The QC screen displays quality metrics for the run and each sample sequenced in the
run. This information is also accessible through the Monitor menu within 72 hours of
starting the run on the sequencer.
To view the QC screen, in the Results > Run Results screen, click the sample name in
the Sample Name column. If you are in the View Results screen, click QC in the
left navigation pane to view the screen.
The data displayed in the screen depend on the assay that was used in the run.
Metric
Description
Run QC
General run quality control information
Key Signal
The average signal after software processing for library ISPs that identically match
the library key (TCAG).
Percent Loading
The number of wells with ISPs divided by the number of the total addressable wells in
a run.
Raw Read Accuracy
The percent of raw reads mapped to the reference genome.
Templating QC—CF-1
Control
Sequencing quality metrics of the control fragment. They indicate templating
success.
Average Reads Per Lane
The number of CF-1 reads divided by the number of chip lanes used in the run.
Base Call Accuracy
The probability that a given base is called correctly.
1 – (total number of errors for all positions in CF-1) / (total number of CF-1 base
reads).
Mean AQ20 Read Length (bp) Average length, in base pairs, at which the accuracy rate is ≥99% for CF
‑
1 reads.
Sample QC—DNA
Sequencing quality metrics of the sample DNA library.
MAPD
MAPD (Median of the Absolute values of all Pairwise Differences) is a quality metric
that estimates coverage variability between adjacent amplicons in CNV analyses. A
MAPD value of ≤0.5 indicates an acceptable level of coverage variability. High MAPD
value typically translates to a lower coverage uniformity. Lower coverage uniformity
can result in missed or erroneous CNV calls.
Mapped Reads
The number of reads that are mapped to the reference file.
Mean AQ20 Read Length (bp) The average length, in base pairs, at which the accuracy rate is ≥99% for all aligned
reads of a library.
Mean Read Length (bp)
The average length, in base pairs, of final library reads for the sample.
Uniformity of Amplicon
Coverage
The percentage of amplicons that had at least 20% of the average number of reads
per amplicon. Cumulative coverage is linearly interpolated between nearest integer
read depth counts.
Median Mol Cov
The median number of functional molecule reads per amplicon calculated over all
amplicons in the assay.
This metric is applicable to Ion AmpliSeq
™
HD library chemistry only.
Median Read Cov
The median number of reads per amplicon calculated over all amplicons in the assay.
QC results
Chapter 9
Review data and results
View sequencing results and run metrics
9
94
Genexus
™
Integrated Sequencer User Guide
