GS_00DDL6X.1

Display Name: USA/GS_00DDL6X.1/2025-03-11
Aufderhar, M.; Franzen, K.; Killian, M.; Lantz, K.; Stuber, T.; Hicks, J.; Norris, C.; Lakin, S.

Submission details

Submission ID
PV573278.1.seg1/PV573279.1.seg2/PV573280.1.seg3/PV573281.1.seg4/PV573282.1.seg5/PV573283.1.seg6/PV573284.1.seg7/PV573285.1.seg8
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2025-04-28 18:00:10 UTC
Date released
2025-04-28 18:01:48 UTC

Authors

Author affiliations
USDA Animal Plant Health Inspection Service-National Veterinary Services Laboratories, National Veterinary Services Laboratories

INSDC

Bioproject accession
PRJNA980729
Biosample accession
SAMN47586940
INSDC accession seg1
PV573278.1
INSDC accession seg2
PV573279.1
INSDC accession seg3
PV573280.1
INSDC accession seg4
PV573281.1
INSDC accession seg5
PV573282.1
INSDC accession seg6
PV573283.1
INSDC accession seg7
PV573284.1
INSDC accession seg8
PV573285.1
NCBI release date
2025-04-28
SRA run accession
SRR32868589

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
363
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
212
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
242
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
173
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
174
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
208
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
58
Total unknown nucs seg7
0

Alignment states and QC metrics seg8

Completeness seg8
96.88%
Frame shifts seg8
NS1:23-26(nt:80-92)
Length seg8
838
Total ambiguous nucs seg8
0
Total deleted nucs seg8
2
Total frame shifts seg8
1
Total inserted nucs seg8
2
Total SNPs seg8
246
Total unknown nucs seg8
0

Sample details

Collection country
USA
Collection subdivision level 1
PA
Collection date
2025-03-11
Isolate name
25-008666-003-original

Host

Host name scientific
Gallus gallus
Host taxon id
9031

INSDC seg4

Subtype seg4
H5

INSDC seg6

Subtype seg6
N1

Nucleotide mutations

Mutations called relative to the NC_007357.1, NC_007358.1, NC_007359.1, NC_007362.1, NC_007360.1, NC_007361.1, NC_007363.1 & NC_007364.1 references

Substitutions

seg1

  • seg1:A33G
  • seg1:A48G
  • seg1:G63A
  • seg1:C69T
  • seg1:A90C
  • seg1:G102T
  • seg1:T105C
  • seg1:T108C
  • seg1:A126G
  • seg1:A141G
  • seg1:G147A
  • seg1:T159A
  • seg1:A165G
  • seg1:T192C
  • seg1:A211C
  • seg1:G222A
  • seg1:T228C
  • seg1:G243A

    • seg2

  • seg2:T42C
  • seg2:A70G
  • seg2:T75C
  • seg2:T96C
  • seg2:A129G
  • seg2:C141A
  • seg2:T171C
  • seg2:A177G
  • seg2:G183A
  • seg2:G195A
  • seg2:G204A
  • seg2:T207C
  • seg2:C216T
  • seg2:T225C
  • seg2:G228A
  • seg2:A237G
  • seg2:T252C
  • seg2:T255C

    • seg3

  • seg3:T63C
  • seg3:G120T
  • seg3:A126G
  • seg3:T129C
  • seg3:C132T
  • seg3:G144T
  • seg3:C147T
  • seg3:A150G
  • seg3:A171G
  • seg3:C180T
  • seg3:T183C
  • seg3:C206T
  • seg3:A211G
  • seg3:A213G
  • seg3:C228A
  • seg3:T235C
  • seg3:T238C
  • seg3:A243G

    • seg4

  • seg4:G27A
  • seg4:A30C
  • seg4:G36A
  • seg4:G52A
  • seg4:C54T
  • seg4:T57C
  • seg4:C63T
  • seg4:C102T
  • seg4:A123G
  • seg4:A132G
  • seg4:T141C
  • seg4:T144C
  • seg4:G174A
  • seg4:A175G
  • seg4:T183C
  • seg4:C195T
  • seg4:A207G
  • seg4:C219G

    • seg5

  • seg5:G57A
  • seg5:T72C
  • seg5:G81A
  • seg5:A96G
  • seg5:T111C
  • seg5:G117A
  • seg5:T147C
  • seg5:T153C
  • seg5:G159A
  • seg5:T162C
  • seg5:T165C
  • seg5:A183G
  • seg5:C195T
  • seg5:C198T
  • seg5:T201C
  • seg5:A207G
  • seg5:T216C
  • seg5:G219A

    • seg6

  • seg6:G35A
  • seg6:C47T
  • seg6:T50C
  • seg6:A53G
  • seg6:T62C
  • seg6:G69A
  • seg6:G74A
  • seg6:T80A
  • seg6:C83T
  • seg6:T84C
  • seg6:T90C
  • seg6:G101A
  • seg6:A116C
  • seg6:C122T
  • seg6:G137A
  • seg6:A140T
  • seg6:G143A
  • seg6:T146C

    • seg7

  • seg7:A76G
  • seg7:G112A
  • seg7:C142T
  • seg7:A196G
  • seg7:A205G
  • seg7:G268A
  • seg7:C274T
  • seg7:T275C
  • seg7:T292C
  • seg7:T301C
  • seg7:T307C
  • seg7:T316C
  • seg7:G319A
  • seg7:A322G
  • seg7:A327G
  • seg7:G331A
  • seg7:C332T
  • seg7:A337G

    • seg8

  • seg8:G29T
  • seg8:A30G
  • seg8:A32G
  • seg8:A33T
  • seg8:C35A
  • seg8:T36A
  • seg8:C37G
  • seg8:G38C
  • seg8:T50C
  • seg8:T53C
  • seg8:A55T
  • seg8:A59T
  • seg8:C65T
  • seg8:A66G
  • seg8:A68C
  • seg8:A69C
  • seg8:A71C
  • seg8:G74A
    • Deletions
    seg4:1054-1056, seg8:90, seg8:93
    Insertions
    ins_seg8:79:TG

    Amino acid mutations

    Mutations called relative to the NC_007357.1, NC_007358.1, NC_007359.1, NC_007362.1, NC_007360.1, NC_007361.1, NC_007363.1 & NC_007364.1 references

    Substitutions

    HA

  • HA:K3N
  • HA:V11I
  • HA:T52A
  • HA:R69K
  • HA:N88R
  • HA:K98R
  • HA:S100N
  • HA:D110S
  • HA:F111L
  • HA:T124I
  • HA:Q131L
  • HA:S139P
  • HA:D142E
  • HA:A143T
  • HA:S145L
  • HA:S149A
  • HA:H154Q
  • HA:R156A

    • M1

  • M1:K101R
  • M1:T140A
  • M1:F144L
  • M1:M165I
  • M1:K230R
  • M1:N232D
  • M1:M248L

    • M2

  • M2:E14G
  • M2:K18N
  • M2:V28I
  • M2:I51V

    • NA

  • NA:V17I
  • NA:H44N
  • NA:Q45H
  • NA:A46P
  • NA:P48T
  • NA:I53V
  • NA:V67I
  • NA:F74L
  • NA:L75I
  • NA:T76A
  • NA:K78Q
  • NA:A81D
  • NA:S82P
  • NA:T84A
  • NA:V99I
  • NA:H100Y
  • NA:H155Y
  • NA:T188I

    • NP

  • NP:V105M
  • NP:I109T
  • NP:M136L
  • NP:A353V
  • NP:S450N
  • NP:S451A

    • NS1

  • NS1:I6V
  • NS1:T7S
  • NS1:Y14F
  • NS1:I18V
  • NS1:L21R
  • NS1:L22F
  • NS1:C28G
  • NS1:D33L
  • NS1:A42S
  • NS1:K44R
  • NS1:L54I
  • NS1:R55E
  • NS1:V56T
  • NS1:M59R
  • NS1:E60A
  • NS1:K63Q
  • NS1:D67R
  • NS1:K70E

    • NS2

  • NS2:I6V
  • NS2:T7S
  • NS2:Q14M
  • NS2:E22G
  • NS2:V26E
  • NS2:E36K
  • NS2:R37S
  • NS2:I40L
  • NS2:S48A
  • NS2:M49V
  • NS2:N60S
  • NS2:A63E
  • NS2:T64K
  • NS2:N67G
  • NS2:E68Q
  • NS2:A81E
  • NS2:C83V
  • NS2:N85H

    • PA

  • PA:T61I
  • PA:I63V
  • PA:T129I
  • PA:K139R
  • PA:I145T
  • PA:V201I
  • PA:C212R
  • PA:K228N
  • PA:R269K
  • PA:I322V
  • PA:V323I
  • PA:I348L
  • PA:R361K
  • PA:S388G
  • PA:R391K
  • PA:K399E
  • PA:I465M
  • PA:A475T

    • PAX

  • PAX:T61I
  • PAX:I63V
  • PAX:T129I
  • PAX:K139R
  • PAX:I145T
  • PAX:R195K
  • PAX:G209E
  • PAX:L210P
  • PAX:L221R
  • PAX:I222T
  • PAX:N228T
  • PAX:R250P

    • PB1

  • PB1:N16D
  • PB1:K134N
  • PB1:G154S
  • PB1:E172D
  • PB1:G177E
  • PB1:I182T
  • PB1:K207R
  • PB1:S375N
  • PB1:R430K
  • PB1:E460Q
  • PB1:T478S
  • PB1:C490F
  • PB1:M535I
  • PB1:D536N
  • PB1:P558T
  • PB1:P598L
  • PB1:A609V
  • PB1:G610C

    • PB2

  • PB2:D195E
  • PB2:N334S
  • PB2:K340R
  • PB2:K355R
  • PB2:A471T
  • PB2:V478I
  • PB2:Q508R
  • PB2:S579P
  • PB2:A588S
  • PB2:S590G
  • PB2:P628Q
  • PB2:T637I
  • PB2:R699K
  • PB2:M727G
  • PB2:F741S
    • Deletions
    HA:344, NS1:27
    Insertions
    None