The Summary screen displays a summary of the variant and fusion calls for each
sample in a run, as well as details about the sample and a summary of the metrics for
the run.
To view the Summary screen for a sample, click the sample name associated with a
run that is listed in the Results > Run Results screen, then in the View Results screen,
click Summary in the left navigation pane.
The information that is displayed depends on the assay that was used in the run.
Section
Description
Sample Details
Sample Name
A unique identifier representing the sample.
Gender
The biological sex of the sample: Female, Male, or Unknown.
Disease Category
The disease type of the sample.
Cancer Stage
The stage of the cancer from which the sample was collected.
Collection Date
The date that the sample was collected.
Sample Type
A term that describes the sample, for example, FFPE, DNA, DNA & RNA
Cancer Type
The type of cancer that is represented by the sample.
% Cellularity
The percentage of tumor cellularity in the sample. This is a whole number between 1
and 100. The % Cellularity attribute is applicable to FFPE samples only.
Metrics
Average Base Coverage
Depth
The average number of reads of all targeted reference bases. This is the total number
of base reads on target divided by the number of targeted bases, and therefore includes
any bases that had no coverage.
Uniformity Of Base
Coverage
The percentage of bases in all targeted regions (or whole genome) that are covered by
at least 20% of the average base coverage depth reads. Cumulative coverage is linearly
interpolated between the nearest integer base read depths.
% Base Reads On Target
The percentage of filtered reads that are mapped to any targeted region relative to all
reads mapped to the reference. A read is considered on target if at least one aligned
base overlaps at least one target region. If no target regions (file) was specified, this
value will be the percentage of reads passing uniquely mapped and/or non-duplicate
filters, or 100% if no filters were specified.
Median Molecular
Coverage
[1]
The median number of molecules per target.
The lower median molecular coverage values result in less sensitive detection of
variants at 0.1% frequency, although still sufficient for sensitive detection of variants
with higher frequency.
Median Read Coverage
[1]
The median number of individual interrogated DNA molecules across the targets.
Variant Summary
SNVs/Indels
Lists and describes the SNV, MNV, and INDEL variants that are detected in the sample.
Summary of the
sample results
Chapter 9
Review data and results
View sequencing results and run metrics
9
Genexus
™
Integrated Sequencer User Guide
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