Schema for xenoMrna
  Database: rheMac2    Primary Table: xenoMrna    Row Count: 5,979,259   Data last updated: 2016-02-16
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 1302int(10) unsigned Number of bases that match that aren't repeats
misMatches 103int(10) unsigned Number of bases that don't match
repMatches 0int(10) unsigned Number of bases that match but are part of repeats
nCount 75int(10) unsigned Number of 'N' bases
qNumInsert 9int(10) unsigned Number of inserts in query
qBaseInsert 391int(10) unsigned Number of bases inserted in query
tNumInsert 13int(10) unsigned Number of inserts in target
tBaseInsert 3200int(10) unsigned Number of bases inserted in target
strand +-char(2) + or - for strand. First character query, second target (optional)
qName M99587varchar(255) Query sequence name
qSize 1884int(10) unsigned Query sequence size
qStart 0int(10) unsigned Alignment start position in query
qEnd 1871int(10) unsigned Alignment end position in query
tName chr1varchar(255) Target sequence name
tSize 228252215int(10) unsigned Target sequence size
tStart 23200int(10) unsigned Alignment start position in target
tEnd 27880int(10) unsigned Alignment end position in target
blockCount 17int(10) unsigned Number of blocks in alignment
blockSizes 27,104,3,164,120,57,227,110...longblob Size of each block
qStarts 0,32,136,139,467,599,793,10...longblob Start of each block in query.
tStarts 228224335,228224362,2282244...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)
      rheMac2.all_est.qName (via xenoMrna.qName)
      rheMac2.all_mrna.qName (via xenoMrna.qName)
      rheMac2.refGene.name (via xenoMrna.qName)
      rheMac2.refSeqAli.qName (via xenoMrna.qName)
      rheMac2.xenoRefFlat.name (via xenoMrna.qName)
      rheMac2.xenoRefGene.name (via xenoMrna.qName)
      rheMac2.xenoRefSeqAli.qName (via xenoMrna.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
58513021030759391133200+-M99587188401871chr122825221523200278801727,104,3,164,120,57,227,110,161,59,104,53,96,29,27,85,54,0,32,136,139,467,599,793,1020,1130,1319,1378,1513,1566,1662,1702,1730,1817,228224335,228224362,228224467,228224472,228224806,228227747,228227944,228228172,228228285,228228476,228228536,228228659,22822871 ...
5856734005156133614++BC13977684924849chr12282522152333227710845,25,148,12,13,162,221,138,24,71,96,245,266,281,443,711,23332,23377,23403,23551,23563,23576,23739,27572,
585151690011511367+-AF0668611481579950chr122825221523669242562189,31,579,919,228227959,228228515,
58564831078430043109+-BC1600311108291086chr122825221523822276885116,12,120,60,449,29,242,308,440,637,228224527,228224740,228224806,228227747,228227944,
58551872069234033197+-BC1602071060341033chr122825221523827276834109,118,288,144,34,288,601,889,228224532,228224807,228227944,228228244,
58551770069234033197+-AF0093679990996chr122825221523830276834109,118,288,141,0,254,567,855,228224532,228224807,228227944,228228244,
5857623001591206+-HP13755435135193chr12282522152387024175272,27,35,166,228228040,228228318,
5852004200122116+-BT028828824427691chr122825221524013242712206,36,427,655,228227944,228228166,
5852004200122116+-BT028860824427691chr122825221524013242712206,36,427,655,228227944,228228166,
5852004200122116+-BT030410271018332097chr122825221524013242712206,36,1833,2061,228227944,228228166,

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