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GS_00BC7HR.1
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Display Name: USA/GS_00BC7HR.1/2025-02-10
USDA Swine Surveillance,
A.; Lin,
K.; Dohrn,
C.
Submission details
Submission ID
PV241390.1.seg4/PV241391.1.seg6
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2025-03-07 05:18:14 UTC
Date released
2025-03-07 05:18:45 UTC
Authors
Author affiliations
Iowa State University Veterinary Diagnostic Lab, Bioinformatics
Clade
Clade ha
6B.1A.5a.2a.1
Clade na
C.5.3.1
Alignment states and QC metrics seg4
Completeness seg4
97.09%
Length seg4
1701
Total ambiguous nucs seg4
0
Total deleted nucs seg4
0
Total frame shifts seg4
0
Total inserted nucs seg4
0
Total SNPs seg4
101
Total unknown nucs seg4
0
Alignment states and QC metrics seg6
Completeness seg6
98.39%
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
14
Total unknown nucs seg6
0
Sample details
Collection country
USA
Collection subdivision level 1
Oklahoma
Collection date
2025-02-10
Isolate name
A02858367
Host
Host name scientific
Sus scrofa
Host taxon id
9823
INSDC
INSDC accession seg4
PV241390.1
INSDC accession seg6
PV241391.1
NCBI release date
2025-03-06
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
seg4
seg4:
C
42
A
seg4:
A
47
G
seg4:
G
57
A
seg4:
A
119
G
seg4:
T
161
C
seg4:
C
164
T
seg4:
G
188
A
seg4:
A
231
C
seg4:
C
281
A
seg4:
C
293
G
seg4:
G
322
A
seg4:
G
360
A
seg4:
G
416
A
seg4:
A
429
G
seg4:
C
443
T
seg4:
A
456
G
seg4:
A
461
T
seg4:
C
480
T
Show more
seg6
seg6:
C
301
T
seg6:
C
452
A
seg6:
G
607
A
seg6:
A
785
G
seg6:
T
799
C
seg6:
A
818
G
seg6:
C
893
T
seg6:
G
914
T
seg6:
A
1049
G
seg6:
C
1187
T
seg6:
A
1208
G
seg6:
A
1304
G
seg6:
G
1365
A
seg6:
T
1403
C
Deletions
None
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:
K
54
Q
HA1:
S
74
R
HA1:
S
84
N
HA1:
D
97
N
HA1:
T
120
A
HA1:
N
129
D
HA1:
K
130
N
HA1:
P
137
S
HA1:
K
142
R
HA1:
N
156
K
HA1:
L
161
I
HA1:
S
162
N
HA1:
K
163
Q
HA1:
S
164
T
HA1:
S
183
P
HA1:
S
185
I
HA1:
A
186
T
HA1:
Q
189
E
Show more
HA2
HA2:
E
29
D
HA2:
I
45
V
HA2:
E
47
K
HA2:
I
91
V
HA2:
S
124
H
HA2:
I
133
T
HA2:
E
172
K
HA2:
E
179
D
HA2:
V
193
A
NA
NA:
A
98
V
NA:
S
200
N
NA:
I
264
T
NA:
V
453
M
SigPep
SigPep:
L
8
M
SigPep:
A
13
T
Deletions
None
Insertions
None
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