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UCSC Genome Browser on SARS-CoV-2 Jan. 2020 (NC_045512.2) (wuhCor1)
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NC_045512v2:1-29,903 29,903 bp.   Quick start guide
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-   Mapping and Sequencing
Base Position
 		Nanopore coverage
ARTIC Primers V3
ARTIC Primers V4
ARTIC Primers V4.1
RAPID/Midnight Primers
Swift Primers
Crowd-Sourced Data
NEB VarSkip Primers
Cas13 CRISPR
Addgene Plasmids
Assembly
CRISPR Detection
Gap
GC Percent
INSDC
Problematic Sites
RefSeq Acc
Restr Enzymes
RT-PCR Primers
Short Match
-   Genes and Gene Predictions
NCBI Genes
NCBI Proteins
 Subgenomic Canonical
 Subgenomic Breakpts
 Subgenomic Observed
Subgenomic RNA Modif.
Protein Interact.
 Weizman ORFs
PDB Structures
PDB Ligand Contacts
AUGUSTUS
Genscan Genes
Nextstrain Genes
 PhyloCSF Genes
-   UniProt Protein Annotations
Precurs. Proteins
Protein Alignments
Protein Products
Highlights
Signal Peptides
Extracellular
Transmem. Domains
Cytoplasmic
Disulf. Bonds
Protein Domains
Glycosyl/Phosph.
Mutations
Other Annot.
Structure
Repeats
Protease Cleavage
-   Immunology
RBD Mut Bind
 RBD Mut Expr
 Antib Pept Array
 S Antib Pept Array
 Antibody Escape
CD8 Escape Muts
CD8 RosettaMHC
 IEDB Predictions
Poran HLA I
Poran HLA II
 T-React. Epitopes
Vaccines
Validated epitopes from IEDB
-   mRNA and EST
SHAPE Struct Pyle
 icSHAPE RNA Struct
Rangan RNA
Rfam
-   Expression and Regulation
CpG Islands
-   Comparative Genomics
44 Bat CoVs
 119 Vertebrate CoVs
 PhyloCSF
Human CoV
-   Variation and Repeats
Phylogeny: Public
 Phylogeny: GISAID
updated Nextstrain Clades
updated Nextstrain Mutations
Intrahost SNPs
 Nat. Selection (Pond)
Drug Resistance Mutations
 Galaxy ENA mutations
Microdeletions
updated Nextstrain Frequency
updated Nextstrain Parsimony
Pot. pathogenic indels
Predicted Resistance
Recomb. Breakpoints
Simple Repeats
Spike Mutations
new Variants of Concern
WM + SDust
track, load time, draw time, total (first window)
NCBI Genes, 6, 3, 9
Precurs. Proteins, 2, 1, 3
Protein Products, 1, 12, 13
Highlights, 3, 26, 29
Protein Domains, 3, 1, 4
Mutations, 5, 0, 5
Bloom Serum Average, 1, 0, 1
Drug Resistance Mutations, 3, 0, 3
Recomb. Breakpoints, 4, 6, 10
Delta AA Muts, 0, 1, 1
Omicron BA.2 AA Muts, 1, 0, 1
Omicron XBB.1.5 AA Muts, 1, 0, 1
Omicron XBB.1.16 AA Muts, 1, 0, 1
Omicron EG.5.1 AA Muts, 1, 0, 1
Omicron JN.1 AA Muts, 1, 0, 1

For information about this browser and related resources, see COVID-19 Research at UCSC.

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™.

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