Schema for xenoRefSeqAli
  Database: geoFor1    Primary Table: xenoRefSeqAli    Row Count: 378,647   Data last updated: 2020-08-19
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 250int(10) unsigned range Number of bases that match that aren't repeats
misMatches 103int(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 19int(10) unsigned range Number of 'N' bases
qNumInsert 2int(10) unsigned range Number of inserts in query
qBaseInsert 144int(10) unsigned range Number of bases inserted in query
tNumInsert 2int(10) unsigned range Number of inserts in target
tBaseInsert 10047int(10) unsigned range Number of bases inserted in target
strand +-char(2) values + or - for strand. First character query, second target (optional)
qName NM_001001290varchar(255) values Query sequence name
qSize 1885int(10) unsigned range Query sequence size
qStart 225int(10) unsigned range Alignment start position in query
qEnd 741int(10) unsigned range Alignment end position in query
tName JH739887varchar(255) values Target sequence name
tSize 30495534int(10) unsigned range Target sequence size
tStart 9140int(10) unsigned range Alignment start position in target
tEnd 19559int(10) unsigned range Alignment end position in target
blockCount 3int(10) unsigned range Number of blocks in alignment
blockSizes 90,156,126,longblob   Size of each block
qStarts 225,327,615,longblob   Start of each block in query.
tStarts 30475975,30480936,30486268,longblob   Start of each block in target.

Connected Tables and Joining Fields
        geoFor1.all_mrna.qName (via xenoRefSeqAli.qName)
      geoFor1.xenoRefFlat.name (via xenoRefSeqAli.qName)
      geoFor1.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
5852501030192144210047+-NM_0010012901885225741JH73988730495534914019559390,156,126,225,327,615,30475975,30480936,30486268,
5852471150192135210038+-NM_001012363340372588JH73988730495534914019559390,156,135,72,174,453,30475975,30480936,30486259,
5852471150192135210038+-NM_0011024143602271787JH73988730495534914019559390,156,135,271,373,652,30475975,30480936,30486259,
5852471150192135210038+-NM_0011024153281271787JH73988730495534914019559390,156,135,271,373,652,30475975,30480936,30486259,
585235880192174210077+-NM_0011308351761140656JH73988730495534914019559390,117,135,140,242,521,30475975,30480936,30486259,
5852501120192135210038+-NM_0011915513384117633JH73988730495534914019559390,156,135,117,219,498,30475975,30480936,30486259,
632663175038111162915++NM_00092515071161103JH7399078707472619260761963987114,60,36,285,97,140,144,116,230,290,326,722,819,959,6192607,6192792,6192935,6193057,6194784,6195815,6196254,
5852471150192135210038+-NM_1455593276266782JH73988730495534914019559390,156,135,266,368,647,30475975,30480936,30486259,
5856231000000+-NM_001140649848366459JH739887304955341444214535193,366,30480999,
5857839000000+-NM_0010204941950262379JH7398873049553414481145981117,262,30480936,

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