Metrics
Category Metrics
Overview
Metrics class for outputs.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. |
| CONTEXT | The sequence context being reported on. |
| TOTAL_SITES | The total number of sites that had at least one base covering them. |
| TOTAL_BASES | The total number of basecalls observed at all sites. |
| REF_NONOXO_BASES | The number of reference alleles observed as C in read 1 and G in read 2. |
| REF_OXO_BASES | The number of reference alleles observed as G in read 1 and C in read 2. |
| REF_TOTAL_BASES | The total number of reference alleles observed |
| ALT_NONOXO_BASES | The count of observed A basecalls at C reference positions and T basecalls at G reference bases that are correlated to instrument read number in a way that rules out oxidation as the cause |
| ALT_OXO_BASES | The count of observed A basecalls at C reference positions and T basecalls at G reference bases that are correlated to instrument read number in a way that is consistent with oxidative damage. |
| OXIDATION_ERROR_RATE | The oxo error rate, calculated as max(ALT_OXO_BASES - ALT_NONOXO_BASES, 1) / TOTAL_BASES |
| OXIDATION_Q | -10 * log10(OXIDATION_ERROR_RATE) |
| C_REF_REF_BASES | The number of ref basecalls observed at sites where the genome reference == C. |
| G_REF_REF_BASES | The number of ref basecalls observed at sites where the genome reference == G. |
| C_REF_ALT_BASES | The number of alt (A/T) basecalls observed at sites where the genome reference == C. |
| G_REF_ALT_BASES | The number of alt (A/T) basecalls observed at sites where the genome reference == G. |
| C_REF_OXO_ERROR_RATE | The rate at which C>A and G>T substitutions are observed at C reference sites above the expected rate if there were no bias between sites with a C reference base vs. a G reference base. |
| C_REF_OXO_Q | C_REF_OXO_ERROR_RATE expressed as a phred-scaled quality score. |
| G_REF_OXO_ERROR_RATE | The rate at which C>A and G>T substitutions are observed at G reference sites above the expected rate if there were no bias between sites with a C reference base vs. a G reference base. |
| G_REF_OXO_Q | G_REF_OXO_ERROR_RATE expressed as a phred-scaled quality score. |
GATK version 4.5.0.0 built at Tue, 9 Jan 2024 14:37:17 -0500.
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