Schema for all_mrna
  Database: caeJap1    Primary Table: all_mrna    Row Count: 12   Data last updated: 2014-09-01
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 877smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 546int(10) unsigned range Number of bases that match that aren't repeats
misMatches 0int(10) unsigned range Number of bases that don't match
repMatches 103int(10) unsigned range Number of bases that match but are part of repeats
nCount 0int(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 1int(10) unsigned range Number of inserts in target
tBaseInsert 46int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName AY589600varchar(255) values Query sequence name
qSize 2059int(10) unsigned range Query sequence size
qStart 1374int(10) unsigned range Alignment start position in query
qEnd 2024int(10) unsigned range Alignment end position in query
tName chrUnvarchar(255) values Target sequence name
tSize 156378573int(10) unsigned range Target sequence size
tStart 38354037int(10) unsigned range Alignment start position in target
tEnd 38354732int(10) unsigned range Alignment end position in target
blockCount 3int(10) unsigned range Number of blocks in alignment
blockSizes 56,293,300,longblob   Size of each block
qStarts 35,92,385,longblob   Start of each block in query.
tStarts 38354037,38354093,38354432,longblob   Start of each block in target.

Connected Tables and Joining Fields
        caeJap1.all_est.qName (via all_mrna.qName)
      caeJap1.mrnaOrientInfo.name (via all_mrna.qName)
      caeJap1.xenoMrna.qName (via all_mrna.qName)
      caeJap1.xenoRefGene.name (via all_mrna.qName)
      caeJap1.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
8775460103011146-AY589600205913742024chrUn1563785733835403738354732356,293,300,35,92,385,38354037,38354093,38354432,
8775460103011146-AY58960115068211471chrUn1563785733835403738354732356,293,300,35,92,385,38354037,38354093,38354432,
9591322032000101376-AY5896002059201374chrUn156378573490574664906019611153,96,128,79,149,222,141,83,86,142,75,685,838,934,1062,1141,1290,1512,1653,1736,1822,1964,49057466,49057668,49057850,49057979,49058111,49058545,49058832,49059023,49059150,49059926,49060121,
9597940700071929-AY589601150620821chrUn15637857349057466490601968153,96,128,79,149,91,30,75,685,838,934,1062,1141,1290,1381,1411,49057466,49057668,49057850,49057979,49058111,49058545,49060038,49060121,
11731061030000160+AY5896092724201111chrUn15637857377074473770756242182,909,20,202,77074473,77074715,
155883131540128249039-AY589604106921054chrUn156378573864175818666767010129,220,89,89,125,103,114,82,79,20,15,146,366,455,544,669,772,886,968,1047,86417581,86417710,86417983,86418114,86420317,86420600,86420750,86421039,86421169,86667650,
13049601174100022406+AY589609272415412686chrUn15637857394347334943508853330,216,599,1541,1871,2087,94347334,94350007,94350286,
1408175101280004297+AY589614190201879chrUn156378573107996361107998537542,578,233,785,241,0,42,620,853,1638,107996361,107996456,107997162,107997457,107998296,
1408162101280003244+AY589615178201749chrUn1563785731079965441079985374490,233,785,241,0,490,723,1508,107996544,107997162,107997457,107998296,
140812221430002116+AY5896161314151281chrUn1563785731079971551079985373240,785,241,15,255,1040,107997155,107997457,107998296,

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