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umbrella-embark.yml
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unique-id: umbrella-embark
phe-label: V-22APR-01
who-label:
alternate-names:
-
belongs-to-lineage:
- PANGO: XD
description: This variant is a recombinant lineage. It comtains BA.2 spike within an AY.4 (Delta) backbone.
information-sources:
- https://github.com/cov-lineages/pango-designation/issues/444
variants:
- amino-acid-change: E172D
codon-change: GAA-GAC
gene: ORF1ab
one-based-reference-position: 1321
predicted-effect: non-synonymous
protein: nsp2
protein-codon-position: 172
reference-base: A
type: SNP
variant-base: C
- amino-acid-change: I57V
codon-change: ATA-GTA
gene: ORF1ab
one-based-reference-position: 8723
predicted-effect: non-synonymous
protein: nsp4
protein-codon-position: 57
reference-base: A
type: SNP
variant-base: G
- amino-acid-change: P323F
codon-change: CCT-TTT
gene: ORF1ab
one-based-reference-position: 14407
predicted-effect: non-synonymous
protein: nsp12
protein-codon-position: 323
reference-base: CCT
type: MNP
variant-base: TTT
- amino-acid-change: A27S
codon-change: GCA-TCA
gene: S
one-based-reference-position: 21641
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 27
reference-base: G
type: SNP
variant-base: T
- amino-acid-change: G496S
codon-change: GGT-AGT
gene: S
one-based-reference-position: 23048
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 496
reference-base: G
type: SNP
variant-base: A
- amino-acid-change: N764K
codon-change: AAC-AAA
gene: S
one-based-reference-position: 23854
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 764
reference-base: C
type: SNP
variant-base: A
- amino-acid-change: L981F
codon-change: CTT-TTT
gene: S
one-based-reference-position: 24503
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 981
reference-base: C
type: SNP
variant-base: T
- amino-acid-change: S92L
codon-change: TCA-TTA
gene: ORF3a
one-based-reference-position: 25667
predicted-effect: non-synonymous
protein: ORF3a protein
protein-codon-position: 92
reference-base: C
type: SNP
variant-base: T
- amino-acid-change: D155Y
codon-change: GAC-TAC
gene: ORF3a
one-based-reference-position: 25855
predicted-effect: non-synonymous
protein: ORF3a protein
protein-codon-position: 155
reference-base: G
type: SNP
variant-base: T
- gene: .
one-based-reference-position: 29540
protein: .
reference-base: G
type: SNP
variant-base: A
- amino-acid-change: V30L
codon-change: GTA-TTA
gene: ORF10
one-based-reference-position: 29645
predicted-effect: non-synonymous
protein: ORF10 protein
protein-codon-position: 30
reference-base: G
type: SNP
variant-base: T
calling-definition:
confirmed:
mutations-required: 9
indels-required: 0
allowed-wildtype: 0
probable:
mutations-required: 6
indels-required: 0
allowed-wildtype: 0
low-qc:
mutations-required: 0
indels-required: 0
allowed-wildtype: 0