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LOC_000PC17.1
Download
Download FASTA
Download metadata TSV
Madagascar/LOC_000PC17.1/1988-02-12
M. Guerbois,
N. L. Forrester,
S. L. Rossi,
K. Hari,
D. Lin &
S. C. Weaver
University of Texas Medical Branch, Microbiology and Immunology
Sample details
Collection date
1988-02-12
Earliest release date
2017-03-25
Sampling location
Madagascar
Isolate name
DAK AR MG 979
Data use terms
Data use terms
OPEN
(history)
Data use terms URL
https://#TODO-MVP/open
INSDC
NCBI release date
2017-03-25
NCBI update date
2017-03-25
INSDC accession
KU978767.1
BioProject accession
PRJNA257008
BioSample accession
SAMN04328129
Raw reads accession
SRR3218228
Host
Host
southern house mosquito (Culex quinquefasciatus)
Submission details
Submission ID
KU978767.1
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2026-09-09 16:34:10 UTC
Date released
2026-09-09 16:48:32 UTC
Lineage
Lineage
2
Files
Annotations
LOC_000PC17.1.embl
Alignment and QC
Total SNPs
2227
Total inserted nucs
33
Total deleted nucs
11
Total frame shifts
1
Frame shifts
NS4B:27-33(nt:6992-7014)
Length
11040 (99.9%)
Amino Acid Mutations from founder clade
NS1:
K
102
R
NS1:
A
146
V
NS1:
R
170
K
NS1:
V
188
I
NS1:
T
338
L
NS2A:
F
46
L
NS2A:
S
126
L
NS3:
S
160
A
NS3:
I
384
V
NS3:
S
421
N
NS3:
H
559
Y
NS4B:
H
19
Y
NS4B:
P
21
L
NS4B:
V
23
A
NS4B:
V
51
A
NS4B:
T
202
A
NS4B:
L
235
V
NS4B:
L
238
F
Show more
Variant
True
Nucleotide mutations
Mutations called relative to the
NC_009942.1
reference
Substitutions
A
56
G
C
123
T
G
126
A
G
128
A
A
156
T
T
167
G
G
168
A
T
180
C
G
186
A
T
199
C
C
204
T
G
207
A
C
210
T
C
216
G
G
219
A
G
222
C
A
231
T
T
234
C
Show more
Deletions
10421, 10468-10471, 10484-10487, 10904, 10921
Insertions
ins_6991:CG, ins_7014:G, ins_10406:GTTGTAT, ins_10411:AGTTGTACAGTTGCAG, ins_10427:G, ins_10451:GAG, ins_10461:AG, ins_10501:T
Amino acid substitutions
Substitutions 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:
K
102
R
NS1:
T
105
A
NS1:
I
113
M
NS1:
L
123
I
NS1:
V
135
I
NS1:
K
141
E
NS1:
Q
146
V
NS1:
L
153
M
NS1:
V
171
I
NS1:
S
174
T
NS1:
V
188
I
NS1:
L
192
M
Show more
NS2A
NS2A:
M
34
I
NS2A:
L
38
M
NS2A:
I
39
L
NS2A:
F
46
L
NS2A:
S
68
A
NS2A:
M
90
L
NS2A:
N
104
S
NS2A:
V
112
A
NS2A:
H
119
Y
NS2A:
R
122
K
NS2A:
Q
123
N
NS2A:
I
124
V
NS2A:
I
129
V
NS2A:
A
137
S
NS2A:
T
147
S
NS2A:
T
150
N
NS2A:
R
167
K
NS2A:
I
183
V
Show more
NS2B
NS2B:
A
41
V
NS2B:
S
61
T
NS2B:
V
103
A
NS2B:
V
120
I
NS3
NS3:
Q
92
H
NS3:
F
130
Y
NS3:
S
160
A
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:
S
421
N
NS3:
T
436
E
Show more
NS4A
NS4A:
I
6
V
NS4A:
K
11
R
NS4A:
T
64
S
NS4A:
M
65
L
NS4A:
A
85
V
NS4A:
V
86
I
NS4A:
V
89
A
NS4B
NS4B:
S
11
N
NS4B:
F
17
L
NS4B:
Q
19
Y
NS4B:
R
20
K
NS4B:
I
21
L
NS4B:
V
23
A
NS4B:
K
24
R
NS4B:
V
51
A
NS4B:
T
116
A
NS4B:
I
168
V
NS4B:
L
183
M
NS4B:
K
193
R
NS4B:
I
202
A
NS4B:
L
235
V
NS4B:
L
238
F
NS5
NS5:
V
11
F
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
162
V
NS5:
R
177
K
NS5:
V
181
I
NS5:
L
197
T
NS5:
R
224
H
NS5:
V
229
I
NS5:
R
247
K
NS5:
R
287
K
NS5:
R
288
K
Show more
capsid
capsid:
S
11
N
capsid:
V
24
G
capsid:
S
100
T
capsid:
K
108
T
capsid:
T
109
A
capsid:
I
111
F
capsid:
A
112
T
capsid:
V
113
I
capsid:
M
114
L
capsid:
I
115
L
capsid:
S
120
C
capsid:
V
121
A
env
env:
E
55
D
env:
T
64
S
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:
L
167
F
env:
A
172
S
env:
E
182
D
env:
N
199
S
env:
T
205
S
env:
T
208
A
env:
T
210
S
env:
V
232
T
env:
I
253
V
Show more
prM
prM:
M
44
L
prM:
D
46
E
prM:
S
57
A
prM:
A
73
S
prM:
M
112
L
prM:
L
136
V
prM:
V
156
A
prM:
V
157
I
Deletions
N/A
Insertions
NS4B
ins_NS4B:25:T
Nucleotide sequence
Aligned nucleotide sequence
Aligned amino acid sequences
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