.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

.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

.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

.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

.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

.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

.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

.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

.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

.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