Schema for refSeqAli
  Database: calJac4    Primary Table: refSeqAli    Row Count: 237   Data last updated: 2020-09-21
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 1425smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 917int(10) unsigned range Number of bases that match that aren't repeats
misMatches 3int(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 5int(10) unsigned range Number of inserts in target
tBaseInsert 11375int(10) unsigned range Number of bases inserted in target
strand +char(2) values + or - for strand. First character query, second target (optional)
qName NM_001267747varchar(255) values Query sequence name
qSize 957int(10) unsigned range Query sequence size
qStart 37int(10) unsigned range Alignment start position in query
qEnd 957int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 217961735int(10) unsigned range Target sequence size
tStart 110217345int(10) unsigned range Alignment start position in target
tEnd 110229640int(10) unsigned range Alignment end position in target
blockCount 6int(10) unsigned range Number of blocks in alignment
blockSizes 63,342,288,108,60,59,longblob   Size of each block
qStarts 37,100,442,730,838,898,longblob   Start of each block in query.
tStarts 110217345,110218319,1102245...longblob   Start of each block in target.

Connected Tables and Joining Fields
        calJac4.all_est.qName (via refSeqAli.qName)
      calJac4.all_mrna.qName (via refSeqAli.qName)
      calJac4.mrnaOrientInfo.name (via refSeqAli.qName)
      calJac4.refFlat.name (via refSeqAli.qName)
      calJac4.refGene.name (via refSeqAli.qName)
      calJac4.xenoMrna.qName (via refSeqAli.qName)
      calJac4.xenoRefGene.name (via refSeqAli.qName)
      calJac4.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
142591730000511375+NM_00126774795737957chr1217961735110217345110229640663,342,288,108,60,59,37,100,442,730,838,898,110217345,110218319,110224511,110227154,110228424,110229581,
2222796300117311296+NM_001205006280002800chr1217961735156301062156615157959,46,81,131,115,22,102,1235,1008,0,59,105,186,317,432,454,556,1792,156301062,156462005,156539496,156552840,156594668,156596008,156602446,156612914,156614149,
22273555001812520238+NM_001371508736907368chr12179617351563010621568286601459,46,81,131,115,22,102,86,2416,179,39,1021,2597,466,0,59,105,186,317,432,454,556,642,3058,3237,3276,4297,6902,156301062,156462005,156539496,156552840,156594668,156596008,156602446,156675505,156792788,156812068,156818036,156824575,15682559 ...
2226950400185117387+NM_001204128696306962chr12179617351567043191568286607236,2416,179,39,1021,2597,466,0,236,2652,2831,2870,3891,6496,156704319,156792788,156812068,156818036,156824575,156825597,156828194,
2226809400184117426+NM_001371507682106821chr12179617351567044181568286576137,2416,179,1021,2597,463,0,137,2553,2732,3753,6358,156704418,156792788,156812068,156824575,156825597,156828194,
1792225130000416629+NM_001204974225402254chr12179617351582477751582666585391,153,471,1229,10,0,391,544,1015,2244,158247775,158260914,158263198,158265418,158266648,
179212500000026556+NM_001204975125001250chr12179617351582754471582832533142,132,976,0,142,274,158275447,158279874,158282277,
18672138100045618613-NM_001267732215302153chr121796173516813558616815634710331,638,18,10,705,138,117,66,36,89,0,333,972,991,1002,1707,1845,1962,2028,2064,168135586,168135918,168136556,168136574,168136584,168141097,168148841,168149983,168152036,168156258,
201816150000082581+NM_001204438161501615chr12179617351878949511878991479228,172,153,161,177,142,188,142,252,0,228,400,553,714,891,1033,1221,1363,187894951,187895838,187896537,187896778,187897397,187897728,187898083,187898656,187898895,
21106871000042055-NM_0011999316880688chr12179617351998884491998911925351,79,35,36,187,0,351,430,465,501,199888449,199888879,199889312,199889562,199891005,

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