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Display Name: GS_001EHQ7.1/2024-10-10
Aufderhar, M.; Franzen, K.; Killian, M.; Lantz, K.; Stuber, T.; Hicks, J.; Norris, C.; Lakin, S.

Submission details

Submission ID
PQ687300.1.seg1/PQ687301.1.seg2/PQ687302.1.seg3/PQ687303.1.seg4/PQ687304.1.seg5/PQ687305.1.seg6/PQ687306.1.seg7/PQ687307.1.seg8
Date submitted
2024-12-11 16:47:38 UTC
Date released
2024-12-11 17:24:58 UTC

Data use terms

Data use terms
OPEN

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
2024-12-06
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
362
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
270
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
162
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
188
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
182
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
150
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
63
Total unknown nucs seg7
0

Alignment states and QC metrics seg8

Completeness seg8
96.88%
Length seg8
838
Total ambiguous nucs seg8
0
Total deleted nucs seg8
11
Total frame shifts seg8
0
Total inserted nucs seg8
11
Total SNPs seg8
215
Total unknown nucs seg8
0

Sample details

Collection country
USA
Collection subdivision level 1
CA
Collection date
2024-10-10
Isolate name
24-030318-003-original

Host

Host name scientific
Bos taurus
Host taxon id

Nucleotide mutations

Substitutions

seg1

  • seg1:A33G
  • seg1:A48G
  • seg1:G63A
  • seg1:C69T
  • seg1:A90C
  • seg1:G102T
  • seg1:T105C
  • seg1:T108C
  • seg1:A126G
  • seg1:G147A
  • seg1:T159A
  • seg1:A211C
  • seg1:G222A
  • seg1:T228C
  • seg1:G243A
  • seg1:G255C
  • seg1:T258C
  • seg1:G267A
  • seg2

  • seg2:T42C
  • seg2:T48C
  • seg2:A54G
  • seg2:G60T
  • seg2:T75C
  • seg2:T81C
  • seg2:T93G
  • seg2:C138T
  • seg2:C153T
  • seg2:G180A
  • seg2:G195A
  • seg2:A199T
  • seg2:G204A
  • seg2:T207C
  • seg2:A210G
  • seg2:C216T
  • seg2:G228A
  • seg2:C241T
  • seg3

  • seg3:G81A
  • seg3:A117G
  • seg3:G120A
  • seg3:G144A
  • seg3:A171G
  • seg3:C180T
  • seg3:T189C
  • seg3:G195A
  • seg3:C206T
  • seg3:A207G
  • seg3:A211G
  • seg3:C228A
  • seg3:G249A
  • seg3:A255G
  • seg3:G270A
  • seg3:A277G
  • seg3:A321G
  • seg3:T324C
  • seg4

  • seg4:A30C
  • seg4:G36A
  • seg4:T39A
  • seg4:C54T
  • seg4:T57C
  • seg4:C63T
  • seg4:C102T
  • seg4:G114A
  • seg4:A123G
  • seg4:T141C
  • seg4:G174A
  • seg4:T183C
  • seg4:C192A
  • seg4:T198C
  • seg4:A207G
  • seg4:T216A
  • 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:T199C
  • seg5:T201C
  • seg5:A207G
  • seg5:T216C
  • seg6

  • seg6:G35A
  • seg6:T43C
  • seg6:G69A
  • seg6:A78G
  • seg6:T80C
  • seg6:T90C
  • seg6:A92G
  • seg6:C122T
  • seg6:T125C
  • seg6:T134C
  • seg6:G137A
  • seg6:C150T
  • seg6:A155G
  • seg6:G156C
  • seg6:T179C
  • seg6:T185C
  • seg6:A191G
  • seg6:A212G
  • seg7

  • seg7:A76G
  • seg7:G112A
  • seg7:A127G
  • seg7:C142T
  • seg7:A196G
  • seg7:A205G
  • seg7:G268A
  • seg7:T275C
  • seg7:A279G
  • seg7:A285C
  • seg7:T292C
  • seg7:T301C
  • seg7:T307C
  • seg7:G310A
  • seg7:T316C
  • seg7:C320T
  • seg7:A322G
  • seg7:A327G
  • seg8

  • seg8:A30T
  • seg8:C34G
  • seg8:T50C
  • seg8:T53C
  • seg8:A55T
  • seg8:A59T
  • seg8:C65T
  • seg8:A66G
  • seg8:A68C
  • seg8:A69C
  • seg8:A71C
  • seg8:G74A
  • seg8:T76G
  • seg8:C78T
  • seg8:T83A
  • seg8:A84C
  • seg8:T85C
  • seg8:G86A
  • Deletions
    seg4:1054-1056, seg8:36-38, seg8:90, seg8:93, seg8:181, seg8:239-242, seg8:494
    Insertions
    ins_seg8:28:TGT, ins_seg8:510:C, ins_seg8:221:GAGG, ins_seg8:176:G, ins_seg8:79:TG

    Amino acid mutations

    Substitutions

    HA

  • HA:K3N
  • HA:R69K
  • HA:N88R
  • HA:K98R
  • HA:S100N
  • HA:D104G
  • HA:D110S
  • HA:F111L
  • HA:L120M
  • HA:T124I
  • HA:S139P
  • HA:D142E
  • HA:A143T
  • HA:S145L
  • HA:S149A
  • HA:H154Q
  • HA:R156A
  • HA:S157P
  • M2

  • M2:E14G
  • M2:K18N
  • M2:V28I
  • M2:I51V
  • M2:R61G
  • M2:D88N
  • NA

  • NA:I8T
  • NA:V17I
  • NA:I20V
  • NA:H44Y
  • NA:A46P
  • NA:V67I
  • NA:N71S
  • NA:T76A
  • NA:K78Q
  • NA:A81T
  • NA:T84A
  • NA:V99I
  • NA:H100Y
  • NA:H155Y
  • NA:T188I
  • NA:M258I
  • NA:L269M
  • NA:E287D
  • NP

  • NP:Y52H
  • NP:V105M
  • NP:I119V
  • NP:M136L
  • NP:A353V
  • NP:S450N
  • NP:S451A
  • NP:E454G
  • NP:S482N
  • NS2

  • NS2:I6V
  • NS2:T7L
  • NS2:Q14M
  • NS2:E22G
  • NS2:V26E
  • NS2:R37S
  • NS2:I40L
  • NS2:S48A
  • NS2:M49V
  • NS2:N60S
  • NS2:A63G
  • NS2:T64K
  • NS2:N67G
  • NS2:E68Q
  • NS2:A81E
  • NS2:C83V
  • NS2:N85H
  • NS2:I86R
  • PAX

  • PAX:T61M
  • PAX:I63V
  • PAX:T85A
  • PAX:K113R
  • PAX:T129I
  • PAX:S193N
  • PAX:G209E
  • PAX:L210P
  • PAX:S219F
  • PAX:L221R
  • PAX:I222T
  • PAX:N228T
  • PAX:R250Q
  • PAX:K252R
  • PB1

  • PB1:T59S
  • PB1:E75D
  • PB1:K134N
  • PB1:M171V
  • PB1:G177E
  • PB1:M179I
  • PB1:I182T
  • PB1:R430K
  • PB1:E460Q
  • PB1:T478S
  • PB1:C490F
  • PB1:M535I
  • PB1:D536N
  • PB1:P558T
  • PB1:A587P
  • PB1:P598L
  • PB1:A609V
  • PB1:G610C
  • PB1:G754R
  • PB2

  • PB2:V109I
  • PB2:V139I
  • PB2:N334S
  • PB2:K340R
  • PB2:K355R
  • PB2:E362G
  • PB2:D441N
  • PB2:A471T
  • PB2:V478I
  • PB2:V495I
  • PB2:Q508R
  • PB2:S579P
  • PB2:S590G
  • PB2:P628Q
  • PB2:M631L
  • PB2:V649I
  • PB2:K670R
  • PB2:T676A
  • Deletions
    HA:344
    Insertions
    None