Schema for xenoRefSeqAli
  Database: rheMac2    Primary Table: xenoRefSeqAli    Row Count: 350,277   Data last updated: 2016-02-16
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 1389int(10) unsigned range Number of bases that match that aren't repeats
misMatches 86int(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 78int(10) unsigned range Number of 'N' bases
qNumInsert 11int(10) unsigned range Number of inserts in query
qBaseInsert 343int(10) unsigned range Number of bases inserted in query
tNumInsert 7int(10) unsigned range Number of inserts in target
tBaseInsert 3130int(10) unsigned range Number of bases inserted in target
strand +-char(2) values + or - for strand. First character query, second target (optional)
qName NM_018942varchar(255) values Query sequence name
qSize 1896int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 1896int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 228252215int(10) unsigned range Target sequence size
tStart 23197int(10) unsigned range Alignment start position in target
tEnd 27880int(10) unsigned range Alignment end position in target
blockCount 14int(10) unsigned range Number of blocks in alignment
blockSizes 27,128,153,12,120,60,531,16...longblob   Size of each block
qStarts 0,32,161,411,477,609,806,13...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 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)
      rheMac2.all_est.qName (via xenoRefSeqAli.qName)
      rheMac2.all_mrna.qName (via xenoRefSeqAli.qName)
      rheMac2.refGene.name (via xenoRefSeqAli.qName)
      rheMac2.refSeqAli.qName (via xenoRefSeqAli.qName)
      rheMac2.xenoMrna.qName (via xenoRefSeqAli.qName)
      rheMac2.xenoRefFlat.name (via xenoRefSeqAli.qName)
      rheMac2.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
5851389860781134373130+-NM_018942189601896chr122825221523197278801427,128,153,12,120,60,531,164,150,27,39,17,68,57,0,32,161,411,477,609,806,1337,1532,1682,1711,1751,1769,1839,228224335,228224362,228224490,228224740,228224806,228227747,228227944,228228476,228228659,228228810,228228837,228228876,22822889 ...
585151690011511367+-NM_2049281481579950chr122825221523669242562189,31,579,919,228227959,228228515,
58553968066234233196+-NM_001108363150401015chr122825221523817276864114,117,285,157,0,261,573,858,228224529,228224808,228227944,228228241,
58552370069234033197+-NM_010445150801002chr122825221523824276834109,118,288,147,0,254,567,855,228224532,228224807,228227944,228228244,
58522734000000+-NM_001007985927537798chr122825221524010242711261,537,228227944,
5852004200122116+-NM_169763269118322096chr122825221524013242712206,36,1832,2060,228227944,228228166,
58519122000000+-NM_2055331131597810chr122825221524058242711213,597,228227944,
58516041000000+-NM_001113526849444645chr122825221524070242711201,444,228227944,
58514451000000+-NM_0010453711446410605chr122825221524073242681195,410,228227947,
58516926000000+-NM_2053861820413608chr122825221524073242681195,413,228227947,

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