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Status
PP_000RH4S.2
Version 2
PP_000RH4S.1
Previous version
PP_000RH4S.2
Latest version
All versions
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Download FASTA
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Display Name: USA/PP_000RH4S.2/2023-08-20
E. H. Davis,
J. Velez &
H. R. Hughes
Submission details
Submission ID
PP445212.1
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2024-10-29 17:09:23 UTC
Date released
2024-10-29 17:17:47 UTC
Data use terms
Data use terms
OPEN
✕
Data Use Terms History
Changed
User
Data Use Terms
2024-10-14 02:31
insdc_ingest_user
OPEN
Close
(history)
Data use terms URL
https://pathoplexus.org/about/terms-of-use/open-data
Authors
Author affiliations
Centers for Disease Control and Prevention, Arboviral Diseases Branch
Alignment and QC metrics
Completeness
98.44%
Length
10704
Total ambiguous nucs
0
Total deleted nucs
167
Total frame shifts
0
Total inserted nucs
14
Total SNPs
2405
Total stop codons
0
Total unknown nucs
0
Sample details
Earliest release date
2024-10-13
Collection subdivision level 1
Nebraska
Collection country
USA
Collection date
2023-08-20
Collection date (lower bound)
2023-08-20
Collection date (upper bound)
2023-08-20
Isolate name
135322a-L3
Host
Host name - scientific
Homo sapiens
Host taxon ID
9606
INSDC
INSDC accession
PP445212.1
NCBI release date
2024-10-13
NCBI update date
2024-10-13
Lineage
Lineage
3
Nucleotide mutations
Mutations called relative to the
NC_009942.1
reference
Substitutions
C
62
T
C
69
T
C
84
T
C
93
T
A
104
G
C
123
A
A
124
G
G
126
T
G
128
A
T
146
A
A
156
T
T
158
A
T
167
G
G
168
A
T
169
G
T
170
G
G
171
A
T
175
C
Show more
Deletions
10398-10404, 10421-10441, 10447-10458, 10471-10485, 10491-10505, 10522-10524, 10813-10906
Insertions
ins_10410:GGAGCGTTCA, ins_10516:TTT, ins_10665:T
Amino acid mutations
Mutations called relative to the
NC_009942.1
reference
Substitutions
2K
2K:
M
15
L
2K:
L
17
F
2K:
V
18
I
2K:
S
19
G
NS1
NS1:
S
9
G
NS1:
M
29
T
NS1:
Y
34
F
NS1:
Y
35
H
NS1:
K
44
R
NS1:
I
45
V
NS1:
K
51
E
NS1:
E
52
S
NS1:
V
54
T
NS1:
L
57
I
NS1:
E
69
D
NS1:
A
70
S
NS1:
L
79
F
NS1:
K
80
R
NS1:
V
84
I
NS1:
V
88
M
NS1:
E
94
S
NS1:
M
96
V
Show more
NS2A
NS2A:
N
2
K
NS2A:
A
3
S
NS2A:
M
34
I
NS2A:
I
39
V
NS2A:
L
42
A
NS2A:
F
46
L
NS2A:
V
58
I
NS2A:
A
66
M
NS2A:
S
68
A
NS2A:
K
84
R
NS2A:
V
112
A
NS2A:
H
119
Y
NS2A:
Q
123
L
NS2A:
I
124
M
NS2A:
L
126
G
NS2A:
I
142
V
NS2A:
T
147
S
NS2A:
T
150
S
Show more
NS2B
NS2B:
I
31
V
NS2B:
S
61
T
NS2B:
E
73
D
NS2B:
R
78
K
NS2B:
M
88
I
NS3
NS3:
K
14
R
NS3:
T
19
A
NS3:
S
33
N
NS3:
A
38
V
NS3:
Q
86
G
NS3:
K
88
R
NS3:
Q
92
M
NS3:
E
120
D
NS3:
F
130
Y
NS3:
N
158
S
NS3:
D
172
E
NS3:
I
175
V
NS3:
A
177
S
NS3:
E
182
D
NS3:
R
203
K
NS3:
N
214
S
NS3:
R
215
K
NS3:
V
221
I
Show more
NS4A
NS4A:
I
6
V
NS4A:
K
11
R
NS4A:
K
35
R
NS4A:
M
42
S
NS4A:
A
55
I
NS4A:
A
58
T
NS4A:
V
67
I
NS4A:
A
85
T
NS4A:
V
89
A
NS4A:
E
98
D
NS4B
NS4B:
S
11
N
NS4B:
I
13
M
NS4B:
S
15
N
NS4B:
F
17
L
NS4B:
R
20
K
NS4B:
I
21
P
NS4B:
E
22
G
NS4B:
V
23
T
NS4B:
K
24
T
NS4B:
N
26
S
NS4B:
F
27
L
NS4B:
S
28
G
NS4B:
G
30
A
NS4B:
E
31
D
NS4B:
F
32
L
NS4B:
R
37
K
NS4B:
V
47
I
NS4B:
T
48
S
Show more
NS5
NS5:
V
11
A
NS5:
M
19
L
NS5:
I
33
T
NS5:
S
38
A
NS5:
A
39
P
NS5:
H
42
Y
NS5:
V
74
I
NS5:
G
129
K
NS5:
P
136
T
NS5:
C
139
A
NS5:
C
140
S
NS5:
I
162
V
NS5:
L
197
V
NS5:
R
224
H
NS5:
V
229
I
NS5:
S
232
A
NS5:
R
247
K
NS5:
Q
253
H
Show more
capsid
capsid:
K
3
R
capsid:
K
10
D
capsid:
S
11
N
capsid:
L
17
Q
capsid:
M
21
K
capsid:
V
24
G
capsid:
L
25
G
capsid:
I
28
M
capsid:
M
34
I
capsid:
K
41
R
capsid:
R
55
K
capsid:
D
67
E
capsid:
L
82
T
capsid:
T
90
I
capsid:
S
93
N
capsid:
N
96
S
capsid:
S
100
E
capsid:
Q
102
K
Show more
env
env:
A
51
T
env:
N
52
S
env:
E
55
G
env:
S
58
D
env:
T
64
A
env:
D
83
E
env:
F
90
Y
env:
V
91
F
env:
R
93
K
env:
S
122
T
env:
T
123
S
env:
I
126
T
env:
R
128
W
env:
T
129
I
env:
L
131
Q
env:
E
150
D
env:
V
159
M
env:
L
167
F
Show more
prM
prM:
T
2
V
prM:
V
10
L
prM:
V
19
I
prM:
D
21
N
prM:
T
27
I
prM:
A
29
S
prM:
I
35
T
prM:
M
39
I
prM:
Y
43
F
prM:
M
44
L
prM:
S
57
A
prM:
S
72
L
prM:
V
74
M
prM:
H
86
Q
prM:
M
150
T
prM:
V
156
M
Deletions
None
Insertions
None
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