Metrics
Category Metrics
Overview
A set of metrics used to describe the general quality of a BAM fileThis table summarizes the values that are specific to this metric.
| Metric | Summary |
|---|---|
| TOTAL_READS |
The total number of reads in the input file |
| PF_READS |
The number of reads that are PF - pass filter |
| MEAN_PF_READ_NUMBER_OF_FLOWS |
The average number of flows in PF reads |
| PF_FLOWS |
The total number of flows in all PF reads |
| PF_Q20_FLOWS |
The number of flows in PF reads that achieve quality score 20 or higher |
| PCT_PF_Q20_FLOWS |
The percentage of flows in all reads that achieve quality score 20 or higher |
| PF_Q30_FLOWS |
The number of flows in PF reads that achieve quality score 30 or higher |
| PCT_PF_Q30_FLOWS |
The percentage of flows in all reads that achieve quality score 30 or higher |
| PF_Q20_EQUIVALENT_YIELD |
The sum of quality scores of all flows in PF reads divided by 20 |
GATK version 4.6.0.0-33-gdffedfb built at Wed, 23 Oct 2024 21:44:48 -0400.
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