-
Notifications
You must be signed in to change notification settings - Fork 19
/
mushroom-android.yml
194 lines (194 loc) · 4.56 KB
/
mushroom-android.yml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
unique-id: mushroom-android
phe-label: V-21MAR-02
who-label: Theta
alternate-names:
- VUI202103/02
- Philippines
belongs-to-lineage:
- PANGO: P.3
description: This variant appeared to be closely associated with the Phillipines and widely divergent from anything else upon discovery.
information-sources:
- https://github.com/cov-lineages/pango-designation/issues/27
- https://www.medrxiv.org/content/10.1101/2021.03.03.21252812v2
variants:
- amino-acid-change: D736G
codon-change: GAC-GGC
gene: ORF1ab
one-based-reference-position: 4926
predicted-effect: non-synonymous
protein: nsp3
protein-codon-position: 736
reference-base: A
type: SNP
variant-base: G
- 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: D112E
codon-change: GAC-GAA
gene: ORF1ab
one-based-reference-position: 11308
predicted-effect: non-synonymous
protein: nsp6
protein-codon-position: 112
reference-base: C
type: SNP
variant-base: A
- amino-acid-change: L71F
codon-change: CTT-TTT
gene: ORF1ab
one-based-reference-position: 12053
predicted-effect: non-synonymous
protein: nsp7
protein-codon-position: 71
reference-base: C
type: SNP
variant-base: T
- amino-acid-change: A368V
codon-change: GCA-GTA
gene: ORF1ab
one-based-reference-position: 17339
predicted-effect: non-synonymous
protein: nsp13
protein-codon-position: 368
reference-base: C
type: SNP
variant-base: T
- gene: S
one-based-reference-position: 21980
protein: surface glycoprotein
reference-base: TTTTTGGGTG
type: deletion
variant-base: T
- amino-acid-change: E484K
codon-change: GAA-AAA
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: A
- amino-acid-change: N501Y
codon-change: AAT-TAT
gene: S
one-based-reference-position: 23063
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 501
reference-base: A
type: SNP
variant-base: T
- amino-acid-change: P681H
codon-change: CCT-CAT
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: A
- amino-acid-change: E1092K
codon-change: GAA-AAA
gene: S
one-based-reference-position: 24836
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 1092
reference-base: G
type: SNP
variant-base: A
- amino-acid-change: H1101Y
codon-change: CAC-TAC
gene: S
one-based-reference-position: 24863
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 1101
reference-base: C
type: SNP
variant-base: T
- amino-acid-change: V1176F
codon-change: GTT-TTT
gene: S
one-based-reference-position: 25088
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 1176
reference-base: G
type: SNP
variant-base: T
- amino-acid-change: K2Q
codon-change: AAA-CAA
gene: ORF8
one-based-reference-position: 27897
predicted-effect: non-synonymous
protein: ORF8
protein-codon-position: 2
reference-base: A
type: SNP
variant-base: C
- codon-change: TCC-TCA
gene: ORF1ab
one-based-reference-position: 7564
predicted-effect: synonymous
protein: nsp3
protein-codon-position: 1615
reference-base: C
type: SNP
variant-base: A
- codon-change: AAC-AAT
gene: ORF1ab
one-based-reference-position: 12049
predicted-effect: synonymous
protein: nsp7
protein-codon-position: 71
reference-base: C
type: SNP
variant-base: T
- codon-change: GGT-GGC
gene: S
one-based-reference-position: 23341
predicted-effect: synonymous
protein: surface glycoprotein
protein-codon-position: 593
reference-base: T
type: SNP
variant-base: C
- codon-change: TCT-TCA
gene: S
one-based-reference-position: 24187
predicted-effect: synonymous
protein: surface glycoprotein
protein-codon-position: 875
reference-base: T
type: SNP
variant-base: A
calling-definition:
confirmed:
mutations-required: 16
indels-required: 0
allowed-wildtype: 0
probable:
mutations-required: 7
indels-required: 0
allowed-wildtype: 0
low-qc:
mutations-required: 0
indels-required: 0
allowed-wildtype: 0
acknowledgements:
curators:
- Nick Ellaby
- Natalie Groves
- Ulf Schaefer
- Nick Loman