# Key QC Metrics

## Key QC Metrics

The following table highlights key quality metrics for evaluating your analysis results. The app has pre-set defaults, but you can set your own QC thresholds based on your application. Additional metrics are described in the DRAGEN documentation.

| Metric                                        | Description                                                               | Source File                              | Unit              | Guidance                                                                                                                                                                                  |
| --------------------------------------------- | ------------------------------------------------------------------------- | ---------------------------------------- | ----------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| Average alignment coverage over target region | Mean de-duplicated coverage of the tumor sample                           | `.target_bed_coverage_metrics_tumor.csv` | Fold (e.g., 200x) | Values of 150x–200x typically provide good sensitivity at 5% VAF. Low values may reduce sensitivity for low-frequency variants.                                                           |
| Uniformity of coverage (PCT > 0.2\*mean)      | Percent of bases with coverage above 0.2x the mean de-duplicated coverage | `.target_bed_coverage_metrics_tumor.csv` | %                 | Low values indicate non-uniform coverage. Positions well below the mean may have reduced sensitivity.                                                                                     |
| Duplicate marked reads                        | Percentage of de-duplicated reads                                         | `mapping_metrics.csv`                    | %                 | High values can indicate issues with library preparation or input nucleic acid quality.                                                                                                   |
| Supplementary (chimeric) alignments           | Percentage of chimeric reads                                              | `mapping_metrics.csv`                    | %                 | Values above 1–2% indicate fixation artifacts. Consider running these samples in [low-quality FFPE mode](/dragen-somatic-for-idt-custom-panels/stage-2-run-variant-calling/ffpe-mode.md). |

## What Happens Next: Interpretation and Reporting

After the DRAGEN for IDT Custom Panels pipeline completes, you can import the VCF output into **Illumina Connected Insights** for variant interpretation, annotation, and clinical research reporting.

See [Connecting to Connected Insights](/dragen-somatic-for-idt-custom-panels/qc-and-interpretation/connected-insights.md).


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