Schema for all_mrna
  Database: ci2    Primary Table: all_mrna    Row Count: 8,543   Data last updated: 2020-08-21
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 1828int(10) unsigned range Number of bases that match that aren't repeats
misMatches 11int(10) unsigned range Number of bases that don't match
repMatches 21int(10) unsigned range Number of bases that match but are part of repeats
nCount 5int(10) unsigned range Number of 'N' bases
qNumInsert 1int(10) unsigned range Number of inserts in query
qBaseInsert 1int(10) unsigned range Number of bases inserted in query
tNumInsert 10int(10) unsigned range Number of inserts in target
tBaseInsert 5142int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName AK112464varchar(255) values Query sequence name
qSize 1883int(10) unsigned range Query sequence size
qStart 1int(10) unsigned range Alignment start position in query
qEnd 1867int(10) unsigned range Alignment end position in query
tName chr01pvarchar(255) values Target sequence name
tSize 6220112int(10) unsigned range Target sequence size
tStart 13853int(10) unsigned range Alignment start position in target
tEnd 20860int(10) unsigned range Alignment end position in target
blockCount 12int(10) unsigned range Number of blocks in alignment
blockSizes 503,70,142,129,54,102,159,1...longblob   Size of each block
qStarts 16,520,590,732,861,915,1017...longblob   Start of each block in query.
tStarts 13853,14356,14427,14991,154...longblob   Start of each block in target.

Connected Tables and Joining Fields
        ci2.all_est.qName (via all_mrna.qName)
      ci2.mrnaOrientInfo.name (via all_mrna.qName)
      ci2.refGene.name (via all_mrna.qName)
      ci2.refSeqAli.qName (via all_mrna.qName)
      ci2.xenoMrna.qName (via all_mrna.qName)
      ci2.xenoRefGene.name (via all_mrna.qName)
      ci2.xenoRefSeqAli.qName (via all_mrna.qName)
      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)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
58518281121511105142-AK112464188311867chr01p6220112138532086012503,70,142,129,54,102,159,171,180,124,184,47,16,520,590,732,861,915,1017,1176,1347,1527,1651,1835,13853,14356,14427,14991,15405,15554,15976,16672,19012,19817,20295,20813,
58537756700012+AK114304148110201469chr01p622011251544519952371,78,1020,1391,51544,51917,
5853771523000012+AK114191174811101732chr01p622011251544521682371,251,1110,1481,51544,51917,
586291221191029145037-AK113258314703133chr01p622011215212516028616125,32,91,795,180,159,143,211,128,159,104,83,503,136,181,94,14,140,172,271,1066,1246,1405,1548,1759,1887,2046,2150,2233,2736,2872,3053,152125,152250,152283,152383,153538,153970,154520,154904,155548,157298,157917,158465,158818,159667,160009,160192,
5861831000000+AK174899932729913chr01p62201121566341568181184,729,156634,
586145920001183735-AK116012149601480chr01p62201121633361685501069,241,77,322,119,153,50,157,166,125,16,85,326,403,725,844,997,1047,1204,1371,163336,163822,164533,164954,165723,166388,166932,167557,168259,168425,
58611482030000-AK115269115701153chr01p622011217185317300611153,4,171853,
586133893300083235+AK115898139801380chr01p62201121838651884809129,51,83,143,164,149,81,453,127,0,129,180,263,406,570,719,800,1253,183865,183996,184325,185776,186290,186760,187283,187899,188353,
58697911154011141677+AK115766117001155chr01p6220112189838192659695,59,146,88,55,701,0,95,154,300,388,454,189838,190474,191016,191812,191903,191958,
5862543000000-AK175023146710741331chr01p62201122488352490921257,136,248835,

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