Metrics
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. |
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