Metrics
Category Metrics
Overview
Pre-adapter artifacts broken down by context.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. |
| CONTEXT |
The sequence context to which the analysis is constrained. |
| PRO_REF_BASES |
The number of REF_BASE:REF_BASE alignments having a read number and orientation that supports the presence of this artifact. |
| PRO_ALT_BASES |
The number of REF_BASE:ALT_BASE alignments having a read number and orientation that supports the presence of this artifact. |
| CON_REF_BASES |
The number of REF_BASE:REF_BASE alignments having a read number and orientation that refutes the presence of this artifact. |
| CON_ALT_BASES |
The number of REF_BASE:ALT_BASE alignments having a read number and orientation that refutes the presence of this artifact. |
| ERROR_RATE |
The estimated error rate due to this artifact. Calculated as max(1e-10, (PRO_ALT_BASES - CON_ALT_BASES) / (PRO_ALT_BASES + PRO_REF_BASES + CON_ALT_BASES + CON_REF_BASES)). |
| QSCORE |
The Phred-scaled quality score of the artifact, calculated as -10 * log10(ERROR_RATE). |
GATK version 4.6.0.0-33-gdffedfb built at Wed, 23 Oct 2024 21:44:48 -0400.
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