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Sample report Illustrative data — not a real person's results Not a diagnosis

VagiX Core Microbiome Profiling Report

VagiX™ Core Microbiome Profiling Report

A genus-level description of this illustrative vaginal sample, with every scored output withheld.

Sample
SAMPLE-VAGIX-000000
Report
sample-vagix-core-v1 · v1
Method
16S · V4 (515F/806R)
Generated
2026-08-22

This page renders from the same report contract a real report uses, with fixture data marked is_sample: true. Nothing here was produced from anyone's sample.

What this report contains

  • 2Reported
  • 1Partly reported
  • 7Withheld
  • 0Not applicable

Partly reported No approved scientific definition

Descriptive genus-level composition is released. Every scored VagiX output is withheld: as of this report's generation date there is no approved, governed definition for the community state type assignment, the Lactobacillus protection index, the anaerobe and opportunist burden scores, or the population percentile. These sections carry no number rather than a provisional one.

  • This sample report shows the VagiX report format honestly, including the parts that are not ready. Most VagiX sections are locked because no approved scientific definition exists for them yet.
  • What is released: the relative abundance of the bacterial genera detected. What is withheld: community state type, Lactobacillus protection, anaerobe and opportunist burden, diversity indices and any population comparison.
  • A locked section carries no number at all. VagiX does not print a provisional value and label it low-confidence.
  • Sequencing used the 16S rRNA gene V4 region (515F/806R primers), which resolves to genus. Species-level identity — including any specific Lactobacillus species — is not reported.
  • Every number on this page is illustrative sample data created to demonstrate the report format.

Sample quality

Warn

Warn on the checks this pipeline performs. 4 checks in this list were not evaluated and are named below rather than counted as passing.

  • LOW_BIOMASS_SITE
  • ASSIGNMENT_RATE_NOT_GATED
  • CLASSIFIER_PARAMETERS_INHERITED
Quality control metrics, thresholds and results
Check Value Threshold applied Result
Reads passing quality filtering 38210 reads 10000 reads QC_Thresholds_Final · QC_01 Pass
Bases at Q30 or above 90.8 % 70 % QC_Thresholds_Final · QC_03 Pass
Reads assigned to a genus Not evaluated No governed threshold Not evaluated
Low-biomass handling Not evaluated No governed threshold Not evaluated
Negative-control contamination screen Not evaluated No governed threshold Not evaluated
Classifier validated for vaginal taxa Not evaluated No governed threshold Not evaluated

Checks this pipeline does not perform

  • Taxonomic assignment rate is not gated. A sample where almost nothing could be assigned would still reach this pipeline, so a high overall QC figure must not be read as evidence that the community was identified.
  • Low-biomass handling is not implemented for this site. Vaginal samples carry far less biological material than stool, which makes background contamination proportionally larger.
  • Negative-control contamination screen — this pipeline does not run one.
  • Classifier parameters were inherited from the gut workflow and have not been validated against vaginal taxa.

Community composition

Partly reported

Relative abundance is the share of assigned sequencing reads attributed to each genus. It describes proportions within this sample only. No proportion below is scored, banded against a reference population, or interpreted.

Genus-level relative abundance is released. Species-level composition is locked: the 16S V4 amplicon cannot separate species within a genus.

  • Lactobacillus (genus total)

    Measured

    61.4%

    Confidence 68%

    • This is the genus total. It is not broken down by species, and no protective interpretation is attached to it in this report.

    vagix-core-profile@0.4.0#genus_relative_abundance

  • Gardnerella

    Measured

    12.8%

    Confidence 68%

    • Gardnerella is detected in people with and without symptoms. Its presence here is a description of the community, not a finding about health.

    vagix-core-profile@0.4.0#genus_relative_abundance

  • Prevotella

    Measured

    5.1%

    Confidence 66%

    vagix-core-profile@0.4.0#genus_relative_abundance

  • Fannyhessea (formerly Atopobium)

    Measured

    3.4%

    Confidence 64%

    vagix-core-profile@0.4.0#genus_relative_abundance

  • Streptococcus

    Measured

    2.2%

    Confidence 64%

    • Group B Streptococcus cannot be distinguished from other Streptococcus species at this resolution. This report does not screen for Group B Strep, and must not be used in place of that test.

    vagix-core-profile@0.4.0#genus_relative_abundance

  • Reads not assignable to a genus

    Measured

    8.6%

    • Reported rather than redistributed. On real vaginal samples this fraction can be very large, and it is not currently gated by QC.

    vagix-core-profile@0.4.0#unassigned_fraction

  • Species-level composition

    Measured

    Needs a different sequencing method TIER_REQUIRED

    Requires a new sample sequenced at a deeper tier. It cannot be unlocked on this result. Required sequencing tier: WGS.

    • The 16S V4 region amplified by the 515F/806R primer pair does not distinguish species within Lactobacillus, Streptococcus, Staphylococcus or Gardnerella.
    • Species-level identity requires shotgun metagenomic sequencing — a different assay on a new sample.
Genus-level composition of the assigned fraction Measured
  • Lactobacillus 61.4 %
  • Gardnerella 12.8 %
  • Prevotella 5.1 %
  • Fannyhessea 3.4 %
  • Streptococcus 2.2 %
  • Other assigned 15.1 %

Share of assigned reads (%)

What this section cannot tell you

  • Classifier parameters used for this site were inherited from the gut workflow and have not been validated against vaginal taxa. Treat genus assignments as provisional.
  • Vaginal samples are low-biomass. Background contamination makes up a proportionally larger share than it would in a stool sample, and this pipeline does not yet correct for it.

Lactobacillus species ecology

Withheld

No approved scientific definition SCIENCE_NOT_APPROVED

Withheld. The only available method for splitting the Lactobacillus genus into species multiplies the genus total by a fixed constant, which would report the same species proportions for every person. No approved definition exists to replace it, so no species breakdown is published.

Withheld until an approved, governed definition exists. No provisional value is published in the meantime.

  • Lactobacillus crispatus

    Measured

    Not reported — no approved scientific definition

    • No governed species-allocation definition exists, and 16S V4 cannot resolve this species directly.

  • Lactobacillus iners

    Measured

    Not reported — no approved scientific definition

    • No governed species-allocation definition exists, and 16S V4 cannot resolve this species directly.

  • Lactobacillus gasseri

    Measured

    Not reported — no approved scientific definition

    • No governed species-allocation definition exists, and 16S V4 cannot resolve this species directly.

  • Lactobacillus jensenii

    Measured

    Not reported — no approved scientific definition

    • No governed species-allocation definition exists, and 16S V4 cannot resolve this species directly.

Community state type

Withheld

No approved scientific definition SCIENCE_NOT_APPROVED

Withheld. The available community state type assignment cannot separate the Lactobacillus-dominant types from one another — the calculation resolves them to the same value in every sample. Publishing an assignment from it would present an arbitrary choice as a finding.

Withheld until an approved, governed definition exists. No provisional value is published in the meantime.

  • Assigned community state type

    Model output

    Not reported — no approved scientific definition

    • The assignment depends on species-level information this assay does not produce.

  • Assignment margin

    Derived

    Not reported — no approved scientific definition

    • The two governing documents specify this margin in different units and have not been reconciled.

Lactobacillus protection index

Withheld

No approved scientific definition SCIENCE_NOT_APPROVED

Withheld. Every weight and offset in this index is unsourced — no governed document defines them. An index built from unsourced constants would look like a measurement and behave like an opinion.

Withheld until an approved, governed definition exists. No provisional value is published in the meantime.

  • Protection index

    Model output

    Not reported — no approved scientific definition

    • The index also depends on the species split, which this assay cannot produce.

Anaerobe ecology

Withheld

No approved scientific definition SCIENCE_NOT_APPROVED

Withheld. The taxa in this panel come from the VagiX blueprint, but the weights that combine them into a burden figure have no approved source, and the banding thresholds conflict between the documents that define them.

Withheld until an approved, governed definition exists. No provisional value is published in the meantime.

  • Combined anaerobe burden

    Model output

    Not reported — no approved scientific definition

    • A weighted burden score is not a test for bacterial vaginosis, and VagiX would not present it as one even once the weights are approved.

Opportunist context

Withheld

No approved scientific definition SCIENCE_NOT_APPROVED

Withheld. The panel is specified at species level, but this assay resolves only to genus — several species in the panel would silently share one genus measurement. No approved definition resolves that conflict.

Withheld until an approved, governed definition exists. No provisional value is published in the meantime.

  • Opportunist context score

    Model output

    Not reported — no approved scientific definition

    • This is not a pathogen screen. Any concern about infection needs a clinical test ordered by a clinician.

Diversity

Withheld

No approved scientific definition SCIENCE_NOT_APPROVED

Withheld. The available diversity calculation includes unassignable reads as if they were a real group and uses an unsourced adjustment constant, and the companion indices the specification requires are not implemented.

Withheld until an approved, governed definition exists. No provisional value is published in the meantime.

  • Shannon index

    Derived

    Not reported — no approved scientific definition

    • In a low-biomass, low-assignment-rate site, a diversity index computed over unassigned reads measures the sequencing run more than the community.

  • Richness estimate

    Derived

    Not reported — no approved scientific definition

    • The specification requires a depth-corrected estimator; only a raw count is available.

Population comparison

Withheld

No governed reference available REFERENCE_UNAVAILABLE

Withheld. No governed reference cohort has been published for the vaginal ecosystem. There is no population to compare this sample against, so no percentile is produced.

Requires a published reference cohort that does not exist yet.

  • Population percentile

    Reference comparison

    Not reported — no governed reference available

    • A percentile is only meaningful against a defined, governed cohort. Until one exists, none is shown.

Vaginal pH — why it is not on this report

Reported

Vaginal pH is frequently discussed alongside the vaginal microbiome, so its absence here is deliberate and worth stating plainly.

Explanatory

  • pH was not measured

    This assay sequences DNA. It does not measure pH, and VagiX does not estimate pH from sequencing data.

  • Why it is not inferred

    Community composition and pH are related, but inferring one from the other would produce a number that looks measured and is not. A pH figure belongs to a pH test.

Method and limits

Reported

What this assay measured, and what it did not. Everything absent from this list is absent from the report by design.

Explanatory

  • What was sequenced

    The V4 hypervariable region of the bacterial 16S rRNA gene, amplified with the 515F/806R primer pair and classified against SILVA 138.1.

  • Resolution reached

    Genus. No Lactobacillus species, no Gardnerella species and no Streptococcus species are named from this assay.

  • What was not measured

    pH, fungi including Candida, viruses, sexually transmitted infections, Group B Streptococcus, human cells and metabolites. None of these were assayed.

  • What this report is not

    It is not a diagnostic test, not a screen for bacterial vaginosis or any infection, and not a basis for starting, stopping or changing treatment. Symptoms need a clinician, not a sequencing report.

How to read the method labels

  • Measured Directly observed in this sample, within the limits of the assay.
  • Model output The result of a scoring model, not a direct measurement.
  • Derived Calculated from measured values using a fixed, versioned formula.
  • Reference comparison Positioned against a governed reference cohort.
  • Explanatory Explanatory text. Carries no data from this sample.

Limitations of this report

  • Every value in this report is illustrative sample data. It did not come from a person and describes no one's sample.
  • Most VagiX sections are locked. No approved, governed scientific definition exists yet for the community state type, the protection index, the anaerobe and opportunist scores, or the diversity indices — so no number is published for them.
  • This is a descriptive profiling report. It does not diagnose, screen for, treat or rule out bacterial vaginosis, thrush, any sexually transmitted infection or any other condition.
  • Sequencing covered the 16S rRNA V4 region only (515F/806R). Results resolve to genus; no species is named, including any Lactobacillus species.
  • Vaginal pH, fungi including Candida, viruses and Group B Streptococcus were not measured.
  • Vaginal samples are low-biomass, and this pipeline runs no negative-control contamination screen and no low-biomass correction. Those checks are reported as not evaluated, never as passed.
  • The taxonomic classifier settings were inherited from the gut workflow and have not been validated against vaginal taxa.
  • No governed reference cohort exists for this ecosystem, so nothing here is a comparison against other people.
  • Cryptographic hashes of the input artifacts are not carried on a sample report. A real report carries a sha256 for every input consumed.

Provenance

Every version that contributed to this report. Fields with nothing behind them are shown as gaps rather than filled with a plausible default.

Report identity

Report ID
sample-vagix-core-v1
Report version
1
Schema version
1.0.0
Sample ID
SAMPLE-VAGIX-000000
Run ID
SAMPLE-RUN-VAGIX-000000
Sequencing tier
16S
Generated
2026-08-22T09:00:00.000Z

Pipeline and reference data

Pipeline
vagix-16s-core@0.4.0
Feature schema
vams-feature-schema@1.2.0
Report specification
vagix-core-profile@0.4.0
Taxonomy database
SILVA
Taxonomy database version
138.1 (99% identity, 515F/806R region-trimmed)
Classifier
QIIME 2 2024.5 · q2-feature-classifier vsearch consensus (parameters inherited from the gut workflow, not tuned for this site)
Classifier SHA-256
Not carried
Functional method
Not carried
Functional method version
Not carried

ATLAS reference

No ATLAS reference artifact was consumed. Nothing in this report compares this sample against a reference cohort or against other people.

Score definition version
Not applicable
Condition taxonomy version
Not applicable
Reference artifact set
Not applicable
Reference cohort version
Not applicable

Input artifact hashes

Not carried on a sample report. A report generated from a real sample carries a SHA-256 for every input artifact consumed.

All provenance fields the contract requires for an auditable report are present.

Sample report · every value on this page is illustrative · not a diagnosis and not medical advice