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 4.6.0.0-33-gdffedfb built at Wed, 23 Oct 2024 21:44:48 -0400.
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