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.
.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
.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
.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
.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:
.userOptions Node
This section gives information about analysis options specified by the user. The fields are relative to .userOptions
.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[]
.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[]
.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[]
.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
.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
.sequenceName*
Name of the sequence
.referenceAccession*
Reference accession
.overallStatus*
.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[]
.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[]
.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[]
.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[]
.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[]
.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
.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[]
.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
Last updated
Was this helpful?