OverlappingErrorMetric

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)

Return to top

GATK version 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.