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GS_0069FD3.1

Display Name: USA/GS_0069FD3.1/2025-11-02
E. B. Fox, J. M. Garrigues & N. M. Green

Submission details

Submission ID
PX637917.1.seg1/PX637918.1.seg2/PX637919.1.seg3/PX637920.1.seg4/PX637921.1.seg5/PX637922.1.seg6/PX637923.1.seg7/PX637924.1.seg8
Submitting group
Date submitted
2025-12-03 06:33:11 UTC
Date released
2025-12-03 10:39:55 UTC

Authors

Author affiliations
Los Angeles County Public Health Lab microbial pathogen submission group, Los Angeles County Public Health Laboratories

Clade

Clade HA
3C.2a1b.2a.2a.3a.1
Clade NA
B.4.2

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
101
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
108
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
87
Total unknown nucs seg3
0

Alignment states and QC metrics seg4

Completeness seg4
97.87%
Length seg4
1701
Total ambiguous nucs seg4
1
Total deleted nucs seg4
0
Total frame shifts seg4
0
Total inserted nucs seg4
0
Total SNPs seg4
121
Total unknown nucs seg4
0

Alignment states and QC metrics seg5

Completeness seg5
95.53%
Length seg5
1497
Total ambiguous nucs seg5
1
Total deleted nucs seg5
0
Total frame shifts seg5
0
Total inserted nucs seg5
0
Total SNPs seg5
54
Total unknown nucs seg5
0

Alignment states and QC metrics seg6

Completeness seg6
98.19%
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
75
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
26
Total unknown nucs seg7
0

Alignment states and QC metrics seg8

Completeness seg8
96.97%
Length seg8
863
Total ambiguous nucs seg8
0
Total deleted nucs seg8
0
Total frame shifts seg8
0
Total inserted nucs seg8
0
Total SNPs seg8
32
Total unknown nucs seg8
0

Sample details

Collection country
USA
Collection subdivision level 1
California
Collection date
2025-11-02
Isolate name
A/California/LACPHL-INF02052/2025

Host

Host name scientific
Homo sapiens
Host taxon id

INSDC

INSDC accession seg1
INSDC accession seg2
INSDC accession seg3
INSDC accession seg4
INSDC accession seg5
INSDC accession seg6
INSDC accession seg7
INSDC accession seg8
NCBI release date
2025-12-01

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:C54T
  • seg1:G57A
  • seg1:T75C
  • seg1:G87A
  • seg1:C192T
  • seg1:C198T
  • seg1:T255C
  • seg1:A282G
  • seg1:C289A
  • seg1:A336G
  • seg1:G343A
  • seg1:G347A
  • seg1:A369G
  • seg1:G375A
  • seg1:A402G
  • seg1:T417C
  • seg1:T426C
  • seg1:T438C

    • seg2

  • seg2:C46T
  • seg2:G57A
  • seg2:C84A
  • seg2:A129G
  • seg2:A132T
  • seg2:A135G
  • seg2:C141T
  • seg2:T171C
  • seg2:A179G
  • seg2:G180A
  • seg2:A213T
  • seg2:A219G
  • seg2:G258A
  • seg2:C282T
  • seg2:C306T
  • seg2:T327C
  • seg2:G336A
  • seg2:A342T

    • seg3

  • seg3:A99G
  • seg3:A120C
  • seg3:C144T
  • seg3:A156G
  • seg3:T174C
  • seg3:T177C
  • seg3:G210A
  • seg3:T222C
  • seg3:G243A
  • seg3:A324T
  • seg3:A333G
  • seg3:C340T
  • seg3:A342G
  • seg3:A345G
  • seg3:G363A
  • seg3:T369C
  • seg3:A396G
  • seg3:A435G

    • seg4

  • seg4:A24G
  • seg4:T42A
  • seg4:G56T
  • seg4:A71C
  • seg4:C72A
  • seg4:T74A
  • seg4:C77T
  • seg4:C89T
  • seg4:G155A
  • seg4:A163G
  • seg4:C189T
  • seg4:G199A
  • seg4:C203A
  • seg4:C208T
  • seg4:G213A
  • seg4:G214A
  • seg4:G222A
  • seg4:A250G

    • seg5

  • seg5:G81A
  • seg5:G96A
  • seg5:T180G
  • seg5:G207A
  • seg5:G219A
  • seg5:G237A
  • seg5:C249T
  • seg5:A351G
  • seg5:G390A
  • seg5:G432T
  • seg5:G436T
  • seg5:T447C
  • seg5:A451C
  • seg5:C459T
  • seg5:G492A
  • seg5:A513G
  • seg5:T525C
  • seg5:A582C

    • seg6

  • seg6:C36T
  • seg6:C51A
  • seg6:A60G
  • seg6:T88C
  • seg6:T96C
  • seg6:C144T
  • seg6:C205T
  • seg6:T245C
  • seg6:G270A
  • seg6:A280G
  • seg6:A281G
  • seg6:T303C
  • seg6:C345A
  • seg6:C380T
  • seg6:G408A
  • seg6:C429T
  • seg6:G442A
  • seg6:G459A

    • seg7

  • seg7:A37T
  • seg7:C188T
  • seg7:G205A
  • seg7:G214T
  • seg7:A241G
  • seg7:T292C
  • seg7:T298C
  • seg7:A466G
  • seg7:A481G
  • seg7:C493T
  • seg7:A517G
  • seg7:G523A
  • seg7:A637G
  • seg7:A658G
  • seg7:G680A
  • seg7:C697T
  • seg7:T703C
  • seg7:C787T

    • seg8

  • seg8:C53T
  • seg8:G83A
  • seg8:A95T
  • seg8:G102A
  • seg8:A104C
  • seg8:C116T
  • seg8:C123A
  • seg8:T125C
  • seg8:G192T
  • seg8:T205C
  • seg8:T218C
  • seg8:A238G
  • seg8:T271C
  • seg8:C275G
  • seg8:G353A
  • seg8:G398A
  • seg8:G416A
  • seg8:G422A
    • Deletions
    None
    Insertions
    None

    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:K2N
  • HA1:L3I
  • HA1:Q33R
  • HA1:S45N
  • HA1:T48I
  • HA1:G50K
  • HA1:D53N
  • HA1:E62G
  • HA1:K83E
  • HA1:K92R
  • HA1:Y94N
  • HA1:N96S
  • HA1:N121K
  • HA1:T131K
  • HA1:T135K
  • HA1:S138A
  • HA1:R142G
  • HA1:N145S

    • HA2

  • HA2:I32R
  • HA2:N46D
  • HA2:I77V
  • HA2:R121K
  • HA2:G155E
  • HA2:D160N
  • HA2:I193M
  • HA2:V200I

    • M1

  • M1:V219I

    • M2

  • M2:P25L
  • M2:S31N
  • M2:L54F
  • M2:N82S
  • M2:D88A

    • NA

  • NA:L81P
  • NA:N93G
  • NA:P126L
  • NA:D147N
  • NA:V194I
  • NA:I215V
  • NA:K220N
  • NA:E221D
  • NA:S245N
  • NA:S247T
  • NA:H264N
  • NA:T267K
  • NA:L285P
  • NA:V303I
  • NA:Y310H
  • NA:S315R
  • NA:N329S
  • NA:D339N

    • NP

  • NP:A131S
  • NP:I136L
  • NP:V197I
  • NP:R236K
  • NP:T472A

    • NS1

  • NS1:E26N
  • NS1:L33I
  • NS1:A56S
  • NS1:V60A
  • NS1:E71G
  • NS1:V82A
  • NS1:M124I
  • NS1:S135N
  • NS1:D139G
  • NS1:I171V
  • NS1:L185F
  • NS1:K221E
  • NS1:K229E

    • PA

  • PA:N142K
  • PA:I155M
  • PA:K158R
  • PA:S208T
  • PA:K222N
  • PA:K256Q
  • PA:N272S
  • PA:I311M
  • PA:Y321C
  • PA:D382E
  • PA:D396E
  • PA:N409S
  • PA:I421V
  • PA:Y437H
  • PA:I602V
  • PA:K605R
  • PA:V668I
  • PA:N675K

    • PA-X

  • PA-X:N142K
  • PA-X:I155M
  • PA-X:K158R
  • PA-X:E209G
  • PA-X:V212A
  • PA-X:N222T

    • PB1

  • PB1:K52R
  • PB1:V113A
  • PB1:V423I
  • PB1:L576I
  • PB1:R586K
  • PB1:A587T
  • PB1:E618D
  • PB1:N667I
  • PB1:*758Q

    • PB1-F2

  • PB1-F2:E4G
  • PB1-F2:Q5L
  • PB1-F2:D6G
  • PB1-F2:P8L
  • PB1-F2:I18T
  • PB1-F2:R21E
  • PB1-F2:H32L
  • PB1-F2:N34S
  • PB1-F2:S47N
  • PB1-F2:T55I
  • PB1-F2:S63F
  • PB1-F2:V70A
  • PB1-F2:R73K
  • PB1-F2:H75L
  • PB1-F2:S82P
  • PB1-F2:K85R
  • PB1-F2:W88*

    • PB2

  • PB2:A106T
  • PB2:S107N
  • PB2:I147T
  • PB2:E249G
  • PB2:K340R
  • PB2:E341D
  • PB2:K353R
  • PB2:I394V
  • PB2:I451V
  • PB2:V560I
  • PB2:I588T
  • PB2:T613A

    • SigPep

  • SigPep:T3A
  • SigPep:Y9N
    • Deletions
    None
    Insertions
    None