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CRG Viral Beacon - Multi Variant Query

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Lineage A

8782 C > T; 28144 T > C

Lineage A.1

17747 C > T; 17858 A > G; 18060 C > T

Lineage A.2

9477 T > A; 14805 C > T; 25979 G > T; 28657 C > T; 28863 C > T

Lineage B.1

241 C > T; 3037 C > T; 14408 C > T; 23403 A > G

Lineage B.1.1

28881 G > A; 28882 G > A; 28883 G > C

Lineage B.2

11083 G > T; 14805 C > T; 26144 G > T

*Pangolin lineages extracted from Tegally, H., Wilkinson, E., Lessells, R.J. et al. Sixteen novel lineages of SARS-CoV-2 in South Africa. Nat Med 27, 440–446 (2021).


Lineage A

S2839 ORF1ab; L84S ORF8

Lineage A.1

P5828L ORF1ab; Y5865C ORF1ab; L5932 ORF1ab

Lineage A.2

F3071Y ORF1ab; Y4847 ORF1ab; G196V ORF3a; D128 N; S197L N

Lineage B.1.1

R203K N; R203 N; G204R N

Lineage B.2

L3606F ORF1ab; Y4847 ORF1ab; G251V ORF3a

*Pangolin lineages extracted from Tegally, H., Wilkinson, E., Lessells, R.J. et al. Sixteen novel lineages of SARS-CoV-2 in South Africa. Nat Med 27, 440–446 (2021).


Nucleotide

Aminoacid

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Variant Annotation Variant Frequency per Dataset
Position Type Ref. Alt. gene region effect functional class locus name locus id aminoacid change ENA-Illumina ENA-ONT ENA-Consensus

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Metadata

frequency per run host age host sex geo origin dataset disease sample type collection date platform run id bioproject accession sample id JBrowse strain id
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