Schema for xenoRefSeqAli
  Database: felCat3    Primary Table: xenoRefSeqAli    Row Count: 716,810   Data last updated: 2020-08-21
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 2201int(10) unsigned Number of bases that match that aren't repeats
misMatches 273int(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 8int(10) unsigned Number of inserts in query
qBaseInsert 2775int(10) unsigned Number of bases inserted in query
tNumInsert 23int(10) unsigned Number of inserts in target
tBaseInsert 45821int(10) unsigned Number of bases inserted in target
strand +-char(2) + or - for strand. First character query, second target (optional)
qName NM_001130823varchar(255) Query sequence name
qSize 5274int(10) unsigned Query sequence size
qStart 23int(10) unsigned Alignment start position in query
qEnd 5272int(10) unsigned Alignment end position in query
tName scaffold_100606varchar(255) Target sequence name
tSize 144313int(10) unsigned Target sequence size
tStart 78078int(10) unsigned Alignment start position in target
tEnd 126373int(10) unsigned Alignment end position in target
blockCount 24int(10) unsigned Number of blocks in alignment
blockSizes 112,110,223,73,3,69,37,86,3...longblob Size of each block
qStarts 23,169,279,546,619,622,699,...longblob Start of each block in query.
tStarts 17940,25614,25917,26778,269...longblob Start of each block in target.

Connected Tables and Joining Fields
        felCat3.all_est.qName (via xenoRefSeqAli.qName)
      felCat3.all_mrna.qName (via xenoRefSeqAli.qName)
      felCat3.refGene.name (via xenoRefSeqAli.qName)
      felCat3.refSeqAli.qName (via xenoRefSeqAli.qName)
      felCat3.xenoMrna.qName (via xenoRefSeqAli.qName)
      felCat3.xenoRefFlat.name (via xenoRefSeqAli.qName)
      felCat3.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
585220127300827752345821+-NM_0011308235274235272scaffold_1006061443137807812637324112,110,223,73,3,69,37,86,36,35,84,45,65,111,119,94,111,136,196,167,117,91,110,244,23,169,279,546,619,622,699,736,822,945,980,1098,1158,1223,1334,1453,1548,4211,4347,4543,4710,4827,4918,5028,17940,25614,25917,26778,26914,28362,31885,32299,34104,36914,37426,39639,39793,39959,42762,43162,43984,62624,63452,63981,64389,65 ...
585103119200225869029+-NM_0010353751600961577scaffold_0756515447156997354,137,113,159,176,232,52,96,450,587,701,860,1036,1525,59952,63876,64618,67886,68382,69624,70152,
58521417000024136++NM_0013843953175332563scaffold_1553582139304657250939362,92,77,332,394,486,46572,49739,50862,
585906172000058732+-NM_00130246750473021380scaffold_0756515847156576312,137,114,159,176,180,302,614,751,865,1024,1200,59994,63876,64618,67886,68382,69624,
585906172000058732+-NM_00130246849962511329scaffold_0756515847156576312,137,114,159,176,180,251,563,700,814,973,1149,59994,63876,64618,67886,68382,69624,
585906172000058732+-NM_01134152555101588scaffold_0756515847156576312,137,114,159,176,180,510,822,959,1073,1232,1408,59994,63876,64618,67886,68382,69624,
585900176001258734+-NM_13041214551011179scaffold_0756515847156576312,137,112,159,176,180,101,413,550,664,823,999,59994,63876,64618,67886,68382,69624,
58595416000211558712+-NM_00131958620852431472scaffold_0756515847156736328,137,113,171,185,180,243,571,708,822,1107,1292,59978,63876,64618,67886,68373,69624,
58564922300221468931+-NM_0010941422756671153scaffold_075651584815651751,171,138,155,178,3,176,67,218,389,641,796,974,977,60000,60136,63877,67888,68380,68560,69627,
585705220001268734+-NM_21308724065141441scaffold_0756515850155097164,137,112,4,157,177,174,514,678,815,927,931,1088,1267,60142,63876,64618,64838,67888,68382,69627,

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