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Status
PP_000RDTH.3
All versions
PP_000RDTH.1
(Revised)
PP_000RDTH.2
(Revised)
PP_000RDTH.3
(Latest version)
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Download FASTA
Download metadata TSV
Display Name: Pakistan/PP_000RDTH.3/2023-04-20
Umair,
M.; Haider,
S. A.; Jamal,
Z.; Ammar,
M.; Hakim,
R.; Ali,
Q.; Salman,
M.
Submission details
Submission ID
OR964923.1.L/OR964934.1.M/OR964912.1.S
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2024-10-29 17:10:51 UTC
Date released
2024-10-29 17:16:10 UTC
Data use terms
Data use terms
OPEN
✕
Data Use Terms History
Changed
User
Data Use Terms
2024-08-27 12:11
insdc_ingest_user
OPEN
Close
(history)
Data use terms URL
https://pathoplexus.org/about/terms-of-use/open-data
Authors
Author affiliations
National Institute of Health, Department of Virology
Alignment states and QC metrics L
Completeness L
99.70%
Frame shifts L
RdRp:792-795(nt:2450-2461)
Length L
12107
Total ambiguous nucs L
0
Total deleted nucs L
5
Total frame shifts L
1
Total inserted nucs L
27
Total SNPs L
1614
Total unknown nucs L
13
Alignment states and QC metrics M
Completeness M
96.53%
Frame shifts M
GPC:1291-1685(nt:3963-5147)
Length M
5290
Total ambiguous nucs M
0
Total deleted nucs M
0
Total frame shifts M
1
Total inserted nucs M
2
Total SNPs M
620
Total unknown nucs M
108
Alignment states and QC metrics S
Completeness S
97.49%
Length S
1594
Total ambiguous nucs S
0
Total deleted nucs S
41
Total frame shifts S
0
Total inserted nucs S
4
Total SNPs S
200
Total unknown nucs S
1
Sample details
Collection country
Pakistan
Collection date
2023-04-20
Isolate name
CCHF/NIHPAK-22/2023
Host
Host name scientific
Homo sapiens
Host taxon id
9606
INSDC
INSDC accession L
OR964923.1
INSDC accession M
OR964934.1
INSDC accession S
OR964912.1
NCBI release date
2023-12-26
Nucleotide mutations
Substitutions
L
L:
G
23
T
L:
A
35
G
L:
G
43
T
L:
T
49
C
L:
C
63
G
L:
C
64
T
L:
T
65
C
L:
T
66
C
L:
T
68
C
L:
G
69
A
L:
G
71
C
L:
C
85
T
L:
G
88
A
L:
G
93
A
L:
A
109
G
L:
C
117
A
L:
A
124
G
L:
T
131
A
Show more
M
M:
C
82
T
M:
C
85
T
M:
A
107
G
M:
A
117
G
M:
C
119
T
M:
C
120
T
M:
T
122
C
M:
A
128
G
M:
G
131
A
M:
T
137
C
M:
G
143
A
M:
A
146
G
M:
G
147
A
M:
C
153
A
M:
T
155
C
M:
T
159
C
M:
A
169
G
M:
A
170
G
Show more
S
S:
A
50
G
S:
G
54
A
S:
G
67
A
S:
T
79
C
S:
A
81
G
S:
G
99
A
S:
A
109
G
S:
A
118
G
S:
C
166
T
S:
G
169
A
S:
T
172
C
S:
C
178
A
S:
T
182
C
S:
G
190
A
S:
G
196
A
S:
T
199
C
S:
C
208
T
S:
C
217
T
Show more
Deletions
L:2449, L:11981, L:11982, L:12076, L:12083, S:1541-1543, S:1626-1663
Insertions
ins_S:1532:CCA, ins_S:1584:C, ins_M:3962:T, ins_M:5238:N, ins_L:12096:GTTC, ins_L:58:T, ins_L:12064:GGTTAACCT, ins_L:11977:A, ins_L:12054:TACAATTT, ins_L:2461:G, ins_L:11973:A, ins_L:11914:GC
Amino acid mutations
Substitutions
GPC
GPC:
I
9
V
GPC:
L
10
F
GPC:
E
19
K
GPC:
H
21
N
GPC:
S
23
P
GPC:
E
26
G
GPC:
R
28
E
GPC:
K
31
N
GPC:
D
33
H
GPC:
T
34
V
GPC:
M
35
L
GPC:
G
39
D
GPC:
N
41
S
GPC:
P
42
Q
GPC:
S
44
P
GPC:
S
53
P
GPC:
I
54
V
GPC:
L
56
P
Show more
NP
NP:
N
9
S
NP:
R
15
K
NP:
V
83
A
NP:
D
116
E
NP:
T
124
S
NP:
G
125
N
NP:
H
195
R
NP:
D
199
E
NP:
I
246
V
NP:
R
270
K
NP:
S
301
G
NP:
A
307
V
NP:
E
322
D
NP:
Q
405
L
NP:
V
436
I
RdRp
RdRp:
S
6
N
RdRp:
A
14
D
RdRp:
S
19
T
RdRp:
Y
60
N
RdRp:
R
63
H
RdRp:
S
67
V
RdRp:
R
80
K
RdRp:
V
82
I
RdRp:
I
114
V
RdRp:
T
163
A
RdRp:
A
168
T
RdRp:
M
172
V
RdRp:
R
174
K
RdRp:
S
205
P
RdRp:
N
206
Y
RdRp:
I
223
V
RdRp:
N
236
S
RdRp:
D
264
N
Show more
Deletions
None
Insertions
None
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