Schema for GC Percent - GC Percent in 5-Base Windows
  Database: tupBel1    Primary Table: gc5Base    Row Count: 610,995   Data last updated: 2006-12-21
Format description: Wiggle track values to display as y-values (first 6 fields are bed6)
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 585smallint(5) unsigned Indexing field to speed chromosome range queries.
chrom scaffold_0.1-13376varchar(255) Reference sequence chromosome or scaffold
chromStart 0int(10) unsigned Start position in chromosome
chromEnd 5120int(10) unsigned End position in chromosome
name scaffold_0.1-13376.0varchar(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/tupBel1/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 865int(10) unsigned number of valid data values in this block
sumData 32730double sum of the data points, for average and stddev calc
sumSquares 1639300double sum of data points squared, for stddev calc

Sample Rows
 
binchromchromStartchromEndnamespancountoffsetfilelowerLimitdataRangevalidCountsumDatasumSquares
585scaffold_0.1-1337605120scaffold_0.1-13376.0510240/gbdb/tupBel1/wib/gc5Base.wib0100865327301639300
585scaffold_0.1-13376512010240scaffold_0.1-13376.1510241024/gbdb/tupBel1/wib/gc5Base.wib0100100538946.72010850
585scaffold_0.1-133761024013375scaffold_0.1-13376.256272048/gbdb/tupBel1/wib/gc5Base.wib010039215480794400
585scaffold_1.1-5113505120scaffold_1.1-51135.3510242675/gbdb/tupBel1/wib/gc5Base.wib0100758419302699300
585scaffold_1.1-51135512010240scaffold_1.1-51135.4510243699/gbdb/tupBel1/wib/gc5Base.wib0100994555003552400
585scaffold_1.1-511351024013480scaffold_1.1-51135.556484723/gbdb/tupBel1/wib/gc5Base.wib0100648380302476500
585scaffold_1.1-511352933534455scaffold_1.1-51135.6510245371/gbdb/tupBel1/wib/gc5Base.wib010093053931.73610670
585scaffold_1.1-511353445539575scaffold_1.1-51135.7510246395/gbdb/tupBel1/wib/gc5Base.wib010085145076.72818950
585scaffold_1.1-511353957544695scaffold_1.1-51135.8510247419/gbdb/tupBel1/wib/gc5Base.wib01001024484802795200
585scaffold_1.1-511354469549815scaffold_1.1-51135.9510248443/gbdb/tupBel1/wib/gc5Base.wib010095951213.33217510

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.