Column
Description
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. Click the link to open the View Annotation Sources window to view
additional information. For more information, see “View annotation sources“ on page 101.
AA Change
Identification of the amino acid change using HGVS nomenclature.
Genotype
Identification of the DNA-level nucleotide change using HGVS nomenclature.
Ref
The reference base or bases at that locus.
Type
The type of variation that is detected.
• SNP (single nucleotide polymorphism)
• SNV (single nucleotide variation) / MNV (multi-nucleotide variation)
• ins (insertion)
• del (deletion)
• complex
No Call Reason
Details about the No Call result in the Filter column.
Qual Score
The relative probability of either the "reference" hypothesis interval [0,cutoff], or the "variant"
hypothesis interval [cutoff,1], Phred-scaled (
‑
10*log10). A higher score means more evidence
for the variant call.
Coverage
The number of reads covering the position.
Allele Ratio
The total read count of variants that are the alternative alleles of the current variant.
Variant ID
The name of the hotspot as defined in the BED file.
Filter
Indicates the presence (PASS) or absence (ABSENT) of an SNV/MNV/INDEL variant, or
insufficient reads to call with confidence (NO CALL).
Nuc Change
The position and identity of the nucleic acid change.
Depth
Total read coverage across amplicon containing SNV/INDEL hotspot locations. Count of chip-
level reads aligned at this locus that participate in variant calling.
Mol Depth
[1]
Reports number of interrogated DNA molecules containing target. It defines limit of
detection at hotspot position in a particular run and sample. For instance, if molecular depth
is ≥1,500, you can have high confidence that no variant is present at 0.2% LOD. If molecular
depth is ≥2,500, you can have high confidence that no variant is present down to 0.1% LOD.
For reference calls, Molecular Depth provides measurable metric that serves as confirmation
for variant absence among a large number of interrogated molecules.
WT Mol Cov.
[1]
The number of wild-type allele reads at the locus.
Chapter 9
Review data and results
View sequencing results and run metrics
9
96
Genexus
™
Integrated Sequencer User Guide
