Metrics
Category Metrics
Overview
Bait bias artifacts broken down by context.This table summarizes the values that are specific to this metric.
| Metric | Summary |
|---|---|
| SAMPLE_ALIAS |
|
| 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. |
| FWD_CXT_REF_BASES |
The number of REF_BASE:REF_BASE alignments at sites with the given reference context. |
| FWD_CXT_ALT_BASES |
The number of REF_BASE:ALT_BASE alignments at sites with the given reference context. |
| REV_CXT_REF_BASES |
The number of ~REF_BASE:~REF_BASE alignments at sites complementary to the given reference context. |
| REV_CXT_ALT_BASES |
The number of ~REF_BASE:~ALT_BASE alignments at sites complementary to the given reference context. |
| FWD_ERROR_RATE |
The substitution rate of REF_BASE:ALT_BASE, calculated as max(1e-10, FWD_CXT_ALT_BASES / (FWD_CXT_ALT_BASES + FWD_CXT_REF_BASES)). |
| REV_ERROR_RATE |
The substitution rate of ~REF_BASE:~ALT_BASE, calculated as max(1e-10, REV_CXT_ALT_BASES / (REV_CXT_ALT_BASES + REV_CXT_REF_BASES)). |
| ERROR_RATE |
The bait bias error rate, calculated as max(1e-10, FWD_ERROR_RATE - REV_ERROR_RATE). |
| 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.
0 comments
Please sign in to leave a comment.