Download all variants

CNV_VCIB

• cn_results.png— A PNG file that represents the CNV amplicons in the X scale and log2 ratio in Y scale.

• amplicon_data.txt— A file that represents the CNV amplicons in the X scale and log2 ratio in Y scale. Open the file with a text editor.

CnvActor

Gene_deletions.xls, a file that contains information about whole gene deletions and amplicon coverage that are found in BRCA analyses. Values in the third column of the file indicate the following information for the BRCA1 and BRCA2 genes in the sample.

• S—Stable.

• SQCFAIL—Calculated overall variation between amplicon coverage is too high.

• LGD=<score>—Large Gene Deletion with Phred scale score = <score>.

• WGD=<score>—Whole Gene Deletion with Phred scale score = <score> (max score = 100).

The Phred scale score is must >=40, for the WGD (subtype = GeneCNV) to be reported in the VCF file. Large gene deletions are not reported in the VCF file.

FusionImbalancePlots

• <sample name>_covPlot.png—Fusion imbalance coverage plots for the sample.

• <sample name>_ImbalanceCalls.png—Plot that shows whether fusion imbalance coverage calls are positive or negative.

• <sample name>_SampleQC.png—Plot that shows the per amplicon QC mean read counts for fusion imbalance calls.

RNACountsActor-00

• driver_WT_assays_Level.txt—Information for the fusion wild type assays. Lists the ExpressionControl, RNAExonTile and RNAExonVariant details for the genes.

• <barcode>_rawlib_RNAExonTile_TotalCounts.txt—Lists the read counts for the RNA Exon tiles.

N/A

fusions_RNAExonVariants_normCounts.png—A coverage plot for the normalized RNA Exon Variants read counts. The data is available in text format in the file <barcode>_rawlib_RNAExonTile_TotalCounts.txt, which is available in the RNACountsActor-00 folder.

HRR_Results

hrr_summary.tsv—A TSV file that contains a summary of the HRR results.

MRR_Results

mmr_summary.json—A JSON file that contains a summary of the MRR results.

signature_prediction

The signature_prediction folder contains:

• A PDF report of the mutational signature prediction results

• Image files that graphically represent the results (Only available if a mutational signature match is found.)

• A TXT file of the trinucleotide distribution of variants

QC

• report.pdf

• Torrent Suite™ Software Quality Control (QC) files. For example, bam_file_basename>.ionstats_alignment.json, analysis.bfmask.stats, explog_final.txt, raw_peak_signal, InitLog.txt, basecaller_results/BaseCaller.json, basecaller_results/ datasets_basecaller.json, basecaller_results/ionstats_tf.json, basecaller_results/TFStats.json

• mapd.txt—output of the copy number variation.

• diffCoverage.seg—output of CNV module.

• RNAQCAndCalls.txt—contains information about the QC for fusion data.

• TotalMappedFusionPanelReads.txt—provides number of total mapped fusion panel reads.

• qc_cnv_display.txt—CNV sample QC for BRCA analyses.

• <analysis name>_QC.pdf—Report of QC metrics. The same QC metrics are available in the Final Report of an analysis.

StatsActor

• • amplicons_low_no_coverage_statistics.txt—A tab-delimited report file that contains detailed coverage metrics for genomic regions (amplicons, genes, or hotspots) that are analyzed during quality control assessment for sequencing runs.

  • analysis_low_no_coverage_statistics.txt—A file that contains coverage statistics for genomic regions below acceptable coverage thresholds. Each row in the file represents a genomic region and tracks the distribution of bases across different coverage levels.

  • genes_low_no_coverage_statistics.txt—A file that identifies problematic genomic regions where sequencing coverage is insufficient for reliable variant calling and analysis.

• AnnotatorActor—

  • variome-stats.csv—The variome-stats.csv file is a Quality Control (QC) report that provides comprehensive variant-level statistics and metrics for a genomic sample.

Variants

Contains VCF and TSV files for the variants, and fusion data if the sequencing run includes a DNA and Fusions or Fusions analysis workflow. You can open these files in Microsoft™ Excel™.

• <sample name>_Non-Filtered_<timestamp>.oncomine.tsv—VCF file that contains information in tab-separated format.

• <sample name>_Non-Filtered_<timestamp>.vcf—VCF file that contains all, filtered, or selected variants based on user action.

• <sample name>-full.tsv—Tab-separated file for all the variants with annotation.

• SmallVariants.filtered.vcf—An intermediate output VCF file from VarinatCallerActor of the Ion Reporter Software. The VCF file is primarily for use in troubleshooting. It contains variants that are blocked by a Sequence Variant Baseline (SVB) or filtered out by a specific filter reason.

• SmallVariants.vcf—An intermediate output VCF file from VarinatCallerActor software component. The file contains the variants to be reported to the user. The file is further processed and annotated by Ion Reporter™ Software.

• Variant.genome.vcf—An output file from VariantCallerActor software component. The VCF file uses the Genomic Variant Call Format (GVCF) format and contains the coverage information of the targeted regions. Variants in the file are reported in the Locus View VCF format in Ion Reporter™ Software.

Workflow_Settings

• Analysis_Settings—Contains a text file that describes settings used for the analysis. Open the file with a text editor.

• Module_Configuration_Files—Contains configuration files for workflows, including VariantCallerActor.json, a JSON file that contains variant finding parameters used to customize variant calling in Ion Reporter™ Software and the settings used in the analysis. The file shows changes made to the parameters in the software. The file is present only for analyses that include variants.

MSI

Files with data about microsatellite instability (MSI) markers. These markers can identify a form of genomic instability in the replication of repetitive DNA. MSI often occurs in tumor cells. It leads to the appearance of multiple alleles at microsatellite loci, which can be easily identified.

A folder for each sample contains the following files.

• MSIQC.json—File contains "flags" and warning messages associated with MSI status that are used by customer support representatives.

• Classify.json —Provides a summary of the MSI status and coverage.

RESULTS

If the Tumor Mutational Burden parameter is enabled, or an analysis workflow for the Tumor Mutation Load Assay is used, a Results folder is generated that contains:

• filter_variants.tsv and somatic_variants.tsv—TSV files that include post-filter and somatic variants.

• <tmb report>.pdf—Report that contains tumor mutational load results.

• statistic.txt—contains tumor mutational burden statistics.

• PNG files that include images of:

  • allele frequency distribution of germline and somatic variants

  • allele frequency distribution of only somatic variants

  • bar plot of signature type and context of somatic mutations

  • pie chart of substitution type of somatic mutations

  • pie chart of signature pattern of somatic mutations

• base_change_file.txt and somatic_mutation_substitution_context_summary.txt— four files that include the data used to generate the substitution type and context of somatic mutations and substitution type and signature pattern of somatic mutations plots

• deamination_metric.txt — contains the TMB score and other TMB metrics

Plugin outputs

Contains ZIP file of the plugin output folder.

Immune repertoire output

The CSV, PNG and PDF files that show the data for Immune repertoire analyses.

• <analysis name><timestamp>.csv

• <analysis name><timestamp>.png

• <analysis name><timestamp>.pdf

Metagenomics Output

Files from a single metagenomics sample, or results from multiple samples that the software compares for Beta diversity, and files that contains reads for the analysis in FASTA format, and other TXT files for the analysis.

To download all results files for metagenomics analyses, use instead the Download results files for all samples link, shown in the Visualization/Downloads section of the metagenomics analysis results. For more information, see View interactive taxonomy charts for metagenomics analyses.