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

# Run QC

The Run Metrics section of the metrics output report provides sequencing run quality metrics along with suggested values to determine if they are within an acceptable range. The overall percentage of reads passing filter is compared to a minimum threshold. For Read 1 and Read 2, the average percentage of bases ≥ Q30, which gives a prediction of the probability of an incorrect base call (Q‑score), are also compared to a minimum threshold.

Review the following metrics to assess run data quality:

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

<table><thead><tr><th width="169.56640625">Metric</th><th>Description</th><th>Recommended Threshold</th></tr></thead><tbody><tr><td>PCT_PF_READS</td><td>Percentage of reads on the sequencing flow cell that pass the filter.</td><td><p>≥ 55.0</p><p>(No lower specification limit for NovaSeq X Plus)</p></td></tr><tr><td>PCT_Q30_R1</td><td>Percentage of bases with a quality score ≥ 30 from Read 1.</td><td><p>≥ 80.0</p><p>(≥ 85.0 for NovaSeq X Plus)</p></td></tr><tr><td>PCT_Q30_R2</td><td>Percentage of bases with a quality score ≥ 30 from Read 2.</td><td><p>≥ 80.0</p><p>(≥ 85.0 for NovaSeq X Plus)</p></td></tr></tbody></table>

The values in the Run Metrics section are listed as NA in the following situations:

* If the analysis was started from FASTQ files.
* If 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.


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