Package picard.analysis
Class GcBiasDetailMetrics
- java.lang.Object
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- htsjdk.samtools.metrics.MetricBase
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- picard.metrics.MultilevelMetrics
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- picard.analysis.GcBiasDetailMetrics
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public class GcBiasDetailMetrics extends MultilevelMetrics
Class that holds detailed metrics about reads that fall within windows of a certain GC bin on the reference genome.
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Field Summary
Fields Modifier and Type Field Description String
ACCUMULATION_LEVEL
double
ERROR_BAR_WIDTH
The radius of error bars in this bin based on the number of observations made.int
GC
The G+C content of the reference sequence represented by this bin.int
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.double
NORMALIZED_COVERAGE
The ratio of "coverage" in this GC bin vs.long
READ_STARTS
The number of reads whose start position is at the start of a window of this GC.String
READS_USED
This option is used to mark including or excluding duplicates.int
WINDOWS
The number of windows on the reference genome that have this G+C content.-
Fields inherited from class picard.metrics.MultilevelMetrics
LIBRARY, READ_GROUP, SAMPLE
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Constructor Summary
Constructors Constructor Description GcBiasDetailMetrics()
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Field Detail
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ACCUMULATION_LEVEL
public String ACCUMULATION_LEVEL
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READS_USED
public String READS_USED
This option is used to mark including or excluding duplicates.
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GC
public int GC
The G+C content of the reference sequence represented by this bin. Values are from 0% to 100%
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WINDOWS
public int WINDOWS
The number of windows on the reference genome that have this G+C content.
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READ_STARTS
public long READ_STARTS
The number of reads whose start position is at the start of a window of this GC.
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MEAN_BASE_QUALITY
public int 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.
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NORMALIZED_COVERAGE
public double 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).
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ERROR_BAR_WIDTH
public double 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.
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