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Influenza A/H1N1pdm
GenSpectrum
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Influenza B/Victoria
Dengue 1
Dengue 2
Dengue 3
Dengue 4
Influenza A/H1N1pdm
Influenza A/H3N2
Influenza A/H5N1
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Influenza B
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Influenza A/H1N1pdm
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Browse data
GS_00GC6P9.1
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Display Name: USA/GS_00GC6P9.1/2025-10-21
A. USDA Swine Influenza Surveillance &
M. Sturos
Submission details
Submission ID
PX596416.1.seg4/PX596417.1.seg6
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2025-11-26 04:56:42 UTC
Date released
2025-11-26 04:57:40 UTC
Authors
Author affiliations
USDA
Clade
Clade HA
6B.1A.5a.2a
Clade NA
D
Alignment states and QC metrics seg4
Completeness seg4
97.03%
Length seg4
1701
Total ambiguous nucs seg4
1
Total deleted nucs seg4
0
Total frame shifts seg4
0
Total inserted nucs seg4
0
Total SNPs seg4
95
Total unknown nucs seg4
0
Alignment states and QC metrics seg6
Completeness seg6
98.39%
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
20
Total unknown nucs seg6
0
Sample details
Collection country
USA
Collection date
2025-10-21
Isolate name
A/swine/Minnesota/A02980717/2025
Host
Host name scientific
Sus scrofa
Host taxon id
9823
INSDC
INSDC accession seg4
PX596416.1
INSDC accession seg6
PX596417.1
NCBI release date
2025-11-24
INSDC seg4
Subtype seg4
H1
INSDC seg6
Subtype seg6
N1
Nucleotide mutations
Mutations called relative to the
NC_026438.1
,
NC_026435.1
,
NC_026437.1
,
CY121680.1
,
NC_026436.1
,
MW626056.1
,
NC_026431.1
&
NC_026432.1
references
Substitutions
seg4
seg4:
C
42
A
seg4:
A
47
G
seg4:
G
57
A
seg4:
A
119
G
seg4:
T
161
C
seg4:
C
164
T
seg4:
G
188
A
seg4:
A
231
C
seg4:
C
293
A
seg4:
T
308
A
seg4:
G
311
A
seg4:
C
318
T
seg4:
G
322
A
seg4:
G
338
T
seg4:
G
360
A
seg4:
A
392
T
seg4:
G
416
A
seg4:
A
429
G
Show more
seg6
seg6:
G
112
A
seg6:
A
428
G
seg6:
C
452
A
seg6:
G
607
A
seg6:
G
611
A
seg6:
A
785
G
seg6:
T
799
C
seg6:
A
818
G
seg6:
T
890
C
seg6:
C
893
T
seg6:
G
914
T
seg6:
G
938
A
seg6:
A
1049
G
seg6:
T
1056
G
seg6:
C
1187
T
seg6:
A
1193
G
seg6:
G
1253
A
seg6:
G
1365
A
seg6:
T
1403
C
seg6:
G
1415
T
Deletions
None
Insertions
None
Amino acid mutations
Mutations called relative to the
NC_026438.1
,
NC_026435.1
,
NC_026437.1
,
CY121680.1
,
NC_026436.1
,
MW626056.1
,
NC_026431.1
&
NC_026432.1
references
Substitutions
HA1
HA1:
K
54
Q
HA1:
S
74
R
HA1:
P
83
S
HA1:
S
84
N
HA1:
D
97
N
HA1:
T
120
A
HA1:
N
129
D
HA1:
N
156
K
HA1:
L
161
I
HA1:
S
162
N
HA1:
K
163
Q
HA1:
S
164
T
HA1:
K
169
Q
HA1:
S
183
P
HA1:
S
185
I
HA1:
A
186
T
HA1:
Q
189
E
HA1:
S
203
T
Show more
HA2
HA2:
E
47
K
HA2:
I
91
V
HA2:
R
106
K
HA2:
S
124
N
HA2:
E
172
K
HA2:
E
179
D
HA2:
I
183
T
NA
NA:
S
35
N
NA:
S
200
N
NA:
I
264
T
NA:
S
350
A
NA:
V
453
M
NA:
K
469
N
SigPep
SigPep:
L
8
M
SigPep:
A
13
T
Deletions
None
Insertions
None
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