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GS_00HREN9.1
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Download FASTA
Download metadata TSV
USA/GS_00HREN9.1/2026-04-02
P. C. Gauger,
G. S. Silva,
M. A. Zeller &
K. Hu
University of Pennsylvania Center of Excellence for Influenza Research and Response (CEIRR), CEIRR Influenza Data Processing and Communication Center
Submission details
Submission ID
PZ411810.1.seg1/PZ411809.1.seg2/PZ411805.1.seg3/PZ411804.1.seg4/PZ411808.1.seg5/PZ411807.1.seg6/PZ411806.1.seg7/PZ411803.1.seg8
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2026-05-18 05:48:21 UTC
Date released
2026-05-18 05:49:02 UTC
INSDC
bioprojectAccession
PRJNA818275
INSDC accession seg1
PZ411810.1
INSDC accession seg2
PZ411809.1
INSDC accession seg3
PZ411805.1
INSDC accession seg4
PZ411804.1
INSDC accession seg5
PZ411808.1
INSDC accession seg6
PZ411807.1
INSDC accession seg7
PZ411806.1
INSDC accession seg8
PZ411803.1
NCBI release date
2026-05-15
Clade
Clade HA
unassigned
Clade NA
None
Sample details
Collection country
USA
Collection date
2026-04-02
Isolate name
A/swine/Nebraska/I033305/2026
Host
Host
Sus scrofa
INSDC seg4
subtype_seg4
H3
INSDC seg6
subtype_seg6
N2
Alignment and QC
Length seg1
2280 (97.4%)
Total SNPs seg1
395
Length seg2
2274 (97.1%)
Total SNPs seg2
204
Length seg3
2151 (96.3%)
Total SNPs seg3
377
Length seg4
1701 (97.9%)
Total SNPs seg4
134
Length seg5
1497 (95.6%)
Total SNPs seg5
287
Length seg6
1410 (98%)
Total SNPs seg6
181
Length seg7
982 (95.6%)
Total SNPs seg7
133
Length seg8
838 (94.2%)
Total SNPs seg8
158
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
seg1
A
33
G
C
49
A
G
51
A
C
54
T
G
57
A
G
87
C
A
90
C
A
93
G
A
99
T
T
120
C
G
123
A
A
132
G
G
135
A
G
138
A
A
141
G
A
147
G
G
156
A
T
157
G
Show more
seg2
T
42
C
G
48
T
A
69
G
T
105
C
C
141
T
G
177
A
A
179
G
G
180
A
G
186
A
G
192
A
A
204
G
A
219
G
C
225
T
A
228
G
G
249
A
G
258
A
G
291
A
T
297
C
Show more
seg3
T
33
C
C
54
T
G
57
A
T
63
C
A
69
G
A
78
G
A
81
G
G
93
A
G
102
A
T
107
C
T
114
C
A
120
T
T
129
C
A
132
T
C
144
A
G
153
A
A
156
C
A
171
T
Show more
seg4
G
23
A
T
26
C
G
33
A
C
34
T
T
36
C
T
42
C
C
44
A
G
52
A
T
60
C
A
80
T
G
91
A
C
94
T
G
113
A
A
125
G
A
156
G
T
185
C
G
199
A
C
202
T
Show more
seg5
C
54
T
G
69
A
T
72
A
A
87
G
A
92
G
T
99
G
A
106
G
A
111
C
T
114
A
G
117
A
T
120
C
G
123
A
C
129
T
G
135
A
A
137
G
G
138
A
A
142
G
A
146
G
Show more
seg6
C
20
A
G
25
A
G
34
A
A
53
G
A
55
T
A
56
C
T
59
G
T
74
C
C
76
T
C
91
T
A
95
G
A
97
G
T
110
C
A
124
G
T
125
C
A
130
T
T
132
G
C
133
T
Show more
seg7
C
31
T
T
55
C
G
68
A
T
70
A
A
73
G
T
109
G
G
113
A
A
114
G
T
124
A
A
163
G
T
178
C
C
179
T
G
205
A
C
277
A
G
283
T
T
292
C
T
298
C
C
307
T
Show more
seg8
T
32
C
C
38
T
T
50
C
C
53
T
T
62
C
C
65
T
T
77
C
G
83
C
A
88
G
A
89
G
G
90
T
T
94
C
C
99
A
A
101
T
A
103
G
C
105
T
A
108
G
C
122
T
Show more
Deletions
N/A
Insertions
N/A
Amino acid substitutions
Substitutions 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:
S
9
N
HA1:
T
10
M
HA1:
N
31
D
HA1:
S
45
N
HA1:
S
46
F
HA1:
G
50
E
HA1:
D
53
N
HA1:
H
56
Y
HA1:
E
62
G
HA1:
K
82
N
HA1:
V
88
I
HA1:
Y
94
H
HA1:
A
106
V
HA1:
D
122
K
HA1:
N
133
D
HA1:
T
135
A
HA1:
R
142
K
HA1:
N
144
S
Show more
HA2
HA2:
I
32
R
HA2:
N
46
D
HA2:
L
102
M
HA2:
R
121
K
HA2:
D
164
N
HA2:
K
179
R
HA2:
G
181
E
HA2:
V
200
A
HA2:
R
216
K
M1
M1:
V
15
I
M1:
D
30
S
M1:
K
95
R
M1:
R
101
K
M1:
I
115
V
M1:
A
116
S
M1:
A
121
T
M1:
A
137
T
M1:
V
142
A
M1:
V
166
A
M1:
A
167
T
M1:
K
174
R
M1:
I
205
V
M1:
S
207
N
M1:
A
209
T
M1:
Q
214
H
M1:
A
218
T
M1:
V
219
I
M1:
R
230
K
M1:
T
239
A
M2
M2:
I
11
T
M2:
N
13
S
M2:
E
14
G
M2:
G
16
E
M2:
C
17
Y
M2:
N
20
S
M2:
V
27
A
M2:
V
28
I
M2:
S
31
N
M2:
L
43
T
M2:
V
51
I
M2:
L
54
R
M2:
H
57
Y
M2:
R
77
Q
M2:
K
78
Q
M2:
N
82
S
M2:
A
86
V
M2:
S
89
G
M2:
S
93
N
NA
NA:
Q
5
K
NA:
T
16
A
NA:
I
17
L
NA:
S
18
A
NA:
F
23
L
NA:
I
30
V
NA:
Y
40
H
NA:
E
41
D
NA:
F
42
C
NA:
N
43
D
NA:
P
45
S
NA:
L
52
F
NA:
I
58
V
NA:
I
62
K
NA:
T
71
I
NA:
I
73
V
NA:
N
86
I
NA:
G
93
S
Show more
NEP
NEP:
L
14
M
NEP:
I
32
V
NEP:
Q
34
R
NEP:
S
37
A
NEP:
A
48
T
NEP:
L
57
Y
NEP:
N
60
K
NEP:
G
63
E
NEP:
T
89
A
NEP:
F
107
L
NP
NP:
D
16
G
NP:
D
18
E
NP:
N
21
D
NP:
K
31
R
NP:
I
33
V
NP:
D
34
G
NP:
R
38
K
NP:
H
52
Y
NP:
L
61
I
NP:
K
65
R
NP:
V
109
I
NP:
I
119
V
NP:
I
186
V
NP:
M
189
I
NP:
V
190
A
NP:
V
197
I
NP:
K
214
R
NP:
S
217
I
Show more
NS1
NS1:
Q
21
R
NS1:
V
22
F
NS1:
V
23
A
NS1:
Q
25
N
NS1:
E
26
G
NS1:
S
28
G
NS1:
R
41
K
NS1:
R
44
I
NS1:
G
51
N
NS1:
K
55
E
NS1:
A
56
T
NS1:
H
59
L
NS1:
K
67
W
NS1:
D
74
S
NS1:
E
75
D
NS1:
A
76
T
NS1:
L
77
I
NS1:
M
79
R
Show more
PA
PA:
L
28
P
PA:
I
54
V
PA:
N
55
D
PA:
Q
57
R
PA:
V
62
I
PA:
L
65
S
PA:
D
66
G
PA:
G
99
E
PA:
A
100
V
PA:
N
142
K
PA:
I
155
M
PA:
N
184
S
PA:
K
204
R
PA:
S
208
T
PA:
K
222
N
PA:
C
225
S
PA:
N
254
S
PA:
I
268
L
Show more
PA-X
PA-X:
L
28
P
PA-X:
I
54
V
PA-X:
N
55
D
PA-X:
Q
57
R
PA-X:
V
62
I
PA-X:
L
65
S
PA-X:
D
66
G
PA-X:
G
99
E
PA-X:
A
100
V
PA-X:
N
142
K
PA-X:
I
155
M
PA-X:
N
184
S
PA-X:
K
195
R
PA-X:
K
199
R
PA-X:
N
204
D
PA-X:
S
207
L
PA-X:
L
210
P
PA-X:
V
212
A
Show more
PB1
PB1:
K
52
R
PB1:
V
113
I
PB1:
K
176
R
PB1:
M
179
I
PB1:
V
212
M
PB1:
G
216
S
PB1:
K
327
R
PB1:
I
339
M
PB1:
R
361
K
PB1:
A
374
S
PB1:
S
384
P
PB1:
D
398
E
PB1:
V
423
I
PB1:
K
433
R
PB1:
K
578
M
PB1:
R
586
K
PB1:
A
587
T
PB1:
N
619
D
Show more
PB1-F2
PB1-F2:
P
8
L
PB1-F2:
R
20
K
PB1-F2:
R
21
E
PB1-F2:
S
23
N
PB1-F2:
R
25
Q
PB1-F2:
K
29
R
PB1-F2:
N
34
S
PB1-F2:
T
36
I
PB1-F2:
Q
37
R
PB1-F2:
R
44
K
PB1-F2:
S
47
N
PB1-F2:
W
58
*
PB1-F2:
L
60
P
PB1-F2:
P
62
L
PB1-F2:
V
70
G
PB1-F2:
S
71
Y
PB1-F2:
T
74
I
PB1-F2:
K
78
R
Show more
PB2
PB2:
S
44
A
PB2:
K
61
R
PB2:
T
64
M
PB2:
E
65
D
PB2:
K
80
R
PB2:
M
81
T
PB2:
S
82
N
PB2:
V
105
T
PB2:
A
106
T
PB2:
D
120
E
PB2:
I
147
T
PB2:
K
187
R
PB2:
R
194
Q
PB2:
K
197
R
PB2:
S
199
A
PB2:
I
227
V
PB2:
E
249
G
PB2:
T
292
V
Show more
SigPep
SigPep:
A
6
I
SigPep:
Y
9
Q
SigPep:
C
12
Y
SigPep:
F
15
L
Deletions
N/A
Insertions
N/A
Load sequences