ErrorSummaryMetrics

Metrics

Category Metrics

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Overview

Summary metrics produced by {@link CollectSequencingArtifactMetrics} as a roll up of the context-specific error rates, to provide global error rates per type of base substitution. Errors are normalized to the lexically lower reference base and summarized together. E.g. G>T is converted to C>A and merged with data from C>A for reporting.

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

Metric	Summary
REF_BASE	The reference base (or it's complement).
ALT_BASE	The alternative base (or it's complement).
SUBSTITUTION	A single string representing the substition from REF_BASE to ALT_BASE for convenience.
REF_COUNT	The number of reference bases observed.
ALT_COUNT	The number of alt bases observed.
SUBSTITUTION_RATE	The rate of the substitution in question.

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GATK version 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.