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| Base Position |
| Chromosome position in bases. (Clicks here zoom in 3x) |
| Nanopore coverage |
| Nanopore coverage of in-vitro-transcribed RNA seq + PCR, Kim et al 2020 |
| ARTIC Primers V3 |
| ARTIC V3 Oxford Nanopore sequencing primers |
| ARTIC Primers V4 |
| ARTIC V4 Oxford Nanopore sequencing primers |
| ARTIC Primers V4.1 |
| ARTIC V4.1 Oxford Nanopore sequencing primers |
| RAPID/Midnight Primers |
| RAPID/Midnight 1200bp amplicon Oxford Nanopore sequencing primers |
| Swift Primers |
| Swift BioSciences sequencing primers |
| Crowd-Sourced Data |
| Crowd-sourced data: annotations contributed via bit.ly/cov2annots |
| NEB VarSkip Primers |
| New England Biolabs (NEB) VarSkip Primers |
| Cas13 CRISPR |
| Cas13 CRISPR targets |
| Addgene Plasmids |
| Addgene Plasmid Sequences alignable to the Genome |
| Assembly |
| Assembly from Fragments |
| CRISPR Detection |
| CRISPR Detection Guides |
| Gap |
| Gap Locations |
| GC Percent |
| GC Percent in 5-Base Windows |
| INSDC |
| Accession at INSDC - International Nucleotide Sequence Database Collaboration |
| Problematic Sites |
| Problematic sites where masking or caution are recommended for analysis |
| RefSeq Acc |
| RefSeq Accession |
| Restr Enzymes |
| Restriction Enzymes from REBASE |
| RT-PCR Primers |
| RT-PCR Detection Kit Primer Sets |
| Short Match |
| Perfect Matches to Short Sequence () |
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| NCBI Genes |
| NCBI Genes from NC_045512.2 |
| NCBI Proteins |
| NCBI Proteins: annotated mature peptide products |
| Subgenomic Canonical |
| Canonical Subgenomic Transcripts |
| Subgenomic Breakpts |
| Subgenomic Transcript Breakpoints from Kim et al 2020: Nanopore and MGISeq |
| Subgenomic Observed |
| Subgenomic Transcripts found in long-read sequences by Kim et al. 2020 |
| Subgenomic RNA Modif. |
| Subgenomic RNA Modifications from Kim et al. 2020: gRNA S 3a E M 6 7a 7b 8 N |
| Protein Interact. |
| Human Interacting Proteins from Gordon et al. (* = druggable) |
| Weizman ORFs |
| New ORFs based on RNA-seq and Ribo-seq by the Weizman Institute |
| Vero6 24hpi |
| Vero6 24hpi Ribo-seq and RNA-seq |
| Vero6 5hpi |
| Vero6 5hpi Ribo-seq and RNA-seq |
| Calu3 7hpi |
| Calu3 7hpi Ribo-seq and RNA-seq |
| ORF predictions |
| Weizman ORF predictions |
| PDB Structures |
| Protein Data Bank (PDB) Sequence Matches |
| PDB Ligand Contacts |
| Potential contact residues in PDB structures of viral proteins |
| AUGUSTUS |
| AUGUSTUS ab initio gene predictions v3.1 |
| Genscan Genes |
| Genscan Gene Predictions |
| Nextstrain Genes |
| Genes annotated by nextstrain.org/ncov |
| PhyloCSF Genes |
| PhyloCSF Genes - Curated conserved genes |
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| Precurs. Proteins |
| UniProt Precursor Proteins (before cleavage into protein products) |
| Protein Alignments |
| UCSC alignment of full-length SwissProt proteins to genome |
| Protein Products |
| UniProt Protein Products (Polypeptide Chains, after cleavage) |
| Highlights |
| UniProt highlighted "Regions of Interest" |
| Signal Peptides |
| UniProt Signal Peptides |
| Extracellular |
| UniProt Extracellular Domain |
| Transmem. Domains |
| UniProt Transmembrane Domains |
| Cytoplasmic |
| UniProt Cytoplasmic Domains |
| Disulf. Bonds |
| UniProt Disulfide Bonds |
| Protein Domains |
| UniProt Domains |
| Glycosyl/Phosph. |
| UniProt Amino Acid Glycosylation/Phosphorylation sites |
| Mutations |
| UniProt Amino Acid Mutations |
| Other Annot. |
| UniProt Other Annotations |
| Structure |
| UniProt Protein Primary/Secondary Structure Annotations |
| Repeats |
| UniProt Repeats |
| Protease Cleavage |
| Protease Cleavage Sites |
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| RBD Mut Bind |
| S RBD Deep Mutational Scanning: ACE2 Binding (Jesse Bloom's Group) |
| RBD Mut Expr |
| S RBD Deep Mutational Scanning: Expression (Jesse Bloom's Group) |
| Antib Pept Array |
| Antibody Proteome Peptide Binding Microarray Raw Data from Wang et al, ACS 2020, Xiaobo Yu group, NCPSB Beijing |
| IgM Z-score - early COVID-19 patients |
| Proteome Peptide Microarray - IgM - early COVID-19 patients |
| IgG Z-score- early COVID-19 patients |
| Proteome Peptide Microarray - IgG - early COVID-19 patients |
| Antib Pept Array Sum (IgM) |
| Antibody Proteome Peptide Binding Microarray, Wang et al 2020 - IgM, Covid - Sum of scores per nucleotide |
| Antib Pept Array Sum (IgG) |
| Antibody Proteome Peptide Binding Microarray, Wang et al 2020 - IgG, Covid - Sum of scores per nucleotide |
| S Antib Pept Array |
| S Protein Antibody Peptide Binding Microarray from Li et al, Cell & Mol Imm 2020, Sheng-ce Tao group, Jiao Tung Univ. |
| S-PBM: IgM Response Frequency |
| S Protein Antibody Peptide Binding Microarray - IgM - Response Frequency |
| S-PBM: IgG Response Frequency |
| S Protein Antibody Peptide Binding Microarray - IgG - Response Frequency |
| S-PBM IgM |
| S Protein Antibody Peptide Binding Microarray - IgM - Sheng-ce Tao group, Jiao Tung Univ. |
| S-PBM IgG |
| S Protein Antibody Peptide Binding Microarray - IgG - Sheng-ce Tao group, Jiao Tung Univ. |
| Antibody Escape |
| Escape from serum or monoclonal antibodies: Whelan, Bloom and Rappuoli groups |
| McCoy Escape |
| McCoy lab: S Mutation impact on neutralization by serum and mAbs |
| Rappuoli Serum Escape |
| Rappuoli lab: S Mutations that lead to escape from neutralizing antibodies from plasma of a single patient |
| Whelan 21 Ab |
| Whelan lab: RBD Mutations that lead to escape from 21 monoclonal antibodies (click to show mutation details) |
| Bloom Total Escape |
| Bloom Lab: S RBD-mutation antibody escape - total escape score per amino acid - 13 MABs and serum from 11 patients (A-K) |
| Bloom Max Escape |
| Bloom Lab: S RBD-mutation antibody escape - maximum escape score per amino acid - 13 MABs and serum from 11 patients (A-K) |
| Bloom Strong Mutations |
| Bloom Lab: Strong S RBD-mutation antibody escape - positions with max score > 0.18 - shading = number of samples where found |
| Bloom MAB Average |
| Bloom Lab: S RBD-mutation monoclonal antibody escape - average score across all 13 MAB samples |
| Bloom Serum Average |
| Bloom Lab: S RBD-mutation patient serum antibody escape - average score across serum samples (patients A-K) |
| CD8 Escape Muts |
| T-Cell MHCI CD8+ Escape Mutations from Agerer et al. Sci Immun 2020 |
| CD8 RosettaMHC |
| CD8 Epitopes predicted by NetMHC and Rosetta |
| IEDB Predictions |
| IEDB-Predicted Epitopes from Grifoni et al 2020 |
| Poran HLA I |
| RECON HLA-I epitopes |
| Poran HLA II |
| RECON HLA-II epitopes |
| T-React. Epitopes |
| T-cell reactive epitopes in patients and donors |
| Vaccines |
| COVID Vaccines BioNTech/Pfizer BNT-162b2 and Moderna mRNA-1273 |
| Validated epitopes from IEDB |
| Validated epitopes from IEDB |
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| SHAPE Struct Pyle |
| RNA SHAPE Structure from the Pyle group |
| icSHAPE RNA Struct |
| icSHAPE RNA Structure |
| Rangan RNA |
| Rangan et al. RNA predictions |
| Rfam |
| Rfam families |
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| CpG Islands |
| CpG Islands (Islands < 300 Bases are Light Green) |
| Unmasked CpG |
| CpG Islands on All Sequence (Islands < 300 Bases are Light Green) |
| CpG Islands |
| CpG Islands (Islands < 300 Bases are Light Green) |
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| 44 Bat CoVs |
| Multiz Alignment & Conservation (44 Strains with bats as hosts) |
| 119 Vertebrate CoVs |
| Multiz Alignment & Conservation (119 strains: strains with vertebrate hosts and human SARS-Cov2) |
| PhyloCSF |
| PhyloCSF |
| Smoothed PhyloCSF-3 |
| Smoothed PhyloCSF Strand - Frame 3 |
| Smoothed PhyloCSF-2 |
| Smoothed PhyloCSF Strand - Frame 2 |
| Smoothed PhyloCSF-1 |
| Smoothed PhyloCSF Strand - Frame 1 |
| Smoothed PhyloCSF+3 |
| Smoothed PhyloCSF Strand + Frame 3 |
| Smoothed PhyloCSF+2 |
| Smoothed PhyloCSF Strand + Frame 2 |
| Smoothed PhyloCSF+1 |
| Smoothed PhyloCSF Strand + Frame 1 |
| PhyloCSF Power |
| Relative branch length of local alignment, a measure of PhyloCSF statistical power |
| Human CoV |
| Multiz Alignment and Conservation of 7 Strains of human coronavirus |
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| Phylogeny: Public |
| Phylogenetic Tree and Nucleotide Substitution Mutations in Sequences in Public Databases |
| Phylogeny: GISAID |
| Phylogenetic Tree and Nucleotide Substitution Mutations in High-coverage Sequences in GISAID EpiCoV TM |
| updated
Nextstrain Clades |
| Nextstrain year-letter clade designations (19A, 19B, 20A, etc.) |
| updated
Nextstrain Mutations |
| Nextstrain Subset of GISAID EpiCoV TM Sample Mutations |
| Intrahost SNPs |
| Intrahost SNP patient data from Todd Treangen's group |
| Nat. Selection (Pond) |
| Natural selection analysis from Sergei Pond's research group |
| Drug Resistance Mutations |
| Mutations that confer drug resistance (Anna Niewiadomska, BV-BRC) |
| Galaxy ENA mutations |
| GalaxyProject surveillance of SARS-CoV-2 mutations through consistent processing of public raw sequencing data |
| Galaxy ENA mutations in top lineages - three quarters ago |
| Most frequent lineages of three quarters ago |
| Galaxy ENA mutations in top lineages - two quarters ago |
| Most frequent lineages of two quarters ago |
| Galaxy ENA mutations in top lineages - a quarter ago |
| Most frequent lineages of a quarter ago |
| Galaxy ENA mutations in top lineages - current quarter |
| Most frequent lineages of current quarter |
| Microdeletions |
| Microdeletions in GISAID sequences |
| updated
Nextstrain Frequency |
| Nextstrain Mutations Alternate Allele Frequency |
| updated
Nextstrain Parsimony |
| Parsimony Scores for Nextstrain Mutations and Phylogenetic Tree |
| Pot. pathogenic indels |
| Potential pathogenic insertions and deletions from Gussow et al, PNAS 2020 |
| Predicted Resistance |
| Mutations that may confer drug resistance - from Coronavirus3d.org (label: count of GISAID sequences with mutation, Feb 2022) |
| Recomb. Breakpoints |
| Recombination Breakpoints from Thurakia et al 2022 |
| Simple Repeats |
| Simple Tandem Repeats by TRF |
| Spike Mutations |
| Spike protein mutations from community annotation (Feb 2021) |
| new
Variants of Concern |
| Mutations in Variants of Concern (VOC), Interest (VOI), or Under Monitoring (VUM) (configure to show more lineages) |
| WM + SDust |
| Genomic Intervals Masked by WindowMasker + SDust |
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