Schema for all_mrna
  Database: canFam4    Primary Table: all_mrna    Row Count: 3,656   Data last updated: 2020-05-05
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 615smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 4120int(10) unsigned range Number of bases that match that aren't repeats
misMatches 100int(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 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 1int(10) unsigned range Number of inserts in target
tBaseInsert 1int(10) unsigned range Number of bases inserted in target
strand +char(2) values + or - for strand. First character query, second target (optional)
qName AB012223varchar(255) values Query sequence name
qSize 4251int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 4220int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 123556469int(10) unsigned range Target sequence size
tStart 3943956int(10) unsigned range Alignment start position in target
tEnd 3948177int(10) unsigned range Alignment end position in target
blockCount 2int(10) unsigned range Number of blocks in alignment
blockSizes 4204,16,longblob   Size of each block
qStarts 0,4204,longblob   Start of each block in query.
tStarts 3943956,3948161,longblob   Start of each block in target.

Connected Tables and Joining Fields
        canFam4.all_est.qName (via all_mrna.qName)
      canFam4.mrnaOrientInfo.name (via all_mrna.qName)
      canFam4.refGene.name (via all_mrna.qName)
      canFam4.refSeqAli.qName (via all_mrna.qName)
      canFam4.xenoMrna.qName (via all_mrna.qName)
      canFam4.xenoRefGene.name (via all_mrna.qName)
      canFam4.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
6154120100000011+AB012223425104220chr11235564693943956394817724204,16,0,4204,3943956,3948161,
62346000000435279+HM1545314600460chr1123556469504504350807825161,129,30,35,105,0,161,290,320,355,5045043,5072902,5074883,5078937,5080677,
679412298000011+AB012223425104220chr1123556469124092281241344924204,16,0,4204,12409228,12413433,
861344800232165544+AB154172137401355chr11235564691381158613978482588,59,209,658,338,0,90,149,359,1017,13811586,13811674,13811959,13812168,13978144,
86665200001165318+AB1161456860667chr112355646913812497139784822329,338,0,329,13812497,13978144,
70814914000011+LC223817151901495chr1123556469162141801621567621393,102,0,1393,16214180,16215574,
8841209800001334753+AB012223425104218chr1123556469164236471676261824163,55,0,4163,16423647,16762563,
7111680000013167-DQ4490721680168chr112355646916558933165622682108,60,0,108,16558933,16562208,
71568200000514866-J05069820138820chr11235564691711519117130739687,58,120,150,110,157,0,87,145,265,415,525,17115191,17115892,17117997,17120237,17124148,17130582,
9226450003318354626+X51448264802648chr1123556469201661712052344222168,63,40,255,73,62,97,65,127,50,106,134,133,68,79,77,204,136,151,230,141,186,0,169,233,274,529,602,664,761,826,953,1003,1109,1243,1376,1444,1523,1600,1804,1940,2091,2321,2462,20166171,20166339,20166402,20166442,20170938,20287827,20290938,20346833,20398090,20398697,20471810,20475497,20481496,20489442,20 ...

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