Microbial 'omics


Brought to you by

variability-profile-txt [artifact]

Table of Contents

TXT

A TXT-type anvi’o artifact. This artifact can be generated, used, and/or exported by anvi’o. It can also be provided by the user for anvi’o to import into its databases, process, and/or use..

Back to the main page of anvi’o programs and artifacts.

Provided by

anvi-gen-variability-profile

Required or used by

anvi-3dev anvi-gen-fixation-index-matrix anvi-script-calculate-pn-ps-ratio anvi-script-snvs-to-interactive anvi-script-variability-to-vcf

Description

This artifact contains various information about the SNVs, SCVs, and SAAVs across a profile-db that is thoroughly described on this blogpost.

This was generated by anvi-gen-variability-profile, which is also described on that blogpost.

Unsure what SNV, SCV, and SAAVs are or looking for a refresher? You can find that information on the same blogpost.

In summary, this contains output matrices for your SNVs, SCVs and SAAVs that annotate them with lots of additional infomration. This way, you can interact with that data by running anvi-script-snvs-to-interactive or incorporate it into your structural analysis when running anvi-3dev.

What kinds of information?

SNVs

For each of your SNVs, this matrix include their position in the contig and gene, sample, coverage data, the A, C, G, and T counts, the reference and consensus nucleotides, entropy value, and more.

SCVs

This information will only appear if you requested it when running your earlier analysis. To do this, use the flag --profile-SCVs when you run anvi-profile or anvi-merge. Then, when running anvi-gen-variability-profile use the flag --engine CDN.

For each SCVs, this matrix details the position, sample, coverage data, count for each of the 64 codons (AAA, AAC, …, TTG, TTT), entropy, synonymity, etc.

SAAVs

Like the information about SCVs, this information will only appear if you requested it when running your earlier analysis. To do this, use the flag --profile-SCVs when you run anvi-profile or anvi-merge. Then, when running anvi-gen-variability-profile use the flag --engine AA.

For each SCVs, this matrix details the position, sample, coverage data, count for each of the 20 amino acids (as well as the stop codon), entropy, BLOSUM62, etc.

Structural information

If you provided anvi-gen-variability-profile with a structure-db, then you’ll also have some additional columns to your matrices. These include structural annotations, how the residue responds to water, information about bond angles, and a list of residues that are in physical contact with the residue you’re looking at.

For more information on any of this, check out this page, where every column in these matrices is not only listed, but explained.

Edit this file to update this information.