> For the complete documentation index, see [llms.txt](https://help.tso500software.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.tso500software.illumina.com/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-output/metrics-output.md).

# Metrics Output

The Metrics Output File ( `MetricsOutput.tsv` ) 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 file 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.

The Metrics Output File contains the following sections for all samples:

<table data-full-width="true"><thead><tr><th>Section</th><th width="463.09375">Metrics</th><th>Interpretation Details</th></tr></thead><tbody><tr><td>Header</td><td>Output date, time and pipeline version</td><td>-</td></tr><tr><td>Run QC Metrics</td><td>Percentage of reads meeting quality scores (PCT_PF_READS, PCT_Q30_R1 (%), PCT_Q30_R2 (%))</td><td><a href="/pages/CLXQ5mvTM0qIHYkUua9C">Run QC page</a></td></tr><tr><td>Analysis Status</td><td>Completion confirmation, failed and not executed steps</td><td>-</td></tr><tr><td>DNA Library QC Metrics</td><td>Contamination score (CONTAMINATION_SCORE)</td><td><a href="/pages/8WrQqdm8wRBAPOR99K4e">Contamination page</a></td></tr><tr><td>DNA Library QC Metrics for Small Variant Calling and TMB</td><td>Median exon coverage (MEDIAN_EXON_COVERAGE (count)), percent of exons with 1000X coverage (PCT_EXON_1000X (%))</td><td><a href="/pages/vCtdzVkvcae53cvfbkIY">Sample QC page</a></td></tr><tr><td>DNA Library QC Metrics for MSI and Fusions</td><td>Median exon coverage (MEDIAN_EXON_COVERAGE (count))</td><td><a href="/pages/vCtdzVkvcae53cvfbkIY">Sample QC page</a></td></tr><tr><td>DNA Library QC Metrics for CNV Calling</td><td>The median of absolute deviations normalized by gene fold change (GENE_SCALED_MAD (count)), the median raw bin count per CNV target.(MEDIAN_BIN_COUNT_CNV_TARGET (count))</td><td><a href="/pages/vCtdzVkvcae53cvfbkIY">Sample QC page</a></td></tr><tr><td>DNA Expanded Metrics</td><td>Total reads, mean family size, chimeric reads, and others</td><td><a href="/pages/qLVvRPCr3lVXCt4Q4YMj">DNA Expanded Metrics</a></td></tr><tr><td>Notes</td><td>Comments</td><td>-</td></tr></tbody></table>


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