Schema for xenoRefSeqAli
  Database: manPen1    Primary Table: xenoRefSeqAli    Row Count: 548,155   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 73smallint(5) unsigned Indexing field to speed chromosome range queries.
matches 291int(10) unsigned Number of bases that match that aren't repeats
misMatches 38int(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 2int(10) unsigned Number of inserts in target
tBaseInsert 144291int(10) unsigned Number of bases inserted in target
strand +-char(2) + or - for strand. First character query, second target (optional)
qName NM_001035277varchar(255) Query sequence name
qSize 3707int(10) unsigned Query sequence size
qStart 162int(10) unsigned Alignment start position in query
qEnd 491int(10) unsigned Alignment end position in query
tName JPTV01024999varchar(255) Target sequence name
tSize 206047int(10) unsigned Target sequence size
tStart 49433int(10) unsigned Alignment start position in target
tEnd 194053int(10) unsigned Alignment end position in target
blockCount 3int(10) unsigned Number of blocks in alignment
blockSizes 118,3,208,longblob Size of each block
qStarts 162,280,283,longblob Start of each block in query.
tStarts 11994,12127,156406,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)
      manPen1.xenoRefFlat.name (via xenoRefSeqAli.qName)
      manPen1.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
732913800002144291+-NM_0010352773707162491JPTV01024999206047494331940533118,3,208,162,280,283,11994,12127,156406,
732943500002144291+-NM_0011098122305101430JPTV01024999206047494331940533117,4,208,101,218,222,11994,12126,156406,
732943500002144291+-NM_0011331933516278607JPTV01024999206047494331940533117,5,207,278,395,400,11994,12241,156407,
732963300002144291+-NM_0012665523820159488JPTV01024999206047494331940533117,5,207,159,276,281,11994,12241,156407,
732893900002144291+-NM_001109945214239367JPTV01024999206047494341940533117,5,206,39,156,161,11994,12241,156407,
732725600002144291+-NM_1388893403109437JPTV01024999206047494341940533118,3,207,109,227,230,11994,12127,156406,
58512168000000+-NM_0010947303330219408JPTV0102499920604749456496451189,219,156402,
58511871000000+-NM_0011030783614197386JPTV0102499920604749456496451189,197,156402,
732059500002144291+-NM_001001760277978378JPTV01024999206047494621940533117,6,177,78,195,201,11994,15116,156408,
585324720041054327718++NR_1109371493341484JPTV0102499920604786005114119536,54,183,36,87,34,83,812,1360,1397,86005,86052,113447,113996,114032,

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