16S Sample JSON

16S Sample JSON

A JSON file is generated for each sample in the analysis and is named <outputFilePrefix>.<sampleId>.ap.json. It contains general metadata, version information, sample QC, statistics, and analysis options specified by the user.

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
.analysisId	Identifier used for the analysis
.analysisPipelineVersion	Analysis Pipeline release version
.deploymentEnvironment	Environment in which the results were produced
.dragenVersion	DRAGEN release version
.errors	List of errors encountered during the analysis
.reportTime	Date and time the report was generated
.runId	Identifier used for the sequencing run
.testName	Full name of test. "DRAGEN 16S Plus Analysis Pipeline"
.testType	Type of test ("Refseq-RDP-v1", "Custom")
.testUse	Test use. "For Research Use Only. Not for use in diagnostic procedures."
.testVersion	Test release version
.warnings	List of warnings encountered during the analysis

.qcReport.sampleQc Node

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

Field	Description
.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
.postQualityMeanReadLength	Average read length after read QC processing
.postQualityReads	Number of reads (or read pairs for paired-end data) in sample after read QC processing, inclusive of any duplicate reads
.postQualityReadsProportion	Proportion of post-quality reads (or read pairs for paired-end data) in sample relative to total raw reads
.preQualityMeanReadLength	Average read length before read QC processing
.totalRawBases	Number of base pairs in sample before read QC processing
.totalRawReads	Number of reads (or read pairs for paired-end data) in sample before read QC processing
.uniqueReads	Number of distinct reads (or read pairs for paired-end data) in sample before read QC processing
.uniqueReadsProportion	Proportion of distinct reads (or read pairs for paired-end data) in sample before read QC processing

.statistics Node

This section contains information about sample statistics. The fields are relative to .statistics.

Field	Description
.classificationCounts	Array of objects containing "count" and "rank" information for each of the seven canonical taxonomic levels
.numberOfSpeciesIdentified	Count of species identified in the sample after any read count threshold is applied
.shannonDiversity	Measure of species diversity within a community that takes into account both species richness and evenness

.userOptions Node

This section gives information about analysis options specified by the user. The fields are relative to .userOptions.

Field	Description
.readCountThreshold	Read count threshold for reporting taxa. Value is an integer >= 0. Default is 0 or unfiltered
.readQcEnabled	Boolean indicating if read QC (trimming and filtering based on quality and read length) is enabled
.customDatabaseFastaFile	Basename of the user-provided FASTA file when a custom reference database is specified