This is a demonstration environment. It may contain non-accurate test data and should not be used for real-world applications. Data will be deleted regularly.
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Loculus
Crimean-Congo Hemorrhagic Fever Virus
Crimean-Congo Hemorrhagic Fever Virus
Test Dummy Organism
Ebola Sudan
Test organism (without alignment)
West Nile Virus
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LOC_000P79W.1
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Display Name: Pakistan/LOC_000P79W.1/2024-07-16
Umair,
M.; Hakim,
R.; Jamal,
Z.; Salman,
M.
Submission details
Submission ID
PQ523729.1.L/PQ523726.1.M/PQ523722.1.S
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2024-12-20 08:39:34 UTC
Date released
2024-12-20 08:43:49 UTC
Data use terms
Data use terms
OPEN
✕
Data Use Terms History
Changed
User
Data Use Terms
2024-12-20 08:39
insdc_ingest_user
OPEN
Close
(history)
Data use terms URL
https://#TODO-MVP/open
Authors
Author affiliations
National Institute of Health, Department of Virology
Alignment states and QC metrics L
Completeness L
97.56%
Frame shifts L
RdRp:792-795(nt:2450-2461)
Length L
12104
Total ambiguous nucs L
0
Total deleted nucs L
12
Total frame shifts L
1
Total inserted nucs L
38
Total SNPs L
1563
Total unknown nucs L
266
Alignment states and QC metrics M
Completeness M
95.75%
Length M
5287
Total ambiguous nucs M
0
Total deleted nucs M
0
Total frame shifts M
0
Total inserted nucs M
0
Total SNPs M
622
Total unknown nucs M
149
Alignment states and QC metrics S
Completeness S
91.93%
Length S
1590
Total ambiguous nucs S
0
Total deleted nucs S
11
Total frame shifts S
0
Total inserted nucs S
4
Total SNPs S
196
Total unknown nucs S
60
Sample details
Earliest release date
2024-11-12
Collection subdivision level 1
Punjab
Collection country
Pakistan
Collection date
2024-07-16
Collection date (lower bound)
2024-07-16
Collection date (upper bound)
2024-07-16
Isolate name
CCHF/NIHPAK-41/2024
Host
Host name scientific
Homo sapiens
Host taxon id
9606
INSDC
INSDC accession L
PQ523729.1
INSDC accession M
PQ523726.1
INSDC accession S
PQ523722.1
NCBI release date
2024-11-12
Nucleotide mutations
Substitutions
L
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
L:
T
139
C
Show more
M
M:
C
82
T
M:
C
85
T
M:
T
86
C
M:
A
107
G
M:
A
117
G
M:
C
119
T
M:
C
120
T
M:
T
122
C
M:
C
126
T
M:
A
128
G
M:
T
137
C
M:
G
143
A
M:
A
146
G
M:
G
147
A
M:
G
149
A
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:
C
115
T
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:
C
208
T
S:
C
217
T
S:
G
229
A
Show more
Deletions
L:2449, L:11920-11924, L:11981, L:11982, L:12054, L:12058, L:12059, L:12073, S:1541-1543, S:1611-1618
Insertions
ins_S:1532:CCA, ins_S:1584:C, ins_L:12096:GTTC, ins_L:11977:CA, ins_L:12101:CGT, ins_L:11917:CATTATC, ins_L:12085:ACTATCCTACTATTCCA, ins_L:58:T, ins_L:2461:G, ins_L:12080:TAA
Amino acid mutations
Substitutions
GPC
GPC:
I
9
V
GPC:
L
10
F
GPC:
E
19
K
GPC:
S
23
P
GPC:
E
26
G
GPC:
R
28
E
GPC:
K
31
N
GPC:
D
33
H
GPC:
T
34
A
GPC:
G
39
D
GPC:
N
41
S
GPC:
P
42
Q
GPC:
S
44
P
GPC:
S
53
P
GPC:
I
54
A
GPC:
L
56
P
GPC:
S
59
P
GPC:
P
80
S
Show more
NP
NP:
N
9
S
NP:
R
15
K
NP:
V
83
A
NP:
D
186
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:
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:
K
275
R
RdRp:
I
279
V
RdRp:
R
302
K
Show more
Deletions
None
Insertions
None
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