Metrics Output
File name: MetricsOutput.tsv
The metrics output file is a final combined metrics report that provides sample status, key analysis metrics, and metadata in a tab-separated values (TSV) file. Sample metrics within the report indicate
Run Metrics
Run metrics from the analysis module indicate the quality of the sequencing run.
Review the following metrics to assess run data quality:
|
Metric |
Description |
Recommended Threshold |
|---|---|---|
|
PCT_PF_READS |
Percentage of reads on the sequencing flow cell that pass the filter. |
≥ 55.0 |
|
PCT_Q30_R1 |
Percentage of bases with a quality score ≥ 30 from Read 1. |
≥ 80.0 |
|
PCT_Q30_R2 |
Percentage of bases with a quality score ≥ 30 from Read 2. |
≥ 80.0 |
The values in the Run Metrics section are listed as NA in the following situations:
| • | The analysis was started from FASTQ files. |
| • | The analysis was started from BCL files and the InterOp files are missing or corrupt. |
Sample QC Metrics
Review the following metrics to assess sample data quality:
|
Metric |
Description |
Recommended Threshold |
Variant Class |
|---|---|---|---|
|
CONTAMINATION_SCORE |
The contamination score based on VAF distribution of SNPs.
|
Contamination Score ≤ 1227 |
All |
|
MEDIAN_EXON_COVERAGE |
Median exon fragment coverage across all exon bases. |
≥ 1300 |
Small variant, TMB, fusion, MSI |
|
PCT_EXON_1000X |
Percent exon bases with 1000X fragment coverage. |
≥ 80.0 |
Small variant, TMB |
|
GENE_SCALED_MAD |
The median of absolute deviations normalized by gene fold change. |
≤ 0.059* |
CNV |
|
CNV_TARGET_MEDIAN_BIN_COUNT |
The median raw bin count per CNV target. |
≥ 6.0 |
CNV |
* The recommended threshold of 0.059 for GENE_SCALED_MAD only applies to
