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spherical-trial.yml
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spherical-trial.yml
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unique-id: spherical-trial
phe-label: V-21APR-03
alternate-names:
- India
- B.1.617 Clade 3
belongs-to-lineage:
- PANGO: B.1.617.3
description: This variant is reported to be circulating in India and has been exported to other countries.
information-sources:
- https://github.com/cov-lineages/pango-designation/issues/49
variants:
- codon-change: TTC-TTT
gene: ORF1ab
one-based-reference-position: 835
predicted-effect: synonymous
protein: nsp2
protein-codon-position: 10
reference-base: C
snp-codon-position: 3
type: SNP
variant-base: T
- amino-acid-change: A1526V
codon-change: GCT-GTT
gene: ORF1ab
one-based-reference-position: 7296
predicted-effect: non-synonymous
protein: nsp3
protein-codon-position: 1526
reference-base: C
type: SNP
variant-base: T
- amino-acid-change: T1830I
codon-change: ACT-ATT
gene: ORF1ab
one-based-reference-position: 8208
predicted-effect: non-synonymous
protein: nsp3
protein-codon-position: 1830
reference-base: C
type: SNP
variant-base: T
- amino-acid-change: A194S
codon-change: GCT-TCT
gene: ORF1ab
one-based-reference-position: 10634
predicted-effect: non-synonymous
protein: nsp5
protein-codon-position: 194
reference-base: G
type: SNP
variant-base: T
- amino-acid-change: A117V
codon-change: GCA-GTA
gene: ORF1ab
one-based-reference-position: 11322
predicted-effect: non-synonymous
protein: nsp6
protein-codon-position: 117
reference-base: C
type: SNP
variant-base: T
- codon-change: TGC-TGT
gene: ORF1ab
one-based-reference-position: 16293
predicted-effect: synonymous
protein: nsp13
protein-codon-position: 19
reference-base: C
snp-codon-position: 3
type: SNP
variant-base: T
- amino-acid-change: T19R
codon-change: ACA-AGA
gene: S
one-based-reference-position: 21618
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 19
reference-base: C
type: SNP
variant-base: G
- amino-acid-change: L452R
codon-change: CTG-CGG
gene: S
one-based-reference-position: 22917
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 452
reference-base: T
type: SNP
variant-base: G
- amino-acid-change: E484Q
codon-change: GAA-CAA
gene: S
one-based-reference-position: 23012
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 484
reference-base: G
type: SNP
variant-base: C
- amino-acid-change: P681R
codon-change: CCT-CGT
gene: S
one-based-reference-position: 23604
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 681
reference-base: C
type: SNP
variant-base: G
- amino-acid-change: D950N
codon-change: GAT-AAT
gene: S
one-based-reference-position: 24410
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 950
reference-base: G
type: SNP
variant-base: A
- codon-change: GAT-GAC
gene: ORF6
one-based-reference-position: 27384
predicted-effect: synonymous
protein: ORF6 protein
protein-codon-position: 61
reference-base: T
snp-codon-position: 3
type: SNP
variant-base: C
- amino-acid-change: V82A
codon-change: GTT-GCT
gene: ORF7a
one-based-reference-position: 27638
predicted-effect: non-synonymous
protein: ORF7a protein
protein-codon-position: 82
reference-base: T
type: SNP
variant-base: C
- amino-acid-change: T26I
codon-change: ACT-ATT
gene: ORF8
one-based-reference-position: 27970
predicted-effect: non-synonymous
protein: ORF8 protein
protein-codon-position: 26
reference-base: C
type: SNP
variant-base: T
- amino-acid-change: P67S
codon-change: CCT-TCT
gene: N
one-based-reference-position: 28472
predicted-effect: non-synonymous
protein: nucleocapsid phosphoprotein
protein-codon-position: 67
reference-base: C
type: SNP
variant-base: T
- amino-acid-change: R203M
codon-change: AGG-ATG
gene: N
one-based-reference-position: 28881
predicted-effect: non-synonymous
protein: nucleocapsid phosphoprotein
protein-codon-position: 203
reference-base: G
type: SNP
variant-base: T
- amino-acid-change: D377Y
codon-change: GAT-TAT
gene: N
one-based-reference-position: 29402
predicted-effect: non-synonymous
protein: nucleocapsid phosphoprotein
protein-codon-position: 377
reference-base: G
type: SNP
variant-base: T
calling-definition:
confirmed:
mutations-required: 17
indels-required: 0
allowed-wildtype: 0
probable:
mutations-required: 8
indels-required: 0
allowed-wildtype: 0
low-qc:
mutations-required: 0
indels-required: 0
allowed-wildtype: 0
acknowledgements:
curators:
- Natalie Groves
- Jeff Barrett