Schema for refSeqAli
  Database: strPur1    Primary Table: refSeqAli    Row Count: 934   Data last updated: 2020-02-07
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 390int(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 1int(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_214542varchar(255) values Query sequence name
qSize 392int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 392int(10) unsigned range Alignment end position in query
tName Scaffold100164varchar(255) values Target sequence name
tSize 823int(10) unsigned range Target sequence size
tStart 410int(10) unsigned range Alignment start position in target
tEnd 802int(10) unsigned range Alignment end position in target
blockCount 1int(10) unsigned range Number of blocks in alignment
blockSizes 392,longblob   Size of each block
qStarts 0,longblob   Start of each block in query.
tStarts 410,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)
      strPur1.all_mrna.qName (via refSeqAli.qName)
      strPur1.mrnaOrientInfo.name (via refSeqAli.qName)
      strPur1.refFlat.name (via refSeqAli.qName)
      strPur1.refGene.name (via refSeqAli.qName)
      strPur1.xenoRefGene.name (via refSeqAli.qName)
      strPur1.xenoRefSeqAli.qName (via refSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
5853901010000-NM_2145423920392Scaffold1001648234108021392,0,410,
5857110031111+NM_2145497150715Scaffold100275192239011053396,44,274,0,397,441,390,786,831,
5853741000000+NM_0010144263750375Scaffold1003019724838581375,0,483,
5853580092815-NM_2145453750375Scaffold100481132091312853311,6,50,0,318,325,913,1229,1235,
5856630000042691+NM_0012426776630663Scaffold1004925105620595239495142,117,173,119,112,0,142,259,432,551,20595,21402,21952,22897,23837,
58540814000023441+NM_00100190614910422Scaffold1006384253737896417593141,105,176,0,141,246,37896,40925,41583,
585144212001191276481-NM_21466512074778411150Scaffold1007963033923881738179,182,25,247,243,219,148,211,924,1103,1285,3222,3469,3712,3931,4079,238,1557,4354,4714,5694,6047,6606,7962,
5853901010000+NM_2145423920392Scaffold1012751517104914411392,0,1049,
5855460000011+NM_001165990168011331679Scaffold101279167401637102195,351,1133,1328,163,359,
585358614906553252419017+NM_001114194936352389363Scaffold101637279240228172895,145,189,166,88,135,201,106,155,123,226,171,117,206,119,49,123,159,20,146,119,159,169,87,115,64,189,159,5238,5333,5478,5667,5833,5921,6056,6257,6363,6518,6740,6966,7137,7254,7460,7580,7630,7753,7915,7935,8302,8421,8580,8749,8836,895 ...0,817,1318,2298,3306,3724,4906,5943,6399,7003,7445,8461,8749,10355,11217,11336,11385,11858,12017,12594,13715,14835,15585,16505,1 ...

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