Schema for refSeqAli
  Database: gasAcu1    Primary Table: refSeqAli    Row Count: 65   Data last updated: 2016-03-30
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 590smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 468int(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 3int(10) unsigned range Number of inserts in target
tBaseInsert 6617int(10) unsigned range Number of bases inserted in target
strand +char(2) values + or - for strand. First character query, second target (optional)
qName NM_001267687varchar(255) values Query sequence name
qSize 468int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 468int(10) unsigned range Alignment end position in query
tName chrIvarchar(255) values Target sequence name
tSize 28185914int(10) unsigned range Target sequence size
tStart 717456int(10) unsigned range Alignment start position in target
tEnd 724541int(10) unsigned range Alignment end position in target
blockCount 4int(10) unsigned range Number of blocks in alignment
blockSizes 141,48,153,126,longblob   Size of each block
qStarts 0,141,189,342,longblob   Start of each block in query.
tStarts 717456,718511,719636,724415,longblob   Start of each block in target.

Connected Tables and Joining Fields
        gasAcu1.all_est.qName (via refSeqAli.qName)
      gasAcu1.all_mrna.qName (via refSeqAli.qName)
      gasAcu1.mrnaOrientInfo.name (via refSeqAli.qName)
      gasAcu1.refFlat.name (via refSeqAli.qName)
      gasAcu1.refGene.name (via refSeqAli.qName)
      gasAcu1.xenoMrna.qName (via refSeqAli.qName)
      gasAcu1.xenoRefGene.name (via refSeqAli.qName)
      gasAcu1.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
5904680000036617+NM_0012676874680468chrI281859147174567245414141,48,153,126,0,141,189,342,717456,718511,719636,724415,
6731574028000181-NM_001267680160201602chrI2818591411579499115811822741,861,0,741,11579499,11580321,
7591611000001311785-NM_001267653161101611chrI28185914228167282283012414261,186,96,152,110,59,81,20,77,128,123,171,84,63,0,261,447,543,695,805,864,945,965,1042,1170,1293,1464,1548,22816728,22817099,22817593,22818725,22819114,22819500,22820101,22821375,22821841,22823937,22824178,22824414,22828354,22830061,
784295500000469484+NM_001267670295502955chrI2818591426108233261806725931,153,186,790,895,0,931,1084,1270,2060,26108233,26135238,26167171,26169677,26179777,
67519584601212153277+NM_001267646205202017chrII23295652118426091184789117276,193,151,148,167,138,137,125,74,74,48,270,35,13,25,123,8,0,276,469,620,768,935,1073,1210,1335,1409,1483,1541,1813,1848,1861,1886,2009,11842609,11844431,11844951,11845214,11845481,11845733,11846329,11846632,11847003,11847197,11847362,11847410,11847683,11847719,11 ...
74622700022947737-NM_0012676315400521chrII232956522117581121176775915,39,39,3,20,6,15,16,74,19,34,73,112,115,135,142,157,466,21175811,21175827,21175867,21175907,21175911,21175932,21175938,21175954,21176701,
751113705100000+NM_001267676118801188chrII23295652217690562177024411188,0,21769056,
587207660000114255-NM_001267662208202082chrIII1679850629898230531912615,392,128,112,65,58,38,136,106,176,233,23,0,615,1007,1135,1247,1312,1370,1408,1544,1650,1826,2059,298982,299794,300714,300972,301177,301400,301542,301665,302192,303117,304018,305296,
610408000003551-NM_0012676824080408chrIV32632948330480633057654111,147,39,111,0,111,258,297,3304806,3305032,3305517,3305654,
610393000003282-NM_0012676833930393chrIV32632948330792833086034108,126,36,123,0,108,234,270,3307928,3308110,3308338,3308480,

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