Metrics
Category Metrics
Overview
Metrics that are calculated during the process of marking duplicates within a stream of SAMRecords using the UmiAwareDuplicateSetIterator.This table summarizes the values that are specific to this metric.
| Metric | Summary |
|---|---|
| LIBRARY | Library that was used to generate UMI data. |
| MEAN_UMI_LENGTH | Number of bases in each UMI |
| OBSERVED_UNIQUE_UMIS | Number of different UMI sequences observed |
| INFERRED_UNIQUE_UMIS | Number of different inferred UMI sequences derived |
| OBSERVED_BASE_ERRORS | Number of errors inferred by comparing the observed and inferred UMIs |
| DUPLICATE_SETS_IGNORING_UMI | Number of duplicate sets found before taking UMIs into account |
| DUPLICATE_SETS_WITH_UMI | Number of duplicate sets found after taking UMIs into account |
| OBSERVED_UMI_ENTROPY | Entropy (in base 4) of the observed UMI sequences, indicating the effective number of bases in the UMIs. If this is significantly smaller than UMI_LENGTH, it indicates that the UMIs are not distributed uniformly. |
| INFERRED_UMI_ENTROPY | Entropy (in base 4) of the inferred UMI sequences, indicating the effective number of bases in the inferred UMIs. If this is significantly smaller than UMI_LENGTH, it indicates that the UMIs are not distributed uniformly. |
| UMI_BASE_QUALITIES | Estimation of Phred scaled quality scores for UMIs |
| PCT_UMI_WITH_N | The percentage of reads that contain an UMI that contains at least one N |
GATK version 4.6.0.0 built at Sat, 29 Jun 2024 20:47:29 -0400.
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