Schema for xenoRefSeqAli
  Database: panTro1    Primary Table: xenoRefSeqAli    Row Count: 508,887   Data last updated: 2020-08-23
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 585smallint(5) unsigned Indexing field to speed chromosome range queries.
matches 1603int(10) unsigned Number of bases that match that aren't repeats
misMatches 34int(10) unsigned Number of bases that don't match
repMatches 0int(10) unsigned Number of bases that match but are part of repeats
nCount 0int(10) unsigned Number of 'N' bases
qNumInsert 1int(10) unsigned Number of inserts in query
qBaseInsert 15int(10) unsigned Number of bases inserted in query
tNumInsert 12int(10) unsigned Number of inserts in target
tBaseInsert 914int(10) unsigned Number of bases inserted in target
strand ++char(2) + or - for strand. First character query, second target (optional)
qName NR_034090varchar(255) Query sequence name
qSize 1652int(10) unsigned Query sequence size
qStart 0int(10) unsigned Alignment start position in query
qEnd 1652int(10) unsigned Alignment end position in query
tName chr1varchar(255) Target sequence name
tSize 229575298int(10) unsigned Target sequence size
tStart 1745int(10) unsigned Alignment start position in target
tEnd 4296int(10) unsigned Alignment end position in target
blockCount 13int(10) unsigned Number of blocks in alignment
blockSizes 354,109,38,541,265,7,25,12,...longblob Size of each block
qStarts 0,354,463,501,1042,1307,131...longblob Start of each block in query.
tStarts 1745,2483,3091,3130,3673,39...longblob Start of each block in target.

Connected Tables and Joining Fields
        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)
      panTro1.all_est.qName (via xenoRefSeqAli.qName)
      panTro1.all_mrna.qName (via xenoRefSeqAli.qName)
      panTro1.refGene.name (via xenoRefSeqAli.qName)
      panTro1.refSeqAli.qName (via xenoRefSeqAli.qName)
      panTro1.xenoMrna.qName (via xenoRefSeqAli.qName)
      panTro1.xenoRefFlat.name (via xenoRefSeqAli.qName)
      panTro1.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
5851603340011512914++NR_034090165201652chr12295752981745429613354,109,38,541,265,7,25,12,15,9,6,3,253,0,354,463,501,1042,1307,1314,1354,1366,1381,1390,1396,1399,1745,2483,3091,3130,3673,3939,3948,3992,4005,4022,4032,4039,4043,
5851596310012512924++NR_045117165201652chr12295752981745429613354,109,38,541,265,7,15,12,15,9,6,3,253,0,354,463,501,1042,1307,1314,1354,1366,1381,1390,1396,1399,1745,2483,3091,3130,3673,3939,3948,3992,4005,4022,4032,4039,4043,
5851603340011512914++NR_046018165201652chr12295752981745429613354,109,38,541,265,7,25,12,15,9,6,3,253,0,354,463,501,1042,1307,1314,1354,1366,1381,1390,1396,1399,1745,2483,3091,3130,3673,3939,3948,3992,4005,4022,4032,4039,4043,
58514433000115111078++NR_051985148801488chr12295752981745429612354,127,397,265,7,25,12,15,9,6,3,253,0,354,481,878,1143,1150,1190,1202,1217,1226,1232,1235,1745,2465,3274,3673,3939,3948,3992,4005,4022,4032,4039,4043,
5851600400011512914++NR_051986165501655chr12295752981745429913354,109,38,541,265,7,25,12,15,9,6,3,256,0,354,463,501,1042,1307,1314,1354,1366,1381,1390,1396,1399,1745,2483,3091,3130,3673,3939,3948,3992,4005,4022,4032,4039,4043,
5851558350025011961++NR_110561164301643chr12295752981745429912354,109,38,541,263,12,15,9,5,3,102,142,0,354,463,501,1042,1354,1366,1381,1391,1396,1399,1501,1745,2483,3091,3130,3673,3992,4005,4022,4033,4039,4043,4157,
585102360011082939++NM_001007319375324332679chr122957529820523129345,55,38,2433,2586,2641,2052,2868,3091,
58515756001333864++NM_001170825369430873333chr122957529820523129444,88,43,38,3087,3131,3252,3295,2052,2480,2880,3091,
585161425002831814374+-NR_0245401786471769chr122957529842482026119152,46,23,35,147,137,136,78,61,59,16,106,42,62,71,134,184,56,94,47,199,245,268,303,450,587,723,801,862,921,974,1080,1122,1230,1301,1435,1619,1675,229555037,229560708,229560755,229560779,229561021,229567037,229567413,229567726,229567805,229567867,229568018,229568080,22956884 ...
5852003420042612118961+-NR_00365925902482554chr122957529842482525422157,144,99,152,46,23,35,147,9,124,136,78,61,63,16,106,105,71,134,184,61,94,248,405,575,826,978,1024,1047,1082,1229,1238,1362,1498,1576,1637,1700,1753,1859,2010,2081,2215,2399,2460,229550044,229550202,229550365,229555037,229560708,229560755,229560779,229561021,229567037,229567050,229567413,229567726,22956780 ...

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