Schema for GC Percent - GC Percent in 5-Base Windows
  Database: cavPor3    Primary Table: gc5Base    Row Count: 528,190   Data last updated: 2008-04-03
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 chrMvarchar(255) Reference sequence chromosome or scaffold
chromStart 0int(10) unsigned Start position in chromosome
chromEnd 5120int(10) unsigned End position in chromosome
name chrM.528186varchar(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 536767012int(10) unsigned offset in File to fetch data
file /gbdb/cavPor3/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 39400double sum of the data points, for average and stddev calc
sumSquares 2040800double sum of data points squared, for stddev calc

Sample Rows
 
binchromchromStartchromEndnamespancountoffsetfilelowerLimitdataRangevalidCountsumDatasumSquares
585chrM05120chrM.52818651024536767012/gbdb/cavPor3/wib/gc5Base.wib01001024394002040800
585chrM512010240chrM.52818751024536768036/gbdb/cavPor3/wib/gc5Base.wib01001024402002094400
585chrM1024015360chrM.52818851024536769060/gbdb/cavPor3/wib/gc5Base.wib01001024396202044400
585chrM1536016800chrM.5281895288536770084/gbdb/cavPor3/wib/gc5Base.wib010028812860715600
585scaffold_005120scaffold_0.0510240/gbdb/cavPor3/wib/gc5Base.wib01001024324601445200
585scaffold_0512010240scaffold_0.1510241024/gbdb/cavPor3/wib/gc5Base.wib01001024472202753200
585scaffold_01024015360scaffold_0.2510242048/gbdb/cavPor3/wib/gc5Base.wib01001024505003030000
585scaffold_01536020480scaffold_0.3510243072/gbdb/cavPor3/wib/gc5Base.wib01001004383201963200
585scaffold_02048025600scaffold_0.4510244096/gbdb/cavPor3/wib/gc5Base.wib080951321501500500
585scaffold_02560027675scaffold_0.554155120/gbdb/cavPor3/wib/gc5Base.wib08041513350596500

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.