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 built at Sat, 29 Jun 2024 20:47:29 -0400.
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