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