Schema for xenoRefSeqAli
  Database: oreNil2    Primary Table: xenoRefSeqAli    Row Count: 461,652   Data last updated: 2020-08-22
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 130int(10) unsigned range Number of bases that match that aren't repeats
misMatches 53int(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 45int(10) unsigned range Number of bases inserted in query
tNumInsert 1int(10) unsigned range Number of inserts in target
tBaseInsert 1244int(10) unsigned range Number of bases inserted in target
strand +-char(2) values + or - for strand. First character query, second target (optional)
qName NM_001097175varchar(255) values Query sequence name
qSize 3171int(10) unsigned range Query sequence size
qStart 2460int(10) unsigned range Alignment start position in query
qEnd 2688int(10) unsigned range Alignment end position in query
tName AERX01071843-2varchar(255) values Target sequence name
tSize 12936int(10) unsigned range Target sequence size
tStart 3430int(10) unsigned range Alignment start position in target
tEnd 4857int(10) unsigned range Alignment end position in target
blockCount 2int(10) unsigned range Number of blocks in alignment
blockSizes 108,75,longblob   Size of each block
qStarts 2460,2613,longblob   Start of each block in query.
tStarts 8079,9431,longblob   Start of each block in target.

Connected Tables and Joining Fields
        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)
      oreNil2.all_est.qName (via xenoRefSeqAli.qName)
      oreNil2.all_mrna.qName (via xenoRefSeqAli.qName)
      oreNil2.refGene.name (via xenoRefSeqAli.qName)
      oreNil2.refSeqAli.qName (via xenoRefSeqAli.qName)
      oreNil2.xenoRefFlat.name (via xenoRefSeqAli.qName)
      oreNil2.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
585130530014511244+-NM_001097175317124602688AERX01071843-212936343048572108,75,2460,2613,8079,9431,
5851791210014533287+-NM_001273228918680968441AERX01071843-212936343070174114,3,105,78,8096,8210,8213,8363,5919,6278,8079,9428,
5851791210014533287+-NM_001273230900979198264AERX01071843-212936343070174114,3,105,78,7919,8033,8036,8186,5919,6278,8079,9428,
5851791210014533287+-NM_001273231890678168161AERX01071843-212936343070174114,3,105,78,7816,7930,7933,8083,5919,6278,8079,9428,
5851791210014533287+-NM_164709918880988443AERX01071843-212936343070174114,3,105,78,8098,8212,8215,8365,5919,6278,8079,9428,
58519610400223727323+-NM_001108868339423892926AERX01071843-2129363430110533120,105,75,2389,2698,2851,1883,8079,9431,
5852039700223727323+-NM_001310332322722062743AERX01071843-2129363430110533120,105,75,2206,2515,2668,1883,8079,9431,
74920110500232432325+-NM_0070011623359989chrLG12346797062152404921526680465,70,90,81,359,424,665,908,13153026,13153193,13154608,13155576,
59017994000000+-NM_0013624281301308581GL831384-19284007550577553301273,308,173070,
5852039500224527331+-NM_001101918368826493192AERX01071843-2129363430110593126,97,75,2649,2964,3117,1877,8079,9431,

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