🐲
Illumina Infectious Disease Software
Illumina Connected Software
  • 👾Illumina Infectious Disease and Microbiology Software
  • DRAGEN Microbial Amplicon
    • ▶️DRAGEN Microbial Amplicon App Documentation
      • 🌀How to start
      • Page
      • 🧬Custom reference
        • 📄Reference BED file format
        • 📄PCR Primer definition file formats
      • 📂Output files
      • 📖Understanding the BaseSpace Reports
        • 📄Summary
        • 📄Sample Report
      • 💠Pipeline Logic
      • ⭐Special considerations for amplicon detection
      • ❓Frequently Asked Questions (FAQ)
  • DRAGEN Targeted Microbial
    • ▶️DRAGEN Targeted Microbial App Documentation
      • 🌀How to set up and run an analysis
      • 🧬Custom genomes and primer sets
        • 📄Genome definition file formats
        • 📄Primer definition file formats
      • ⚙️App Settings
      • 📖Understanding the BaseSpace Reports
        • 📄Summary Report
        • 📄Result Reports
      • 📂Output files
      • 💠Pipeline Logic
      • ⭐Special considerations for amplicon sequencing with IMAP protocols
      • ❓Frequently Asked Questions (FAQ)
      • 🚩Known issues
  • DRAGEN Microbial Enrichment Plus
    • ▶️DRAGEN Microbial Enrichment Plus App Documentation
      • 🌀How to set up and run an analysis
        • 🧬Custom reference FASTA and BED files
        • 📄Microorganism Reporting File format
      • 📂Output files
        • 📖Understanding the BaseSpace HTML reports
        • 📖Report JSON format
      • 💠Pipeline logic
      • ⭐Test information
        • 📄RPIP
        • 📄UPIP
        • 📄RVOP/RVEK
        • 📄VSP
        • 📄VSP V2
        • 📄Custom Panel
      • 🕵️‍♀️Scientific evidence
      • ❓Frequently Asked Questions (FAQ)
      • 🚩Release notes
Powered by GitBook
On this page

Was this helpful?

Export as PDF
  1. DRAGEN Microbial Enrichment Plus
  2. DRAGEN Microbial Enrichment Plus App Documentation
  3. Output files

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

.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[]

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

.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

PreviousUnderstanding the BaseSpace HTML reportsNextPipeline logic

Last updated 7 months ago

Was this helpful?

Description

Description

Overall status

Description

▶️
📂
📖
[Source]
[Source]
quality control
[Source]