Schema for GC Percent - GC Percent in 5-Base Windows

Schema for GC Percent - GC Percent in 5-Base Windows

Database: bosTau4 Primary Table: gc5Base Row Count: 545,767
Format description: Wiggle track values to display as y-values (first 6 fields are bed6)

field	example	SQL type	description
`bin`	585	`smallint unsigned`	Indexing field to speed chromosome range queries.
`chrom`	chr1	`varchar(255)`	Reference sequence chromosome or scaffold
`chromStart`	0	`int unsigned`	Start position in chromosome
`chromEnd`	5120	`int unsigned`	End position in chromosome
`name`	chr1.16313	`varchar(255)`	Name of item
`span`	5	`int unsigned`	each value spans this many bases
`count`	1024	`int unsigned`	number of values in this block
`offset`	16590744	`int unsigned`	offset in File to fetch data
`file`	/gbdb/bosTau4/wib/gc5Base.wib	`varchar(255)`	path name to data file, one byte per value
`lowerLimit`	0	`double`	lowest data value in this block
`dataRange`	80	`double`	lowerLimit + dataRange = upperLimit
`validCount`	925	`int unsigned`	number of valid data values in this block
`sumData`	29623.3	`double`	sum of the data points, for average and stddev calc
`sumSquares`	1395210	`double`	sum of data points squared, for stddev calc

Sample Rows

bin	chrom	chromStart	chromEnd	name	span	count	offset	file	dataRange	validCount	sumData	sumSquares
585	chr1	0	5120	chr1.16313	5	1024	16590744	/gbdb/bosTau4/wib/gc5Base.wib	80	925	29623.3	1395210
585	chr1	5120	10240	chr1.16314	5	1024	16591768	/gbdb/bosTau4/wib/gc5Base.wib	100	1024	43380	2342800
585	chr1	10240	15360	chr1.16315	5	1024	16592792	/gbdb/bosTau4/wib/gc5Base.wib	100	1024	31700	1515600
585	chr1	15360	20480	chr1.16316	5	1024	16593816	/gbdb/bosTau4/wib/gc5Base.wib	100	1024	38380	2006800
585	chr1	20480	25600	chr1.16317	5	1024	16594840	/gbdb/bosTau4/wib/gc5Base.wib	100	1024	39180	2003600
585	chr1	25600	30720	chr1.16318	5	1024	16595864	/gbdb/bosTau4/wib/gc5Base.wib	100	1024	39940	1998800
585	chr1	30720	35840	chr1.16319	5	1024	16596888	/gbdb/bosTau4/wib/gc5Base.wib	100	1024	39620	2023600
585	chr1	35840	40960	chr1.16320	5	1024	16597912	/gbdb/bosTau4/wib/gc5Base.wib	100	1024	39100	1980400
585	chr1	40960	46080	chr1.16321	5	1024	16598936	/gbdb/bosTau4/wib/gc5Base.wib	100	1024	39220	1994000
585	chr1	46080	51200	chr1.16322	5	1024	16599960	/gbdb/bosTau4/wib/gc5Base.wib	100	1024	36760	1795200

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 aspects 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.