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Influenza A/H1N1pdm
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GS_00DKQ0S.1
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Display Name: USA/GS_00DKQ0S.1/2025-02-16
Leonard,
A. S.; Mendoza,
L.; John,
A. O.; Hensley,
S. E.
Submission details
Submission ID
PV466125.1.seg1/PV466122.1.seg3/PV466128.1.seg4/PV466126.1.seg5/PV466123.1.seg6/PV466127.1.seg7/PV466124.1.seg8
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2025-04-10 00:13:31 UTC
Date released
2025-04-10 00:13:52 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
PRJNA818282
INSDC accession seg1
PV466125.1
INSDC accession seg3
PV466122.1
INSDC accession seg4
PV466128.1
INSDC accession seg5
PV466126.1
INSDC accession seg6
PV466123.1
INSDC accession seg7
PV466127.1
INSDC accession seg8
PV466124.1
NCBI release date
2025-04-09
Clade
Clade HA
3C.2a1b.2a.2a.3a.1
Clade NA
B.4.2
Alignment states and QC metrics seg1
Completeness seg1
98.93%
Length seg1
2316
Total ambiguous nucs seg1
0
Total deleted nucs seg1
0
Total frame shifts seg1
0
Total inserted nucs seg1
0
Total SNPs seg1
97
Total unknown nucs seg1
0
Alignment states and QC metrics seg3
Completeness seg3
98.84%
Length seg3
2208
Total ambiguous nucs seg3
0
Total deleted nucs seg3
0
Total frame shifts seg3
0
Total inserted nucs seg3
0
Total SNPs seg3
90
Total unknown nucs seg3
1
Alignment states and QC metrics seg4
Completeness seg4
100.00%
Length seg4
1737
Total ambiguous nucs seg4
0
Total deleted nucs seg4
0
Total frame shifts seg4
0
Total inserted nucs seg4
0
Total SNPs seg4
115
Total unknown nucs seg4
0
Alignment states and QC metrics seg5
Completeness seg5
98.40%
Length seg5
1540
Total ambiguous nucs seg5
0
Total deleted nucs seg5
1
Total frame shifts seg5
0
Total inserted nucs seg5
0
Total SNPs seg5
53
Total unknown nucs seg5
0
Alignment states and QC metrics seg6
Completeness seg6
99.86%
Length seg6
1439
Total ambiguous nucs seg6
0
Total deleted nucs seg6
0
Total frame shifts seg6
0
Total inserted nucs seg6
4
Total SNPs seg6
77
Total unknown nucs seg6
1
Alignment states and QC metrics seg7
Completeness seg7
97.57%
Length seg7
1002
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
96.18%
Length seg8
859
Total ambiguous nucs seg8
0
Total deleted nucs seg8
0
Total frame shifts seg8
0
Total inserted nucs seg8
0
Total SNPs seg8
28
Total unknown nucs seg8
3
Sample details
Collection country
USA
Collection date
2025-02-16
Host
Host name scientific
Homo sapiens
Host taxon id
9606
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
seg1
seg1:
T
27
C
seg1:
C
54
T
seg1:
G
57
A
seg1:
T
75
C
seg1:
C
192
T
seg1:
C
198
T
seg1:
T
255
C
seg1:
A
282
G
seg1:
C
289
A
seg1:
A
330
G
seg1:
A
336
G
seg1:
G
343
A
seg1:
G
347
A
seg1:
A
369
G
seg1:
G
375
A
seg1:
A
402
G
seg1:
T
426
C
seg1:
T
438
C
Show more
seg3
seg3:
G
22
A
seg3:
A
99
G
seg3:
C
144
T
seg3:
A
156
G
seg3:
T
177
C
seg3:
G
210
A
seg3:
T
222
C
seg3:
G
243
A
seg3:
A
324
T
seg3:
A
333
G
seg3:
C
340
T
seg3:
A
342
G
seg3:
A
345
G
seg3:
G
363
A
seg3:
T
369
C
seg3:
A
396
G
seg3:
A
435
G
seg3:
C
450
A
Show more
seg4
seg4:
A
24
G
seg4:
T
42
A
seg4:
G
56
T
seg4:
C
72
A
seg4:
T
74
A
seg4:
C
77
T
seg4:
C
89
T
seg4:
A
125
G
seg4:
G
155
A
seg4:
A
163
G
seg4:
A
170
G
seg4:
C
189
T
seg4:
G
199
A
seg4:
C
203
A
seg4:
C
208
T
seg4:
G
213
A
seg4:
G
214
A
seg4:
G
222
A
Show more
seg5
seg5:
A
16
G
seg5:
C
29
T
seg5:
A
40
C
seg5:
G
96
A
seg5:
G
207
A
seg5:
G
219
A
seg5:
C
249
T
seg5:
A
345
C
seg5:
A
351
G
seg5:
G
390
A
seg5:
G
432
T
seg5:
G
436
T
seg5:
T
447
C
seg5:
A
451
C
seg5:
C
459
T
seg5:
G
492
A
seg5:
A
513
G
seg5:
T
525
C
Show more
seg6
seg6:
C
51
A
seg6:
A
60
G
seg6:
T
88
C
seg6:
C
129
A
seg6:
C
132
A
seg6:
C
144
T
seg6:
C
205
T
seg6:
T
245
C
seg6:
G
247
A
seg6:
G
270
A
seg6:
A
280
G
seg6:
A
281
G
seg6:
T
303
C
seg6:
C
345
A
seg6:
C
380
T
seg6:
G
408
A
seg6:
C
421
A
seg6:
C
429
T
Show more
seg7
seg7:
A
37
T
seg7:
C
188
T
seg7:
G
205
A
seg7:
G
214
T
seg7:
A
241
G
seg7:
T
292
C
seg7:
T
298
C
seg7:
A
466
G
seg7:
A
481
G
seg7:
C
493
T
seg7:
A
517
G
seg7:
G
625
A
seg7:
A
637
G
seg7:
A
658
G
seg7:
G
680
A
seg7:
C
697
T
seg7:
T
703
C
seg7:
T
718
C
Show more
seg8
seg8:
C
53
T
seg8:
T
68
C
seg8:
G
102
A
seg8:
A
104
C
seg8:
C
116
T
seg8:
C
123
A
seg8:
T
125
C
seg8:
G
192
T
seg8:
T
205
C
seg8:
T
218
C
seg8:
A
238
G
seg8:
T
271
C
seg8:
C
275
G
seg8:
C
302
T
seg8:
G
398
A
seg8:
G
416
A
seg8:
G
430
A
seg8:
A
442
G
Show more
Deletions
seg5:1543
Insertions
ins_seg6:0:AGTA
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:
L
3
I
HA1:
Q
33
R
HA1:
S
45
N
HA1:
T
48
I
HA1:
G
50
K
HA1:
D
53
N
HA1:
E
62
G
HA1:
K
83
E
HA1:
K
92
R
HA1:
Y
94
N
HA1:
N
96
S
HA1:
D
104
N
HA1:
N
121
K
HA1:
T
131
K
HA1:
S
138
A
HA1:
R
142
G
HA1:
N
144
S
HA1:
H
156
S
Show more
HA2
HA2:
I
32
R
HA2:
N
46
D
HA2:
N
49
S
HA2:
I
77
V
HA2:
R
121
K
HA2:
G
155
E
HA2:
D
160
N
HA2:
I
193
M
HA2:
V
200
I
M1
M1:
V
219
I
M1:
T
239
A
M2
M2:
P
25
L
M2:
S
31
N
M2:
L
54
F
M2:
N
82
S
NA
NA:
F
42
L
NA:
N
43
K
NA:
L
81
P
NA:
A
82
T
NA:
N
93
G
NA:
P
126
L
NA:
L
140
I
NA:
D
147
N
NA:
V
194
I
NA:
I
215
V
NA:
K
220
N
NA:
E
221
D
NA:
S
245
N
NA:
S
247
T
NA:
T
267
K
NA:
L
285
P
NA:
V
303
I
NA:
Y
310
H
Show more
NP
NP:
A
131
S
NP:
I
136
L
NP:
V
197
I
NP:
R
236
K
NP:
T
472
A
NS1
NS1:
E
26
N
NS1:
L
33
I
NS1:
A
56
S
NS1:
V
60
A
NS1:
E
71
G
NS1:
V
82
A
NS1:
M
124
I
NS1:
S
135
N
NS1:
D
139
G
NS1:
K
221
E
NS1:
K
229
E
PA
PA:
N
142
K
PA:
I
155
M
PA:
K
158
R
PA:
S
208
T
PA:
K
222
N
PA:
K
256
Q
PA:
I
311
M
PA:
Y
321
C
PA:
D
382
E
PA:
D
396
E
PA:
N
409
S
PA:
I
421
V
PA:
Y
437
H
PA:
A
472
S
PA:
I
602
V
PA:
K
605
R
PA:
V
668
I
PA:
N
675
K
PA:
K
716
E
PA-X
PA-X:
N
142
K
PA-X:
I
155
M
PA-X:
K
158
R
PA-X:
E
209
G
PA-X:
V
212
A
PA-X:
N
222
T
PB2
PB2:
A
106
T
PB2:
S
107
N
PB2:
I
147
T
PB2:
E
249
G
PB2:
K
340
R
PB2:
K
353
R
PB2:
I
451
V
PB2:
M
467
I
PB2:
I
588
T
PB2:
T
613
A
SigPep
SigPep:
T
3
A
SigPep:
Y
9
N
Deletions
None
Insertions
None
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