# 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             |


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