Metrics
Category Metrics
Overview
Holds summary statistics from RRBS processing QC @author jgentryThis table summarizes the values that are specific to this metric.
| Metric | Summary |
|---|---|
| READS_ALIGNED |
Number of mapped reads processed |
| NON_CPG_BASES |
Number of times a non-CpG cytosine was encountered |
| NON_CPG_CONVERTED_BASES |
Number of times a non-CpG cytosine was converted (C->T for +, G->A for -) |
| PCT_NON_CPG_BASES_CONVERTED |
NON_CPG_CONVERTED_BASES / NON_CPG_BASES (fraction) |
| CPG_BASES_SEEN |
Number of CpG sites encountered |
| CPG_BASES_CONVERTED |
Number of CpG sites that were converted (TG for +, CA for -) |
| PCT_CPG_BASES_CONVERTED |
CPG_BASES_CONVERTED / CPG_BASES_SEEN (fraction) |
| MEAN_CPG_COVERAGE |
Mean coverage of CpG sites |
| MEDIAN_CPG_COVERAGE |
Median coverage of CpG sites |
| READS_WITH_NO_CPG |
Number of reads discarded for having no CpG sites |
| READS_IGNORED_SHORT |
Number of reads discarded due to being too short |
| READS_IGNORED_MISMATCHES |
Number of reads discarded for exceeding the mismatch threshold |
GATK version 4.6.0.0-33-gdffedfb built at Wed, 23 Oct 2024 21:44:48 -0400.
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