Section
Description
Fusions
Lists and describes the fusions that are detected in the sample.
CNVs
Lists and describes the copy number variants (CNVs) that are detected in the sample.
[1]
Column appears in analyses of Ion AmpliSeq
™
HD sequencing data only.
The Run Metrics screen provides various metrics on the chip, wells, and Ion Sphere
™
Particles (ISPs) used in a run. For runs with multiple assays, metrics are provided for
each assay in the run. The screen has summary information is at the top, followed by
sample-specific information in the Run Samples table and data on barcodes that were
not assigned in the run but have reads detected in the Barcodes With Reads Reported
table.
To view the run metrics, in the Results > Run Results screen, click the run name in
the Run Plan column. Note that for runs with multiple assays, only the metrics for the
first assay are shown in the initial View Results screen. Use the dropdown list at top
of the screen to select a different assay.
Alternatively, in the Results > Run Results screen, click the sample name in the
Sample Name column, then in the the View Results screen, click Run Metrics in
the left navigation pane.
Run Metrics
Metric
Description
Loading
The number and percentage of total addressable wells on the chip that contain an ISP.
Enrichment
The number and percentage of wells ISPs that contain live ISPs.
Library
The number and percentage of wells with live ISPs that contain Library ISPs.
Final Reads
Library reads passing all filters that are recorded in the output BAM files. This value
can be different from the total number of reads due to technicalities associated with
read trimming beyond a minimal requirement.
Total Bases
The number of filtered and trimmed base pairs that are reported in the output BAM file.
Mean Raw Accuracy 1x
The mean raw accuracy across each individual base position in a read calculated as,
(1−[total errors in the sequenced reads]/[total bases sequenced]) × 100. Raw read
accuracy is measured at each base across the length of the read and is based on 1x
sequencing coverage; raw read accuracy is
not based on consensus accuracy across
multiple reads for the same base position.
Wells with ISPs
The number of wells that contain an ISP.
Total Addressable Wells
Wells on the chip that can be physically reached by a library.
Empty Wells
The percentage of total addressable wells on the chip that do not contain an ISP.
Wells with Live ISPs
Loaded wells with ISPs with a signal of sufficient strength and composition to be
associated with the library or control fragment key.
Wells with Library ISPs
Loaded wells with live ISPs with a key signal that is identical to the library key signal.
Wells with Control ISPs
Loaded wells with live ISPs with a key signal that is identical to the control fragment
key signal.
Run metrics
Chapter 9
Review data and results
View sequencing results and run metrics
9
92
Genexus
™
Integrated Sequencer User Guide
