target sequence size
tStart 2121689int(10) unsigned range Alignment start position in target
tEnd 2121839int(10) unsigned range Alignment end position in target
blockCount 1int(10) unsigned range Number of blocks in alignment
blockSizes 150,longblob   Size of each block
qStarts 0,longblob   Start of each block in query.
tStarts 2121689,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)
      sarHar1.all_mrna.qName (via refSeqAli.qName)
      sarHar1.mrnaOrientInfo.name (via refSeqAli.qName)
      sarHar1.refFlat.name (via refSeqAli.qName)
      sarHar1.refGene.name (via refSeqAli.qName)
      sarHar1.xenoMrna.qName (via refSeqAli.qName)
      sarHar1.xenoRefGene.name (via refSeqAli.qName)
      sarHar1.xenoRefSeqAli.qName (via refSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
6011500000000+NR_1056761500150chr1_GL834484_random3839433212168921218391150,0,2121689,
6031100000000+NR_1056771100110chr1_GL834637_random2638213248583424859441110,0,2485834,
5921500000000+NR_1056781500150chr1_GL834650_random2003497102444610245961150,0,1024446,
6041500000000+NR_1056791500150chr1_GL834659_random3630962257423925743891150,0,2574239,
5891500000000-NR_1056801500150chr1_GL834685_random6586856382106383601150,0,638210,
5901500000000+NR_1056821500150chr1_GL834730_random13233007410117411611150,0,741011,
5921500000000+NR_1056831500150chr1_GL834734_random1590404100376310039131150,0,1003763,
5921500000000+NR_1056841500150chr1_GL834734_random1590404101994110200911150,0,1019941,
5991500000000+NR_1056851500150chr1_GL834769_random1938635190949919096491150,0,1909499,
5851500000000+NR_1056861500150chr1_GL834949_random145045422143711150,0,4221,

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