Schema for all_mrna
  Database: oryLat2    Primary Table: all_mrna    Row Count: 1,315   Data last updated: 2020-08-19
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 587smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 353int(10) unsigned range Number of bases that match that aren't repeats
misMatches 2int(10) unsigned range Number of bases that don't match
repMatches 20int(10) unsigned range Number of bases that match but are part of repeats
nCount 0int(10) unsigned range Number of 'N' bases
qNumInsert 0int(10) unsigned range Number of inserts in query
qBaseInsert 0int(10) unsigned range Number of bases inserted in query
tNumInsert 0int(10) unsigned range Number of inserts in target
tBaseInsert 0int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName AB435638varchar(255) values Query sequence name
qSize 375int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 375int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 39973033int(10) unsigned range Target sequence size
tStart 297266int(10) unsigned range Alignment start position in target
tEnd 297641int(10) unsigned range Alignment end position in target
blockCount 1int(10) unsigned range Number of blocks in alignment
blockSizes 375,longblob   Size of each block
qStarts 0,longblob   Start of each block in query.
tStarts 297266,longblob   Start of each block in target.

Connected Tables and Joining Fields
        hgFixed.gbCdnaInfo.acc (via all_mrna.qName)
      hgFixed.gbMiscDiff.acc (via all_mrna.qName)
      hgFixed.gbSeq.acc (via all_mrna.qName)
      hgFixed.gbWarn.acc (via all_mrna.qName)
      hgFixed.imageClone.acc (via all_mrna.qName)
      oryLat2.all_est.qName (via all_mrna.qName)
      oryLat2.mrnaOrientInfo.name (via all_mrna.qName)
      oryLat2.refGene.name (via all_mrna.qName)
      oryLat2.refSeqAli.qName (via all_mrna.qName)
      oryLat2.xenoMrna.qName (via all_mrna.qName)
      oryLat2.xenoRefGene.name (via all_mrna.qName)
      oryLat2.xenoRefSeqAli.qName (via all_mrna.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
58735322000000-AB4356383750375chr1399730332972662976411375,0,297266,
5921037095000813360-EF544584113201132chr1399730339709629854549121,136,129,169,101,135,105,65,171,0,121,257,386,555,656,791,896,961,970962,972711,973861,978165,979552,979824,980836,984340,985283,
59535322000000+AB4356383750375chr139973033131857413189491375,0,1318574,
59535502000000-AB4356383750375chr139973033136121913615941375,0,1361219,
601561120300233155+AJ6352285850585chr139973033212756821613083188,232,165,0,188,420,2127568,2140494,2161143,
6028412201121394+AB2482748460846chr13997303322600942262333435,172,155,483,0,36,208,363,2260094,2260129,2260411,2261850,
60435502000000+AB4356383750375chr139973033250516425055391375,0,2505164,
60735502000000-AB4356383750375chr139973033293988429402591375,0,2939884,
60735322000000-AB4356383750375chr139973033294774529481201375,0,2947745,
63111400270133675466-AB693199120001200chr139973033605152861281617109,326,94,140,194,201,103,0,109,435,529,669,863,1097,6051528,6056494,6061064,6072534,6081809,6083343,6128058,

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