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