Metrics
Category Metrics
Overview
Metrics produced by the GetHiSeqXPFFailMetrics program. Used to diagnose lanes from HiSeqX Sequencing, providing the number and fraction of each of the reasons that reads could have not passed PF. Possible reasons are EMPTY (reads from empty wells with no template strand), POLYCLONAL (reads from wells that had more than one strand cloned in them), MISALIGNED (reads from wells that are near the edge of the tile), UNKNOWN (reads that didn't pass PF but couldn't be diagnosed)This table summarizes the values that are specific to this metric.
| Metric | Summary |
|---|---|
| TILE | The Tile that is described by this metric. Can be a string (like "All") to mean some marginal over tiles. * |
| READS | The total number of reads examined |
| PF_FAIL_READS | The number of non-PF reads in this tile. |
| PCT_PF_FAIL_READS | The fraction of PF_READS |
| PF_FAIL_EMPTY | The number of non-PF reads in this tile that are deemed empty. |
| PCT_PF_FAIL_EMPTY | The fraction of non-PF reads in this tile that are deemed empty (as fraction of all non-PF reads). |
| PF_FAIL_POLYCLONAL | The number of non-PF reads in this tile that are deemed multiclonal. |
| PCT_PF_FAIL_POLYCLONAL | The fraction of non-PF reads in this tile that are deemed multiclonal (as fraction of all non-PF reads). |
| PF_FAIL_MISALIGNED | The number of non-PF reads in this tile that are deemed "misaligned". |
| PCT_PF_FAIL_MISALIGNED | The fraction of non-PF reads in this tile that are deemed "misaligned" (as fraction of all non-PF reads). |
| PF_FAIL_UNKNOWN | The number of non-PF reads in this tile that have not been classified. |
| PCT_PF_FAIL_UNKNOWN | The fraction of non-PF reads in this tile that have not been classified (as fraction of all non-PF reads). |
GATK version 4.6.0.0 built at Sat, 29 Jun 2024 20:47:29 -0400.
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