Column
Description
Oncomine Variant
Class
The type of CNV at the locus based on Oncomine
™
annotations:
• Amplification — indicates a duplication event at the locus
• Deletion — indicates a deletion event at the locus
This information is available if the Apply Oncomine Variant Annotations checkbox is selected
in the assay used in the run.
Oncomine Gene Class The change in molecular function of the altered gene product due to the mutation, based on
Oncomine
™
annotations:
• Gain-of-function — the altered gene product has a new molecular function or pattern of
gene expression, compared to the wild-type gene
• Loss-of-function — the altered gene product lacks the molecular function of the wild-
type gene
This information is available if the Apply Oncomine Variant Annotations checkbox is selected
in the assay used in the run.
Gene
The gene name, which provides a link to the View Annotation Sources dialog box with
additional information about the HotSpot ID.
For more information, see “View annotation sources“ on page 101.
Copy Number
The copy number of a CNV gene locus per genome. This column is available when a positive
call is made.
No Call Reason
Details about the No Call result in the Filter column.
CNV Confidence
The CNV confidence interval associated with the call. The 5% lower confidence bound value is
the ploidy estimate, where there is a 5% chance that the true ploidy is below that value. The
95% upper confidence bound is the ploidy estimate, where it is 95% certain that the true
ploidy is below that value.
Variant ID
The name of the hotspot as defined in the BED file.
Filter
Indicates the presence (PASS) or absence (FAIL) of a CNV variant, or insufficient reads to call
with confidence (NOCALL). For calls that are positive for CNV, GAIN indicates gene
amplification and LOSS indicates gene deletion.
CNV Ratio
The ratio of measured CNV gene locus coverage relative to coverage of non-CNV loci.
P-value
The statistical significance of the CNV ratio measurement.
Med Mol Cov Gene
The median molecular coverage of targeted CNV gene.
Med Mol Cov Ref
The median molecular coverage of non-CNV reference loci.
Med Read Cov Gene
The median read coverage of targeted CNV gene.
Med Read Cov Ref
The median read coverage of non-CNV reference loci.
Valid CNV Amplicons The number of amplicons spanning the CNV call.
Chapter 9
Review data and results
View sequencing results and run metrics
9
100
Genexus
™
Integrated Sequencer User Guide