Metrics Output

The MetricsOutput.tsv file contains the following quality control metrics for all samples:

This TSV file also includes expanded DNA library QC metrics per sample, based on total reads, collapsed reads, chimeric reads, and on-target reads. Analysis using RNA samples also produces RNA library QC metrics and expanded RNA library QC metrics per sample based on total reads and coverage.

The MetricsOutput.tsv file is a final combined metrics report with sample status, key analysis metrics, and metadata. Sample metrics within the report include suggested lower specification limits (LSL) and upper specification limits (USL) for each sample in the run.

For troubleshooting information, refer to Troubleshooting.

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:

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If the analysis was started from FASTQ files.

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If 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 and CONTAMINATION_P_VALUE	The contamination score based on VAF distribution of SNPs. The contamination p-value used to assess highly rearranged genomes. A p‑value ≤ 0.049 suggests that the sample has large-scale rearrangements that could lead to high-contamination scores without actual sample contamination. The contamination p-value is only needed when the contamination score is above USL.	Contamination Score ≤ 1672 OR Contamination Score > 1672 AND Contamination p‑value ≤ 0.049	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
MEDIAN_BIN_COUNT_CNV_TARGET	The median raw bin count per CNV target.	≥ 6.0	CNV

* The recommended threshold of 0.059 for GENE_SCALED_MAD only applies to real cell‑free DNA.