This is a demo instance. You can upload any data you like, including test data to try things out. You can find test data to upload in the
example data
repository. This instance should not be used for analysis.
X
Pathoplexus
Crimean-Congo Hemorrhagic Fever Virus
Crimean-Congo Hemorrhagic Fever Virus
Ebola Sudan
Ebola Zaire
West Nile Virus
Browse
Submit
SeqSets
News
About
Docs
Login
Loculus
Browse
Submit
SeqSets
News
About
Docs
Login
API docs
Governance
Contact
Status
PPD_0039B4U.1
Download
Download FASTA
Download metadata TSV
Display Name: Pakistan/PPD_0039B4U.1/2023-05-01
Umair,
M.; Haider,
S. A.; Jamal,
Z.; Ammar,
M.; Hakim,
R.; Ali,
Q.; Salman,
M.
Submission details
Submission ID
OR964921.1.L/OR964932.1.M/OR964910.1.S
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2024-11-19 16:17:00 UTC
Date released
2024-11-19 16:30:17 UTC
Data use terms
Data use terms
OPEN
✕
Data Use Terms History
Changed
User
Data Use Terms
2024-11-19 16:17
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
99.98%
Frame shifts L
RdRp:792-795(nt:2450-2461)
Length L
12158
Total ambiguous nucs L
0
Total deleted nucs L
11
Total frame shifts L
1
Total inserted nucs L
61
Total SNPs L
1627
Total unknown nucs L
2
Alignment states and QC metrics M
Completeness M
98.43%
Length M
5334
Total ambiguous nucs M
0
Total deleted nucs M
0
Total frame shifts M
0
Total inserted nucs M
1
Total SNPs M
653
Total unknown nucs M
51
Alignment states and QC metrics S
Completeness S
98.68%
Length S
1651
Total ambiguous nucs S
0
Total deleted nucs S
3
Total frame shifts S
0
Total inserted nucs S
4
Total SNPs S
211
Total unknown nucs S
0
Sample details
Collection country
Pakistan
Collection date
2023-05-01
Isolate name
CCHF/NIHPAK-31/2023
Host
Host name scientific
Homo sapiens
Host taxon id
9606
INSDC
INSDC accession L
OR964921.1
INSDC accession M
OR964932.1
INSDC accession S
OR964910.1
NCBI release date
2023-12-26
Nucleotide mutations
Substitutions
L
L:
T
10
C
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
Show more
M
M:
T
65
C
M:
A
69
G
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:
G
131
A
M:
T
137
C
M:
G
143
A
M:
A
146
G
M:
G
147
A
M:
C
153
A
Show more
S
S:
A
50
G
S:
G
54
A
S:
G
67
A
S:
T
79
C
S:
A
81
G
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
S:
G
229
A
Show more
Deletions
L:2449, L:11920-11924, L:11981, L:11982, L:12034, L:12076, L:12083, S:1541-1543
Insertions
ins_S:1532:CCA, ins_S:1584:C, ins_M:5169:G, ins_L:12108:TGTGGGGGGAACGATTT, ins_L:12098:TCATGTCCGTTTTATT, ins_L:58:T, ins_L:11917:CATTATC, ins_L:12064:GGTTAACCT, ins_L:11977:A, ins_L:12054:TACAATTT, ins_L:11973:A, ins_L:2461:G
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:
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
GPC:
T
64
S
Show more
NP
NP:
N
9
S
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:
K
275
R
Show more
Deletions
None
Insertions
None
Load sequences