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LOC_0005CQX.1
Download
Download FASTA
Download metadata TSV
Pakistan/LOC_0005CQX.1/2024-05
S. Aiman,
A. Zia,
M. U. Khattak,
Y. M. Yousafzai,
M. Umair,
M. Salman,
R. Hakim,
Z. Jamal,
H. Khan &
A. Islam
Khyber Medical University, Institute of Pathology and Diagnostic Medicine (IPDM), Microbiology
Sample details
Collection date
2024-05
Earliest release date
2026-09-07
Sampling location
Pakistan (Peshawar)
Isolate name
CCHFV/PHRL/140
Data use terms
Data use terms
OPEN
(history)
Data use terms URL
https://#TODO-MVP/open
INSDC
NCBI release date
2026-09-07
INSDC accession L segment
PZ816504.1
INSDC accession M segment
PZ816503.1
INSDC accession S segment
PZ816502.1
Host
Host
human (Homo sapiens)
Submission details
Submission ID
PZ816504.1.L/PZ816503.1.M/PZ816502.1.S
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2026-11-04 12:14:37 UTC
Date released
2026-11-04 12:19:56 UTC
Clade & Lineage
Closest reference L segment
singleReference (variant)
Closest reference M segment
M (MH396653.1)
Closest reference S segment
S1 (OL774851.1) (variant)
Files
Annotations
LOC_0005CQX.1.embl
Alignment and QC
Total SNPs L segment
1551
Total inserted nucs L segment
19
Total deleted nucs L segment
7
Total unknown nucs L segment
698
Length L segment
12099 (94.1%)
Total SNPs M segment
35
Total inserted nucs M segment
1
Total unknown nucs M segment
448
Length M segment
5284 (88.6%)
Total SNPs S segment
153
Total unknown nucs S segment
97
Length S segment
1459 (75.4%)
Nucleotide mutations
Mutations called relative to the
NC_005301.3
,
MH396653.1
&
OL774851.1
references
Substitutions
L segment
G
23
T
A
35
G
G
43
T
T
49
C
A
53
G
C
63
G
C
64
T
T
65
C
T
66
C
T
68
C
G
69
A
G
71
C
C
85
T
G
88
A
G
93
A
A
109
G
C
117
A
A
124
G
Show more
M segment
C
245
A
A
251
G
T
326
C
C
576
T
A
888
G
T
1000
C
A
1130
G
G
1224
A
A
1382
G
C
1423
T
G
1521
A
A
1591
G
A
1621
G
A
1885
G
T
1894
C
A
1948
G
G
2107
A
T
2125
C
Show more
S segment
T
16
A
C
31
G
T
63
C
A
65
G
A
84
G
A
93
G
A
98
T
A
102
G
C
150
T
G
153
A
T
156
C
T
166
C
A
173
G
G
174
A
G
180
A
A
186
G
C
192
T
C
201
T
Show more
Deletions
L segment
12028-12034
Insertions
L segment
ins_58:T, ins_11917:CA, ins_12053:CTAC, ins_12086:CTACTATTCCAC
M segment
ins_5234:N
Amino acid substitutions
Substitutions called relative to the
NC_005301.3
,
MH396653.1
&
OL774851.1
references
Substitutions
GPC
GPC:
P
53
T
GPC:
T
55
A
GPC:
S
80
P
GPC:
P
163
L
GPC:
K
267
R
GPC:
T
348
A
GPC:
R
379
Q
GPC:
I
432
V
GPC:
R
478
K
GPC:
R
852
Q
GPC:
V
893
I
GPC:
T
1394
N
GPC:
S
1571
G
NP
NP:
N
9
S
NP:
Y
20
F
NP:
K
45
R
NP:
V
83
A
NP:
D
116
E
NP:
A
124
S
NP:
Q
179
L
NP:
D
199
E
NP:
R
270
K
NP:
A
307
V
NP:
E
322
D
NP:
Q
405
L
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:
A
202
V
RdRp:
S
205
P
RdRp:
N
206
Y
RdRp:
I
223
V
RdRp:
K
275
R
Show more
Deletions
N/A
Insertions
N/A
Nucleotide sequences
Reference-aligned nucleotide sequences
Reference-aligned amino acid sequences
L segment
M segment
S segment
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