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imagines-viewable.yml
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/
imagines-viewable.yml
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unique-id: imagines-viewable
phe-label: VOC-22JAN-01
who-label: Omicron
alternate-names:
- BA.2
belongs-to-lineage:
- PANGO: BA.2
description: This variant is a sub-lineage of B.1.1.529
information-sources:
- https://github.com/cov-lineages/pango-designation/issues/361
- https://github.com/cov-lineages/pango-designation/issues/359
requires: plausible-scanner
variants:
- amino-acid-change: T24I
codon-change: ACT-ATT
gene: ORF1ab
one-based-reference-position: 2790
predicted-effect: non-synonymous
protein: nsp3
protein-codon-position: 24
reference-base: C
type: SNP
variant-base: T
- amino-acid-change: L438F
codon-change: CTT-TTT
gene: ORF1ab
one-based-reference-position: 9866
predicted-effect: non-synonymous
protein: nsp4
protein-codon-position: 438
reference-base: C
type: SNP
variant-base: T
- amino-acid-change: Q493R
codon-change: CAA-CGA
gene: S
one-based-reference-position: 23040
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 493
reference-base: A
type: SNP
variant-base: G
- amino-acid-change: D61L
codon-change: GAT-CTC
gene: ORF6
one-based-reference-position: 27382
predicted-effect: non-synonymous
protein: ORF6 protein
protein-codon-position: 61
reference-base: GAT
type: MNP
variant-base: CTC
- codon-change: TTC-TTT
gene: M
one-based-reference-position: 26858
predicted-effect: synonymous
protein: M
protein-codon-position: 112
snp-codon-position: 3
reference-base: C
type: SNP
variant-base: T
calling-definition:
confirmed:
mutations-required: 3
indels-required: 0
allowed-wildtype: 0
probable:
mutations-required: 3
indels-required: 0
allowed-wildtype: 1
alt-probable:
mutations-required: 3
indels-required: 0
allowed-wildtype: 0
variants:
- amino-acid-change: T24I
codon-change: ACT-ATT
gene: ORF1ab
one-based-reference-position: 2790
predicted-effect: non-synonymous
protein: nsp3
protein-codon-position: 24
reference-base: C
type: SNP
variant-base: T
- amino-acid-change: F486P
codon-change: TTT-CCT
gene: S
one-based-reference-position: 23018
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 486
reference-base: TTT
type: MNP
variant-base: CCN
- amino-acid-change: D61L
codon-change: GAT-CTC
gene: ORF6
one-based-reference-position: 27382
predicted-effect: non-synonymous
protein: ORF6 protein
protein-codon-position: 61
reference-base: GAT
type: MNP
variant-base: CTC
- codon-change: TTC-TTT
gene: M
one-based-reference-position: 26858
predicted-effect: synonymous
protein: M
protein-codon-position: 112
snp-codon-position: 3
reference-base: C
type: SNP
variant-base: T
low-qc:
mutations-required: 0
indels-required: 0
allowed-wildtype: 1
acknowledgements:
- Tulio de Oliveira and colleagues, CERI, Centre for Epidemic Response and Innovation, Stellenbosch University and KRISP, KZN Research Innovation and Sequencing Platform, UKZN, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, South Africa
- Thomas Peacock, Imperial College, UK
curators:
- Natalie Groves