GS_00EZ5L9.1

Display Name: USA/GS_00EZ5L9.1/2025-07-01
M. Aufderhar, K. Franzen, M. L. Killian, K. Lantz, T. Stuber, J. Hicks, C. Norris & S. Lakin

Submission details

Submission ID
PX104421.1.seg1/PX104422.1.seg2/PX104423.1.seg3/PX104424.1.seg4/PX104425.1.seg5/PX104426.1.seg6/PX104427.1.seg7/PX104428.1.seg8
Submitting group
Date submitted
2025-08-12 17:02:48 UTC
Date released
2025-08-13 07:57:51 UTC

Authors

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

INSDC

Bioproject accession
Biosample accession
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
2025-08-08
SRA run accession

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
366
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
207
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
243
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
171
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
177
Total unknown nucs seg5
0

Alignment states and QC metrics seg6

Completeness seg6
96.71%
Length seg6
1338
Total ambiguous nucs seg6
0
Total deleted nucs seg6
72
Total frame shifts seg6
0
Total inserted nucs seg6
0
Total SNPs seg6
195
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
57
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
244
Total unknown nucs seg8
0

Sample details

Collection country
USA
Collection subdivision level 1
PA
Collection date
2025-07-01
Isolate name
A/Chukar/PA/25-019408-003-original/2025

Host

Host name scientific
Alectoris chukar
Host taxon id

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:A70G
  • seg2:T75C
  • seg2:T96C
  • seg2:A129G
  • seg2:C141A
  • seg2:A177G
  • seg2:G183A
  • seg2:G195A
  • seg2:G204A
  • seg2:T207C
  • seg2:C216T
  • seg2:C220A
  • seg2:T225C
  • seg2:G228A
  • seg2:A237G
  • seg2:T252C
  • seg2:T255C
  • seg2:G258A

    • seg3

  • seg3:T63C
  • seg3:G120T
  • seg3:A126G
  • seg3:T129C
  • seg3:C132T
  • seg3:G144T
  • seg3:C147T
  • seg3:A150G
  • seg3:A171G
  • seg3:C180T
  • seg3:T183C
  • seg3:A184G
  • seg3:C206T
  • seg3:A211G
  • seg3:A213G
  • seg3:C228A
  • seg3:T235C
  • seg3:T238C

    • seg4

  • seg4:G27A
  • seg4:A30C
  • seg4:G36A
  • seg4:G52A
  • seg4:C54T
  • seg4:T57C
  • seg4:C63T
  • seg4:C102T
  • seg4:A123G
  • seg4:T141C
  • seg4:T144C
  • seg4:G174A
  • seg4:A175G
  • seg4:T183C
  • seg4:C195T
  • seg4:A207G
  • seg4:C219G
  • seg4:G225A

    • 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:G38A
  • seg6:C47T
  • seg6:T50C
  • seg6:A53G
  • seg6:T62C
  • seg6:G66A
  • seg6:G69A
  • seg6:G74A
  • seg6:T80A
  • seg6:C83T
  • seg6:T84C
  • seg6:A87G
  • seg6:T90C
  • seg6:G101A
  • seg6:C122T
  • seg6:G137A
  • seg6:A140T

    • 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, seg6:143-214, 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:V16I
  • NA:V17I
  • NA:M23V
  • NA:V67I
  • NA:F74L
  • NA:L75I
  • NA:T76A
  • NA:K78Q
  • NA:A81D
  • NA:S82P
  • NA:T84A
  • NA:V99I
  • NA:H100Y
  • NA:H155Y
  • NA:Y170C
  • NA:T188I
  • NA:N221S
  • NA:V234I

    • NP

  • NP:V105M
  • NP:M136L
  • NP:A146T
  • NP:I316T
  • NP:A353V
  • NP:D375N
  • 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:I54V
  • PA:T61I
  • PA:I63V
  • PA:I120V
  • PA:T129I
  • PA:V201I
  • PA:C212R
  • PA:N222D
  • PA:K228N
  • PA:R269K
  • PA:Y305C
  • PA:I322V
  • PA:V323I
  • PA:I348L
  • PA:R361K
  • PA:S388G
  • PA:R391K
  • PA:K399E

    • PAX

  • PAX:I54V
  • PAX:T61I
  • PAX:I63V
  • PAX:I120V
  • PAX:T129I
  • PAX:R195K
  • PAX:G209E
  • PAX:L210P
  • PAX:L221R
  • PAX:I222T
  • PAX:N228T
  • PAX:R250P

    • PB1

  • PB1:N16D
  • PB1:L66I
  • 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

    • PB2

  • PB2:T106A
  • PB2:N334S
  • PB2:K340R
  • PB2:K355R
  • PB2:I461V
  • PB2:A471T
  • PB2:V478I
  • PB2:Q508R
  • PB2:S579P
  • PB2:S590G
  • PB2:P628Q
  • PB2:R699K
  • PB2:M727G
  • PB2:F741S
    • Deletions
    HA:344, NA:42-65, NS1:27
    Insertions
    None