Schema for all_est
  Database: galGal3    Primary Table: all_est    Row Count: 619,129   Data last updated: 2020-05-08
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 870smallint(5) unsigned Indexing field to speed chromosome range queries.
matches 511int(10) unsigned Number of bases that match that aren't repeats
misMatches 1int(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 5int(10) unsigned Number of inserts in query
qBaseInsert 8int(10) unsigned Number of bases inserted in query
tNumInsert 21int(10) unsigned Number of inserts in target
tBaseInsert 3027int(10) unsigned Number of bases inserted in target
strand +char(2) + or - for strand. First character query, second target (optional)
qName AA495708varchar(255) Query sequence name
qSize 529int(10) unsigned Query sequence size
qStart 0int(10) unsigned Alignment start position in query
qEnd 520int(10) unsigned Alignment end position in query
tName chr1varchar(255) Target sequence name
tSize 200994015int(10) unsigned Target sequence size
tStart 37380327int(10) unsigned Alignment start position in target
tEnd 37383866int(10) unsigned Alignment end position in target
blockCount 22int(10) unsigned Number of blocks in alignment
blockSizes 24,86,77,113,63,17,13,13,14...longblob Size of each block
qStarts 0,24,110,187,300,363,380,39...longblob Start of each block in query.
tStarts 37380327,37380812,37381342,...longblob Start of each block in target.

Connected Tables and Joining Fields
        galGal3.all_mrna.qName (via all_est.qName)
      galGal3.est.qName (via all_est.qName)
      galGal3.estOrientInfo.name (via all_est.qName)
      galGal3.intronEst.qName (via all_est.qName)
      galGal3.refGene.name (via all_est.qName)
      galGal3.refSeqAli.qName (via all_est.qName)
      galGal3.xenoMrna.qName (via all_est.qName)
      galGal3.xenoRefGene.name (via all_est.qName)
      galGal3.xenoRefSeqAli.qName (via all_est.qName)
      hgFixed.gbCdnaInfo.acc (via all_est.qName)
      hgFixed.gbMiscDiff.acc (via all_est.qName)
      hgFixed.gbSeq.acc (via all_est.qName)
      hgFixed.gbWarn.acc (via all_est.qName)
      hgFixed.imageClone.acc (via all_est.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
87051110058213027+AA4957085290520chr120099401537380327373838662224,86,77,113,63,17,13,13,14,7,5,7,6,7,9,5,7,5,9,11,5,9,0,24,110,187,300,363,380,393,409,423,430,436,443,451,458,467,473,480,486,495,506,511,37380327,37380812,37381342,37382453,37383443,37383507,37383525,37383539,37383557,37383573,37383581,37383588,37383596,37383607,37 ...
1199271000137104-AA495701510193467chr1200994015805125678051294289,5,17,15,15,71,56,83,43,52,57,77,92,107,178,234,80512567,80512593,80512599,80512621,80512637,80512653,80512725,80512859,
155247321011623586-AA4957195710548chr12009940151267740061267750784174,216,52,44,23,197,413,527,126774006,126774181,126774676,126775034,
7423496048336206-AA495715561131523chr11219280952070673920707304117,7,28,12,4,9,24,12,62,69,125,38,46,56,84,97,104,115,144,157,219,305,20706739,20706746,20706754,20706855,20706867,20706872,20706881,20706908,20706920,20707094,20707179,
589569101234486+AA4956965750574chr199939723645459646516612,41,133,232,146,7,0,12,55,188,420,567,645459,645651,645695,646020,646363,646509,
698422301297927+AA49569955047482chr21548737671493381114935164885,41,246,4,18,14,13,5,47,132,173,419,423,448,464,477,14933811,14933897,14934846,14935093,14935098,14935127,14935145,14935159,
66743530911652051+AA4957044630463chr20139862351084817610850674668,36,133,151,24,35,0,68,120,253,404,428,10848176,10849417,10849464,10850171,10850614,10850639,
6264170022261010+AA4957005430421chr23604221754877655489194753,22,53,148,90,49,4,0,53,76,129,277,368,417,5487765,5487819,5487843,5488464,5489048,5489140,5489190,
6085330011157240+AA49571457136571chr26510243830694483077222772,84,69,57,141,56,55,36,108,192,261,318,459,516,3069448,3072034,3073502,3074479,3075158,3077111,3077167,
61047810744661682+AA4957186350532chr27484197033125723314740930,126,162,63,40,16,6,17,26,0,30,156,318,383,423,440,448,506,3312572,3313103,3313609,3314274,3314337,3314378,3314394,3314401,3314714,

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