Metrics
This 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 |
See also General Documentation | Tool Docs Index Tool Documentation Index | Support Forum
GATK version 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.