Schema for Affy GNF1H - Alignments of Affymetrix Consensus/Exemplars from GNF1H
  Database: hg38    Primary Table: affyGnf1h    Row Count: 12,626   Data last updated: 2015-01-08
Format description: Summary info about a patSpace alignment
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 70int(10) unsigned range Number of bases that match that aren't repeats
misMatches 0int(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 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 gnf1h03908_s_atvarchar(255) values Query sequence name
qSize 70int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 70int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 248956422int(10) unsigned range Target sequence size
tStart 14969int(10) unsigned range Alignment start position in target
tEnd 15039int(10) unsigned range Alignment end position in target
blockCount 1int(10) unsigned range Number of blocks in alignment
blockSizes 70,longblob   Size of each block
qStarts 0,longblob   Start of each block in query.
tStarts 14969,longblob   Start of each block in target.

Connected Tables and Joining Fields
        hg38.gnfAtlas2.name (via affyGnf1h.qName)
      hg38.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
585700000000-gnf1h03908_s_at70070chr12489564221496915039170,0,14969,
5853381000000-gnf1h01690_s_at3390339chr124895642216934172731339,0,16934,
5852500024204335+gnf1h07742_at2720272chr12489564222141121998525,77,48,25,77,0,30,112,165,195,21411,21467,21649,21737,21921,
5853751000000-gnf1h03342_at3760376chr124895642224347247231376,0,24347,
5854560000000+gnf1h04689_at4560456chr124895642263332637881456,0,63332,
58611200015161+gnf1h11145_s_at1170117chr1248956422132022132195274,38,0,79,132022,132157,
586188200001506-gnf1h03516_x_at1933193chr12489564221329471336432116,74,0,116,132947,133569,
5865323000022156-gnf1h03907_at5350535chr12489564221836941863853397,69,69,0,397,466,183694,185490,186316,
586700000000-gnf1h03908_s_at70070chr1248956422185490185560170,0,185490,
5863372000000-gnf1h01690_s_at3390339chr12489564221874561877951339,0,187456,

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

Affy GNF1H (affyGnf1h) Track Description
 

Description

This track shows the location of the sequences used for the selection of probes on the Affymetrix GNF1H chips. This contains 11406 predicted genes that do not overlap with the Affy U133A chip.

Methods

The sequences were mapped to the genome using blat followed by pslReps with the parameters:

-minCover=0.3 -minAli=0.95 -nearTop=0.005

Credits

Thanks to the Genomics Institute of the Novartis Research Foundation (GNF) for the data underlying this track.

References

Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A. 2004 Apr 20;101(16):6062-7. PMID: 15075390; PMC: PMC395923