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GS_00HTCSZ.1
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Download FASTA
Download metadata TSV
USA/GS_00HTCSZ.1/2026-04-02
K. Lantz &
T. Stuber
USDA Animal Plant Health Inspection Service-National Veterinary Services Laboratories, National Veterinary Services Laboratories
Submission details
Submission ID
PZ479124.1.seg1/PZ479125.1.seg2/PZ479126.1.seg3/PZ479127.1.seg4/PZ479128.1.seg5/PZ479129.1.seg6/PZ479130.1.seg7/PZ479131.1.seg8
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2026-06-02 06:02:31 UTC
Date released
2026-06-02 06:03:08 UTC
INSDC
bioprojectAccession
PRJNA1230736
biosampleAccession
SAMN57648952
INSDC accession seg1
PZ479124.1
INSDC accession seg2
PZ479125.1
INSDC accession seg3
PZ479126.1
INSDC accession seg4
PZ479127.1
INSDC accession seg5
PZ479128.1
INSDC accession seg6
PZ479129.1
INSDC accession seg7
PZ479130.1
INSDC accession seg8
PZ479131.1
NCBI release date
2026-06-01
SRA run accession
SRR38343103
Clade
Clade HA
unassigned
Clade NA
None
Sample details
Collection country
USA
Collection subdivision level 1
KS
Collection date
2026-04-02
Isolate name
A/Domestic Pig/KS/26G05637-001-original/2026
Host
Host
Sus scrofa domesticus
INSDC seg4
subtype_seg4
H3
INSDC seg6
subtype_seg6
N2
Alignment and QC
Length seg1
2280 (97.4%)
Total SNPs seg1
389
Length seg2
2274 (97.1%)
Total SNPs seg2
209
Length seg3
2151 (96.3%)
Total SNPs seg3
374
Length seg4
1701 (97.9%)
Total SNPs seg4
140
Length seg5
1497 (95.6%)
Total SNPs seg5
271
Length seg6
1410 (98%)
Total SNPs seg6
167
Length seg7
982 (95.6%)
Total SNPs seg7
136
Length seg8
838 (94.2%)
Total SNPs seg8
149
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
A
52
G
G
57
A
T
69
C
G
87
C
A
90
T
A
93
G
A
99
T
T
120
C
G
123
A
C
129
T
G
135
A
G
138
A
A
141
G
G
156
C
T
157
G
Show more
seg2
T
42
C
G
48
T
A
63
G
A
69
G
T
105
C
C
138
T
G
177
A
A
179
G
G
180
A
G
186
A
C
216
T
A
219
G
C
225
T
A
228
G
G
249
A
C
288
T
T
297
C
C
303
T
Show more
seg3
G
31
A
C
54
T
G
57
A
T
63
C
A
69
G
A
75
G
A
81
G
G
93
A
G
102
A
T
107
C
T
114
C
A
120
C
A
126
G
T
129
C
A
132
T
C
144
G
G
153
A
A
171
G
Show more
seg4
A
22
G
G
23
A
T
26
C
C
34
T
T
35
G
T
42
C
C
44
A
T
51
C
G
52
A
A
69
G
C
77
T
A
80
T
G
91
A
C
94
T
G
113
A
A
125
G
A
157
G
C
161
T
Show more
seg5
C
54
T
G
69
A
T
72
A
G
81
A
A
92
G
G
96
A
T
99
G
A
106
G
A
111
T
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
146
C
Show more
seg6
G
34
A
C
40
T
A
55
C
T
59
G
C
76
T
A
95
G
A
97
G
G
104
A
T
110
C
T
125
C
T
127
C
G
128
A
A
130
C
T
132
G
A
134
G
C
140
T
A
147
C
T
148
C
Show more
seg7
C
31
T
T
55
C
C
61
T
G
68
A
T
70
A
A
73
G
A
76
G
C
97
T
T
109
G
G
113
A
C
118
T
T
124
A
G
127
A
A
130
G
C
133
T
T
139
C
T
178
C
C
179
T
Show more
seg8
T
32
C
C
38
T
T
50
C
C
53
T
T
62
C
C
65
T
T
68
C
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
A
108
G
T
134
C
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:
K
2
E
HA1:
S
9
N
HA1:
T
10
M
HA1:
N
31
S
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:
G
78
D
HA1:
K
82
S
HA1:
D
85
E
HA1:
Y
94
H
HA1:
A
106
V
HA1:
D
122
N
HA1:
T
135
A
HA1:
R
142
G
Show more
HA2
HA2:
I
32
R
HA2:
N
46
D
HA2:
R
121
K
HA2:
D
164
N
HA2:
G
181
E
HA2:
K
212
R
HA2:
R
216
K
M1
M1:
V
15
I
M1:
D
30
N
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
Show more
M2
M2:
G
16
E
M2:
D
21
G
M2:
V
27
A
M2:
V
28
I
M2:
S
31
N
M2:
L
43
A
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:
S
18
A
NA:
I
30
V
NA:
V
33
I
NA:
Y
40
H
NA:
E
41
N
NA:
F
42
C
NA:
N
43
D
NA:
P
45
S
NA:
N
47
T
NA:
Q
49
H
NA:
L
52
F
NA:
E
54
K
NA:
I
62
K
NA:
T
69
N
NA:
I
73
V
NA:
I
77
T
NA:
A
82
I
NA:
G
93
N
Show more
NEP
NEP:
L
14
M
NEP:
I
32
V
NEP:
Q
34
R
NEP:
S
37
A
NEP:
A
48
T
NEP:
M
52
T
NEP:
L
57
Y
NEP:
G
63
E
NEP:
F
107
L
NP
NP:
D
16
G
NP:
D
18
E
NP:
N
21
D
NP:
K
31
R
NP:
D
34
A
NP:
H
52
Y
NP:
L
61
V
NP:
K
65
R
NP:
A
85
T
NP:
V
100
I
NP:
V
109
T
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
V
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
K
NS1:
D
53
N
NS1:
K
55
E
NS1:
A
56
T
NS1:
H
59
L
NS1:
K
67
W
NS1:
D
74
S
NS1:
A
76
T
NS1:
M
81
I
NS1:
V
82
A
NS1:
T
84
I
Show more
PA
PA:
D
3
N
PA:
L
28
P
PA:
N
55
D
PA:
V
62
I
PA:
L
65
S
PA:
D
66
G
PA:
A
100
I
PA:
I
118
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
239
I
PA:
N
254
G
PA:
K
256
Q
Show more
PA-X
PA-X:
D
3
N
PA-X:
L
28
P
PA-X:
N
55
D
PA-X:
V
62
I
PA-X:
L
65
S
PA-X:
D
66
G
PA-X:
A
100
I
PA-X:
I
118
V
PA-X:
N
142
K
PA-X:
I
155
M
PA-X:
N
184
S
PA-X:
K
195
R
PA-X:
E
196
G
PA-X:
A
197
G
PA-X:
K
199
R
PA-X:
N
204
D
PA-X:
S
207
L
PA-X:
L
210
P
Show more
PB1
PB1:
K
52
R
PB1:
V
113
I
PB1:
M
179
I
PB1:
I
181
M
PB1:
V
212
M
PB1:
G
216
S
PB1:
K
327
R
PB1:
I
339
M
PB1:
A
374
S
PB1:
D
398
E
PB1:
V
423
I
PB1:
K
433
R
PB1:
I
459
V
PB1:
D
464
N
PB1:
R
586
K
PB1:
N
619
D
PB1:
E
638
D
PB1:
N
642
S
Show more
PB1-F2
PB1-F2:
T
7
I
PB1-F2:
R
20
K
PB1-F2:
R
21
E
PB1-F2:
S
23
N
PB1-F2:
P
33
L
PB1-F2:
N
34
S
PB1-F2:
T
36
I
PB1-F2:
Q
37
R
PB1-F2:
R
44
K
PB1-F2:
S
57
F
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:
S
82
L
PB1-F2:
F
83
S
PB1-F2:
Q
86
R
PB1-F2:
T
89
I
PB2
PB2:
N
9
D
PB2:
S
44
A
PB2:
K
61
R
PB2:
T
64
M
PB2:
E
65
D
PB2:
V
67
I
PB2:
M
81
T
PB2:
S
82
N
PB2:
V
89
I
PB2:
V
105
T
PB2:
A
106
T
PB2:
D
120
E
PB2:
I
147
T
PB2:
K
157
R
PB2:
R
194
Q
PB2:
S
199
A
PB2:
I
227
V
PB2:
T
292
I
Show more
SigPep
SigPep:
K
2
R
SigPep:
A
6
V
SigPep:
Y
9
Q
SigPep:
C
12
H
Deletions
N/A
Insertions
N/A
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