Schema for affyGnf1h
  Database: hg16    Primary Table: affyGnf1h    Row Count: 11,988   Data last updated: 2004-03-30
Format description: Summary info about a patSpace alignment
fieldexampleSQL type info description
bin 790smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 496int(10) unsigned range Number of bases that match that aren't repeats
misMatches 1int(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 0int(10) unsigned range Number of inserts in query
qBaseInsert 0int(10) unsigned range Number of bases inserted in query
tNumInsert 1int(10) unsigned range Number of inserts in target
tBaseInsert 713int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName gnf1h00031_atvarchar(255) values Query sequence name
qSize 497int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 497int(10) unsigned range Alignment end position in query
tName chr7varchar(255) values Target sequence name
tSize 158545518int(10) unsigned range Target sequence size
tStart 26980148int(10) unsigned range Alignment start position in target
tEnd 26981358int(10) unsigned range Alignment end position in target
blockCount 2int(10) unsigned range Number of blocks in alignment
blockSizes 185,312,longblob   Size of each block
qStarts 0,185,longblob   Start of each block in query.
tStarts 26980148,26981046,longblob   Start of each block in target.

Connected Tables and Joining Fields
        hg16.gnfAtlas2.name (via affyGnf1h.qName)
      hg16.knownToGnfAtlas2.value (via affyGnf1h.qName)
      hgFixed.gladHumESOtherData.name (via affyGnf1h.qName)
      hgFixed.gnfHumanAtlas2All.name (via affyGnf1h.qName)
      hgFixed.gnfHumanAtlas2AllRatio.name (via affyGnf1h.qName)
      hgFixed.gnfHumanAtlas2Median.name (via affyGnf1h.qName)
      hgFixed.gnfHumanAtlas2MedianRatio.name (via affyGnf1h.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
790496100001713-gnf1h00031_at4970497chr715854551826980148269813582185,312,0,185,26980148,26981046,
13515461001100-gnf1h00032_at5480548chr41917319591005032921005038392316,231,0,317,100503292,100503608,
14611150000011513-gnf1h00033_at1150115chr4191731959114835772114837400225,90,0,25,114835772,114837310,
146141500000555506-gnf1h00034_s_at4150415chr41917319591148374271148933486112,95,76,49,38,45,0,112,207,283,332,370,114837427,114840122,114845504,114880438,114889613,114893303,
88248800000217345+gnf1h00035_at4880488chr61709145763902724239045075326,122,340,0,26,148,39027242,39041176,39044735,
66353510000315652+gnf1h00036_at5360536chr31993440501023948610255674429,63,201,243,0,29,92,293,10239486,10243054,10251142,10255431,
96652520000312458-gnf1h00037_at5281528chr1213207837950009766500227514118,146,137,126,0,118,264,401,50009766,50019910,50021294,50022625,
7155630000053913-gnf1h00038_at5630563chr1113448295417075652170801286124,126,110,73,118,12,0,124,250,360,433,551,17075652,17077189,17077402,17077851,17078014,17080116,
11763250000000+gnf1h00039_at3250325chr1113448295477501236775015611325,0,77501236,
13474901000053261+gnf1h00040_at4910491chr7158545518100002998100006750639,139,141,100,47,25,0,39,178,319,419,466,100002998,100003138,100004214,100006384,100006595,100006725,

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