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Status
PPD_00483PY.1
Download
Download FASTA
Download metadata TSV
Display Name: Senegal/PPD_00483PY.1/2022-08-01
Sene,
O.
Submission details
Submission ID
PP894721.1.L/PP894745.1.M/PP894740.1.S
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2025-01-22 09:27:21 UTC
Date released
2025-01-22 09:27:44 UTC
Data use terms
Data use terms
OPEN
✕
Data Use Terms History
Changed
User
Data Use Terms
2025-01-22 09:27
insdc_ingest_user
OPEN
Close
(history)
Data use terms URL
https://pathoplexus.org/about/terms-of-use/open-data
Authors
Author affiliations
Institut Pasteur, Dakar, Virology
Alignment and QC metrics L
Completeness L
99.85%
Length L
12090
Total ambiguous nucs L
0
Total deleted nucs L
0
Total frame shifts L
0
Total inserted nucs L
0
Total SNPs L
294
Total unknown nucs L
0
Alignment and QC metrics M
Completeness M
94.89%
Length M
5092
Total ambiguous nucs M
0
Total deleted nucs M
0
Total frame shifts M
0
Total inserted nucs M
0
Total SNPs M
135
Total unknown nucs M
0
Alignment and QC metrics S
Completeness S
93.72%
Length S
1569
Total ambiguous nucs S
1
Total deleted nucs S
0
Total frame shifts S
0
Total inserted nucs S
1
Total SNPs S
126
Total unknown nucs S
0
Sample details
Earliest release date
2025-01-18
Collection country
Senegal
Collection date
2022-08
Collection date (lower bound)
2022-08-01
Collection date (upper bound)
2022-08-31
Host
Host name scientific
Rhipicephalus senegalensis
Host taxon id
1104677
INSDC
INSDC accession L
PP894721.1
INSDC accession M
PP894745.1
INSDC accession S
PP894740.1
NCBI release date
2025-01-18
Nucleotide mutations
Mutations called relative to the
NC_005301.3
,
NC_005300.2
&
NC_005302.1
references
Substitutions
L
L:
A
40
G
L:
T
65
C
L:
T
70
C
L:
G
93
A
L:
G
130
T
L:
T
151
C
L:
C
244
T
L:
T
254
A
L:
A
280
G
L:
T
292
C
L:
A
298
G
L:
C
313
T
L:
T
340
C
L:
A
409
G
L:
C
427
T
L:
A
460
G
L:
T
550
G
L:
G
553
A
Show more
M
M:
A
178
G
M:
A
203
G
M:
C
217
T
M:
G
236
A
M:
T
259
C
M:
C
269
T
M:
T
301
C
M:
C
320
T
M:
T
360
C
M:
A
377
G
M:
T
385
C
M:
C
404
T
M:
T
406
C
M:
C
410
T
M:
G
414
A
M:
C
426
T
M:
C
428
T
M:
C
431
T
Show more
S
S:
G
47
C
S:
A
50
G
S:
G
54
A
S:
G
67
A
S:
G
99
A
S:
G
100
A
S:
C
178
A
S:
T
181
C
S:
G
189
A
S:
T
199
C
S:
G
202
A
S:
G
229
A
S:
C
235
T
S:
A
247
G
S:
G
271
A
S:
C
295
T
S:
A
298
G
S:
A
322
G
Show more
Deletions
None
Insertions
ins_S:1577:A
Amino acid mutations
Mutations called relative to the
NC_005301.3
,
NC_005300.2
&
NC_005302.1
references
Substitutions
GPC
GPC:
H
29
R
GPC:
P
42
L
GPC:
L
56
P
GPC:
L
70
S
GPC:
S
90
P
GPC:
V
98
A
GPC:
L
105
S
GPC:
G
108
S
GPC:
P
112
S
GPC:
A
122
T
GPC:
P
123
L
GPC:
N
131
S
GPC:
S
171
P
GPC:
Q
191
R
GPC:
L
216
P
GPC:
P
226
L
GPC:
H
238
S
GPC:
K
250
E
Show more
NP
NP:
R
15
K
NP:
R
45
K
NP:
K
91
R
NP:
T
124
A
NP:
G
125
N
NP:
L
179
Q
NP:
H
195
R
NP:
I
246
V
NP:
S
301
G
NP:
K
428
R
NP:
V
436
I
RdRp
RdRp:
S
6
N
RdRp:
Y
60
N
RdRp:
I
505
T
RdRp:
T
767
A
RdRp:
K
809
R
RdRp:
G
812
E
RdRp:
T
876
S
RdRp:
A
1038
T
RdRp:
G
1047
E
RdRp:
V
1228
I
RdRp:
N
1367
D
RdRp:
N
1514
S
RdRp:
M
1647
L
RdRp:
P
1660
T
RdRp:
T
1675
N
RdRp:
R
1676
K
RdRp:
I
1949
V
RdRp:
I
1996
V
Show more
Deletions
None
Insertions
None
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