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Hub: UMassMed ZHub
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Genes and Gene Predictions
NCBI Genes hide dense squish pack full	NCBI Proteins hide dense squish pack full	Subgenomic Canonical hide dense squish pack full	Subgenomic Breakpts hide dense full	Subgenomic Observed hide dense squish pack full	Subgenomic RNA Modif. hide dense squish pack full	Protein Interact. hide dense squish pack full	Weizman ORFs hide show
PDB Structures hide dense squish pack full	PDB Ligand Contacts hide dense squish pack full	AUGUSTUS hide dense squish pack full	Nextstrain Genes hide dense squish pack full	PhyloCSF Genes hide dense squish pack full	Simple Repeats hide dense squish pack full
Variation and Repeats
Phylogeny: Public hide dense squish pack full	Phylogeny: GISAID hide dense squish pack full	updated Nextstrain Clades hide dense squish pack full	updated Nextstrain Mutations hide dense squish pack full	Intrahost SNPs hide dense squish pack full	Nat. Selection (Pond) hide dense squish pack full	Drug Resistance Mutations hide dense squish pack full	Galaxy ENA mutations hide show
Microdeletions hide dense squish pack full	updated Nextstrain Frequency hide dense full	updated Nextstrain Parsimony hide dense full	Pot. pathogenic indels hide dense squish pack full	Predicted Resistance hide dense squish pack full	Recomb. Breakpoints hide dense squish pack full	Spike Mutations hide dense squish pack full	new Variants of Concern hide dense squish pack full
WM + SDust hide dense squish pack full
UniProt Protein Annotations
Precurs. Proteins hide dense squish pack full	Protein Alignments hide dense squish pack full	Protein Products hide dense squish pack full	Highlights hide dense squish pack full	Signal Peptides hide dense squish pack full	Extracellular hide dense squish pack full	Transmem. Domains hide dense squish pack full	Cytoplasmic hide dense squish pack full
Disulf. Bonds hide dense squish pack full	Protein Domains hide dense squish pack full	Glycosyl/Phosph. hide dense squish pack full	Mutations hide dense squish pack full	Other Annot. hide dense squish pack full	Structure hide dense squish pack full	Repeats hide dense squish pack full	Protease Cleavage hide dense squish pack full
Immunology
RBD Mut Bind hide dense full	RBD Mut Expr hide dense full	Antib Pept Array hide show	S Antib Pept Array hide show	Antibody Escape hide show	CD8 Escape Muts hide dense squish pack full	CD8 RosettaMHC hide dense squish pack full	IEDB Predictions hide dense squish pack full
Poran HLA I hide dense squish pack full	Poran HLA II hide dense squish pack full	T-React. Epitopes hide dense squish pack full	Vaccines hide dense squish pack full	Validated epitopes from IEDB hide dense squish pack full
Expression and Regulation
CpG Islands hide show
Comparative Genomics
44 Bat CoVs hide dense squish pack full	119 Vertebrate CoVs hide dense squish pack full	PhyloCSF hide show	Human CoV hide dense squish pack full
Mapping and Sequencing
Base Position hide dense full	Nanopore coverage hide dense full	ARTIC Primers V3 hide dense squish pack full	ARTIC Primers V4 hide dense squish pack full	ARTIC Primers V4.1 hide dense squish pack full	RAPID/Midnight Primers hide dense squish pack full	Swift Primers hide dense squish pack full	Crowd-Sourced Data hide dense squish pack full
NEB VarSkip Primers hide dense squish pack full	Assembly hide dense squish pack full	Gap hide dense squish pack full	Cas13 CRISPR hide dense squish pack full	Short Match hide dense squish pack full	Restr Enzymes hide dense squish pack full	Addgene Plasmids hide dense squish pack full	CRISPR Detection hide dense squish pack full
GC Percent hide dense full	INSDC hide dense squish pack full	Problematic Sites hide dense squish pack full	RefSeq Acc hide dense squish pack full	RT-PCR Primers hide dense squish pack full
mRNA and EST
SHAPE Struct Pyle hide dense full	icSHAPE RNA Struct hide dense full	Rangan RNA hide dense squish pack full	Rfam hide dense squish pack full
other
Genscan Genes hide dense squish pack full

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GISAID data displayed in the Genome Browser are subject to GISAID's Terms and Conditions. SARS-CoV-2 genome sequences and metadata are available for download from GISAID EpiCoV™.