📖Report JSON format

The DRAGEN Microbial Enrichment Plus app outputs a comprehensive sample-level report.json file containing general metadata, version information, sample QC, microorganism, and AMR marker results, as well as detailed test information. The additional convenience file formats generated by the DRAGEN Microbial Enrichment Plus app do not contain novel content.

(*) indicates results generated by the application layer as opposed to the DRAGEN secondary analysis pipeline

Top-Level Node

The top-level section of the report JSON contains general metadata and version information.

.qcReport.sampleQc Node

This section contains information about sample quality control (QC). The fields are relative to .qcReport.sampleQc

.qcReport.enrichmentFactor Node

This section contains information about the enrichment factor calculation and is relevant to RPIP, UPIP, and VSP V2 only. Detection of an appropriate Internal Control is required. The fields are relative to .qcReport.enrichmentFactor

.qcReport.sampleComposition Node

This section contains information about the composition of the sample and is provided for RPIP, UPIP, and VSP V2 only. The fields are relative to .qcReport.sampleComposition

.qcReport.internalControls Node

This section contains information about internal control detection and is relevant to RPIP, UPIP, and VSP V2 only. The value of the .qcReport.internalControls field is an array of objects containing name and RPKM information for each Internal Control. See the code block below for an example:

[
    {
        "name": "Allobacillus halotolerans",
        "rpkm": 0
    },
    {
        "name": "Armored RNA Quant Internal Process Control",
        "rpkm": 0
    },
    {
        "name": "Enterobacteria phage T7",
        "rpkm": 180323
    },
    {
        "name": "Escherichia virus MS2",
        "rpkm": 0
    },
    {
        "name": "Escherichia virus Qbeta",
        "rpkm": 0
    },
    {
        "name": "Escherichia virus T4",
        "rpkm": 0
    },
    {
        "name": "Imtechella halotolerans",
        "rpkm": 0
    },
    {
        "name": "Phocid alphaherpesvirus 1",
        "rpkm": 0
    },
    {
        "name": "Phocine morbillivirus",
        "rpkm": 0
    },
    {
        "name": "Truepera radiovictrix",
        "rpkm": 0
    }
]

.userOptions Node

This section gives information about analysis options specified by the user. The fields are relative to .userOptions

.targetReport.microorganisms[] Node

The value of the .targetReport.microorganisms[] field is an array of objects containing information about detected microorganisms. The following table describes one .targetReport.microorganisms[] object. The fields are relative to .targetReport.microorganisms[]

.targetReport.microorganisms[].predictionInformation[].relatedMicroorganisms[] Node

The value of the .targetReport.microorganisms[].predictionInformation[].relatedMicroorganisms[] field is an array of objects containing information about genetically related microorganisms. The following table describes one .targetReport.microorganisms[].predictionInformation[].relatedMicroorganisms[] object. The fields are relative to .targetReport.microorganisms[].predictionInformation[].relatedMicroorganisms[]

.targetReport.microorganisms[].variants[] Node

The value of the .targetReport.microorganisms[].variants[] field is an array of objects containing information about viral variants for all RVOP/RVEK, VSP, and VSP V2 viruses, RPIP: SARS-CoV-2 & FluA/B/C only. The following table describes one .targetReport.microorganisms[].variants[] object. The fields are relative to .targetReport.microorganisms[].variants[]

.targetReport.microorganisms[].pangoLineage[] Node

The value of the .targetReport.microorganisms[].pangoLineage[] field is an array of objects containing information about SARS-CoV-2 Pango lineage prediction results. The following table describes one .targetReport.microorganisms[].pangoLineage[] object. The fields are relative to .targetReport.microorganisms[].pangoLineage[].

.targetReport.microorganisms[].nextclade[] Node

The value of the .targetReport.microorganisms[].nextclade[] field is an array of objects containing information about viral clade assignment results for applicable viruses. The following table describes one .targetReport.microorganisms[].nextclade[] object. The fields are relative to .targetReport.microorganisms[].nextclade[].

.targetReport.amrMarkers[] Node

The value of the .targetReport.amrMarkers[] field is an array of objects containing information about detected bacterial AMR markers. The following table describes one .targetReport.amrMarkers[] object. The fields are relative to .targetReport.amrMarkers[]

.targetReport.amrMarkers[].variants[] Node

The value of the .targetReport.amrMarkers[].variants[] field is an array of objects containing information about variants for bacterial AMR markers with "protein variant" or "rRNA variant" model types. The following table describes one .targetReport.amrMarkers[].variants[] object. The fields are relative to .targetReport.amrMarkers[].variants[]

.targetReport.customReferences[] Node

This section contains information about custom reference detection results and is only present for custom database analyses. When only a custom reference FASTA file is provided (no BED file), each .targetReport.customReferences[] object contains information for a single reference sequence. When both a FASTA and BED file are provided, each .targetReport.customReferences[] object contains information for a single genome/microorganism, which can be a collection of one or more reference sequences. The fields are relative to .targetReport.customReferences[]

.targetReport.customReferences[].consensusSequences[] Node

The value of the .targetReport.customReferences[].consensusSequences[] field is an array of objects containing majority consensus sequence information for a single custom reference sequence. When only a FASTA file is provided (no BED file), there will be only one object in the array. When both a FASTA and BED file are provided, there may be more than one object in the array. The fields are relative to .targetReport.customReferences[].consensusSequences[]

.targetReport.customReferences[].variants[] Node

The value of the .targetReport.customReferences[].variants[] field is an array of objects containing information about a single detected variant. The fields are relative to .targetReport.customReferences[].variants[]

.targetReport.customReferences[].pangoLineage[] Node

The value of the .targetReport.customReferences[].pangoLineage[] field is an array of objects containing information about SARS-CoV-2 Pango lineage prediction results. The following table describes one .targetReport.customReferences[].pangoLineage[] object. The fields are relative to .targetReport.customReferences[].pangoLineage[]

.additionalInformation[] Node

The value of the .additionalInformation[] field is an array of objects containing additional information about the test and data analysis solution. The fields are relative to .additionalInformation[]