Quality Control

The software calculates several quality control metrics for runs and samples.

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. The following tables show run metric and quality threshold information for different systems.

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.

NovaSeq 6000 or NovaSeq 6000Dx (RUO)

Metric	Description	Recommended Guideline Quality Threshold	Variant Class
PCT_PF_READS (%)	Total percentage of reads passing filter.	≥55.0	All
PCT_Q30_R1 (%)	Percentage of Read 1 reads with quality score ≥ 30.	≥80.0	All
PCT_Q30_R2 (%)	Percentage of Read 2 reads with quality score ≥ 30.	≥80.0	All

NovaSeq X

Metric	Description	Recommended Guideline Quality Threshold	Variant Class
PCT_Q30_R1 (%)	Percentage of Read 1 reads with quality score ≥ 30.	≥85.0	All
PCT_Q30_R2 (%)	Percentage of Read 2 reads with quality score ≥ 30.	≥85.0	All

There is no PCT_PF_READS value in NovaSeqX Plus runs, so the PCT_PF_READS value will always be NA

DNA Sample QC

DRAGEN TruSight Oncology 500 uses QC metrics to assess the validity of analysis for DNA libraries that pass contamination quality control. If the library fails one or more quality metrics, then the corresponding variant type or biomarker is not reported, and the associated QC category in the report header displays FAIL.

DNA library QC results are available in the MetricsOutput.tsv file. Refer to Metrics Output for details.

Metric	Description	Recommended Guideline Quality Threshold	Variant Class
CONTAMINATION_SCORE	The contamination score is based on VAF distribution of SNPs.	≤ 1227	All
MEDIAN_EXON_COVERAGE	Median exon fragment coverage across all exon bases.	≥ 1300	Small variant, TMB, Fusion, MSI
PCT_EXON_1000X	Percent exon bases with 1000x fragment coverage.	≥ 80.0	Small variant, TMB
GENE_SCALED_MAD	The median of absolute deviations normalized by gene fold change.	≤ 0.059*	CNV
MEDIAN_BIN_COUNT_CNV_TARGET	The median raw bin count per CNV target.	≥ 6.0	CNV