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 |
| READ_LENGTH | The average read length of all the reads (will be fixed for a lane) |
| TOTAL_BASES | The total number of bases in all reads |
| PF_BASES | The total number of bases in all PF reads |
| Q20_BASES | The number of bases in all reads that achieve quality score 20 or higher |
| PF_Q20_BASES | The number of bases in PF reads that achieve quality score 20 or higher |
| Q30_BASES | The number of bases in all reads that achieve quality score 30 or higher |
| PF_Q30_BASES | The number of bases in PF reads that achieve quality score 30 or higher |
| Q20_EQUIVALENT_YIELD | The sum of quality scores of all bases divided by 20 |
| PF_Q20_EQUIVALENT_YIELD | The sum of quality scores of all bases divided by 20 |
GATK version 4.5.0.0 built at Tue, 9 Jan 2024 14:37:17 -0500.
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