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.

Field	Description
.accession	Identifier used for the sample
.deploymentEnvironment	Environment in which the results were produced
.batchId	Identifier used for the batch of samples processed together
.analysisId	Identifier used for the analysis
.runId	Identifier used for the sequencing run
.controlFlag	Indicates whether the sample is a control. It is set to “POS” if the substring “PosCon” is found in the sample name, “NEG” if the substring “NegCon” is found, or “BLANK” if the substring “controlBlk” is found. Otherwise, it is set to “-”
.dragenVersion	DRAGEN release version
.analysisPipelineVersion	Analysis Pipeline release version
.testType	Type of test panel ("RPIP", "UPIP", "RVOP", "VSPv1", "VSPv2", "Custom")
.testVersion	Test panel release version
.testName	Full name of test panel
.testUse	Test use. "For Research Use Only. Not for use in diagnostic procedures"
.reportTime	Date and time the report was generated
.warnings	List of warnings encountered during the analysis
.errors	List of errors encountered during the analysis
.results*	High level result: “One or more potential pathogens predicted” or ”No potential pathogens predicted”
.appVersion*	DRAGEN Microbial Enrichment plus application release version

.qcReport.sampleQc Node

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

Field	Description
.totalRawBases	Number of base pairs in sample before read QC processing
.totalRawReads	Number of reads in sample before read QC processing
.uniqueReads	Number of distinct reads in sample before read QC processing
.uniqueReadsProportion	Proportion of distinct reads in sample before read QC processing
.preQualityMeanReadLength	Average read length before read QC processing
.postQualityMeanReadLength	Average read length after read QC processing
.postQualityReads	Number of reads in sample after read QC processing, inclusive of any duplicate reads
.postQualityReadsProportion	Proportion of post-quality reads in sample relative to total raw reads
.removedInDehostingReads	Number of host reads in sample removed during dehosting (host = human)
.removedInDehostingReadsProportion	Proportion of host reads in sample removed relative to total raw reads (host = human)
.entropy	Shannon entropy of the counts of 5-mers in the reads after read QC processing, which is a measure of randomness
.gContent	Proportion of guanine (G) base calls in reads after read QC processing
.libraryQScore	Quality score of the library after read QC processing

.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

Field	Description
.value	Enrichment factor value reflecting how well targeted regions were enriched
.category	Enrichment factor category: "poor", "fair", "good", or "not calculated"

.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

Field	Description
.readClassification	Proportion of post-quality reads classified to the following categories:
.readClassification.targetedMicrobial	Targeted microbial
.readClassification.targetedInternalControl	Targeted Internal Control
.readClassification.untargeted	Untargeted
.readClassification.ambiguous	More than one category
.readClassification.unclassified	No category
.readClassification.lowComplexity	Low complexity
.targetedMicrobial	Proportion of post-quality targeted microbial reads classified to the following sub-categories:
.targetedMicrobial.viral	Viral targeted
.targetedMicrobial.bacterial	Bacterial targeted
.targetedMicrobial.fungal	Fungal targeted
.targetedMicrobial.parasitic	Parasitic targeted
.targetedMicrobial.bacterialAmr	Bacterial AMR targeted
.untargeted	Proportion of post-quality untargeted reads classified to the following sub-categories:
.untargeted.viral	Viral untargeted
.untargeted.bacterial	Bacterial untargeted
.untargeted.fungal	Fungal untargeted
.untargeted.parasitic	Parasitic untargeted
.untargeted.bacterialAmr	Bacterial AMR untargeted
.untargeted.internalControl	Internal Control untargeted
.untargeted.human	Human untargeted
.viral	Proportion of post-quality viral reads classified to the following categories:
.viral.targeted	Viral targeted
.viral.untargeted	Viral untargeted
.viral.untargetedSubcategories	Proportion of post-quality viral untargeted reads classified to the following sub-categories:
.viral.untargetedSubcategories.panel	Viral panel members
.viral.untargetedSubcategories.phage	Viral phage
.viral.untargetedSubcategories.other	Viral other (not a panel member or phage)
.bacterial	Proportion of post-quality bacterial reads classified to the following categories:
.bacterial.targeted	Bacterial targeted
.bacterial.untargeted	Bacterial untargeted
.bacterial.untargetedSubcategories	Proportion of post-quality bacterial untargeted reads classified to the following sub-categories:
.bacterial.untargetedSubcategories.panel	Bacterial panel members
.bacterial.untargetedSubcategories.ribosomalDna	Bacterial ribosomal DNA (16S)
.bacterial.untargetedSubcategories.plasmid	Bacterial plasmids
.bacterial.untargetedSubcategories.other	Bacterial other (not a panel member, ribosomal DNA, or plasmid)
.fungal	Proportion of post-quality fungal reads classified to the following categories:
.fungal.targeted	Fungal targeted
.fungal.untargeted	Fungal untargeted
.fungal.untargetedSubcategories	Proportion of post-quality fungal untargeted reads classified to the following sub-categories:
.fungal.untargetedSubcategories.panel	Fungal panel members
.fungal.untargetedSubcategories.ribosomalDna	Fungal ribosomal DNA (18S)
.fungal.untargetedSubcategories.other	Fungal other (not a panel member or ribosomal DNA)
.parasitic	Proportion of post-quality parasitic reads classified to the following categories:
.parasitic.targeted	Parasitic targeted
.parasitic.untargeted	Parasitic untargeted
.parasitic.untargetedSubcategories	Proportion of post-quality parasitic untargeted reads classified to the following sub-categories:
.parasitic.untargetedSubcategories.panel	Parasitic panel members
.parasitic.untargetedSubcategories.ribosomalDna	Parasitic ribosomal DNA (18S)
.parasitic.untargetedSubcategories.other	Parasitic other (not a panel member or ribosomal DNA)
.human	Proportion of post-quality human reads classified to the following categories:
.human.untargeted	Human untargeted
.human.untargetedSubcategories	Proportion of post-quality human untargeted reads classified to the following sub-categories:
.human.untargetedSubcategories.ribosomalDna	Human ribosomal DNA
.human.untargetedSubcategories.codingSequence	Human coding sequence
.human.untargetedSubcategories.other	Human other (not ribosomal DNA or coding sequence)
.internalControl	Proportion of post-quality Internal Control reads classified to the following categories:
.internalControl.targeted	Internal Control targeted
.internalControl.untargeted	Internal Control untargeted
.microbialAndInternalControl	Proportion of post-quality Microbial and Internal Control reads classified to the following categories:
.microbialAndInternalControl.targeted	Microbial and Internal Control targeted
.microbialAndInternalControl.untargeted	Microbial and Internal Control untargeted
.bacterialAmr	Proportion of post-quality bacterial AMR reads classified to the following categories:
.bacterialAmr.targeted	Bacterial AMR targeted
.bacterialAmr.untargeted	Bacterial AMR untargeted

.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

Field	Description
.quantitativeInternalControlName	Quantitative Internal Control used for microorganism absolute quantification (recommendation: Enterobacteria phage T7)
.quantitativeInternalControlConcentration	Quantitative Internal Control concentration (recommendation: 1.21 x 10^7 copies/mL of sample)
.readQcEnabled	Boolean indicating if read QC (trimming and filtering based on quality and read length) is enabled
.readClassificationSensitivity	(RVOP/RVEK, VSP, VSP V2 only) Sensitivity threshold for classifying reads. Determines whether alignment should proceed for a microorganism and/or reference sequence. Value is an integer with a valid range of 1 to 1000, inclusive
.customPanelFastaFile	(Custom Panel only) Name of the custom reference FASTA file
.customPanelBedFile	(Custom Panel only) Name of the custom reference BED file
.belowThresholdEnabled*	Boolean indicating if microorganisms and/or AMR markers below detection thresholds are reported
.bacterialAmrMarkersOnly*	(RPIP, UPIP only) Boolean indicating if only bacterial AMR markers are reported
.bacterialAmrMarkerMicroorganismRequired*	(RPIP, UPIP only) Boolean indicating if bacterial AMR markers are reported only when an associated microorganism is reported
.preDefinedMicroorganismReportingList*	(RPIP, UPIP only) Pre-defined microorganism reporting list, if specified
.userDefinedMicroorganismReportingListUsed*	Boolean indicating if a user-defined microorganism reporting file is specified
.userDefinedMicroorganismReportingListFile*	Name of the user-defined microorganism reporting file, if specified
.providedAnalysisName*	User-provided analysis name

.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[]

Field	Description
.class	Microorganism class ("viral", "bacterial", "fungal", "parasite")
.name	Name of microorganism
.coverage	Proportion of targeted microorganism reference sequence bases that appear in sample sequencing reads
.ani	Average nucleotide identity of consensus sequence to targeted microorganism reference sequences
.medianDepth	Median depth of sample sequencing reads aligned to targeted microorganism reference sequences, indicating the median number of times each targeted microorganism reference sequence base appears in sample sequencing reads
.condensedDepthVector	Read depth across the targeted microorganism reference sequences, condensed to 256 bins
.rpkm	Normalized representation of the number of sample sequencing reads aligned to targeted microorganism reference sequences (targeted Reads mapped Per Kilobase of targeted sequence per Million quality-filtered reads)
.alignedReadCount	Number of sample sequencing reads that aligned to targeted microorganism reference sequences
.kmerReadCount	(UPIP only) Number of sample sequencing reads classified to targeted microorganism reference sequences
.absoluteQuantityRatio	Numerical absolute quantification value. Quantitative internal control required for calculation
.absoluteQuantityRatioFormatted	Formatted absolute quantification value with units. Quantitative internal control required for calculation
.phenotypicGroup	(RPIP, UPIP only) Grouping indicating general association with normal flora, colonization, or contamination from the environment or other sources, as well as general association with disease
.associatedAmrMarkers	(Bacteria only) Information about the bacterial AMR markers associated with the microorganism
.associatedAmrMarkers.applicable	Boolean indicating whether one or more bacterial AMR markers are associated with the microorganism
.associatedAmrMarkers.detected	List of detected bacterial AMR markers associated with the microorganism
.associatedAmrMarkers.predicted	List of predicted bacterial AMR markers associated with the microorganism
.consensusGenomeSequences	(RPIP, RVOP/RVEK, VSP, VSP V2 viruses only) Information about the majority consensus genome (or segment) sequence
.consensusGenomeSequences.sequence	Consensus genome (or segment) sequence bases
.consensusGenomeSequences.referenceAccession	Accession of the reference genome (or segment) sequence
.consensusGenomeSequences.referenceDescription	Description of the reference genome (or segment) sequence
.consensusGenomeSequences.referenceLength	Length of the reference genome (or segment) sequence
.consensusGenomeSequences.maximumAlignmentLength	Longest contiguous alignment between consensus sequence and reference genome (or segment) sequence
.consensusGenomeSequences.maximumGapLength	Longest contiguous alignment gap (insertion or deletion) between consensus sequence and reference genome (or segment) sequence
.consensusGenomeSequences.maximumUnalignedLength	Longest section of the reference genome (or segment) sequence not aligned to by consensus sequence
.consensusGenomeSequences.coverage	Proportion of reference genome (or segment) sequence bases that appear in sample sequencing reads
.consensusGenomeSequences.ani	Average nucleotide identity of consensus sequence to reference genome (or segment) sequence
.consensusGenomeSequences.alignedReadCount	Number of sample sequencing reads that aligned to reference genome (or segment) sequence
.consensusGenomeSequences.medianDepth	Median depth of sample sequencing reads aligned to reference genome (or segment) sequence, indicating the median number of times each reference genome (or segment) sequence base appears in sample sequencing reads
.consensusGenomeSequences.targetAnnotation	List of targeted region annotations for the reference genome (or segment) sequence. Each annotation is a JSON object with the following fields: start (int), end (int), strand (string: "+", "-"), target_name (string), type (string)
.consensusGenomeSequences.condensedDepthVector	Read depth across the reference genome (or segment) sequence, condensed to 256 bins
.consensusTargetSequences	(RPIP viruses only) Information about the majority targeted region consensus sequences
.consensusTargetSequences.sequence	Consensus targeted region sequence bases
.consensusTargetSequences.name	Name of the targeted region
.consensusTargetSequences.referenceAccession	Accession of the targeted region reference sequence
.consensusTargetSequences.depthVector	Read depth across the targeted region reference sequence, not condensed
.consensusTargetSequences.scaledDepthVector*	Read depth across the targeted region reference sequence, condensed and scaled such that the longest targeted region for the microorganism has a maximum length of 256 bins
.predictionInformation	Information about microorganism prediction results
.predictionInformation.predictedPresent	Boolean indicating whether the microorganism passed its reporting logic algorithm
.predictionInformation.notes	List of notes about the prediction result
.predictionInformation.subpanels	List of pre-defined subpanels that the microorganism belongs to
.predictionInformation.relatedMicroorganisms	Array of objects with information about genetically related microorganisms. See below for details
.predictionInformation.userDefined*	User-defined reporting prediction logic for microorganism, if specified
.variants	(all RVOP/RVEK, VSP, and VSP V2 viruses, RPIP: SARS-CoV-2 & FluA/B/C only) Information about viral variants. See below for details
.comments*	List of additional information regarding the microorganism
.abundance*	Relative abundance of the microorganism within the microorganism class
.pangoLineage*	(SARS-CoV-2 only) Information about SARS-CoV-2 Pango lineage prediction results. See below for details
.nextclade*	(applicable viruses only) Information about viral clade assignment results. See below for details
.potentialAmrDetected*	(Bacteria only) Potential AMR detection flag for microorganism. Can be "Yes", “Not Detected”, or “n/a”
.potentialAmrPredicted*	(Bacteria only) Potential AMR prediction flag for microorganism. Can be "Yes", “Not Predicted”, or “n/a”
.flags*	(Bacteria only) Flag for potential resistance to an important drug class ("Potential ESBL", "Potential Carbapenemase")
.intrinsicResistance*	(Bacteria only) List of antimicrobials to which the reported bacteria is intrinsically resistant, based on CLSI Performance Standards for Antimicrobial Susceptibility Testing, M100 34th Edition, Appendix B
.intrinsicResistanceDrugClasses*	(Bacteria only) List of drug classes to which the reported bacteria is intrinsically resistant, based on CLSI Performance Standards for Antimicrobial Susceptibility Testing, M100 34th Edition, Appendix B

.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[]

Field	Description
.name	Name of related microorganism
.onPanel	Boolean indicating whether the related microorganism is a panel member
.kmerReadCount	(UPIP only) Number of sample sequencing reads classified to related microorganism reference sequences
.coverage	Proportion of related microorganism reference sequence bases that appear in sample sequencing reads
.ani	Average nucleotide identity of consensus sequence to related microorganism reference sequences
.alignedReadCount	Number of sample sequencing reads that aligned to related microorganism reference sequences

.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[]

Field	Description
.referenceAccession	Accession of reference genome (or segment) sequence used for variant calling
.segment	(Segmented viruses only) Segment number of reference segment sequence
.ntChange	Nucleotide change associated with variant
.referencePosition	Variant position in viral reference genome (or segment) sequence
.referenceAllele	Reference allele at variant position
.variantAllele	Variant allele
.depth	Variant depth, indicating the number of times variant position appears in sample sequencing reads
.alleleFrequency	Frequency of variant allele in sample sequencing reads
.category*	Variant category ("Viral Variant; Known AMR", "Viral Variant")
.comments*	List of additional information regarding the variant
.gene*	(SARS-CoV-2, Flu A/B/C only) Gene name
.product*	Protein product of gene
.annotation*	Type of change (e.g., "Nonsynonymous Variant")
.aachange*	Amino acid change associated with variant
.epistaticGroups*	List of epistatic groups variant is associated with
.standardNomenclatureEpistaticGroups*	(Flu A/B only) List of epistatic groups variant is associated with using standard nomenclature coordinates
.standardNomenclatureAaChange*	(Flu A/B only) Amino acid change associated with variant using standard nomenclature coordinates
.standardNomenclatureAccession*	(Flu A/B only) NCBI accession of the reference sequence used to establish standard nomenclature coordinates
.drugClasses*	List of drug classes variant is predicted to confer resistance to
.representativeAntimicrobials*	List of representative antimicrobials variant is predicted to confer resistance to
.inhibitionLevel*	(Flu A/B only) Level of inhibition per cited publications (see pmids)
.pmids*	PubMed IDs of publications associated with variant

.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[].

Field	Description [Source]
.lineage*	From Pangolin: "The most likely lineage assigned to a given sequence based on the inference engine used and the SARS-CoV-2 diversity designated. This assignment may be sensitive to missing data at key sites"
.conflict*	From Pangolin: "In the pangoLEARN model, a given sequence gets assigned to the most likely category based on known diversity. If a sequence can fit into more than one category, the conflict score will be greater than 0 and reflect the number of categories the sequence could fit into. If the conflict score is 0, this means that within the current decision tree there is only one category that the sequence could be assigned to"
.ambiguityScore*	From Pangolin: "This score is a function of the quantity of missing data in a sequence. It represents the proportion of relevant sites in a sequnece which were imputed to the reference values. A score of 1 indicates that no sites were imputed, while a score of 0 indicates that more sites were imputed than were not imputed. This score only includes sites which are used by the decision tree to classify a sequence"
.version*	Version of the PUSHER database
.pangolinVersion*	Version of the Pangolin software

.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[].

Field	Description [Source]
.sequenceName*	Name of the sequence
.referenceAccession*	Reference accession
.overallStatus*	Overall quality control status
.clade*	Assigned clade
.pangoLineage*	Pango lineage assigned by Nextclade
.cladeWho*	World Health Organization (WHO) nomenclature
.substitutions*	Total number of detected nucleotide substitutions
.totalNonACGTNs*	Total number of detected ambiguous nucleotides (nucleotide characters that are not A, C, G, T, N)
.totalMissing*	Total number of detected missing nucleotides (nucleotide character N)
.coverage*	Proportion of consensus genome (or segment) sequence bases that aligned to reference accession
.totalInsertions*	Total number of inserted nucleotide bases
.totalFrameShifts*	Total number of detected frame shifts
.stopCodons*	Total number of detected stop codons
.version*	Version of the Nextclade software

.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[]

Field	Description
.class	Microorganism class ("bacterial")
.cardModelType	Bacterial AMR marker model type in the Comprehensive Antibiotic Resistance Database (CARD) ("homolog", "protein variant", "rRNA variant")
.cardGeneFamily	Bacterial AMR marker gene family in the Comprehensive Antibiotic Resistance Database (CARD)
.name	Bacterial AMR marker name
.cardName	Bacterial AMR marker name in the Comprehensive Antibiotic Resistance Database (CARD)
.ncbiName	Bacterial AMR marker name in the National Center for Biotechnology Information (NCBI) Reference Gene Catalog
.referenceAccession	Accession of the bacterial AMR marker reference sequence
.coverage	Proportion of bacterial AMR marker reference sequence residues that appear in sample sequencing reads (protein alignment for "homolog" and "protein variant" model types; nucleotide alignment for "rRNA variant" model type)
.pid	Percent identity of consensus sequence aligned to bacterial AMR marker reference sequence (protein alignment for "homolog" and "protein variant" model types; nucleotide alignment for "rRNA variant" model type)
.medianDepth	Median depth of sample sequencing reads aligned to bacterial AMR marker reference sequence, indicating the median number of times each bacterial AMR marker sequence residue appears in sample sequencing reads (protein alignment for "homolog" and "protein variant" model types; nucleotide alignment for "rRNA variant" model type)
.rpkm	Normalized representation of the number of sample sequencing reads aligned to bacterial AMR reference sequence (protein alignment for "homolog" and "protein variant" model types; nucleotide alignment for "rRNA variant" model type)
.alignedReadCount	Number of sample sequencing reads that aligned to bacterial AMR reference sequence (protein alignment for "homolog" and "protein variant" model types; nucleotide alignment for "rRNA variant" model type)
.nucleotideConsensusSequence	Nucleotide consensus sequence bases
.proteinConsensusSequence	Protein consensus sequence bases
.nucleotideDepthVector	Read depth across the bacterial AMR marker nucleotide reference sequence, not condensed
.proteinDepthVector	Read depth across the bacterial AMR marker protein reference sequence, not condensed
.associatedMicroorganisms	Information about the microorganisms associated with the bacterial AMR marker
.associatedMicroorganisms.all	List of all microorganisms associated with the bacterial AMR marker
.associatedMicroorganisms.detected	List of detected microorganisms associated with the bacterial AMR marker
.associatedMicroorganisms.predicted	List of predicted microorganisms associated with the bacterial AMR marker
.predictionInformation	Information about bacterial AMR marker prediction results
.predictionInformation.predictedPresent	Boolean indicating whether the bacterial AMR marker passed its reporting logic algorithm
.predictionInformation.confidence	Confidence level of bacterial AMR marker prediction ("high", "medium", "low")
.predictionInformation.notes	List of notes about the prediction result
.flags*	Flag indicating AMR marker is an extended-spectrum beta-lactamase (ESBL) or carbapenemase (Carbapenemase)
.representativeAntimicrobials*	List of representative antimicrobials the AMR marker is predicted to confer resistance to
.drugClasses*	List of drug classes the AMR marker is predicted to confer resistance to

.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[]

Field	Description
.category	Variant category ("Bacterial Variant; Known AMR")
.referenceSourceMicroorganism	Microorganism that reference sequence is associated with in NCBI
.comments	List of additional information regarding the variant
.product	Protein product of gene
.ntChange	Nucleotide change associated with variant
.referencePosition	Variant position in reference sequence
.referenceAllele	Reference allele at variant position
.variantAllele	Variant allele
.depth	Variant depth, indicating the number of times variant position appears in sample sequencing reads
.alleleFrequency	Frequency of variant allele in sample sequencing reads
.annotation	Type of change (e.g. "Nonsynonymous Variant")
.aaChange	Amino acid change associated with variant
.epistaticGroups	List of epistatic groups variant is associated with
.representativeAntimicrobials*	List of representative antimicrobials variant is predicted to confer resistance to
.drugClasses*	List of drug classes variant is predicted to confer resistance to
.confidenceLevel*	(MTB only) Confidence level is given for Mycobacterium tuberculosis variants if provided by the WHO Catalogue of mutations in Mycobacterium tuberculosis (Final Grading Confidence; for rpoB only), or the Comprehensive Antibiotic Resistance Database (CARD), as part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data Platform (ReSeqTB)
.pmids*	PubMed IDs of publications associated with variant

.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[]

Field	Description
.name	Provided name of custom reference sequence, accession, genome, or microorganism
.coverage	Proportion of custom reference sequence bases that appear in sample sequencing reads
.ani	Average nucleolotide identity of consensus sequence to custom reference sequence or, if specified, collection of one or more custom reference sequences
.medianDepth	Median depth of sample sequencing reads aligned to custom reference sequence or, if specified, collection of one or more custom reference sequences, indicating the med\ian number of times each custom reference sequence base appears in sample sequencing reads
.condensedDepthVector	Read depth across custom reference sequence or, if specified, collection of one or more custom reference sequences, condensed to 256 bins
.rpkm	Normalized number of sample sequencing reads aligned to custom reference sequence or, if specified, collection of one or more custom reference sequences (targeted Reads mapped Per Kilobase of targeted sequence per Million quality-filtered reads)
.alignedReadCount	Number of sample sequencing reads that aligned to custom reference sequence or, if specified, collection of one or more custom reference sequences
.consensusSequences	Array of objects with information about each consensus sequence. See below for details
.variants	Array of objects with information about variants detected in custom reference sequence or, if specified, collection of one or more custom reference sequences. See below for details
.pangoLineage*	Array of objects with information about SARS-CoV-2 Pango lineage prediction results. See below for details

.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[]

Field	Description
.sequence	Majority consensus sequence bases
.referenceAccession	Accession of custom reference sequence
.referenceDescription	Description of custom reference sequence
.referenceLength	Length of custom reference sequence
.coverage	Proportion of custom reference sequence bases that appear in sample sequencing reads
.ani	Average nucleolotide identity of consensus sequence to custom reference sequence
.medianDepth	Median depth of sample sequencing reads aligned to custom reference sequence, indicating the median number of times each custom reference sequence base appears in sample sequencing reads
.depthVector	Read depth across custom reference sequence, not condensed
.alignedReadCount	Number of sample sequencing reads that aligned to custom reference sequence
.maximumAlignmentLength	Longest contiguous alignment between consensus sequence and custom reference sequence
.maximumGapLength	Longest contiguous alignment gap (insertion or deletion) between consensus sequence and custom reference sequence
.maximumUnalignedLength	Longest section of custom reference sequence not aligned to by consensus sequence

.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[]

Field	Description
.ntChange	Nucleotide change associated with variant
.referenceAccession	Accession of custom reference sequence used for variant calling
.referencePosition	Variant position in custom reference sequence
.referenceAllele	Reference allele at variant position
.variantAllele	Variant allele
.depth	Variant depth, indicating the number of times variant position appears in sample sequencing reads
.alleleFrequency	Frequency of variant allele in sample sequencing reads

.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[]

Field	Description [Source]
.lineage*	The most likely lineage assigned to a given sequence based on the inference engine used and the SARS-CoV-2 diversity designated. This assignment may be is sensitive to missing data at key sites
.conflict*	In the pangoLEARN model, a given sequence gets assigned to the most likely category based on known diversity. If a sequence can fit into more than one category, the conflict score will be greater than 0 and reflect the number of categories the sequence could fit into. If the conflict score is 0, this means that within the current decision tree there is only one category that the sequence could be assigned to
.ambiguityScore*	This score is a function of the quantity of missing data in a sequence. It represents the proportion of relevant sites in a sequnece which were imputed to the reference values. A score of 1 indicates that no sites were imputed, while a score of 0 indicates that more sites were imputed than were not imputed. This score only includes sites which are used by the decision tree to classify a sequence
.version*	Version of the PUSHER database
.pangolinVersion*	Version of the Pangolin software

.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[]

Field	Description
.abbreviations*	Information about abbreviations relevant to test
.abbreviations.abbreviation*	Abbreviation
.abbreviations.definition*	Abbreviation definition
.interpretiveData*	Information about test
.interpretiveData.header*	Test information category
.interpretiveData.paragraph*	Test information text