---
title: Interpreting Metagenomics outputs
description: >-
  Taxonomy reports, abundance profiles, diversity indices, distance matrices,
  and differentially abundant taxa.
tags:
  - metagenomics
  - outputs
---

Each tool returns taxonomy reports, abundance profiles, diversity indices and distance matrices, or a table of differentially abundant taxa with statistics. These let you take the next step: an abundance profile feeds diversity and differential-abundance testing, differentially abundant taxa point to microbiome-disease associations, and abundant species can hand off to genomics for functional annotation.

## Interpreting Metagenomics outputs

## Metagenomics Classify output

| Field | Type | Description |
|-------|------|-------------|
| `sample_id` | string | Sample identifier |
| `total_reads` | number | Total reads processed |
| `classified_reads` | number | Reads successfully classified |
| `classification_rate` | number | Fraction of reads classified (0-1) |
| `taxa` | array | Taxonomic hits, sorted by abundance |

### Taxa entry fields

| Field | Type | Description |
|-------|------|-------------|
| `taxon_id` | number | NCBI taxonomy ID |
| `name` | string | Taxonomic name |
| `rank` | string | Taxonomic rank (kingdom, phylum, class, order, family, genus, species) |
| `abundance` | number | Relative abundance (0-1) |
| `read_count` | number | Number of reads assigned |
| `confidence` | number | Classification confidence (0-1) |

### Classification rate interpretation

| Classification rate | Interpretation |
|--------------|----------------|
| > 80% | Good classification rate for human gut metagenomes |
| 50-80% | Typical for environmental samples (soil, ocean) |
| 20-50% | Many novel/uncharacterized organisms |
| < 20% | Consider host contamination or database mismatch |

## Metagenomics Profile output

| Field | Type | Description |
|-------|------|-------------|
| `sample_id` | string | Sample identifier |
| `richness` | number | Number of distinct taxa detected |
| `evenness` | number | Pielou evenness index (0-1) |
| `dominant_taxon` | string | Most abundant taxon name |
| `dominant_abundance` | number | Relative abundance of the dominant taxon (0-1) |
| `phylum_abundances` | object | Map of phylum name to relative abundance |

The profile is a per-sample community summary, not a full per-taxon abundance table — pass its `sample_id` and abundance data through to `microbiome_diversity` or `microbiome_differential` for further analysis.

## Microbiome Diversity output

| Field | Type | Description |
|-------|------|-------------|
| `sample_id` | string | Sample identifier |
| `shannon` | number | Shannon diversity index |
| `simpson` | number | Simpson diversity index (0-1) |
| `chao1` | number | Chao1 richness estimator |
| `observed_species` | number | Number of observed species |
| `beta_distances` | object | Bray-Curtis distance to each other sample, keyed by `sample_id` |

The alpha metrics (Shannon, Simpson, Chao1, observed species) are always returned per sample; `beta_distances` is populated when `metrics` includes `"beta"` or `"both"`. There is no ordination (PCoA/NMDS) output and no PERMANOVA test — those aren't part of this tool's result.

### Alpha diversity interpretation

| Metric | Low Value | High Value |
|--------|-----------|------------|
| Shannon (H') | < 2.0 (low diversity) | > 4.0 (high diversity) |
| Simpson (1-D) | < 0.7 (dominated by few species) | > 0.9 (even community) |
| Observed species | Context-dependent | Context-dependent |
| Chao1 | Close to observed (few unseen species) | >> observed (many unseen rare species) |

### Beta distance interpretation

| Bray-Curtis distance | Interpretation |
|-------|----------------|
| 0.0 | Identical communities |
| 0.0 - 0.3 | Similar communities |
| 0.3 - 0.6 | Moderately different |
| 0.6 - 1.0 | Very different communities |

## Microbiome Differential output

| Field | Type | Description |
|-------|------|-------------|
| `group1_label` | string | Label for group 1 |
| `group2_label` | string | Label for group 2 |
| `n_group1` | number | Number of samples in group 1 |
| `n_group2` | number | Number of samples in group 2 |
| `significant_taxa` | array | Taxa with adjusted p-value < 0.05 |
| `total_tested` | number | Total taxa tested |

### Significant taxa fields

| Field | Type | Description |
|-------|------|-------------|
| `taxon_name` | string | Taxon name |
| `taxon_rank` | string | Taxonomic rank |
| `log2_fold_change` | number | Log2 fold change between groups |
| `p_value` | number | Raw p-value |
| `adjusted_p_value` | number | FDR-adjusted p-value |
| `mean_abundance_group1` | number | Mean abundance in group 1 |
| `mean_abundance_group2` | number | Mean abundance in group 2 |

`significant_taxa` is pre-filtered to adjusted p-value < 0.05 — there's no separate `significant` boolean or prevalence field in the result.

### Fold change interpretation

| Log2 Fold Change | Raw Fold Change | Interpretation |
|-------------------|-----------------|----------------|
| > 3.0 | > 8x | Very strong enrichment |
| 2.0 to 3.0 | 4x to 8x | Strong enrichment |
| 1.0 to 2.0 | 2x to 4x | Moderate enrichment |
| -1.0 to 1.0 | 0.5x to 2x | Not biologically significant |
| -2.0 to -1.0 | 0.25x to 0.5x | Moderate depletion |
| < -2.0 | < 0.25x | Strong depletion |

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