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perfume-sprint.yml
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unique-id: perfume-sprint
phe-label: V-21JUN-01
who-label: Lambda
alternate-names:
belongs-to-lineage:
- PANGO: C.37
- WHO: Lambda
description: This variant is a clade first associated with South America but now observed in USA and Europe
information-sources:
- https://github.com/cov-lineages/pango-designation/issues/52
variants:
- amino-acid-change: F1569V
codon-change: TTT-GTT
gene: ORF1ab
one-based-reference-position: 7424
predicted-effect: non-synonymous
protein: nsp3
protein-codon-position: 1569
reference-base: T
type: SNP
variant-base: G
- codon-change: CTA-TTA
gene: ORF1ab
one-based-reference-position: 9857
predicted-effect: synonymous
protein: nsp4
protein-codon-position: 435
reference-base: C
snp-codon-position: 1
type: SNP
variant-base: T
- amino-acid-change: L438P
codon-change: CTT-CCT
gene: ORF1ab
one-based-reference-position: 9867
predicted-effect: non-synonymous
protein: nsp4
protein-codon-position: 438
reference-base: T
type: SNP
variant-base: C
- amino-acid-change: T492I
codon-change: ACC-ATC
gene: ORF1ab
one-based-reference-position: 10029
predicted-effect: non-synonymous
protein: nsp4
protein-codon-position: 492
reference-base: C
type: SNP
variant-base: T
- gene: ORF1ab
one-based-reference-position: 11287
protein: nsp6
reference-base: GTCTGGTTTT
type: deletion
variant-base: G
- gene: S
one-based-reference-position: 22298
protein: surface glycoprotein
reference-base: AGAAGTTATTTGACTCCTGGTG
type: deletion
variant-base: A
- amino-acid-change: L452Q
codon-change: CTG-CAG
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: A
- amino-acid-change: F490S
codon-change: TTT-TCT
gene: S
one-based-reference-position: 23031
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 490
reference-base: T
type: SNP
variant-base: C
- amino-acid-change: T859N
codon-change: ACT-AAT
gene: S
one-based-reference-position: 24138
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 859
reference-base: C
type: SNP
variant-base: A
- amino-acid-change: G214C
codon-change: GGC-TGC
gene: N
one-based-reference-position: 28913
predicted-effect: non-synonymous
protein: nucleocapsid phosphoprotein
protein-codon-position: 214
reference-base: G
type: SNP
variant-base: T
- codon-change: TTC-TTT
gene: N
one-based-reference-position: 29311
predicted-effect: synonymous
protein: nucleocapsid phosphoprotein
protein-codon-position: 346
reference-base: C
snp-codon-position: 3
type: SNP
variant-base: T
calling-definition:
confirmed:
mutations-required: 9
indels-required: 0
allowed-wildtype: 0
probable:
mutations-required: 5
indels-required: 0
allowed-wildtype: 0
low-qc:
mutations-required: 0
indels-required: 0
allowed-wildtype: 0
acknowledgements:
curators:
- Natalie Groves
- Francesco Strino