# 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 guideline‑suggested lower specification limits (LSL) and upper specification limits (USL) for each sample in the run.

One metrics output file is generated for the entire run. An additional file is generated for each sample.

{% hint style="success" %}
All metrics and guidelines are applicable to all versions of DRAGEN TSO 500 ctDNA analysis software (v2.1 and above).
{% endhint %}

#### 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. | <p>≥ 55.0</p><p>(No lower specification limit for NovaSeq X Plus)</p> |
| PCT\_Q30\_R1   | Percentage of bases with a quality score ≥ 30 from Read 1.            | <p>≥ 80.0</p><p>(≥ 85.0 for NovaSeq X Plus)</p>                       |
| PCT\_Q30\_R2   | Percentage of bases with a quality score ≥ 30 from Read 2.            | <p>≥ 80.0</p><p>(≥ 85.0 for NovaSeq X Plus)</p>                       |

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.
* \[NovaSeqX Plus only] There is no PCT\_PF\_READS value in NovaSeqX Plus runs, so the PCT\_PF\_READS value will always be NA.

#### Sample QC Metrics

Review the following metrics to assess sample data quality:

<table data-full-width="true"><thead><tr><th>Metric</th><th>Description</th><th>Recommended Threshold</th><th>Variant Class</th></tr></thead><tbody><tr><td>CONTAMINATION_SCORE</td><td>The contamination score based on VAF distribution of SNPs.</td><td>≤ 1227</td><td>All</td></tr><tr><td>MEDIAN_EXON_COVERAGE</td><td>Median exon fragment coverage across all exon bases.</td><td>≥ 1300</td><td>Small variant, TMB, fusion, MSI</td></tr><tr><td>PCT_EXON_1000X</td><td>Percent exon bases with 1000X fragment coverage.</td><td>≥ 80.0</td><td>Small variant, TMB</td></tr><tr><td>GENE_SCALED_MAD</td><td>The median of absolute deviations normalized by gene fold change.</td><td>≤ 0.059*</td><td>CNV</td></tr><tr><td>MEDIAN_BIN_COUNT_CNV_TARGET</td><td>The median raw bin count per CNV target.</td><td>≥ 6.0</td><td>CNV</td></tr></tbody></table>

\*The recommended threshold of 0.059 for GENE\_SCALED\_MAD only applies to real cell‑free DNA.

For troubleshooting information, refer to [Troubleshooting](https://help.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/troubleshooting)