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GS_00513YT.1
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Display Name: USA/GS_00513YT.1/2025-02-28
Gauger,
P. C.; Moraes,
D.; Silva,
G. S.; Linhares,
D. C.
Submission details
Submission ID
PV434088.1.seg1/PV434090.1.seg2/PV434089.1.seg3/PV434095.1.seg4/PV434091.1.seg5/PV434092.1.seg6/PV434093.1.seg7/PV434094.1.seg8
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2025-04-03 08:01:46 UTC
Date released
2025-04-03 10:23:07 UTC
Authors
Author affiliations
University of Pennsylvania Center of Excellence for Influenza Research and Response (CEIRR), CEIRR Influenza Data Processing and Communication Center
INSDC
Bioproject accession
PRJNA818275
INSDC accession seg1
PV434088.1
INSDC accession seg2
PV434090.1
INSDC accession seg3
PV434089.1
INSDC accession seg4
PV434095.1
INSDC accession seg5
PV434091.1
INSDC accession seg6
PV434092.1
INSDC accession seg7
PV434093.1
INSDC accession seg8
PV434094.1
NCBI release date
2025-04-02
Clade
Clade HA
6
Alignment states and QC metrics seg1
Completeness seg1
100.00%
Length seg1
2280
Total ambiguous nucs seg1
0
Total deleted nucs seg1
0
Total frame shifts seg1
0
Total inserted nucs seg1
0
Total SNPs seg1
173
Total unknown nucs seg1
0
Alignment states and QC metrics seg2
Completeness seg2
100.00%
Length seg2
2274
Total ambiguous nucs seg2
0
Total deleted nucs seg2
0
Total frame shifts seg2
0
Total inserted nucs seg2
0
Total SNPs seg2
180
Total unknown nucs seg2
0
Alignment states and QC metrics seg3
Completeness seg3
100.00%
Length seg3
2151
Total ambiguous nucs seg3
0
Total deleted nucs seg3
0
Total frame shifts seg3
0
Total inserted nucs seg3
0
Total SNPs seg3
107
Total unknown nucs seg3
0
Alignment states and QC metrics seg4
Completeness seg4
97.09%
Length seg4
1695
Total ambiguous nucs seg4
0
Total deleted nucs seg4
6
Total frame shifts seg4
0
Total inserted nucs seg4
0
Total SNPs seg4
271
Total unknown nucs seg4
0
Alignment states and QC metrics seg5
Completeness seg5
100.00%
Length seg5
1497
Total ambiguous nucs seg5
0
Total deleted nucs seg5
0
Total frame shifts seg5
0
Total inserted nucs seg5
0
Total SNPs seg5
60
Total unknown nucs seg5
0
Alignment states and QC metrics seg7
Completeness seg7
100.00%
Length seg7
982
Total ambiguous nucs seg7
0
Total deleted nucs seg7
0
Total frame shifts seg7
0
Total inserted nucs seg7
0
Total SNPs seg7
27
Total unknown nucs seg7
0
Alignment states and QC metrics seg8
Completeness seg8
97.10%
Length seg8
838
Total ambiguous nucs seg8
0
Total deleted nucs seg8
0
Total frame shifts seg8
0
Total inserted nucs seg8
0
Total SNPs seg8
65
Total unknown nucs seg8
0
Sample details
Collection country
USA
Collection date
2025-02-28
Host
Host name scientific
Sus scrofa
Host taxon id
9823
Is lab host
True
Alignment states and QC metrics seg6
Length seg6
1410
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
seg1
seg1:
C
19
T
seg1:
G
21
A
seg1:
C
87
T
seg1:
G
99
A
seg1:
A
111
G
seg1:
G
123
A
seg1:
G
161
A
seg1:
T
171
C
seg1:
C
195
T
seg1:
G
236
A
seg1:
A
245
C
seg1:
A
264
C
seg1:
G
303
A
seg1:
A
316
G
seg1:
T
321
C
seg1:
T
330
C
seg1:
G
339
A
seg1:
A
360
G
Show more
seg2
seg2:
T
18
C
seg2:
A
33
G
seg2:
A
34
G
seg2:
T
36
C
seg2:
A
45
G
seg2:
C
57
T
seg2:
T
81
C
seg2:
A
129
C
seg2:
C
147
T
seg2:
A
155
G
seg2:
G
156
A
seg2:
A
159
G
seg2:
G
162
A
seg2:
C
174
T
seg2:
T
186
G
seg2:
C
201
T
seg2:
G
225
A
seg2:
G
243
A
Show more
seg3
seg3:
R
53
A
seg3:
G
84
A
seg3:
G
102
A
seg3:
T
105
C
seg3:
T
123
C
seg3:
G
126
A
seg3:
T
132
C
seg3:
C
169
A
seg3:
C
201
T
seg3:
G
204
A
seg3:
C
211
T
seg3:
T
214
C
seg3:
C
222
T
seg3:
A
246
G
seg3:
C
250
A
seg3:
A
252
G
seg3:
A
253
G
seg3:
T
254
C
Show more
seg4
seg4:
A
35
G
seg4:
G
36
T
seg4:
A
38
G
seg4:
T
41
C
seg4:
C
42
T
seg4:
T
48
C
seg4:
T
54
C
seg4:
T
78
A
seg4:
A
110
T
seg4:
C
113
T
seg4:
A
119
T
seg4:
C
122
T
seg4:
A
128
G
seg4:
C
129
T
seg4:
A
134
G
seg4:
A
143
G
seg4:
T
161
C
seg4:
C
164
T
Show more
seg5
seg5:
T
48
G
seg5:
G
54
A
seg5:
A
126
G
seg5:
T
159
A
seg5:
C
180
T
seg5:
A
225
G
seg5:
T
228
C
seg5:
A
282
T
seg5:
A
306
G
seg5:
T
326
C
seg5:
R
341
A
seg5:
T
365
A
seg5:
C
408
A
seg5:
C
426
T
seg5:
C
427
T
seg5:
C
438
A
seg5:
G
447
A
seg5:
A
450
G
Show more
seg7
seg7:
T
6
C
seg7:
G
89
A
seg7:
A
174
G
seg7:
G
258
A
seg7:
G
270
A
seg7:
G
342
A
seg7:
A
348
G
seg7:
G
414
A
seg7:
T
429
C
seg7:
T
435
C
seg7:
T
483
C
seg7:
A
489
G
seg7:
G
492
A
seg7:
T
498
C
seg7:
C
504
T
seg7:
C
514
T
seg7:
G
540
T
seg7:
G
600
A
Show more
seg8
seg8:
C
12
T
seg8:
C
15
T
seg8:
A
16
G
seg8:
T
51
C
seg8:
G
60
A
seg8:
A
63
G
seg8:
A
78
G
seg8:
A
114
G
seg8:
A
122
G
seg8:
T
127
C
seg8:
A
129
G
seg8:
A
131
T
seg8:
G
139
A
seg8:
G
151
A
seg8:
G
152
A
seg8:
G
157
A
seg8:
T
159
C
seg8:
G
183
A
Show more
Deletions
seg4:450-455
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:
L
3
I
HA1:
R
45
G
HA1:
V
47
K
HA1:
A
48
S
HA1:
H
51
Y
HA1:
I
61
L
HA1:
S
69
P
HA1:
L
70
I
HA1:
S
71
L
HA1:
A
73
V
HA1:
P
83
S
HA1:
S
84
N
HA1:
D
94
S
HA1:
I
96
T
HA1:
D
97
N
HA1:
R
113
K
HA1:
K
119
I
HA1:
T
120
E
Show more
HA2
HA2:
E
29
D
HA2:
L
38
Q
HA2:
N
43
R
HA2:
E
47
G
HA2:
V
55
I
HA2:
H
72
N
HA2:
K
75
R
HA2:
K
82
R
HA2:
Y
110
F
HA2:
S
124
N
HA2:
K
127
R
HA2:
D
158
N
HA2:
P
160
L
HA2:
A
166
S
HA2:
E
179
D
HA2:
I
183
V
HA2:
L
199
I
HA2:
V
200
L
HA2:
I
206
L
M1
M1:
S
30
N
M1:
M
248
I
M2
M2:
C
19
Y
M2:
I
39
V
M2:
T
43
A
M2:
F
47
L
M2:
F
55
L
NEP
NEP:
M
6
V
NEP:
S
37
A
NEP:
M
52
T
NEP:
L
58
F
NEP:
S
60
N
NEP:
M
83
V
NEP:
H
85
N
NEP:
A
89
T
NEP:
A
115
T
NP
NP:
D
53
E
NP:
I
109
T
NP:
X
114
E
NP:
L
122
Q
NP:
V
183
I
NP:
A
366
S
NP:
M
426
L
NP:
S
450
N
NP:
K
452
R
NS1
NS1:
M
6
V
NS1:
K
41
R
NS1:
K
44
I
NS1:
G
47
S
NS1:
G
51
N
NS1:
D
53
N
NS1:
E
75
D
NS1:
R
78
K
NS1:
S
87
P
NS1:
S
91
A
NS1:
L
95
P
NS1:
L
119
M
NS1:
M
124
L
NS1:
V
129
I
NS1:
Y
171
N
NS1:
V
178
I
NS1:
V
194
S
NS1:
I
198
L
Show more
PA
PA:
X
18
E
PA:
I
85
A
PA:
M
86
I
PA:
K
142
M
PA:
S
186
G
PA:
K
204
R
PA:
K
213
R
PA:
P
224
S
PA:
N
254
S
PA:
R
262
K
PA:
L
275
P
PA:
H
277
S
PA:
V
323
I
PA:
E
327
D
PA:
K
328
R
PA:
M
336
L
PA:
R
356
K
PA:
A
404
S
PA:
R
626
K
PA:
L
711
I
PA-X
PA-X:
X
18
E
PA-X:
I
85
A
PA-X:
M
86
I
PA-X:
K
142
M
PA-X:
S
186
G
PA-X:
K
195
R
PA-X:
N
204
D
PA-X:
R
206
K
PA-X:
L
210
P
PA-X:
S
213
G
PA-X:
S
219
F
PA-X:
*
233
W
PB1
PB1:
I
12
V
PB1:
K
52
R
PB1:
V
113
I
PB1:
N
175
D
PB1:
V
200
I
PB1:
L
212
M
PB1:
G
216
S
PB1:
I
298
L
PB1:
I
364
L
PB1:
M
372
L
PB1:
A
374
S
PB1:
K
386
R
PB1:
K
433
R
PB1:
I
435
T
PB1:
V
517
I
PB1:
V
587
A
PB1:
D
618
E
PB1:
N
642
S
PB1:
V
728
I
PB2
PB2:
R
54
K
PB2:
S
79
N
PB2:
N
82
T
PB2:
T
106
A
PB2:
A
184
V
PB2:
E
249
K
PB2:
R
299
K
PB2:
I
315
M
PB2:
R
355
K
PB2:
R
368
K
PB2:
S
453
P
PB2:
N
456
S
PB2:
M
473
T
PB2:
V
511
I
PB2:
I
559
S
PB2:
V
560
L
PB2:
S
684
A
PB2:
D
740
N
SigPep
SigPep:
V
6
L
SigPep:
Y
10
H
SigPep:
F
12
L
Deletions
HA1:127, HA1:128
Insertions
None
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