Output files

Note: Some files may not be generated depending on the selected analysis options and analysis results

Sample-level output files

Filename
Type
Description

Samplename.Panelname.report.json

json

Comprehensive report file. See Report JSON format for further details

Samplename.Panelname.report.html

html

Visual report file. See Understanding the BaseSpace HTML reports for further details

Samplename.Panelname.viral_variants.vcf

vcf

Viral variant call file describing variant calls between viral consensus genome (or segment) sequences and best-match reference sequences (all RVOP/RVEK, VSP, and VSP V2 viruses, RPIP: SARS-CoV-2 & FluA/B/C only)

Samplename.Panelname.viral_genomes_consensus.fa

fasta

Viral genome (or segment) nucleotide consensus sequence(s) for all viruses reported in the sample (RPIP, RVOP/RVEK, VSP, VSP V2 only)

Samplename.Panelname.viral_targets_consensus.fa

fasta

Viral targeted region nucleotide consensus sequence(s) for all viruses reported in the sample (RPIP only)

Samplename.Panelname.bacterial_amr_nucleotide_consensus.fa

fasta

Bacterial AMR gene nucleotide consensus sequence(s) for all bacterial AMR markers reported in the sample (RPIP, UPIP only)

Samplename.Panelname.bacterial_amr_protein_consensus.fa

fasta

Bacterial AMR gene protein consensus sequence(s) for all bacterial AMR markers reported in the sample (RPIP, UPIP only)

viral_consensus_genomes

Dataset

Directory containing viral genome (or segment) nucleotide consensus sequence(s) per virus reported in the sample (RPIP, RVOP/RVEK, VSP, VSP V2 only)

Analysis-level output files

Filename
Type
Description

AnalysisIDnumber.Panelname.results.zip

zip

Compressed file containing all output files for single-click download

AnalysisIDnumber.Panelname.report.xlsx

xlsx

Aggregate Excel report file that summarizes results for all samples across 4 tabs: Samples, Microorganisms, AMR, and Variants. See below for further details

report.html

html

Visual report file. See Understanding the BaseSpace HTML reports for further details

RPIP, UPIP, RVOP/RVEK, VSP, VSP V2: Description of aggregate Excel report file fields
Custom Panel: Description of aggregate Excel report file fields

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