Output

The output of the Explify Analysis Pipeline is a report.json file written to the specified output directory. It is similar to the JSON reports available in BaseSpace applications, but contains more information. In contrast with the Explify BaseSpace App, all the information is in the JSON file. There is not a separate PDF, consensus FASTA files, or convenient XLSX file.

Some information available in BaseSpace reports is not available in the core DRAGEN Explify pipeline, including Pangolin SARS-CoV-2 lineage assignment (RPIP), viral AMR marker reporting (RPIP), organism relative abundance, footnotes/abbreviations/interpretive data, and clinical tertiary drug and drug class resistance results (intrinsic or acquired).

Report.json format

The fields in the top-level node of the JSON report provide general metadata and version information.

Field

Description

.accession

Sample identifier

.deploymentEnvironment

Environment in which the results were produced

.batchId

Identifier used for a batch of samples prepared in the lab at the same time

.analysisId

Identifier for the Explify analysis

.runId

Identifier used for a sequencing run

.controlFlag

Indicates whether the sample is a control. It is based on the ControlFlag field in the sample TSV and can be set to POS, NEG, BLANK, or -

.dragenVersion

DRAGEN release version

.analysisPipelineVersion

Analysis pipeline version

.testType

RPIP or UPIP

.testVersion

Version of the test

.testName

Name of the test, eg Explify® Respiratory Pathogen ID/AMR Panel (RPIP) - Data Analysis Solution

.testUse

For Research Use Only. Not for use in diagnostic procedures.

.reportTime

Time the report was generated

The fields are relative to .qcReport. This section provides information about the FASTQ file before and after read trimming.

Field

Description

.sampleQc

Read QC information

.sampleQc.entropy

Kmer entropy of reads after read QC processing

.sampleQc.gContent

Proportion of guanine (G) base calls in reads after read QC processing

.sampleQc.libraryQScore

Quality score of the library after read QC processing

.sampleQc.postQualityMeanReadLength

Average read length after read QC processing

.sampleQc.postQualityReads

Number of reads in sample after QC processing

.sampleQc.preQualityMeanReadLength

Average read length before read QC processing

.sampleQc.totalRawReads

Number of reads in sample before read QC processing

.sampleQc.uniqueReads

Number of unique reads in sample before read QC processing

.sampleQc.uniqueReadsProportion

Proportion of unique reads in sample before read QC processing

All of the fields are relative to .qcReport.sampleComposition. This section provides information about the composition of the sample.

Field

Description

.readClassification

Proportion of reads classified to the following groups:

.readClassification.targeted

Targeted reference sequences

.readClassification.untargeted

Untargeted reference sequences

.readClassification.ambiguous

More than one pathogen class

.readClassification.unclassified

Could not be classified

Field

Description

.targeted

Proportion of targeted reads classified to the following groups:

.targeted.viral

Viral targeted sequences

.targeted.bacterial

Bacterial targeted sequences

.targeted.fungal

Fungal targeted sequences

.targeted.parasitic

Parasitic targeted sequences

.targeted.amr

Bacterial AMR targeted sequences

.targeted.internalControl

Internal Control (IC) targeted sequences

Field

Description

.untargeted

Proportion of untargeted reads classified to the following groups:

.untargeted.viral

Viral untargeted sequences

.untargeted.bacterial

Bacterial untargeted sequences

.untargeted.fungal

Fungal untargeted sequences

.untargeted.parasitic

Parasitic untargeted sequences

.untargeted.amr

Bacterial AMR untargeted sequences

.untargeted.internalControl

Internal Control (IC) untargeted sequences

.untargeted.human

Human sequences

.untargeted.lowComplexity

Sequences with low complexity in base composition (eg poly-A tails)

The internalControls object is a list that gives the name and RPKM for the 10 commercially available spike-in control options. Refer to the following code block:

[

{

"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

}

]

Copy
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
    }
]

The fields are relative to .userOptions.

Field

Description

.quantitativeInternalControlName

Indicates the Internal Control used for absolute quantification (recommendation: Enterobacteria phage T7)

.quantitativeInternalControlConcentration

Internal Control concentration used in absolute quantification calculations (recommendation: 1.21 x 10^7 copies/mL)

.readQcEnabled

Boolean field that indicates whether read trimming was enabled

The fields are relative to .targetReport.microorganisms. The value of the microorganisms field is an array of objects describing microorganism detection metrics and metadata. The following table describes a microorganism’s array of objects.

Field

Description

.class

Microorganism class (viral, bacterial, fungal, parasite)

.name

Name of detected microorganism

.coverage

Proportion of targeted microorganism sequence bases that appear in sequencing reads

.ani

Average nucleotide identity of majority consensus sequence to targeted microorganism reference sequences

.medianDepth

Median depth of reads aligned to targeted microorganism reference sequences, indicating the median number of times each targeted microorganism sequence base appears in sequencing reads

.condensedDepthVector

Read depth across the targeted microorganism reference sequences, concatenated and condensed (if needed) down to 256 items.

.rpkm

Normalized representation of the number of reads aligned to targeted microorganism reference sequences (aligned reads per kilobase of targeted sequence per million reads)

.alignedReadCount

Number of reads aligned to reference genome (or segment)

.kmerReadCount

Number of reads assigned to targeted microorganism reference sequences by k-mer classification

.absoluteQuantityRatio

Numerical absolute quantification value

.absoluteQuantityRatioFormatted

Formatted absolute quantification value and units

.phenotypicGroup

Grouping indicating general association with normal flora, colonization, or contamination from the environment or other sources, as well as general association with disease

Field

Description

.associatedAmrMarkers

Information about the detected and predicted AMR markers associated with this bacterium. Only present for bacteria.

.associatedAmrMarkers.detected

A list of the detected AMR markers associated with this bacterium. Only present for bacteria.

.associatedAmrMarkers.predicted

A list of the predicted AMR markers associated with this bacterium. Only present for bacteria.

Field

Description

.consensusGenomeSequences

(RPIP viruses only) Information about genome (or segment) consensus sequence

.consensusGenomeSequences.sequence

The consensus genome (or segment) sequence

.consensusGenomeSequences.referenceAccession

Accession of the reference genome (or segment)

.consensusGenomeSequences.referenceDescription

Description of the reference genome (or segment)

.consensusGenomeSequences.referenceLength

The length of the reference genome

.consensusGenomeSequences.maximumAlignmentLength

Longest contiguous alignment between consensus and reference genome (or segment)

.consensusGenomeSequences.maximumGapLength

Longest contiguous gap between consensus and reference genome (or segment)

.consensusGenomeSequences.coverage

Proportion of reference genome sequence bases that appear in sequencing reads

.consensusGenomeSequences.ani

Average nucleotide identity (ANI) of majority consensus sequence to reference genome (or segment)

.consensusGenomeSequences.alignedReadCount

Number of reads aligned to targeted microorganism reference genome sequences

.consensusGenomeSequences.medianDepth

Median depth of reads aligned to reference genome (or segment), indicating the median number of times each reference genome (or segment) base appears in sequencing reads

.consensusGenomeSequences.targetAnnotation

List of target annotations for the reference genome (or segment). Each annotation is a JSON object with the following fields: start (int), end (int), strand (string), target_name (string), type (string).

Field

Description

.consensusTargetSequences

(RPIP viruses only) Information about targeted region consensus sequence

.consensusTargetSequences.sequence

Targeted region consensus sequence

.consensusTargetSequences.name

Targeted region name

.consensusTargetSequences.referenceAccession

Targeted region reference accession

.consensusTargetSequences.depthVector

Read depth across the targeted region

Field

Description

.explifyInterpretation

Information about Explify's automated interpretation results

.explifyInterpretation.predictedPresent

Explify prediction that microorganism is present (true/false)

.explifyInterpretation.notes

List of notes about the Explify prediction result

.explifyInterpretation.subpanels

List of subpanels that microorganism belongs to

.explifyInterpretation.relatedOrganisms

Object that gives key metrics for closely related on- and off-panel microorganisms that were detected. See below for details.

The relatedOrganisms object includes a list of the organisms that were considered as part of this organism's interpretation. The fields below describe an object in the relatedOrganisms array.

Field

Description

.name

Related microorganism's name

.onPanel

Whether the related microorganism is on the panel or not

.kmerReadCount

The number of reads assigned to the microorganism using a k-mer based approach. This field is only present when this approach is applied. Currently, it is present for UPIP but not RPIP

.coverage

The coverage to the microorganism resulting from alignment

.ani

The ANI to the microorganism resulting from alignment

.alignedReadCount

Number of reads aligned to related microorganism reference sequences

The fields are relative to .targetReport.microorganisms.variants. The variants object is only present for select viruses.

Field

Description

.referenceAccession

NCBI accession of reference sequence used for variant calling

.segment

(Influenza A only). Segment number of reference sequence

.ntChange

Nucleotide change associated with the variant

.referencePosition

Variant position in reference sequence

.referenceAllele

Reference allele at same position as the variant

.variantAllele

Variant allele

.depth

Variant depth, indicating the number of times the variant appears in sequencing reads.

.alleleFrequency

Frequency of the variant allele in the sequencing reads

The fields are relative to .targetReport.amrMarkers. This section provides information about the detected bacterial AMR markers.

Field

Description

.class

Microorganism class (eg bacterial)

.modelType

AMR marker detection model specified by CARD (homolog, protein variant, rRNA variant)

.geneFamily

AMR marker family name in CARD

.name

AMR marker name

.referenceAccession

NCBI or CARD accession of AMR marker reference sequence

.coverage

Proportion of reference genome (or segment) bases that appear in sequencing reads (protein alignment for homolog and protein variant model types; DNA alignment for rRNA variant model type)

.pid

Percent identity of majority consensus sequence aligned to reference sequence (protein alignment for homolog and protein variant model types; DNA alignment for rRNA variant model type)

.medianDepth

Median depth of reads aligned to AMR marker reference sequence, indicating the median number of times each AMR marker sequence residue appears in sequencing reads (protein alignment for homolog and protein variant model types; DNA alignment for rRNA variant model type)

.rpkm

Median depth of reads aligned to AMR marker reference sequence, indicating the median number of times each AMR marker sequence residue appears in sequencing reads (protein alignment for homolog and protein variant model types; DNA alignment for rRNA variant model type)

.alignedReadCount

The read count to the marker resulting from alignment

.nucleotideConsensusSequence

(UPIP only) The nucleotide consensus sequence

.proteinConsensusSequence

(UPIP only) The protein consensus sequence

.nucleotideDepthVector

The depths across the nucleotide alignment, not condensed

.proteinDepthVector

The depths across the protein alignment, not condensed

.associatedMicroorganisms

Lists of the detected and predicted organisms associated with this marker

.associatedMicroorganisms.all

A list of all organisms associated with this marker

.associatedMicroorganisms.detected

A list of the detected organisms associated with this marker

.associatedMicroorganisms.predicted

A list of the predicted organisms associated with this marker

.explifyInterpretation

Information about Explify's automated interpretation results

.explifyInterpretation.predictedPresent

Whether Explify interpretation predicts that the marker is present (true/false)

.explifyInterpretation.confidence

Whether the AMR marker is predicted with high or medium confidence

.explifyInterpretation.notes

List of notes about the interpretation result

The fields are relative to targetReport.amrMarkers.variants. This section provides information about variants detected on select bacterial AMR markers.

Field

Description

.category

"Bacterial Variant; Known AMR"

.referenceSourceMicroorganism

Microorganism that reference sequence is associated with in NCBI

.product

The protein product of the gene

.ntChange

The nucleotide change

.referencePosition

The position on the reference sequence

.referenceAllele

The reference sequence at the position of the variant

.variantAllele

The variant sequence

.depth

The depth at the variant position

.alleleFrequency

The frequency of the variant allele in the read pile up

.annotation

Type of change (eg "Nonsynonymous Variant")

.aaChange

Amino acid change

.epistaticGroups

List of epistatic groups the variant is associated with