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mutations

README.md

Common mutations observed in SARS-CoV-2 genome assemblies

A list of mutations observed by public health or academic institutions engaged in sequencing SARS-CoV-2 clinical specimens. Listed mutations are submitted by the community and come with no guarantees or endorsements. Mutations relative to reference NC_045512.2 are provided in both table and VCF formats (coming soon) as described below. Previous versions of the table are stored in previous_tsv with filenames timestamped to indicate their revision date. A detailed history of updates to the table can be found in the changelog.

See also: https://github.com/W-L/ProblematicSites_SARS-CoV2

Intended use

  1. Facilitate sample review by public health laboratories.
  2. Aid review of assemblies flagged by QC processes due to presumed disruptive mutations.
  3. Improve submission of SARS-CoV-2 genome sequence assemblies to public data repositories.
  4. Compile problematic sites that may impact downstream bioinformatic analyses.
  5. Inform further development of targeted assays for SARS-CoV-2.

Inclusion criteria

Before adding, submitters are expected to confirm the validity of mutations by inspecting read mapping results (for example, upload your FASTA and BAM files to IGV) to ensure high confidence according to the suggested criteria:

  1. Minimum 90% genome-wide coverage breadth
  2. Mimimum 30x coverage depth at mutation
  3. Mimimum 80% read agreement for mutation
  4. Optional: confirm by Sanger sequencing

How to contribute mutations

  1. Download /import/mut_template.csv and save with a filename containing an unique identifier using format: [YYYYMMDD].[YourName].[0-9]{3}.csv that can be used to link entries between the table and changelog (eg. 20210812.Weigand.123.csv).
  2. Enter mutation information according to the column descriptions below, entering 'NA' for any missing attributes except those marked as required. You may add multiple entries to this file.
  3. Create a new GitHub issue with title "Add: mutation table entry" (Do you need a GitHub account?).
  4. Drag-and-drop the new csv file containing your entries.
  5. Submit your issue. The new entry will be reviewed and you will be notified when the mutation table has been updated.

Table column definitions

Header Description
Chrom * Name of the reference sequence NC_045512.2
Gene * Annotated gene in the reference
Position * Base position in the reference
Reference * Reference sequence
Mutation * Mutation sequence change (use '-' for deletion)
Description * Human-readable description of mutation
Example GenBank and/or SRA accession of example genome with confirmed mutation
Library Primer set or library method information
Platform Sequencing platform information
Analysis Bioinformatic pipeline information (version)
Lineage Affected PANGO lineages (Pangolin version)
Submitter * Name and affiliation of mutation submitter
Date * Date added to table

(* required)

VCF column definitions -- coming soon

Header Description
CHROM Name of the reference sequence
POS 1-based position of the variation on the reference
ID ????
REF Reference base
ALT List of alternative alleles at the position (IUPAC ambiguity code)
QUAL ????
FILTER ????
INFO ????

Feedback

Please submit suggested revisions to inclusion criteria, table updates, or other feedback by opening an new GitHub issue and including "mutation table" somewhere in the title.

This resource is maintained by CDC's Technical Outreach and Asstance for States Team (TOAST), 🍞.