QC Metrics

The following tables provide information on quantitation and sequencing metrics and boundaries.

Metric	Description	Lower Bound	Upper Bound	Rationale
standard_r_squared	R-squared value of the standards curve model.	0.980	N/A	Standards curve models showing poor linearity in log-log space are not good predictors of true sample concentrations.
standard_slope	Slope of the standards curve model.	0.95	1.15	Standards curve models that slope outside expected performance bands indicate an unreliable model.
ccn_library_pg_ul	Maximum allowable sample concentration.	N/A	1000 pg/µl	Samples with calculated DNA concentrations that exceed specifications indicate excess genomic DNA contamination.
median_ccn_pg_ul	Median calculated concentration value for all samples in batch.	16 pg/µl	N/A	A sequencing pool of appropriate volume cannot have an excessive number of overly dilute samples. Batches with high numbers of dilute samples indicate sample prep process failure.

Metric	Description	Lower Bound	Upper Bound	Rationale
cluster_density	Sequencing cluster density.	152,000 per mm²	338,000 per mm²	Flow cell with low cluster density does not generate enough reads. Over clustered flow cells usually produce sequencing data of low quality.
pct_pf	Percent reads passing chastity filter.	≥50%	N/A	Flow cells with extremely low %PF can have abnormal base representation and are likely to indicate problems with PF reads.
prephasing	Fraction of prephasing.	N/A	≤0.003	Empirically optimized recommendations for the VeriSeq NIPT Solution v2 – RUO.
phasing	Fraction of phasing.	N/A	≤0.004	Empirically optimized recommendations for the VeriSeq NIPT Solution v2 – RUO.
predicted_aligned_reads	Estimated average number of uniquely mapped fragments per sample.	≥4,000,000	N/A	Determined as minimal observed NES across normal population.