Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Quality control of low-frequency variants in SARS-CoV-2 genomes

View ORCID ProfileMikhail Rayko, Aleksey Komissarov
doi: https://doi.org/10.1101/2020.04.26.062422
Mikhail Rayko
1Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, Saint Petersburg, Russia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Mikhail Rayko
  • For correspondence: m.rayko@spbu.ru
Aleksey Komissarov
2Applied Genomics Laboratory, SCAMT Institute, ITMO University, Saint Petersburg, Russia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Data/Code
  • Preview PDF
Loading

Abstract

During the current outbreak of COVID-19, research labs around the globe submit sequences of the local SARS-CoV-2 genomes to the GISAID database to provide a comprehensive analysis of the variability and spread of the virus during the outbreak. We explored the variations in the submitted genomes and found a significant number of variants that can be seen only in one submission (singletons). While it is not completely clear whether these variants are erroneous or not, these variants show lower transition/transversion ratio. These singleton variants may influence the estimations of the viral mutation rate and tree topology. We suggest that genomes with multiple singletons even marked as high-covered should be considered with caution. We also provide a simple script for checking variant frequency against the database before submission.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Supplemental files updated, minor cosmetic fixes

  • https://github.com/ablab/covid19_variation_analysis

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
Back to top
PreviousNext
Posted May 07, 2020.
Download PDF

Supplementary Material

Data/Code
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Quality control of low-frequency variants in SARS-CoV-2 genomes
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Quality control of low-frequency variants in SARS-CoV-2 genomes
Mikhail Rayko, Aleksey Komissarov
bioRxiv 2020.04.26.062422; doi: https://doi.org/10.1101/2020.04.26.062422
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Quality control of low-frequency variants in SARS-CoV-2 genomes
Mikhail Rayko, Aleksey Komissarov
bioRxiv 2020.04.26.062422; doi: https://doi.org/10.1101/2020.04.26.062422

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Genomics
Subject Areas
All Articles
  • Animal Behavior and Cognition (4113)
  • Biochemistry (8815)
  • Bioengineering (6518)
  • Bioinformatics (23462)
  • Biophysics (11789)
  • Cancer Biology (9208)
  • Cell Biology (13322)
  • Clinical Trials (138)
  • Developmental Biology (7436)
  • Ecology (11409)
  • Epidemiology (2066)
  • Evolutionary Biology (15150)
  • Genetics (10436)
  • Genomics (14043)
  • Immunology (9171)
  • Microbiology (22154)
  • Molecular Biology (8812)
  • Neuroscience (47568)
  • Paleontology (350)
  • Pathology (1428)
  • Pharmacology and Toxicology (2491)
  • Physiology (3730)
  • Plant Biology (8080)
  • Scientific Communication and Education (1437)
  • Synthetic Biology (2221)
  • Systems Biology (6037)
  • Zoology (1253)