Schema for Predicted Resistance - Mutations that may confer drug resistance - from Coronavirus3d.org (label: count of GISAID sequences with mutation, Feb 2022)
  Database: wuhCor1    Primary Table: resistPred Data last updated: 2022-03-04
Big Bed File: /gbdb/wuhCor1/resistPred/resistPred.bb
Item Count: 1,566
Format description: Browser extensible data (9 fields) plus other mutation annotations
fieldexampledescription
chromNC_045512v2Chromosome (or contig, scaffold, etc.)
chromStart21601Start position in chromosome
chromEnd21605End position in chromosome
name105Name of item
score105Score from 0-1000
strand.+ or -
thickStart21601Start of where display should be thick (start codon)
thickEnd21605End of where display should be thick (stop codon)
reserved0Used as itemRgb as of 2004-11-22
count105Frequency in Mar 2022
mutstop_gained; missense_variant; inframe_deletion; Mutation Type
annotDeletion; SNP; Annotations Type
changeFreqC>T:5; 21602-21622del:1; C>A:93; C>G:12; 21602-21619del:11; 21602-21625del:14; Base change and frequency for each
aa14:Q>*; 14:14-20del; 14:Q>K; 14:Q>E; 14:14-19del; 14:14-21del; AA change
res14Residue number in PDB structure

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedcountmutannotchangeFreqaares
NC_045512v22160121605105105.21601216050105stop_gained; missense_variant; inframe_deletion;Deletion; SNP;C>T:5; 21602-21622del:1; C>A:93; C>G:12; 21602-21619del:11; 21602-21625del:14;14:Q>*; 14:14-20del; 14:Q>K; 14:Q>E; 14:14-19del; 14:14-21del;14
NC_045512v22160221606937937.21602216060937coding_sequence_variant; missense_variant;Deletion; SNP;A>C:3; 21603-21608del:1; A>G:757; A>T:177;14:Q>P; 14:QCV>L; 14:Q>R; 14:Q>L;14
NC_045512v2216032160757671000.216032160705767missense_variant; frameshift_variant; coding_sequence_variant;SNP; Deletion;G>C:712; 21604-21606del:3; 21604-21605del:1; 21604-21657del:1; G>T:5055;14:Q>H; 14:QC>H; 14:fs; 14:QCVNLTTRTQLPPAYTNSF>H; 14:Q>H;14
NC_045512v221604216085454.2160421608054inframe_deletion; missense_variant;SNP; Deletion;TGT>GAA:1; T>G:15; 21605-21643del:3; T>A:1; T>C:37;15:C>E; 15:C>G; 15:15-27del; 15:C>S; 15:C>R;15
NC_045512v22160521609670670.21605216090670coding_sequence_variant; missense_variant;SNP; Deletion;G>C:21; G>T:608; GTG>CAA:1; G>A:41; 21606-21707del:1; 21606-21611del:1; 21606-21641del:1; 21606-21620del:3;15:C>S; 15:C>F; 15:CV>SI; 15:C>Y; 15:CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLH>Y; 15:CVN>Y; 15:CVNLTTRTQLPPA>S; 15:CVNLTT>S;15
NC_045512v2216062161022.216062161002inframe_deletion; missense_variant; coding_sequence_variant; frameshift_variant;SNP; Deletion;21607-21607del:1; T>G:2; 21607-21609del:2; TG>CT:1;15:fs; 15:C>W; 16:16-16del; 15:CV>CF;15
NC_045512v2216072161162961000.216072161106296coding_sequence_variant; missense_variant;SNP; Insertion;G>C:264; G>GCAACTTTGAGGA:2; GT>AA:1; G>T:5770; G>A:261;16:V>L; 16:V>ATLRI; 16:V>N; 16:V>F; 16:V>I;16
NC_045512v22160821612325325.21608216120325inframe_deletion; missense_variant; coding_sequence_variant; frameshift_variant;Deletion; SNP;T>A:1; T>G:11; 21609-21614del:8; T>C:313; 21609-21609del:1; 21609-21611del:11;16:V>D; 16:V>G; 17:17-18del; 16:V>A; 16:fs; 16:VN>D;16
NC_045512v22161021614181181.21610216140181missense_variant; inframe_deletion;SNP; Deletion;21611-21622del:1; 21611-21625del:1; A>T:13; A>G:167; 21611-21646del:1; A>C:1; 21611-21619del:2;17:17-20del; 17:17-21del; 17:N>Y; 17:N>D; 17:17-28del; 17:N>H; 17:17-19del;17
NC_045512v2216112161524101000.216112161502410missense_variant; coding_sequence_variant; frameshift_variant;Deletion; SNP;21612-21646del:1; A>G:2383; 21612-21614del:27; A>T:13; A>C:14;17:fs; 17:N>S; 17:NL>I; 17:N>I; 17:N>T;17

Predicted Resistance (resistPred) Track Description
 

Description

This track lists amino acid positions that are close to certain Covid drug target protein binding sites; potentially relevant for viral drug resistance. The protein products are the S, NSP3, and NSP5 proteins. The data is derived from 3D Protein Data Bank (PDB) X-ray crystal structures and was imported from Coronavirus3d.org, a project funded by NIAID, NIGMS and UCR. For more information, please visit that site and look through the 9 protein-drug structures listed.

Display Conventions

The display shows amino acids within 5 Angstroms of an inhibitor binding site on the S, NSP3, and NSP5 proteins. The label of the annotations is the number of GISAID sequences with at least one mutation at this position as of March 3, 2022. Click or mouse-over the mutations to show the full list of nucleotide changes and the frequency of each.

Data Access

You can see the original data as tables on Coronavirus3d.org. The data can be explored interactively at the Genome Browser with the Table Browser or the Data Integrator. For automated analysis, the genome annotation is stored in a bigBed file that can be downloaded from the download server or the API.

Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.

Credits

Thanks to Anna Niewiadomska from the BV-BRC team at the J. Craig Venter Institute for finding the dataset and testing the track. Thanks to the Godzik Lab for making available the data in .tsv format on the coronavirus3d.org website.