Schema for xenoRefSeqAli
  Database: droVir2    Primary Table: xenoRefSeqAli    Row Count: 277,208   Data last updated: 2020-08-18
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 267int(10) unsigned range Number of bases that match that aren't repeats
misMatches 93int(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 6int(10) unsigned range Number of bases inserted in query
tNumInsert 0int(10) unsigned range Number of inserts in target
tBaseInsert 0int(10) unsigned range Number of bases inserted in target
strand +-char(2) values + or - for strand. First character query, second target (optional)
qName NM_068800varchar(255) values Query sequence name
qSize 384int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 366int(10) unsigned range Alignment end position in query
tName scaffold_9504varchar(255) values Target sequence name
tSize 5434int(10) unsigned range Target sequence size
tStart 4056int(10) unsigned range Alignment start position in target
tEnd 4416int(10) unsigned range Alignment end position in target
blockCount 2int(10) unsigned range Number of blocks in alignment
blockSizes 33,327,longblob   Size of each block
qStarts 0,39,longblob   Start of each block in query.
tStarts 1018,1051,longblob   Start of each block in target.

Connected Tables and Joining Fields
        droVir2.all_est.qName (via xenoRefSeqAli.qName)
      droVir2.all_mrna.qName (via xenoRefSeqAli.qName)
      droVir2.xenoMrna.qName (via xenoRefSeqAli.qName)
      droVir2.xenoRefFlat.name (via xenoRefSeqAli.qName)
      droVir2.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
58526793001600+-NM_0688003840366scaffold_9504543440564416233,327,0,39,1018,1051,
58527783001600++NM_0746313840366scaffold_9503532652412233,327,0,39,52,85,
5856913000000++NR_003280157183scaffold_100019183149231182,1,149,
5857013000000++NR_003285157285scaffold_54781773537620183,2,537,
5856913000000++NR_045133157284scaffold_100019183149231182,2,149,
5856913000000++NR_046238156284scaffold_100019183149231182,2,149,
5856913000000++NR_046250156183scaffold_100019183149231182,1,149,
5851211000000++NR_1335441231123scaffold_1000191831492711122,1,149,
5851220000000++NR_1335511231123scaffold_1000191831492711122,1,149,
5851220000000++NR_1335561231123scaffold_1000191831492711122,1,149,

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