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. |
GATK version 4.6.0.0-33-gdffedfb built at Wed, 23 Oct 2024 21:44:48 -0400.
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