Package picard.analysis

Class GcBiasDetailMetrics

  • 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.

    • Field Detail

      • ACCUMULATION_LEVEL

        public String ACCUMULATION_LEVEL

      • READS_USED

        public String READS_USED
        This option is used to mark including or excluding duplicates.

      • GC

        public int GC
        The G+C content of the reference sequence represented by this bin. Values are from 0% to 100%

      • WINDOWS

        public int WINDOWS
        The number of windows on the reference genome that have this G+C content.

      • READ_STARTS

        public long READ_STARTS
        The number of reads whose start position is at the start of a window of this GC.

      • 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.

      • 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).

      • 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.

    • Constructor Detail

      • GcBiasDetailMetrics

        public GcBiasDetailMetrics()