QC Metric
Description
Sample Balance Factor
For a given sample in a system install qualification run, Sample Balance
Factor = Number of mapped reads / Mean number of mapped reads for
four tested samples A–D.
Uniformity Of Base Coverage
The percentage of bases having a depth of coverage ≥20% of the mean
coverage at each position.
Performance Qualification results
For a Performance Qualification run, basic information about the verification run is
provided, and the reference range and pass/fail QC status for the following metrics
are reported for the samples and controls that are used in the run.
Manager- and administrator-level users can sign off on the PQ Report, at which point
it becomes a locked PQ Report. However, we recommend that only qualified support
specialists sign off on a PQ Report.
QC metric
Description
Pass threshold
Run QC
AQ20 Mean Read Length (bp)
Average read length, in base pairs, at which the error rate is ≤1%
for all aligned reads.
≥95
Raw Read Accuracy
The percentage of raw reads mapped to the reference genome.
≥98.5
Run Balance Factor
The minimum Sample Balance Factor in a set of four tested
samples A–D.
≥0.5
Total Reads
The total number of filtered and trimmed reads with the listed
barcodes assigned to the samples.
≥10,000,000
Templating Control QC – CF-1
Average Reads Per Lane
Average number of CF-1 reads per GX5
™
Chip lane.
≥0
Base Call Accuracy
1 – (total number of errors for all positions in the control / total
number of aligned bases).
≥0
Mean AQ20 read length (bp)
Average read length, in base pairs, at which the error rate is ≤1%
for all aligned reads of the CF-1 control fragment.
≥0
Control QC – DNA
COSM12558
Detection of variant yields call of PRESENT and QC Status = Pass
Present
COSM28747
COSM476
COSM521
COSM6223
COSM6224
COSM760
Chapter 9
Review data and results
Verification runs
9
Genexus
™
Integrated Sequencer User Guide
115
