Microbial 'omics

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# variability-profile [artifact]

A CONCEPT-type anvi’o artifact. This artifact is typically generated, used, and/or exported by anvi’o (and not provided by the user)..

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anvi-profile

## Description

As an artifact, this describes the variability information about a single sample calculated when you ran anvi-profile. To examine variability across samples, you’ll want to use this information (which is stored within your profile-db) to run anvi-gen-variability-profile.

In the context of anvi’o, variability means divergence of environmental populations from the reference used to perform metagenomic read recruitment.

Here, the term “population” describes an assemblage of co-existing microbial genomes in an environment that are similar enough to map to the context of the same reference genome.

The variability profile of a metagenome enables studies of microbial population genetics with anvi’o.

There are two types of variability the program anvi-profile can characterize and store: substitutions and indels.

### Substitutions: SNVs, SCVs, SAAVs

You can learn the name of the table in which anvi’o stores this in a given profile-db by running this command in your anvi’o environment:

python -c 'import anvio.tables as t; print(t.variable_nts_table_name)'


This will tell you about its structure:

python -c 'import anvio.tables as t; print(t.variable_nts_table_structure)'


### Indels: insertions and deletions

Anvi’o can also characterize insertions and deletions found within an environment based on short-read recruitment results and will store in the following table:

python -c 'import anvio.tables as t; print(t.indels_table_name)'


Notes for programmers: The convention for the start position of an insertion is defined like so:

    pos_in_contig ...0123456 7890123456
reference     ...CTACTAC TACTTCATGA...