Schema for Nat. Selection (Pond) - Natural selection analysis from Sergei Pond's research group
  Database: wuhCor1    Primary Table: Negative_Selection Data last updated: 2022-05-18
Big Bed File Download: /gbdb/wuhCor1/pond/neg.bb
Item Count: 2,908
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
chromStart19983Start position in chromosome
chromEnd19986End position in chromosome
nameName of item
score0Score from 0-1000 (might not be applicable)
strand.+, - or . for unknown
thickStart19983Start of where display should be thick
thickEnd19986End of where display should be thick
seqs4216Number of sequences
alpha9.94253Dn
beta0.0Ds
p2.68011e-09P-Value

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndseqsalphabetap
NC_045512v219983199860.199831998642169.942530.02.68011e-09
NC_045512v219983199860.1998319986455910.02910.01.69848e-09
NC_045512v219983199860.199831998645859.892680.04.3797e-09
NC_045512v219983199860.1998319986457210.01060.02.82761e-09
NC_045512v220055200580.2005520058421669.93270.02.22045e-16
NC_045512v220055200580.2005520058455969.8950.01.00142e-13
NC_045512v220055200580.2005520058458552.21850.05.56755e-11
NC_045512v220055200580.2005520058457245.86460.04.07012e-10
NC_045512v220148201510.201482015142163.520970.07.34457e-05
NC_045512v220148201510.201482015145595.36190.05.48222e-07

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 Contact us or Sergei if you believe that the data shown is too outdated for your analyses.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