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GS_005DQXJ.1
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Display Name: USA/GS_005DQXJ.1/2025-02-18
USDA Swine Surveillance,
A.; Lin,
K.; Dohrn,
C.
Submission details
Submission ID
PV353946.1.seg4/PV353947.1.seg6
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2025-04-03 08:07:10 UTC
Date released
2025-04-03 11:33:09 UTC
Authors
Author affiliations
Iowa State University Veterinary Diagnostic Lab, Bioinformatics
Clade
Clade HA
unassigned
Clade NA
unassigned
Alignment states and QC metrics seg4
Completeness seg4
97.93%
Length seg4
1701
Total ambiguous nucs seg4
0
Total deleted nucs seg4
0
Total frame shifts seg4
0
Total inserted nucs seg4
0
Total SNPs seg4
113
Total unknown nucs seg4
0
Alignment states and QC metrics seg6
Completeness seg6
98.19%
Length seg6
1410
Total ambiguous nucs seg6
0
Total deleted nucs seg6
0
Total frame shifts seg6
0
Total inserted nucs seg6
0
Total SNPs seg6
142
Total unknown nucs seg6
0
Sample details
Collection country
USA
Collection subdivision level 1
Oklahoma
Collection date
2025-02-18
Isolate name
A02858392
Host
Host name scientific
Sus scrofa
Host taxon id
9823
INSDC
INSDC accession seg4
PV353946.1
INSDC accession seg6
PV353947.1
NCBI release date
2025-03-20
INSDC seg4
Subtype seg4
H3
INSDC seg6
Subtype seg6
N2
Nucleotide mutations
Mutations called relative to the
NC_007373.1
,
NC_007372.1
,
NC_007371.1
,
CY163680.1
,
NC_007369.1
,
CY114383.1
,
NC_007367.1
&
NC_007370.1
references
Substitutions
seg4
seg4:
T
42
C
seg4:
G
56
A
seg4:
C
76
A
seg4:
C
77
T
seg4:
A
80
T
seg4:
T
83
C
seg4:
G
91
A
seg4:
C
94
T
seg4:
G
113
A
seg4:
A
125
G
seg4:
A
165
G
seg4:
A
206
T
seg4:
C
208
A
seg4:
G
210
A
seg4:
G
214
A
seg4:
G
222
A
seg4:
C
224
T
seg4:
T
230
C
Show more
seg6
seg6:
G
30
A
seg6:
C
50
T
seg6:
T
55
G
seg6:
C
72
T
seg6:
A
79
G
seg6:
T
88
C
seg6:
A
91
C
seg6:
C
95
T
seg6:
A
102
G
seg6:
A
116
G
seg6:
T
121
C
seg6:
T
123
C
seg6:
A
126
T
seg6:
T
128
G
seg6:
C
144
A
seg6:
G
153
A
seg6:
G
156
A
seg6:
C
157
T
Show more
Deletions
None
Insertions
None
Amino acid mutations
Mutations called relative to the
NC_007373.1
,
NC_007372.1
,
NC_007371.1
,
CY163680.1
,
NC_007369.1
,
CY114383.1
,
NC_007367.1
&
NC_007370.1
references
Substitutions
HA1
HA1:
P
4
H
HA1:
S
9
N
HA1:
T
10
M
HA1:
I
34
V
HA1:
T
48
K
HA1:
G
49
S
HA1:
G
50
E
HA1:
D
53
N
HA1:
K
82
S
HA1:
Y
94
H
HA1:
V
112
I
HA1:
N
121
T
HA1:
D
122
N
HA1:
N
133
D
HA1:
K
158
N
HA1:
F
159
S
HA1:
N
165
E
HA1:
K
173
Q
Show more
HA2
HA2:
I
32
R
HA2:
N
46
D
HA2:
N
116
S
HA2:
R
121
K
HA2:
N
168
S
HA2:
G
181
E
HA2:
R
216
K
NA
NA:
T
16
I
NA:
S
18
A
NA:
I
26
V
NA:
I
30
L
NA:
T
31
I
NA:
K
38
R
NA:
Y
40
H
NA:
E
41
D
NA:
F
42
C
NA:
N
47
K
NA:
M
51
I
NA:
L
52
F
NA:
I
58
L
NA:
I
62
K
NA:
T
69
I
NA:
I
73
V
NA:
L
81
P
NA:
N
86
D
Show more
SigPep
SigPep:
Y
9
H
Deletions
None
Insertions
None
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