Warning: Development or Keycloak main database is enabled. Development environment only.
X
GenSpectrum
Influenza A/H5N1
Influenza A/H5N1
RSV-A
RSV B
Browse
Loculus
Browse
Docs
API docs
GS_001EHQ7.1
Download
Download FASTA
Download metadata TSV
Display Name: GS_001EHQ7.1/2024-10-10
Aufderhar,
M.; Franzen,
K.; Killian,
M.; Lantz,
K.; Stuber,
T.; Hicks,
J.; Norris,
C.; Lakin,
S.
Submission details
Submission ID
PQ687300.1.seg1/PQ687301.1.seg2/PQ687302.1.seg3/PQ687303.1.seg4/PQ687304.1.seg5/PQ687305.1.seg6/PQ687306.1.seg7/PQ687307.1.seg8
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2024-12-11 16:47:38 UTC
Date released
2024-12-11 17:24:58 UTC
Data use terms
Data use terms
OPEN
✕
Data Use Terms History
Changed
User
Data Use Terms
2024-12-11 16:48
insdc_ingest_user
OPEN
Close
(history)
Authors
Author affiliations
USDA Animal Plant Health Inspection Service-National Veterinary Services Laboratories, National Veterinary Services Laboratories
INSDC
Bioproject accession
PRJNA1102327
Biosample accession
SAMN44611594
INSDC accession seg1
PQ687300.1
INSDC accession seg2
PQ687301.1
INSDC accession seg3
PQ687302.1
INSDC accession seg4
PQ687303.1
INSDC accession seg5
PQ687304.1
INSDC accession seg6
PQ687305.1
INSDC accession seg7
PQ687306.1
INSDC accession seg8
PQ687307.1
NCBI release date
2024-12-06
SRA run accession
SRR31254373
Clade
Clade
2.3.4.4b
Alignment states and QC metrics seg1
Completeness seg1
97.39%
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
362
Total unknown nucs seg1
0
Alignment states and QC metrics seg2
Completeness seg2
97.14%
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
270
Total unknown nucs seg2
0
Alignment states and QC metrics seg3
Completeness seg3
96.33%
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
162
Total unknown nucs seg3
0
Alignment states and QC metrics seg4
Completeness seg4
96.99%
Length seg4
1704
Total ambiguous nucs seg4
0
Total deleted nucs seg4
3
Total frame shifts seg4
0
Total inserted nucs seg4
0
Total SNPs seg4
188
Total unknown nucs seg4
0
Alignment states and QC metrics seg5
Completeness seg5
95.65%
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
182
Total unknown nucs seg5
0
Alignment states and QC metrics seg6
Completeness seg6
96.71%
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
150
Total unknown nucs seg6
0
Alignment states and QC metrics seg7
Completeness seg7
95.62%
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
63
Total unknown nucs seg7
0
Alignment states and QC metrics seg8
Completeness seg8
96.88%
Length seg8
838
Total ambiguous nucs seg8
0
Total deleted nucs seg8
11
Total frame shifts seg8
0
Total inserted nucs seg8
11
Total SNPs seg8
215
Total unknown nucs seg8
0
Sample details
Collection country
USA
Collection subdivision level 1
CA
Collection date
2024-10-10
Isolate name
24-030318-003-original
Host
Host name scientific
Bos taurus
Host taxon id
9913
Nucleotide mutations
Substitutions
seg1
seg1:
A
33
G
seg1:
A
48
G
seg1:
G
63
A
seg1:
C
69
T
seg1:
A
90
C
seg1:
G
102
T
seg1:
T
105
C
seg1:
T
108
C
seg1:
A
126
G
seg1:
G
147
A
seg1:
T
159
A
seg1:
A
211
C
seg1:
G
222
A
seg1:
T
228
C
seg1:
G
243
A
seg1:
G
255
C
seg1:
T
258
C
seg1:
G
267
A
Show more
seg2
seg2:
T
42
C
seg2:
T
48
C
seg2:
A
54
G
seg2:
G
60
T
seg2:
T
75
C
seg2:
T
81
C
seg2:
T
93
G
seg2:
C
138
T
seg2:
C
153
T
seg2:
G
180
A
seg2:
G
195
A
seg2:
A
199
T
seg2:
G
204
A
seg2:
T
207
C
seg2:
A
210
G
seg2:
C
216
T
seg2:
G
228
A
seg2:
C
241
T
Show more
seg3
seg3:
G
81
A
seg3:
A
117
G
seg3:
G
120
A
seg3:
G
144
A
seg3:
A
171
G
seg3:
C
180
T
seg3:
T
189
C
seg3:
G
195
A
seg3:
C
206
T
seg3:
A
207
G
seg3:
A
211
G
seg3:
C
228
A
seg3:
G
249
A
seg3:
A
255
G
seg3:
G
270
A
seg3:
A
277
G
seg3:
A
321
G
seg3:
T
324
C
Show more
seg4
seg4:
A
30
C
seg4:
G
36
A
seg4:
T
39
A
seg4:
C
54
T
seg4:
T
57
C
seg4:
C
63
T
seg4:
C
102
T
seg4:
G
114
A
seg4:
A
123
G
seg4:
T
141
C
seg4:
G
174
A
seg4:
T
183
C
seg4:
C
192
A
seg4:
T
198
C
seg4:
A
207
G
seg4:
T
216
A
seg4:
C
219
G
seg4:
G
225
A
Show more
seg5
seg5:
G
57
A
seg5:
T
72
C
seg5:
G
81
A
seg5:
A
96
G
seg5:
T
111
C
seg5:
G
117
A
seg5:
T
147
C
seg5:
T
153
C
seg5:
G
159
A
seg5:
T
162
C
seg5:
T
165
C
seg5:
A
183
G
seg5:
C
195
T
seg5:
C
198
T
seg5:
T
199
C
seg5:
T
201
C
seg5:
A
207
G
seg5:
T
216
C
Show more
seg6
seg6:
G
35
A
seg6:
T
43
C
seg6:
G
69
A
seg6:
A
78
G
seg6:
T
80
C
seg6:
T
90
C
seg6:
A
92
G
seg6:
C
122
T
seg6:
T
125
C
seg6:
T
134
C
seg6:
G
137
A
seg6:
C
150
T
seg6:
A
155
G
seg6:
G
156
C
seg6:
T
179
C
seg6:
T
185
C
seg6:
A
191
G
seg6:
A
212
G
Show more
seg7
seg7:
A
76
G
seg7:
G
112
A
seg7:
A
127
G
seg7:
C
142
T
seg7:
A
196
G
seg7:
A
205
G
seg7:
G
268
A
seg7:
T
275
C
seg7:
A
279
G
seg7:
A
285
C
seg7:
T
292
C
seg7:
T
301
C
seg7:
T
307
C
seg7:
G
310
A
seg7:
T
316
C
seg7:
C
320
T
seg7:
A
322
G
seg7:
A
327
G
Show more
seg8
seg8:
A
30
T
seg8:
C
34
G
seg8:
T
50
C
seg8:
T
53
C
seg8:
A
55
T
seg8:
A
59
T
seg8:
C
65
T
seg8:
A
66
G
seg8:
A
68
C
seg8:
A
69
C
seg8:
A
71
C
seg8:
G
74
A
seg8:
T
76
G
seg8:
C
78
T
seg8:
T
83
A
seg8:
A
84
C
seg8:
T
85
C
seg8:
G
86
A
Show more
Deletions
seg4:1054-1056, seg8:36-38, seg8:90, seg8:93, seg8:181, seg8:239-242, seg8:494
Insertions
ins_seg8:28:TGT, ins_seg8:510:C, ins_seg8:221:GAGG, ins_seg8:176:G, ins_seg8:79:TG
Amino acid mutations
Substitutions
HA
HA:
K
3
N
HA:
R
69
K
HA:
N
88
R
HA:
K
98
R
HA:
S
100
N
HA:
D
104
G
HA:
D
110
S
HA:
F
111
L
HA:
L
120
M
HA:
T
124
I
HA:
S
139
P
HA:
D
142
E
HA:
A
143
T
HA:
S
145
L
HA:
S
149
A
HA:
H
154
Q
HA:
R
156
A
HA:
S
157
P
Show more
M2
M2:
E
14
G
M2:
K
18
N
M2:
V
28
I
M2:
I
51
V
M2:
R
61
G
M2:
D
88
N
NA
NA:
I
8
T
NA:
V
17
I
NA:
I
20
V
NA:
H
44
Y
NA:
A
46
P
NA:
V
67
I
NA:
N
71
S
NA:
T
76
A
NA:
K
78
Q
NA:
A
81
T
NA:
T
84
A
NA:
V
99
I
NA:
H
100
Y
NA:
H
155
Y
NA:
T
188
I
NA:
M
258
I
NA:
L
269
M
NA:
E
287
D
Show more
NP
NP:
Y
52
H
NP:
V
105
M
NP:
I
119
V
NP:
M
136
L
NP:
A
353
V
NP:
S
450
N
NP:
S
451
A
NP:
E
454
G
NP:
S
482
N
NS2
NS2:
I
6
V
NS2:
T
7
L
NS2:
Q
14
M
NS2:
E
22
G
NS2:
V
26
E
NS2:
R
37
S
NS2:
I
40
L
NS2:
S
48
A
NS2:
M
49
V
NS2:
N
60
S
NS2:
A
63
G
NS2:
T
64
K
NS2:
N
67
G
NS2:
E
68
Q
NS2:
A
81
E
NS2:
C
83
V
NS2:
N
85
H
NS2:
I
86
R
Show more
PAX
PAX:
T
61
M
PAX:
I
63
V
PAX:
T
85
A
PAX:
K
113
R
PAX:
T
129
I
PAX:
S
193
N
PAX:
G
209
E
PAX:
L
210
P
PAX:
S
219
F
PAX:
L
221
R
PAX:
I
222
T
PAX:
N
228
T
PAX:
R
250
Q
PAX:
K
252
R
PB1
PB1:
T
59
S
PB1:
E
75
D
PB1:
K
134
N
PB1:
M
171
V
PB1:
G
177
E
PB1:
M
179
I
PB1:
I
182
T
PB1:
R
430
K
PB1:
E
460
Q
PB1:
T
478
S
PB1:
C
490
F
PB1:
M
535
I
PB1:
D
536
N
PB1:
P
558
T
PB1:
A
587
P
PB1:
P
598
L
PB1:
A
609
V
PB1:
G
610
C
PB1:
G
754
R
PB2
PB2:
V
109
I
PB2:
V
139
I
PB2:
N
334
S
PB2:
K
340
R
PB2:
K
355
R
PB2:
E
362
G
PB2:
D
441
N
PB2:
A
471
T
PB2:
V
478
I
PB2:
V
495
I
PB2:
Q
508
R
PB2:
S
579
P
PB2:
S
590
G
PB2:
P
628
Q
PB2:
M
631
L
PB2:
V
649
I
PB2:
K
670
R
PB2:
T
676
A
Show more
Deletions
HA:344
Insertions
None
Load sequences