Schema for GC Percent - GC Percent in 5-Base Windows
  Database: mm9    Primary Table: gc5Base    Row Count: 512,038   Data last updated: 2007-07-19
Format description: Wiggle track values to display as y-values (first 6 fields are bed6)
fieldexampleSQL type description
bin 607smallint(5) unsigned Indexing field to speed chromosome range queries.
chrom chr1varchar(255) Reference sequence chromosome or scaffold
chromStart 3000000int(10) unsigned Start position in chromosome
chromEnd 3005120int(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/mm9/wib/gc5Base.wibvarchar(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 37240double sum of the data points, for average and stddev calc
sumSquares 1866400double sum of data points squared, for stddev calc

Sample Rows
 
binchromchromStartchromEndnamespancountoffsetfilelowerLimitdataRangevalidCountsumDatasumSquares
607chr130000003005120chr1.0510240/gbdb/mm9/wib/gc5Base.wib01001024372401866400
607chr130051203010240chr1.1510241024/gbdb/mm9/wib/gc5Base.wib01001024389801858800
75chr130102403015360chr1.2510242048/gbdb/mm9/wib/gc5Base.wib01001024405002017200
608chr130153603020480chr1.3510243072/gbdb/mm9/wib/gc5Base.wib01001024428402256000
608chr130204803025600chr1.4510244096/gbdb/mm9/wib/gc5Base.wib01001024389201907200
608chr130256003030720chr1.5510245120/gbdb/mm9/wib/gc5Base.wib01001024422402211200
608chr130307203035840chr1.6510246144/gbdb/mm9/wib/gc5Base.wib01001024422402193600
608chr130358403040960chr1.7510247168/gbdb/mm9/wib/gc5Base.wib01001024413602096000
608chr130409603046080chr1.8510248192/gbdb/mm9/wib/gc5Base.wib01001024425802294000
608chr130460803051200chr1.9510249216/gbdb/mm9/wib/gc5Base.wib01001024380601909200

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.