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LOC_000Q3SX.1
Download
Download FASTA
Download metadata TSV
Uganda/LOC_000Q3SX.1/2019
E. M. Wampande,
P. Waiswa,
D. J. Allen,
R. Hewson,
S. D. W. Frost &
S. C. B. Stubbs
London School of Hygiene and Tropical Medicine, Infectious Disease Epidemiology
Sample details
Collection date
2019
Earliest release date
2021-02-10
Sampling location
Uganda (Kampala)
Isolate name
CW-024
Data use terms
Data use terms
OPEN
(history)
Data use terms URL
https://#TODO-MVP/open
INSDC
NCBI release date
2021-02-10
INSDC accession L
MW452935.1
INSDC accession M
MW452934.1
INSDC accession S
MW452933.1
Host
Host
hard ticks; hardbacked ticks; scale ticks (Rhipicephalus decoloratus)
Submission details
Submission ID
MW452935.1.L/MW452934.1.M/MW452933.1.S
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2026-10-30 18:26:46 UTC
Date released
2026-10-30 18:30:16 UTC
Lineage
Segment S Lineage
II
Files
Annotations
LOC_000Q3SX.1.embl
Alignment and QC
Total SNPs S
272
Total inserted nucs S
1
Length S
1662 (99.3%)
Total SNPs L
1944
Length L
11838 (97.8%)
Total SNPs M
1578
Total inserted nucs M
134
Total deleted nucs M
69
Total frame shifts M
1
Frame shifts M
GPC:21-38(nt:152-206)
Length M
5431 (100%)
Nucleotide mutations
Mutations called relative to the
NC_005301.3
,
NC_005300.2
&
NC_005302.1
references
Substitutions
L
C
82
A
G
93
A
A
109
G
T
115
C
T
131
A
C
148
T
T
151
C
T
154
A
T
157
C
T
160
C
G
175
T
G
190
T
C
193
T
C
199
T
C
205
T
G
217
A
T
218
C
T
229
C
Show more
M
G
38
A
T
40
C
G
50
T
A
51
G
A
52
T
G
56
T
T
58
A
T
59
G
A
64
G
T
65
A
T
67
A
T
68
G
A
69
T
A
70
G
T
71
A
A
75
G
G
76
T
A
80
G
Show more
S
A
50
G
G
54
A
A
61
G
C
64
T
G
67
A
A
78
C
A
81
G
A
85
G
A
118
G
G
122
A
A
124
C
A
130
T
G
136
A
T
144
A
C
154
T
T
157
C
C
166
T
T
175
C
Show more
Deletions
M
72, 207-216, 471-485, 645-659, 5263-5290
Insertions
M
ins_0:GGGAAAAGAAGGAAGAAGAA, ins_151:CACCAATGGGATCAGTGCAAAT, ins_332:TTAATTATCAGTAAAGCAACTTCTCCTAGC, ins_368:CCCACAACCCCAAGACCAAAC, ins_5200:GTGCTTTCCCGCTAAA, ins_5366:TTAGGTCAGAACTAGGGCGGTATCC
S
ins_1581:C
Amino acid substitutions
Substitutions called relative to the
NC_005301.3
,
NC_005300.2
&
NC_005302.1
references
Substitutions
GPC
GPC:
M
1
K
GPC:
H
2
P
GPC:
I
3
M
GPC:
S
4
L
GPC:
L
5
W
GPC:
M
6
V
GPC:
A
8
F
GPC:
I
9
A
GPC:
L
12
Q
GPC:
Q
13
L
GPC:
C
15
W
GPC:
G
16
S
GPC:
L
17
D
GPC:
G
18
V
GPC:
E
19
G
GPC:
P
46
Q
GPC:
P
47
G
GPC:
V
48
P
Show more
NP
NP:
N
8
T
NP:
N
9
S
NP:
G
23
S
NP:
F
30
Y
NP:
D
116
G
NP:
T
124
A
NP:
G
125
N
NP:
H
195
R
NP:
D
199
E
NP:
I
246
V
NP:
S
275
N
NP:
I
277
V
NP:
S
301
G
NP:
A
307
P
NP:
Y
311
F
NP:
T
320
S
NP:
Q
370
E
NP:
V
436
I
RdRp
RdRp:
D
2
E
RdRp:
S
6
N
RdRp:
S
19
T
RdRp:
Y
60
N
RdRp:
S
67
E
RdRp:
R
80
K
RdRp:
V
82
I
RdRp:
E
87
D
RdRp:
I
114
V
RdRp:
I
131
L
RdRp:
I
157
M
RdRp:
T
163
A
RdRp:
R
166
K
RdRp:
A
168
T
RdRp:
M
172
V
RdRp:
R
174
K
RdRp:
S
201
G
RdRp:
A
202
S
Show more
Deletions
GPC
GPC:39-42, GPC:104-131, GPC:178-222
Insertions
GPC
ins_GPC:22:GI, ins_GPC:61:VGMTNVQVTTDDGSGESSTDPLIISKATSPSPIISTQVQKAE, ins_GPC:243:QIGPTTPGAISVTQTTQRQEVKESVTTTTTAATTLADSIS
Nucleotide sequences
Reference-aligned nucleotide sequences
Reference-aligned amino acid sequences
L
M
S
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