Schema for Nat. Selection (Pond) - Natural selection analysis from Sergei Pond's research group
  Database: wuhCor1    Primary Table: Positive_Selection Data last updated: 2022-05-18
Big Bed File Download: /gbdb/wuhCor1/pond/pos.bb
Item Count: 2,113
The data is stored in the binary BigBed format.

Format description: Items with thin (outer) and/or thick (inner) regions and an arbitrary set of attributes
fieldexampledescription
chromNC_045512v2Reference sequence chromosome or scaffold
chromStart19947Start position in chromosome
chromEnd19950End position in chromosome
nameName of item
score0Score from 0-1000 (might not be applicable)
strand.+, - or . for unknown
thickStart19947Start of where display should be thick
thickEnd19950End of where display should be thick
seqs4216Number of sequences
alpha0.0Dn
beta2.68111Ds
p0.00659394P-Value

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndseqsalphabetap
NC_045512v219947199500.199471995042160.02.681110.00659394
NC_045512v219947199500.199471995045590.02.83050.00701117
NC_045512v219947199500.199471995045850.02.637210.00844327
NC_045512v220061200640.200612006442160.02.327820.00703353
NC_045512v220061200640.200612006445590.02.428430.00535201
NC_045512v220061200640.200612006445720.04.414650.000340507
NC_045512v220070200730.200702007342160.2888453.041930.00947289
NC_045512v220103201060.201032010645850.02.414820.00601626
NC_045512v220103201060.201032010645720.03.737410.00102447
NC_045512v220106201090.201062010945590.01.550190.0075911

Nat. Selection (Pond) (pond) Track Description
 

Description

This track shows data from Sergei Pond's research group, updated several times between 2020 and 2022, with results published in 2022. The current dataset is from February 2022 and is scheduled to be updated soon. Contact us or Sergei if you believe that the data shown is too outdated for your analyses.

The authors use several statistical techniques to identify selection sites of interest in SARS-CoV-2 data from GISAID.

Display Conventions and Configuration

This track has two subtracks:

Positive Selection: "On average along interior tree branches, this site has a dN/dS>1 is accumulating non-synonymous changes (some of which might have a functional impact, but most probably don't) faster relative to synonymous changes than would be expected under neutral evolution."

Negative Selection: "On average along interior tree branches, this site has a dN/dS<1, meaning that it is conserved, i.e. non-synonymous changes might be selected against. Note that sites with no changes (i.e. perfectly conserved sites) cannot be detected by dN/dS based methods"

Methods

The CSV used to generate the genomic coordinates of selection sites was parsed and the position, gene, site_in_gene, score, and type fields were used to generate the resulting fields provided for each site in the data.

References

Pond et al, 2020 "Natural selection analysis of SARS-CoV-2/COVID-19"

Pond et al, 2020 "Natural selection analysis of SARS-CoV-2/COVID-19, V2"

Martin DP, Lytras S, Lucaci AG, Maier W, Grüning B, Shank SD, Weaver S, MacLean OA, Orton RJ, Lemey P et al. Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function. Mol Biol Evol. 2022 Apr 11;39(4). PMID: 35325204; PMC: PMC9037384