Metrics
Category Metrics
Overview
An error metric for the errors invovling bases in the overlapping region of a read-pair. The resulting metric includes error rate information which can be assigned to the reading of the molecular insert {@link #DISAGREES_WITH_REF_AND_MATE_ONLY_Q}, error rate which can be assigned to events that occured to to the molecular insert before it was loaded onto the flowcell/sequencer {@link #DISAGREES_WITH_REFERENCE_ONLY_Q}, and an error rate which cannot be explained nicely {@link #THREE_WAYS_DISAGREEMENT_ONLY_Q}.This table summarizes the values that are specific to this metric.
| Metric | Summary |
|---|---|
| NUM_BASES_WITH_OVERLAPPING_READS |
The number of bases for which an overlapping base from the mate read was found |
| NUM_DISAGREES_WITH_REFERENCE_ONLY |
The number of bases that disagree with the reference, but agree with their mate |
| DISAGREES_WITH_REFERENCE_ONLY_Q |
The (phred) rate of bases that disagree with the reference, but agree with their mate |
| NUM_DISAGREES_WITH_REF_AND_MATE |
The number of bases that disagree with both the reference and their mate (which agree with each other) |
| DISAGREES_WITH_REF_AND_MATE_ONLY_Q |
The (phred) rate of bases that disagree with both the reference and their mate (which agree with each other) |
| NUM_THREE_WAYS_DISAGREEMENT |
The number of bases that disagree with both the reference and their mate (which also disagree) |
| THREE_WAYS_DISAGREEMENT_ONLY_Q |
The (phred) rate of bases that disagree with both the reference and their mate (which also disagree) |
GATK version 4.6.0.0-33-gdffedfb built at Wed, 23 Oct 2024 21:44:48 -0400.
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