GenSpectrum
Influenza B/Victoria
Influenza B/Victoria
Influenza A/H1N1pdm
Influenza A/H3N2
Influenza A/H5N1
Influenza A
Influenza B
RSV-A
RSV B
Browse
Loculus
Browse
Docs
API docs
GS_00BTP45.1
Download
Download FASTA
Download metadata TSV
Display Name: USA/GS_00BTP45.1/2024-12-05
Fox,
E. B.; Garrigues,
J. M.; Green,
N. M.
Submission details
Submission ID
PV075218.1.seg1/PV075219.1.seg2/PV075217.1.seg3/PV075213.1.seg4/PV075215.1.seg5/PV075214.1.seg7/PV075216.1.seg8
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2025-03-11 10:32:49 UTC
Date released
2025-03-11 11:06:02 UTC
Authors
Author affiliations
Los Angeles County Public Health Lab microbial pathogen submission group, Los Angeles County Public Health Laboratories
Clade
Clade ha
V1A.3a.2
Alignment states and QC metrics seg3
Completeness seg3
97.15%
Length seg3
2181
Total ambiguous nucs seg3
0
Total deleted nucs seg3
0
Total frame shifts seg3
0
Total inserted nucs seg3
0
Total SNPs seg3
49
Total unknown nucs seg3
0
Alignment states and QC metrics seg4
Completeness seg4
93.26%
Length seg4
1749
Total ambiguous nucs seg4
0
Total deleted nucs seg4
9
Total frame shifts seg4
0
Total inserted nucs seg4
0
Total SNPs seg4
48
Total unknown nucs seg4
0
Alignment states and QC metrics seg5
Completeness seg5
96.17%
Length seg5
1683
Total ambiguous nucs seg5
0
Total deleted nucs seg5
0
Total frame shifts seg5
0
Total inserted nucs seg5
0
Total SNPs seg5
28
Total unknown nucs seg5
0
Alignment states and QC metrics seg7
Completeness seg7
99.30%
Length seg7
1139
Total ambiguous nucs seg7
0
Total deleted nucs seg7
0
Total frame shifts seg7
0
Total inserted nucs seg7
0
Total SNPs seg7
18
Total unknown nucs seg7
0
Alignment states and QC metrics seg8
Completeness seg8
97.00%
Length seg8
1034
Total ambiguous nucs seg8
0
Total deleted nucs seg8
0
Total frame shifts seg8
0
Total inserted nucs seg8
0
Total SNPs seg8
17
Total unknown nucs seg8
0
Sample details
Collection country
USA
Collection subdivision level 1
California
Collection date
2024-12-05
Isolate name
LACPHL-INF01083
Host
Host name scientific
Homo sapiens
Host taxon id
9606
INSDC
INSDC accession seg1
PV075218.1
INSDC accession seg2
PV075219.1
INSDC accession seg3
PV075217.1
INSDC accession seg4
PV075213.1
INSDC accession seg5
PV075215.1
INSDC accession seg7
PV075214.1
INSDC accession seg8
PV075216.1
NCBI release date
2025-02-06
Alignment states and QC metrics seg1
Length seg1
2263
Alignment states and QC metrics seg2
Length seg2
2313
INSDC seg4
Lineage seg4
vic
Nucleotide mutations
Mutations called relative to the
CY115157.1
,
CY115158.1
,
CY115156.1
,
KX058884.1
,
CY115154.1
,
CY073894.1
,
CY115152.1
&
CY115155.1
references
Substitutions
seg3
seg3:
T
111
C
seg3:
C
117
T
seg3:
T
339
C
seg3:
G
414
A
seg3:
T
423
C
seg3:
G
549
A
seg3:
A
618
G
seg3:
T
654
C
seg3:
T
657
C
seg3:
A
771
G
seg3:
C
813
T
seg3:
G
867
A
seg3:
C
897
T
seg3:
C
928
T
seg3:
A
935
G
seg3:
G
936
A
seg3:
A
987
G
seg3:
C
1006
T
Show more
seg4
seg4:
G
144
A
seg4:
A
234
C
seg4:
C
252
A
seg4:
C
270
T
seg4:
G
297
A
seg4:
G
312
T
seg4:
A
318
G
seg4:
A
351
G
seg4:
C
375
T
seg4:
C
378
T
seg4:
A
427
G
seg4:
C
441
T
seg4:
T
444
C
seg4:
G
457
A
seg4:
A
484
G
seg4:
C
509
T
seg4:
T
510
C
seg4:
C
528
A
Show more
seg5
seg5:
T
46
C
seg5:
A
55
G
seg5:
C
178
T
seg5:
C
193
T
seg5:
A
224
G
seg5:
T
298
C
seg5:
C
313
T
seg5:
G
361
A
seg5:
A
373
G
seg5:
C
380
T
seg5:
A
454
G
seg5:
C
523
T
seg5:
C
608
T
seg5:
A
634
G
seg5:
A
763
G
seg5:
C
841
T
seg5:
G
850
A
seg5:
A
883
G
Show more
seg7
seg7:
C
33
T
seg7:
C
46
T
seg7:
T
125
A
seg7:
G
316
A
seg7:
A
419
G
seg7:
G
482
A
seg7:
G
500
T
seg7:
G
521
A
seg7:
G
536
A
seg7:
A
566
G
seg7:
C
656
T
seg7:
A
681
G
seg7:
G
687
T
seg7:
G
698
A
seg7:
G
824
A
seg7:
A
919
G
seg7:
A
967
G
seg7:
A
1079
G
seg8
seg8:
A
118
G
seg8:
T
163
C
seg8:
G
190
A
seg8:
A
195
G
seg8:
T
341
C
seg8:
A
352
C
seg8:
T
391
C
seg8:
C
419
T
seg8:
C
604
T
seg8:
A
610
T
seg8:
C
632
T
seg8:
G
661
A
seg8:
T
775
C
seg8:
C
882
T
seg8:
A
950
G
seg8:
T
963
C
seg8:
A
1016
G
Deletions
seg4:562-570
Insertions
None
Amino acid mutations
Mutations called relative to the
CY115157.1
,
CY115158.1
,
CY115156.1
,
KX058884.1
,
CY115154.1
,
CY073894.1
,
CY115152.1
&
CY115155.1
references
Substitutions
BM2
BM2:
G
26
R
HA1
HA1:
K
52
N
HA1:
I
117
V
HA1:
A
127
T
HA1:
K
136
E
HA1:
P
144
L
HA1:
N
150
K
HA1:
G
184
E
HA1:
N
197
E
HA1:
A
199
T
HA1:
K
203
R
HA1:
R
279
K
HA1:
V
282
I
M1
M1:
T
15
I
M1:
R
105
K
M1:
K
227
E
M1:
V
229
L
NEP
NEP:
L
30
S
NEP:
S
93
P
NP
NP:
I
9
M
NP:
T
66
A
NP:
V
453
A
NP:
N
544
S
NS1
NS1:
K
55
R
NS1:
Y
104
H
NS1:
K
107
N
NS1:
L
130
F
NS1:
H
201
Y
PA
PA:
K
312
R
PA:
T
352
A
PA:
S
530
T
PA:
G
708
A
PA:
F
709
V
PA:
N
714
S
PA:
I
723
V
Deletions
HA1:162-164
Insertions
None
Load sequences