Schema for kgTargetAli
  Database: hg18    Primary Table: kgTargetAli    Row Count: 66,803   Data last updated: 2008-11-01
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 2122int(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 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 2int(10) unsigned range Number of inserts in target
tBaseInsert 884int(10) unsigned range Number of bases inserted in target
strand +char(2) values + or - for strand. First character query, second target (optional)
qName uc001aaa.2varchar(255) values Query sequence name
qSize 2122int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 2122int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 247249719int(10) unsigned range Target sequence size
tStart 1115int(10) unsigned range Alignment start position in target
tEnd 4121int(10) unsigned range Alignment end position in target
blockCount 3int(10) unsigned range Number of blocks in alignment
blockSizes 975,109,1038,longblob   Size of each block
qStarts 0,975,1084,longblob   Start of each block in query.
tStarts 1115,2475,3083,longblob   Start of each block in target.

Connected Tables and Joining Fields
        hg18.bioCycPathway.kgID (via kgTargetAli.qName)
      hg18.ccdsKgMap.geneId (via kgTargetAli.qName)
      hg18.ceBlastTab.query (via kgTargetAli.qName)
      hg18.dmBlastTab.query (via kgTargetAli.qName)
      hg18.drBlastTab.query (via kgTargetAli.qName)
      hg18.foldUtr3.name (via kgTargetAli.qName)
      hg18.foldUtr5.name (via kgTargetAli.qName)
      hg18.gnfAtlas2Distance.query (via kgTargetAli.qName)
      hg18.gnfAtlas2Distance.target (via kgTargetAli.qName)
      hg18.gnfU95Distance.query (via kgTargetAli.qName)
      hg18.gnfU95Distance.target (via kgTargetAli.qName)
      hg18.humanHprdP2P.query (via kgTargetAli.qName)
      hg18.humanHprdP2P.target (via kgTargetAli.qName)
      hg18.humanVidalP2P.query (via kgTargetAli.qName)
      hg18.humanVidalP2P.target (via kgTargetAli.qName)
      hg18.humanWankerP2P.query (via kgTargetAli.qName)
      hg18.humanWankerP2P.target (via kgTargetAli.qName)
      hg18.keggPathway.kgID (via kgTargetAli.qName)
      hg18.kgAlias.kgID (via kgTargetAli.qName)
      hg18.kgColor.kgID (via kgTargetAli.qName)
      hg18.kgProtAlias.kgID (via kgTargetAli.qName)
      hg18.kgProtMap2.qName (via kgTargetAli.qName)
      hg18.kgSpAlias.kgID (via kgTargetAli.qName)
      hg18.kgTxInfo.name (via kgTargetAli.qName)
      hg18.kgXref.kgID (via kgTargetAli.qName)
      hg18.knownBlastTab.query (via kgTargetAli.qName)
      hg18.knownBlastTab.target (via kgTargetAli.qName)
      hg18.knownCanonToDecipher.name (via kgTargetAli.qName)
      hg18.knownCanonical.protein (via kgTargetAli.qName)
      hg18.knownCanonical.transcript (via kgTargetAli.qName)
      hg18.knownGene.name (via kgTargetAli.qName)
      hg18.knownGeneMrna.name (via kgTargetAli.qName)
      hg18.knownGenePep.name (via kgTargetAli.qName)
      hg18.knownIsoforms.transcript (via kgTargetAli.qName)
      hg18.knownToAllenBrain.name (via kgTargetAli.qName)
      hg18.knownToDecipher.name (via kgTargetAli.qName)
      hg18.knownToEnsembl.name (via kgTargetAli.qName)
      hg18.knownToGnf1h.name (via kgTargetAli.qName)
      hg18.knownToGnfAtlas2.name (via kgTargetAli.qName)
      hg18.knownToHInv.name (via kgTargetAli.qName)
      hg18.knownToHprd.name (via kgTargetAli.qName)
      hg18.knownToKeggEntrez.name (via kgTargetAli.qName)
      hg18.knownToLocusLink.name (via kgTargetAli.qName)
      hg18.knownToMupit.name (via kgTargetAli.qName)
      hg18.knownToPfam.name (via kgTargetAli.qName)
      hg18.knownToRefSeq.name (via kgTargetAli.qName)
      hg18.knownToSuper.gene (via kgTargetAli.qName)
      hg18.knownToTreefam.name (via kgTargetAli.qName)
      hg18.knownToU133.name (via kgTargetAli.qName)
      hg18.knownToU133Plus2.name (via kgTargetAli.qName)
      hg18.knownToU95.name (via kgTargetAli.qName)
      hg18.knownToVisiGene.name (via kgTargetAli.qName)
      hg18.mmBlastTab.query (via kgTargetAli.qName)
      hg18.rnBlastTab.query (via kgTargetAli.qName)
      hg18.scBlastTab.query (via kgTargetAli.qName)
      hg18.ucscScop.ucscId (via kgTargetAli.qName)
      knownGeneV39.bioCycPathway.kgID (via kgTargetAli.qName)
      knownGeneV39.ceBlastTab.query (via kgTargetAli.qName)
      knownGeneV39.dmBlastTab.query (via kgTargetAli.qName)
      knownGeneV39.drBlastTab.query (via kgTargetAli.qName)
      knownGeneV39.foldUtr3.name (via kgTargetAli.qName)
      knownGeneV39.foldUtr5.name (via kgTargetAli.qName)
      knownGeneV39.gnfAtlas2Distance.query (via kgTargetAli.qName)
      knownGeneV39.gnfAtlas2Distance.target (via kgTargetAli.qName)
      knownGeneV39.kgAlias.kgID (via kgTargetAli.qName)
      knownGeneV39.kgColor.kgID (via kgTargetAli.qName)
      knownGeneV39.kgProtAlias.kgID (via kgTargetAli.qName)
      knownGeneV39.kgSpAlias.kgID (via kgTargetAli.qName)
      knownGeneV39.kgTargetAli.qName (via kgTargetAli.qName)
      knownGeneV39.kgXref.kgID (via kgTargetAli.qName)
      knownGeneV39.knownAttrs.kgID (via kgTargetAli.qName)
      knownGeneV39.knownBlastTab.query (via kgTargetAli.qName)
      knownGeneV39.knownBlastTab.target (via kgTargetAli.qName)
      knownGeneV39.knownCanonical.protein (via kgTargetAli.qName)
      knownGeneV39.knownCanonical.transcript (via kgTargetAli.qName)
      knownGeneV39.knownCds.name (via kgTargetAli.qName)
      knownGeneV39.knownGene.name (via kgTargetAli.qName)
      knownGeneV39.knownGeneMrna.name (via kgTargetAli.qName)
      knownGeneV39.knownGenePep.name (via kgTargetAli.qName)
      knownGeneV39.knownIsoforms.transcript (via kgTargetAli.qName)
      knownGeneV39.knownToEnsembl.name (via kgTargetAli.qName)
      knownGeneV39.knownToGnfAtlas2.name (via kgTargetAli.qName)
      knownGeneV39.knownToHprd.name (via kgTargetAli.qName)
      knownGeneV39.knownToLocusLink.name (via kgTargetAli.qName)
      knownGeneV39.knownToMrna.name (via kgTargetAli.qName)
      knownGeneV39.knownToMrnaSingle.name (via kgTargetAli.qName)
      knownGeneV39.knownToMupit.name (via kgTargetAli.qName)
      knownGeneV39.knownToPfam.name (via kgTargetAli.qName)
      knownGeneV39.knownToRefSeq.name (via kgTargetAli.qName)
      knownGeneV39.knownToSuper.gene (via kgTargetAli.qName)
      knownGeneV39.knownToTag.name (via kgTargetAli.qName)
      knownGeneV39.knownToU133.name (via kgTargetAli.qName)
      knownGeneV39.knownToU95.name (via kgTargetAli.qName)
      knownGeneV39.knownToVisiGene.name (via kgTargetAli.qName)
      knownGeneV39.knownToWikipedia.name (via kgTargetAli.qName)
      knownGeneV39.mmBlastTab.query (via kgTargetAli.qName)
      knownGeneV39.rnBlastTab.query (via kgTargetAli.qName)
      knownGeneV39.scBlastTab.query (via kgTargetAli.qName)
      knownGeneV39.ucscScop.ucscId (via kgTargetAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
5852122000002884+uc001aaa.2212202122chr1247249719111541213975,109,1038,0,975,1084,1115,2475,3083,
5852772000001385+uc009vip.1277202772chr1247249719111542722975,1797,0,975,1115,2475,
58517020000098794-uc001aab.2170201702chr124724971942681476410424,69,152,159,202,136,137,147,112,164,0,424,493,645,804,1006,1142,1279,1426,1538,4268,4832,5658,6469,6716,7095,7468,7777,8130,14600,
585158100000613372-uc009viq.1158101581chr12472497194268192217424,152,159,198,456,154,38,0,424,576,735,933,1389,1543,4268,5658,6469,6720,7468,14600,19183,
585195000000913003-uc009vir.1195001950chr124724971942681922110424,69,152,159,198,510,147,99,154,38,0,424,493,645,804,1002,1512,1659,1758,1912,4268,4832,5658,6469,6720,7095,7777,8130,14600,19183,
5851690000001013263-uc001aac.2169001690chr124724971942681922111424,69,152,159,198,110,137,147,102,154,38,0,424,493,645,804,1002,1112,1249,1396,1498,1652,4268,4832,5658,6469,6720,7121,7468,7777,8130,14600,19183,
5857990000031561-uc009vis.17990799chr1247249719426866284424,69,147,159,0,424,493,640,4268,4832,5658,6469,
58526050000082749-uc009vit.1260502605chr1247249719426896229424,69,152,159,198,510,147,99,847,0,424,493,645,804,1002,1512,1659,1758,4268,4832,5658,6469,6720,7095,7777,8130,8775,
58526620000092692-uc009viu.1266202662chr12472497194268962210424,69,152,159,198,510,147,102,54,847,0,424,493,645,804,1002,1512,1659,1761,1815,4268,4832,5658,6469,6720,7095,7777,8130,8363,8775,
58523680000092986-uc001aae.2236802368chr12472497194268962210424,69,152,159,198,136,137,147,99,847,0,424,493,645,804,1002,1138,1275,1422,1521,4268,4832,5658,6469,6720,7095,7468,7777,8130,8775,

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