# Output files

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Note: Some files may not be generated depending on the selected analysis options and analysis results
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## Sample-level output files

| Filename                                                      | Type    | Description                                                                                                                                                                                                                                                            |
| ------------------------------------------------------------- | ------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| Samplename.Panelname.report.json                              | json    | Comprehensive report file. See [Report JSON format](https://help.connected.illumina.com/infectious-disease/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/output-files/report-json-format) for further details                                      |
| Samplename.Panelname.report.html                              | html    | Visual report file. See [Understanding the BaseSpace HTML reports](https://help.connected.illumina.com/infectious-disease/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/output-files/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](https://help.connected.illumina.com/infectious-disease/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/output-files/understanding-the-basespace-html-reports) for further details |

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

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Custom Panel: Description of aggregate Excel report file fields
{% endfile %}