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LOC_000L5S3.1
Download
Download FASTA
Download metadata TSV
Display Name: South_Africa/LOC_000L5S3.1/2017
C. MacIntyre
Sample details
Collection date
2017
Collection date (lower bound)
2017-01-01
Collection date (upper bound)
2017-12-31
Earliest release date
2025-11-23
Collection country
South Africa
Isolate name
ZRU358/17
Data use terms
Data use terms
OPEN
✕
Data use terms history
Changed
User
Data use terms
2025-12-05 17:40
insdc_ingest_user
OPEN
Close
(history)
Data use terms URL
https://#TODO-MVP/open
Authors
Author affiliations
University of Pretoria, Medical Virology
INSDC
NCBI release date
2025-11-23
NCBI update date
2025-11-23
INSDC accession
OR879073.1
Host
Host taxon id
9615
Host name scientific
Canis lupus familiaris
Alignment and QC metrics
Length
10844
Total SNPs
2180
Total inserted nucs
40
Total deleted nucs
25
Total ambiguous nucs
0
Total unknown nucs
221
Total frame shifts
0
Frame shifts
[]
Completeness
96.18%
Stop codons
[]
Total stop codons
0
Submission details
Submission ID
OR879073.1
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2025-12-05 17:40:35 UTC
Date released
2025-12-05 18:03:19 UTC
Lineage
Lineage
2
Files
Annotations
LOC_000L5S3.1.embl
Nucleotide mutations
Mutations called relative to the
NC_009942.1
reference
Substitutions
C
52
T
A
82
G
G
126
A
G
128
A
A
156
T
T
167
G
G
168
A
T
180
A
A
196
T
T
199
C
C
204
T
C
210
T
C
216
G
G
222
C
T
227
C
A
231
T
T
234
C
C
246
T
Show more
Deletions
6994-6996, 10426, 10442-10444, 10457-10462, 10467-10470, 10487-10494
Insertions
ins_7006:TTGNNN, ins_10401:ACAAAGCTGTATTGAGTAGTTGTATAG, ins_10405:T, ins_10416:TC, ins_10483:GAT, ins_10501:T
Amino acid mutations
Mutations called relative to the
NC_009942.1
reference
Substitutions
2K
2K:
M
15
L
NS1
NS1:
S
9
G
NS1:
Y
34
F
NS1:
K
51
A
NS1:
V
71
I
NS1:
E
94
N
NS1:
S
99
A
NS1:
T
105
A
NS1:
I
113
M
NS1:
L
123
I
NS1:
V
135
I
NS1:
K
141
E
NS1:
Q
146
A
NS1:
L
153
M
NS1:
K
170
R
NS1:
V
171
I
NS1:
S
174
T
NS1:
L
192
M
NS1:
I
194
V
Show more
NS2A
NS2A:
M
34
I
NS2A:
L
38
M
NS2A:
I
39
L
NS2A:
I
49
V
NS2A:
T
52
I
NS2A:
S
68
A
NS2A:
M
90
L
NS2A:
N
104
S
NS2A:
H
119
Y
NS2A:
Q
123
N
NS2A:
I
124
V
NS2A:
L
126
S
NS2A:
E
128
K
NS2A:
I
129
V
NS2A:
P
130
L
NS2A:
A
137
S
NS2A:
T
147
S
NS2A:
T
150
N
Show more
NS2B
NS2B:
A
41
V
NS2B:
S
61
T
NS2B:
M
88
V
NS2B:
L
100
I
NS2B:
V
103
A
NS2B:
V
120
I
NS3
NS3:
Q
92
H
NS3:
E
101
D
NS3:
F
130
Y
NS3:
D
172
E
NS3:
I
175
A
NS3:
R
203
K
NS3:
R
215
K
NS3:
A
233
S
NS3:
P
249
H
NS3:
N
253
S
NS3:
V
283
I
NS3:
S
302
A
NS3:
S
331
A
NS3:
L
336
M
NS3:
S
347
T
NS3:
T
356
V
NS3:
K
367
R
NS3:
V
384
I
Show more
NS4A
NS4A:
I
6
V
NS4A:
K
11
R
NS4A:
D
49
N
NS4A:
A
58
V
NS4A:
T
64
S
NS4A:
M
65
L
NS4A:
A
85
I
NS4A:
V
86
I
NS4A:
V
89
A
NS4B
NS4B:
S
11
N
NS4B:
S
14
G
NS4B:
F
17
L
NS4B:
Q
19
H
NS4B:
R
20
K
NS4B:
I
21
P
NS4B:
C
120
L
NS4B:
A
123
V
NS4B:
M
134
T
NS4B:
A
137
V
NS4B:
A
149
V
NS4B:
I
168
V
NS4B:
L
183
M
NS4B:
K
193
R
NS4B:
I
202
T
NS5
NS5:
Q
18
H
NS5:
I
33
T
NS5:
K
45
R
NS5:
V
49
I
NS5:
I
78
V
NS5:
R
101
K
NS5:
C
139
A
NS5:
C
140
S
NS5:
I
147
V
NS5:
I
162
V
NS5:
R
177
K
NS5:
V
181
I
NS5:
L
197
T
NS5:
R
224
H
NS5:
V
229
I
NS5:
V
230
I
NS5:
R
247
K
NS5:
Y
254
F
Show more
capsid
capsid:
S
11
N
capsid:
V
24
G
capsid:
M
34
L
capsid:
I
44
T
capsid:
T
57
I
capsid:
S
100
T
capsid:
K
108
T
capsid:
T
109
A
capsid:
I
111
F
capsid:
A
112
T
capsid:
V
113
T
capsid:
M
114
L
capsid:
I
115
L
capsid:
S
120
C
capsid:
V
121
A
env
env:
V
43
I
env:
E
55
D
env:
T
64
S
env:
K
71
R
env:
D
83
E
env:
R
93
K
env:
S
122
T
env:
I
126
T
env:
R
128
W
env:
T
129
I
env:
L
131
Q
env:
V
159
I
env:
L
167
F
env:
A
172
S
env:
I
196
M
env:
N
199
S
env:
T
205
S
env:
T
208
A
Show more
prM
prM:
T
17
A
prM:
M
44
L
prM:
D
46
E
prM:
S
57
A
prM:
A
73
S
prM:
M
112
L
prM:
V
156
A
prM:
V
157
I
Deletions
NS4B:32-37
Insertions
ins_NS4B:22:ARETTLG
Nucleotide sequence
Aligned nucleotide sequence
Aligned amino acid sequences
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