Metrics
Category Metrics
Overview
Metrics class for the analysis of reads obtained from targeted pcr experiments e.g. the TruSeq Custom Amplicon (TSCA) kit (Illumina).This table summarizes the values that are specific to this metric.
| Metric | Summary |
|---|---|
| CUSTOM_AMPLICON_SET | The name of the amplicon set used in this metrics collection run |
| AMPLICON_TERRITORY | The number of unique bases covered by the intervals of all amplicons in the amplicon set |
| ON_AMPLICON_BASES | The number of PF_BASES_ALIGNED that mapped to an amplified region of the genome. |
| NEAR_AMPLICON_BASES | The number of PF_BASES_ALIGNED that mapped to within a fixed interval of an amplified region, but not on a baited region. |
| OFF_AMPLICON_BASES | The number of PF_BASES_ALIGNED that mapped neither on or near an amplicon. |
| PCT_AMPLIFIED_BASES | The fraction of PF_BASES_ALIGNED that mapped to or near an amplicon, (ON_AMPLICON_BASES + NEAR_AMPLICON_BASES)/PF_BASES_ALIGNED. |
| PCT_OFF_AMPLICON | The fraction of PF_BASES_ALIGNED that mapped neither onto or near an amplicon, OFF_AMPLICON_BASES/PF_BASES_ALIGNED |
| ON_AMPLICON_VS_SELECTED | The fraction of bases mapping to regions on or near amplicons, which mapped directly to but not near amplicons, ON_AMPLICON_BASES/(NEAR_AMPLICON_BASES + ON_AMPLICON_BASES) |
| MEAN_AMPLICON_COVERAGE | The mean read coverage of all amplicon regions in the experiment. |
| FOLD_ENRICHMENT | The fold by which the amplicon region has been amplified above genomic background. |
GATK version 4.6.0.0 built at Sat, 29 Jun 2024 20:47:29 -0400.
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