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empathy-serve.yml
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unique-id: empathy-serve
phe-label: V-21APR-02
who-label: delta
alternate-names:
- India
- B.1.617 Clade 2
- VUI-21APR-02
belongs-to-lineage:
- PANGO: B.1.617.2
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:
- 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: T478K
codon-change: ACA-AAA
gene: S
one-based-reference-position: 22995
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 478
reference-base: C
type: SNP
variant-base: A
- 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: S26L
codon-change: TCA-TTA
gene: ORF3a
one-based-reference-position: 25469
predicted-effect: non-synonymous
protein: ORF3a protein
protein-codon-position: 26
reference-base: C
type: SNP
variant-base: T
- amino-acid-change: I82T
codon-change: ATC-ACC
gene: M
one-based-reference-position: 26767
predicted-effect: non-synonymous
protein: membrane glycoprotein
protein-codon-position: 82
reference-base: T
type: SNP
variant-base: C
- amino-acid-change: T120I
codon-change: ACA-ATA
gene: ORF7a
one-based-reference-position: 27752
predicted-effect: non-synonymous
protein: ORF7a protein
protein-codon-position: 120
reference-base: C
type: SNP
variant-base: T
- amino-acid-change: D63G
codon-change: GAC-GGC
gene: N
one-based-reference-position: 28461
predicted-effect: non-synonymous
protein: nucleocapsid phosphoprotein
protein-codon-position: 63
reference-base: A
type: SNP
variant-base: G
- 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
additional-mutations:
- 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: 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
- 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: 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: 8
indels-required: 0
allowed-wildtype: 0
probable:
mutations-required: 4
indels-required: 0
allowed-wildtype: 0
low-qc:
mutations-required: 0
indels-required: 0
allowed-wildtype: 0
acknowledgements:
curators:
- Natalie Groves
- Jeff Barrett