Schema for GC Percent - GC Percent in 5-Base Windows
  Database: hg19    Primary Table: gc5Base    Row Count: 584,652   Data last updated: 2020-02-18
Format description: Wiggle track values to display as y-values (first 6 fields are bed6)
fieldexampleSQL type description
bin 585smallint(5) unsigned Indexing field to speed chromosome range queries.
chrom chr1varchar(255) Reference sequence chromosome or scaffold
chromStart 10000int(10) unsigned Start position in chromosome
chromEnd 15120int(10) unsigned End position in chromosome
name chr1.0varchar(255) Name of item
span 5int(10) unsigned each value spans this many bases
count 1024int(10) unsigned number of values in this block
offset 0int(10) unsigned offset in File to fetch data
file /gbdb/hg19/wib/gc5Base.p13....varchar(255) path name to data file, one byte per value
lowerLimit 0double lowest data value in this block
dataRange 100double lowerLimit + dataRange = upperLimit
validCount 1024int(10) unsigned number of valid data values in this block
sumData 60360double sum of the data points, for average and stddev calc
sumSquares 4024000double sum of data points squared, for stddev calc

Sample Rows
 
binchromchromStartchromEndnamespancountoffsetfilelowerLimitdataRangevalidCountsumDatasumSquares
585chr11000015120chr1.0510240/gbdb/hg19/wib/gc5Base.p13.plusMT.wib01001024603604024000
585chr11512020240chr1.1510241024/gbdb/hg19/wib/gc5Base.p13.plusMT.wib01001024604603966800
585chr12024025360chr1.2510242048/gbdb/hg19/wib/gc5Base.p13.plusMT.wib01001024549003370000
585chr12536030480chr1.3510243072/gbdb/hg19/wib/gc5Base.p13.plusMT.wib01001024500803089600
585chr13048035600chr1.4510244096/gbdb/hg19/wib/gc5Base.p13.plusMT.wib01001024475602695200
585chr13560040720chr1.5510245120/gbdb/hg19/wib/gc5Base.p13.plusMT.wib01001024504202998800
585chr14072045840chr1.6510246144/gbdb/hg19/wib/gc5Base.p13.plusMT.wib01001024336001520000
585chr14584050960chr1.7510247168/gbdb/hg19/wib/gc5Base.p13.plusMT.wib01001024361001710800
585chr15096056080chr1.8510248192/gbdb/hg19/wib/gc5Base.p13.plusMT.wib01001024389401975600
585chr15608061200chr1.9510249216/gbdb/hg19/wib/gc5Base.p13.plusMT.wib01001024363601720800

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

GC Percent (gc5Base) Track Description
 

Description

The GC percent track shows the percentage of G (guanine) and C (cytosine) bases in 5-base windows. High GC content is typically associated with gene-rich areas.

This track may be configured in a variety of ways to highlight different apsects of the displayed information. Click the "Graph configuration help" link for an explanation of the configuration options.

Credits

The data and presentation of this graph were prepared by Hiram Clawson.