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

26KB

DMEplus_aggregate_report_descriptions.xlsx

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

20KB

DMEplus_custom_aggregate_report_descriptions.xlsx

Custom Panel: Description of aggregate Excel report file fields