Metrics Output
File Name: MetricsOutput.tsv
The metrics output file is a final combined metrics report that provides sample status, key analysis metrics, and metadata in a tab-separated values (TSV) file. Sample metrics within the report indicate guideline‑suggested lower specification limits (LSL) and upper specification limits (USL) for each sample in the run.
One metrics output file is generated for the entire run. An additional file is generated for each sample
Run Metrics
Run metrics from the analysis module indicate the quality of the sequencing run.
Review the following metrics to assess run data quality:
PCT_PF_READS
Percentage of reads on the sequencing flow cell that pass the filter.
≥ 55.0
(No lower specification limit for NovaSeq X Plus)
PCT_Q30_R1
Percentage of bases with a quality score ≥ 30 from Read 1.
≥ 80.0
(≥ 85.0 for NovaSeq X Plus)
PCT_Q30_R2
Percentage of bases with a quality score ≥ 30 from Read 2.
≥ 80.0
(≥ 85.0 for NovaSeq X Plus)
The values in the Run Metrics section are listed as NA in the following situations:
The analysis was started from FASTQ files.
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.
Sample QC Metrics
Review the following metrics to assess sample data quality:
CONTAMINATION_SCORE
The contamination score 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
*The recommended threshold of 0.059 for GENE_SCALED_MAD only applies to real cell‑free DNA.
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