Single-nucleotide conservation state annotation of the SARS-CoV-2 genome

We applied ConsHMM to sequence alignments of coronaviruses (CoV) and learned annotations for the SARS-CoV-2 genome that capture underlying alignment patterns among CoV and their relationship to observed SARS-CoV-2 mutations.

Files in this repository or the following public URL can be used to view the annotations on UCSC SARS-CoV-2 Genome Browser.

• 30 ConsHMM conservation states learned from the Sarbecovirus sequence alignment
• 30 ConsHMM conservation states learned from the vertebrate CoV sequence alignment
• Mutation depletion score track based on significant enrichment/depletion of nonsingleton SARS-CoV-2 mutations
  • Based on all conservation states
  • Based on states learned from Sarbecovirus alignment
  • Based on states learend from vertebrate CoV alignment

Reference

Kwon S.B., Ernst J. Single-nucleotide conservation state annotation of the SARS-CoV-2 genome. Communications Biology, 4:698, 2021. (link)