Metrics
Category Metrics
Overview
Metrics that are calculated during the process of marking duplicates within a stream of SAMRecords.This table summarizes the values that are specific to this metric.
| Metric | Summary |
|---|---|
| LIBRARY |
The library on which the duplicate marking was performed. |
| UNPAIRED_READS_EXAMINED |
The number of mapped reads examined which did not have a mapped mate pair, either because the read is unpaired, or the read is paired to an unmapped mate. |
| READ_PAIRS_EXAMINED |
The number of mapped read pairs examined. (Primary, non-supplemental) |
| SECONDARY_OR_SUPPLEMENTARY_RDS |
The number of reads that were either secondary or supplementary |
| UNMAPPED_READS |
The total number of unmapped reads examined. (Primary, non-supplemental) |
| UNPAIRED_READ_DUPLICATES |
The number of fragments that were marked as duplicates. |
| READ_PAIR_DUPLICATES |
The number of read pairs that were marked as duplicates. |
| READ_PAIR_OPTICAL_DUPLICATES |
The number of read pairs duplicates that were caused by optical duplication. Value is always < READ_PAIR_DUPLICATES, which counts all duplicates regardless of source. |
| PERCENT_DUPLICATION |
The fraction of mapped sequence that is marked as duplicate. |
| ESTIMATED_LIBRARY_SIZE |
The estimated number of unique molecules in the library based on PE duplication. |
GATK version 4.6.0.0-33-gdffedfb built at Wed, 23 Oct 2024 21:44:48 -0400.
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