Schema for xenoRefSeqAli
  Database: papHam1    Primary Table: xenoRefSeqAli    Row Count: 635,835   Data last updated: 2020-08-19
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 585smallint(5) unsigned Indexing field to speed chromosome range queries.
matches 487int(10) unsigned Number of bases that match that aren't repeats
misMatches 51int(10) unsigned Number of bases that don't match
repMatches 0int(10) unsigned Number of bases that match but are part of repeats
nCount 0int(10) unsigned Number of 'N' bases
qNumInsert 0int(10) unsigned Number of inserts in query
qBaseInsert 0int(10) unsigned Number of bases inserted in query
tNumInsert 0int(10) unsigned Number of inserts in target
tBaseInsert 0int(10) unsigned Number of bases inserted in target
strand ++char(2) + or - for strand. First character query, second target (optional)
qName NM_001192546varchar(255) Query sequence name
qSize 1440int(10) unsigned Query sequence size
qStart 362int(10) unsigned Alignment start position in query
qEnd 900int(10) unsigned Alignment end position in query
tName Contig1000002varchar(255) Target sequence name
tSize 11873int(10) unsigned Target sequence size
tStart 9446int(10) unsigned Alignment start position in target
tEnd 9984int(10) unsigned Alignment end position in target
blockCount 1int(10) unsigned Number of blocks in alignment
blockSizes 538,longblob Size of each block
qStarts 362,longblob Start of each block in query.
tStarts 9446,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)
      papHam1.all_mrna.qName (via xenoRefSeqAli.qName)
      papHam1.refGene.name (via xenoRefSeqAli.qName)
      papHam1.refSeqAli.qName (via xenoRefSeqAli.qName)
      papHam1.xenoRefFlat.name (via xenoRefSeqAli.qName)
      papHam1.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
58548751000000++NM_0011925461440362900Contig100000211873944699841538,362,9446,
58549543000000++NM_00124480616404911029Contig100000211873944699841538,491,9446,
58549345000000++NM_0229301937449987Contig100000211873944699841538,449,9446,
585417121000000++NM_2047601455368906Contig100000211873944699841538,368,9446,
58522861490066641325537+-NM_017556331413100scaffold21095405136670346421853,190,270,160,109,170,179,118,114,174,214,75,36,42,84,374,25,48,1,54,244,514,696,805,975,1154,1272,1388,1562,2374,2449,2486,2528,2615,2989,3052,5871,12203,12671,17012,18144,19698,24208,25985,32056,32170,32347,33148,33225,33261,33304,33388,33770,33795,
58547262000000++NM_00108110420036901224Contig100000211873945099841534,690,9450,
585388146000000++NM_00112443920855661100Contig100000211873945099841534,566,9450,
585399135000000++NM_00112451919425151049Contig100000211873945099841534,515,9450,
585367137000000++NM_0010448041584378882Contig100000211873948099841504,378,9480,
585366138000000++NM_0011010361359399903Contig100000211873948099841504,399,9480,

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