GcBiasDetailMetrics – GATK

Metrics

Overview

Class that holds detailed metrics about reads that fall within windows of a certain GC bin on the reference genome. @author Tim Fennell

This table summarizes the values that are specific to this metric.

Metric	Summary
ACCUMULATION_LEVEL
READS_USED	This option is used to mark including or excluding duplicates.
GC	The G+C content of the reference sequence represented by this bin. Values are from 0% to 100%
WINDOWS	The number of windows on the reference genome that have this G+C content.
READ_STARTS	The number of reads whose start position is at the start of a window of this GC.
MEAN_BASE_QUALITY	The mean quality (determined via the error rate) of all bases of all reads that are assigned to windows of this GC.
NORMALIZED_COVERAGE	The ratio of "coverage" in this GC bin vs. the mean coverage of all GC bins. A number of 1 represents mean coverage, a number less than one represents lower than mean coverage (e.g. 0.5 means half as much coverage as average) while a number greater than one represents higher than mean coverage (e.g. 3.1 means this GC bin has 3.1 times more reads per window than average).
ERROR_BAR_WIDTH	The radius of error bars in this bin based on the number of observations made. For example if the normalized coverage is 0.75 and the error bar width is 0.1 then the error bars would be drawn from 0.65 to 0.85.

GATK version 4.5.0.0 built at Tue, 9 Jan 2024 14:37:17 -0500.