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Status
PP_002YQN0.1
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Download FASTA
Download metadata TSV
Display Name: Senegal/PP_002YQN0.1/2022-09-01
Sene, O.
Submission details
Submission ID
PP894724.1.M/PP894729.1.S
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2025-06-10 09:14:43 UTC
Date released
2025-06-10 09:15:28 UTC
Data use terms
Data use terms
OPEN
✕
Data Use Terms History
Changed
User
Data Use Terms
2025-06-10 09:14
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 M
Completeness M
99.89%
Length M
5360
Total ambiguous nucs M
0
Total deleted nucs M
0
Total frame shifts M
0
Total inserted nucs M
0
Total SNPs M
173
Total unknown nucs M
0
Alignment and QC metrics S
Completeness S
100.00%
Length S
1686
Total ambiguous nucs S
0
Total deleted nucs S
16
Total frame shifts S
0
Total inserted nucs S
30
Total SNPs S
285
Total unknown nucs S
0
Sample details
Earliest release date
2025-01-18
Collection country
Senegal
Collection date
2022-09
Collection date (lower bound)
2022-09-01
Collection date (upper bound)
2022-09-30
Isolate name
ARD407209
Host
Host name - scientific
Hyalomma impeltatum
Host taxon ID
563069
INSDC
INSDC accession M
PP894724.1
INSDC accession S
PP894729.1
NCBI release date
2025-01-18
Nucleotide mutations
Mutations called relative to the
NC_005301.3
,
NC_005300.2
&
NC_005302.1
references
Substitutions
M
M:
G
124
A
M:
T
140
C
M:
A
214
G
M:
C
217
T
M:
G
220
T
M:
T
259
C
M:
C
320
T
M:
C
334
T
M:
A
339
G
M:
C
344
T
M:
G
345
A
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
Show more
S
S:
C
38
A
S:
T
39
C
S:
G
54
A
S:
A
61
G
S:
G
67
A
S:
G
73
A
S:
T
79
C
S:
A
92
C
S:
G
99
A
S:
G
100
A
S:
A
109
G
S:
A
118
G
S:
T
127
C
S:
A
130
G
S:
C
139
T
S:
C
142
T
S:
C
160
T
S:
T
163
C
Show more
Deletions
S:1551-1553, S:1564-1572, S:1586-1588, S:1639
Insertions
ins_S:1531:GTG, ins_S:1625:T, ins_S:1616:A, ins_S:1535:TG, ins_S:1580:ACAGTCACCAAAACC, ins_S:1546:AA, ins_S:1506:C, ins_S:1520:CCATT
Amino acid mutations
Mutations called relative to the
NC_005301.3
,
NC_005300.2
&
NC_005302.1
references
Substitutions
GPC
GPC:
C
11
Y
GPC:
N
41
S
GPC:
P
42
L
GPC:
S
43
I
GPC:
L
56
P
GPC:
P
81
L
GPC:
T
83
A
GPC:
G
85
R
GPC:
S
90
P
GPC:
V
98
A
GPC:
L
105
S
GPC:
G
108
S
GPC:
P
112
S
GPC:
P
123
L
GPC:
N
131
S
GPC:
G
167
D
GPC:
K
168
R
GPC:
S
171
P
Show more
NP
NP:
M
13
L
NP:
R
15
K
NP:
S
39
N
NP:
S
52
G
NP:
F
73
Y
NP:
K
91
R
NP:
A
100
T
NP:
T
124
A
NP:
G
125
N
NP:
A
154
S
NP:
H
195
K
NP:
V
198
I
NP:
D
199
E
NP:
V
205
I
NP:
I
220
V
NP:
I
246
V
NP:
D
248
E
NP:
N
258
K
Show more
Deletions
None
Insertions
None
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