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.

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.