Thermo Scientific Ion Torrent A45727, Руководство пользователя

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Column Description
Mol Counts
[1]
The total read coverage across an amplicon containing SNV / INDEL hotspot locations. Count
of chip-level reads aligned at this locus that participate in variant calling.
Mol Freq %
[1]
Molecular frequency percentage. The percentage of mutant reads over total reads at the
locus.
% LOD
[1]
Limit of detection (LOD) of a variant allele expressed as a percentage of the WT allele. LOD is
the lowest possible variant frequency in the sample that can be detected by the system with a
true positive rate greater than 98% for FFPE samples or 95% for cfTNA samples. LOD is
dependent on the molecular read depth at the locus. %LOD is reported when there are no
variant calls for the gene.
[1]
Column appears in analyses of Ion AmpliSeq ™ HD sequencing data only.
The Fusions table lists the calls and other information for the fusions analyzed in each
sample in a run.
To view the Fusions table, in the Results > Run Results screen, click the sample name
in the Sample Name column, then click Fusions in the left navigation pane of the
View Results screen.
The data displayed in the table depend on the assay that was used in the run. Filter
the results list in the table using the filtering tools. For more information, see “Filter
results“ on page 102.
Click Export in the upper right corner of the screen to export the results data in
tabular format.
Column Description
User Classifications A user-defined classification selected from the list.
For more information, see “Create and assign variant classifications“ on page 102.
Locus The chromosome positions in the reference genome that define the fusion junction.
Oncomine Variant
Class
Variants that are known Oncomine ™ annotated hotspots.
Oncomine Gene Class Gain-of-function, or Loss-of-function
Genes (Exon) The name of fusion target and representative acceptor and donor exons.
Read Counts The frequency that the fusion was detected in the sample.
Type Assay type (for example, Fusion, RNA exon variant (exon skipping), RNAExon Tile, Proc
Control).
No Call Reason The reason for reporting a fusion as NOCALL in Filter column.
Failed Reason The reason for FAIL in Filter column.
Variant ID The name of the hotspot as defined in the BED file.
Filter Indicates the presence (PASS) or absence (FAIL) of a fusion, or insufficient reads to call with
confidence (NOCALL).
Fusion results
Chapter 9 Review data and results
View sequencing results and run metrics
9
Genexus
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Integrated Sequencer User Guide 97