Schema for xenoRefSeqAli
  Database: bosTau9    Primary Table: xenoRefSeqAli    Row Count: 213,526   Data last updated: 2019-05-21
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 587smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 370int(10) unsigned range Number of bases that match that aren't repeats
misMatches 104int(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 1int(10) unsigned range Number of inserts in query
qBaseInsert 15int(10) unsigned range Number of bases inserted in query
tNumInsert 2int(10) unsigned range Number of inserts in target
tBaseInsert 3892int(10) unsigned range Number of bases inserted in target
strand +-char(2) values + or - for strand. First character query, second target (optional)
qName NM_001017103varchar(255) values Query sequence name
qSize 1485int(10) unsigned range Query sequence size
qStart 299int(10) unsigned range Alignment start position in query
qEnd 788int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 158534110int(10) unsigned range Target sequence size
tStart 342546int(10) unsigned range Alignment start position in target
tEnd 346912int(10) unsigned range Alignment end position in target
blockCount 3int(10) unsigned range Number of blocks in alignment
blockSizes 138,161,175,longblob   Size of each block
qStarts 299,452,613,longblob   Start of each block in query.
tStarts 158187198,158187348,158191389,longblob   Start of each block in target.

Connected Tables and Joining Fields
        bosTau9.all_est.qName (via xenoRefSeqAli.qName)
      bosTau9.all_mrna.qName (via xenoRefSeqAli.qName)
      bosTau9.refGene.name (via xenoRefSeqAli.qName)
      bosTau9.refSeqAli.qName (via xenoRefSeqAli.qName)
      bosTau9.xenoRefFlat.name (via xenoRefSeqAli.qName)
      bosTau9.xenoRefGene.name (via xenoRefSeqAli.qName)
      hgFixed.gbCdnaInfo.acc (via xenoRefSeqAli.qName)
      hgFixed.gbMiscDiff.acc (via xenoRefSeqAli.qName)
      hgFixed.gbSeq.acc (via xenoRefSeqAli.qName)
      hgFixed.gbWarn.acc (via xenoRefSeqAli.qName)
      hgFixed.imageClone.acc (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
5873701040011523892+-NM_0010171031485299788chr11585341103425463469123138,161,175,299,452,613,158187198,158187348,158191389,
589336870026633971++NM_0010171031485299788chr1158534110626165630559493,45,108,177,299,452,503,611,626165,626313,626363,630382,
589332910026633971++NM_0010916201669287776chr1158534110626165630559493,45,108,177,287,440,491,599,626165,626313,626363,630382,
5906562000034239982++NM_146817107660958chr1158534110689221700059540,201,303,99,213,60,100,307,645,745,689221,699204,699409,699747,699846,
59073417500436224++NM_1466439450945chr1158534110703148704081550,225,256,150,228,0,51,278,537,717,703148,703198,703424,703680,703853,
59071914000330219++NM_00100549698748937chr11585341107031957040734228,254,156,221,48,279,536,716,703195,703425,703679,703852,
590733187001100++NM_1466459420921chr11585341107150107159302383,537,0,384,715010,715393,
731567386001219531954917+-NM_00131700941021804086chr115853411076402182089120138,63,99,195,63,60,69,5,172,116,126,107,182,221,27,11,23,11,132,133,180,323,519,754,1144,1255,1363,1432,1437,1648,1764,1890,1997,2179,2400,2438,2453,3148,3278,3953,157713219,157713362,157713597,157713802,157714072,157714192,157714303,157714373,157714383,157753987,157755018,157755713,15775697 ...
731558380001119141954932+-NM_05327740481804032chr115853411076402182089120138,63,99,195,63,60,69,5,163,110,126,107,182,221,27,11,23,11,132,133,180,323,519,754,1144,1255,1363,1432,1437,1600,1710,1836,1943,2125,2346,2384,2399,3094,3224,3899,157713219,157713362,157713597,157713802,157714072,157714192,157714303,157714373,157714383,157753993,157755018,157755713,15775697 ...
73690121002888653021+-NM_17607822524512150chr1158534110765979819811742,78,108,128,105,182,168,451,1379,1457,1565,1693,1800,1982,157714299,157714468,157753993,157755016,157755713,157756976,157767963,

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