> For the complete documentation index, see [llms.txt](https://help.connected.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.connected.illumina.com/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/quality-control/sample-qc.md).

# Sample QC

DRAGEN TruSight Oncology 500 ctDNA uses QC metrics to assess the validity of analysis for DNA libraries that pass contamination quality control. The metrics are available in the `MetricsOutput.tsv` file, refer to [Metrics Output ](/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-output/metrics-output.md)for details.

<table data-full-width="true"><thead><tr><th>Metric</th><th>Description</th><th>Recommended Guideline Quality Threshold</th><th>Variant Class</th></tr></thead><tbody><tr><td>CONTAMINATION_SCORE</td><td>The contamination score is 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](/tso500/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/troubleshooting.md)


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