PreAdapterSummaryMetrics

Metrics

Category Metrics

Overview

Summary analysis of a single pre-adapter artifact. These artifacts occur on the original template strand, before the addition of adapters, so they correlate with read number / orientation in a specific way. For example, the well-known "Oxo-G" artifact occurs when a G on the template strand is oxidized, giving it an affinity for binding to A rather than the usual C. Thus PCR will introduce apparent G>T substitutions in read 1 and C>A in read 2. In the resulting alignments, a given G>T or C>A observation could either be: 1. a true mutation 2. an OxoG artifact 3. some other kind of artifact On average, we assume that 1 and 3 will not display this read number / orientation bias, so their contributions will cancel out in the calculation.

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

Metric Summary
SAMPLE_ALIAS
The name of the sample being assayed.
LIBRARY
The name of the library being assayed.
REF_BASE
The (upper-case) original base on the reference strand.
ALT_BASE
The (upper-case) alternative base that is called as a result of DNA damage.
TOTAL_QSCORE
The total Phred-scaled Q-score for this artifact. A lower Q-score means a higher probability that a REF_BASE:ALT_BASE observation randomly picked from the data will be due to this artifact, rather than a true variant.
WORST_CXT
The sequence context (reference bases surrounding the locus of interest) having the lowest Q-score among all contexts for this artifact.
WORST_CXT_QSCORE
The Q-score for the worst context.
WORST_PRE_CXT
The pre-context (reference bases leading up to the locus of interest) with the lowest Q-score.
WORST_PRE_CXT_QSCORE
The Q-score for the worst pre-context.
WORST_POST_CXT
The post-context (reference bases trailing after the locus of interest) with the lowest Q-score.
WORST_POST_CXT_QSCORE
The Q-score for the worst post-context.
ARTIFACT_NAME
A "nickname" of this artifact, if it is a known error mode.

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