Schema for xenoRefSeqAli
  Database: caePb1    Primary Table: xenoRefSeqAli    Row Count: 298,212   Data last updated: 2020-08-20
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 1766int(10) unsigned range Number of bases that match that aren't repeats
misMatches 543int(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 91int(10) unsigned range Number of 'N' bases
qNumInsert 9int(10) unsigned range Number of inserts in query
qBaseInsert 162int(10) unsigned range Number of bases inserted in query
tNumInsert 19int(10) unsigned range Number of inserts in target
tBaseInsert 2091int(10) unsigned range Number of bases inserted in target
strand +-char(2) values + or - for strand. First character query, second target (optional)
qName NM_076416varchar(255) values Query sequence name
qSize 2562int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 2562int(10) unsigned range Alignment end position in query
tName chrUnvarchar(255) values Target sequence name
tSize 207333000int(10) unsigned range Target sequence size
tStart 4676int(10) unsigned range Alignment start position in target
tEnd 9167int(10) unsigned range Alignment end position in target
blockCount 20int(10) unsigned range Number of blocks in alignment
blockSizes 102,90,90,98,130,90,105,135...longblob   Size of each block
qStarts 0,105,207,303,401,567,681,7...longblob   Start of each block in query.
tStarts 207323833,207323989,2073241...longblob   Start of each block in target.

Connected Tables and Joining Fields
        caePb1.all_mrna.qName (via xenoRefSeqAli.qName)
      caePb1.xenoMrna.qName (via xenoRefSeqAli.qName)
      caePb1.xenoRefFlat.name (via xenoRefSeqAli.qName)
      caePb1.xenoRefGene.name (via xenoRefSeqAli.qName)
      hgFixed.gbCdnaInfo.acc (via xenoRefSeqAli.qName)
      hgFixed.gbMiscDiff.acc (via xenoRefSeqAli.qName)
      hgFixed.gbSeq.acc (via xenoRefSeqAli.qName)
      hgFixed.gbWarn.acc (via xenoRefSeqAli.qName)
      hgFixed.imageClone.acc (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
58517665430919162192091+-NM_076416256202562chrUn2073330004676916720102,90,90,98,130,90,105,135,421,2,76,83,296,37,81,207,3,102,91,161,0,105,207,303,401,567,681,786,924,1345,1347,1423,1506,1802,1872,1959,2166,2169,2310,2401,207323833,207323989,207324150,207324295,207324436,207324647,207324807,207325079,207325264,207325715,207325732,207325856,20732598 ...
77634720101921622156+-NM_00137536539935331262chrUn20733300025164656251653793174,306,87,533,788,1175,182167621,182167870,182168257,
5991156279005425142342++NM_171632186861866chrUn207333000195528819590651585,262,66,102,144,77,42,69,90,281,99,56,17,24,21,6,91,356,422,524,668,745,815,884,975,1256,1355,1411,1538,1845,1955288,1955678,1955992,1956105,1956253,1956493,1957015,1957140,1957345,1958067,1958397,1958499,1958560,1958684,1959044,
1114168400240011++NM_001384271992445654797chrUn20733300069456025694562582181,51,4565,4746,69456025,69456207,
585944001300++NR_07094511110111chrUn2073330002351923617215,83,10,28,23519,23534,
162115563019157192+-NM_0013805911071192486chrUn207333000135859148135859477245,192,192,294,71473523,71473660,
162149819501921702236++NM_07227717616061488chrUn2073330001358514881358524363249,241,222,606,999,1266,135851488,135851887,135852214,
1621765259023512565878++NM_001383324238322305chrUn2073330001358528121358547376135,75,267,174,258,138,2,748,1219,1681,1864,2167,135852812,135852984,135853587,135854067,135854296,135854599,
5858610001112++NR_07094714128125chrUn2073330003151531613260,36,28,89,31515,31577,
585116900136131++NR_070949279105266chrUn2073330003524435400278,47,105,219,35244,35353,

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