Schema for xenoRefSeqAli
  Database: vicPac1    Primary Table: xenoRefSeqAli    Row Count: 632,143   Data last updated: 2020-09-01
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 137int(10) unsigned Number of bases that match that aren't repeats
misMatches 70int(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_001011357varchar(255) Query sequence name
qSize 1905int(10) unsigned Query sequence size
qStart 472int(10) unsigned Alignment start position in query
qEnd 679int(10) unsigned Alignment end position in query
tName scaffold_0varchar(255) Target sequence name
tSize 5516956int(10) unsigned Target sequence size
tStart 3443int(10) unsigned Alignment start position in target
tEnd 3650int(10) unsigned Alignment end position in target
blockCount 1int(10) unsigned Number of blocks in alignment
blockSizes 207,longblob Size of each block
qStarts 472,longblob Start of each block in query.
tStarts 3443,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)
      vicPac1.all_est.qName (via xenoRefSeqAli.qName)
      vicPac1.xenoRefFlat.name (via xenoRefSeqAli.qName)
      vicPac1.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
58513770000000++NM_0010113571905472679scaffold_05516956344336501207,472,3443,
58513671000000++NM_0010919362142249456scaffold_05516956344336501207,249,3443,
58517830000000++NM_0010797312501299507scaffold_05516956344336511208,299,3443,
58525627001156144899++NM_0012772962393497936scaffold_055169563443486252208,75,497,861,3443,48550,
58525627001156144899++NM_0012772972205309748scaffold_055169563443486252208,75,309,673,3443,48550,
58525627001156144899++NM_0281052314418857scaffold_055169563443486252208,75,418,782,3443,48550,
58525722001158144901++NM_0012669022021251688scaffold_055169563444486242207,72,251,616,3444,48552,
58527013001156144899++NM_0010768952274285724scaffold_055169563444486262207,76,285,648,3444,48550,
5859558000000++NM_0012999221901515668scaffold_05516956344635991153,515,3446,
5859558000000++NM_1381031736350503scaffold_05516956344635991153,350,3446,

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