Schema for xenoMrna
  Database: rn3    Primary Table: xenoMrna    Row Count: 6,789,755   Data last updated: 2018-12-08
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 73smallint(5) unsigned Indexing field to speed chromosome range queries.
matches 1579int(10) unsigned Number of bases that match that aren't repeats
misMatches 295int(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 9int(10) unsigned Number of inserts in query
qBaseInsert 1406int(10) unsigned Number of bases inserted in query
tNumInsert 11int(10) unsigned Number of inserts in target
tBaseInsert 311124int(10) unsigned Number of bases inserted in target
strand ++char(2) + or - for strand. First character query, second target (optional)
qName AF011426varchar(255) Query sequence name
qSize 3896int(10) unsigned Query sequence size
qStart 233int(10) unsigned Alignment start position in query
qEnd 3513int(10) unsigned Alignment end position in query
tName chr1varchar(255) Target sequence name
tSize 268121971int(10) unsigned Target sequence size
tStart 8989int(10) unsigned Alignment start position in target
tEnd 321987int(10) unsigned Alignment end position in target
blockCount 13int(10) unsigned Number of blocks in alignment
blockSizes 809,2,219,124,241,159,102,1...longblob Size of each block
qStarts 233,1042,1044,1264,1388,163...longblob Start of each block in query.
tStarts 8989,9803,10773,14683,16491...longblob Start of each block in target.

Connected Tables and Joining Fields
        hgFixed.gbCdnaInfo.acc (via xenoMrna.qName)
      hgFixed.gbMiscDiff.acc (via xenoMrna.qName)
      hgFixed.gbSeq.acc (via xenoMrna.qName)
      hgFixed.gbWarn.acc (via xenoMrna.qName)
      hgFixed.imageClone.acc (via xenoMrna.qName)
      rn3.all_est.qName (via xenoMrna.qName)
      rn3.all_mrna.qName (via xenoMrna.qName)
      rn3.refGene.name (via xenoMrna.qName)
      rn3.refSeqAli.qName (via xenoMrna.qName)
      rn3.xenoRefFlat.name (via xenoMrna.qName)
      rn3.xenoRefGene.name (via xenoMrna.qName)
      rn3.xenoRefSeqAli.qName (via xenoMrna.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
731579295009140611311124++AF01142638962333513chr1268121971898932198713809,2,219,124,241,159,102,11,7,11,11,111,67,233,1042,1044,1264,1388,1631,2488,2657,2674,2767,2872,2958,3446,8989,9803,10773,14683,16491,16732,17476,17637,17652,17749,17851,17941,321920,
73931170028100611439261++AK03968930163002409chr12681219711221545257912126,83,59,98,89,39,90,21,47,223,124,104,300,426,548,607,777,876,974,1083,1125,1228,1451,2305,12215,107272,109958,314246,314416,314516,316236,316374,316414,316521,317975,452475,
58576150012812494+-JU57201756474193chr12681219711349816083245,46,74,147,268105888,268108427,
58575190170000+-LE216231548100211chr126812197113668137791111,100,268108192,
5859651001121100155++LE57786935142201chr1268121971146801149822114,33,42,168,14680,114949,
58515390000000++LE399469361114357chr126812197116102163451243,114,16102,
5855013000000+-LE331630271063chr12681219711614616209163,0,268105762,
58522711500148148++JN80573941116406chr126812197116261166512117,225,16,181,16261,16426,
58514874000000++JN805736411181403chr126812197116426166481222,181,16426,
585408000000++JT843713222172220chr12681219719484594893148,172,94845,

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