Display Name: GS_001EGS4.1/2024-11-12
Kirby, M. K.; Steel, J.; Garten, R.; Davis, T.; Dugan, V.; Sheffield, S.; Liddell, J.; Frederick, J. C.; Di, H.; Radford, K.; De La Cruz, J.; Keong, L.; Lacek, K. A.; Shu, B.; Molinar, B.; Wright, C.; Guevara, H.; Pan, C.-Y.; Morales, C.; Wadford, D.

Submission details

Submission ID
PQ686580.1.seg2/PQ686583.1.seg4/PQ686582.1.seg5/PQ686585.1.seg6/PQ686584.1.seg7/PQ686581.1.seg8
Date submitted
2024-12-06 16:08:20 UTC
Date released
2024-12-06 16:08:28 UTC

Data use terms

Data use terms
OPEN

Authors

Author affiliations
Centers for Disease Control and Prevention, WHO Collaborating Center for Surveillance, Epidemiology and Control of Influenza, Influenza Division

INSDC

Bioproject accession
INSDC accession seg2
INSDC accession seg4
INSDC accession seg5
INSDC accession seg6
INSDC accession seg7
INSDC accession seg8
NCBI release date
2024-12-06

Clade

Clade
2.3.4.4b

Alignment states and QC metrics seg2

Completeness seg2
98.42%
Length seg2
2304
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 seg4

Completeness seg4
98.64%
Length seg4
1733
Total ambiguous nucs seg4
0
Total deleted nucs seg4
3
Total frame shifts seg4
0
Total inserted nucs seg4
0
Total SNPs seg4
191
Total unknown nucs seg4
0

Alignment states and QC metrics seg5

Completeness seg5
98.40%
Length seg5
1540
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
96.91%
Length seg6
1413
Total ambiguous nucs seg6
0
Total deleted nucs seg6
0
Total frame shifts seg6
0
Total inserted nucs seg6
0
Total SNPs seg6
149
Total unknown nucs seg6
0

Alignment states and QC metrics seg7

Completeness seg7
97.57%
Length seg7
1002
Total ambiguous nucs seg7
0
Total deleted nucs seg7
0
Total frame shifts seg7
0
Total inserted nucs seg7
0
Total SNPs seg7
64
Total unknown nucs seg7
0

Alignment states and QC metrics seg8

Completeness seg8
100.00%
Length seg8
865
Total ambiguous nucs seg8
0
Total deleted nucs seg8
11
Total frame shifts seg8
0
Total inserted nucs seg8
11
Total SNPs seg8
217
Total unknown nucs seg8
0

Sample details

Collection country
USA
Collection subdivision level 1
California
Collection date
2024-11-12
Isolate name
EPI_ISL_19590706

Host

Host name scientific
Homo sapiens
Host taxon id

Nucleotide mutations

Substitutions

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
  • seg4

  • seg4:A30C
  • 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
  • seg4:G227A
  • seg4:A228G
  • seg5

  • seg5:A40C
  • 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
  • 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:A25G
  • 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
  • seg8

  • seg8:G9A
  • 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
  • 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:V147M
  • HA:S149A
  • HA:H154Q
  • HA:R156A
  • 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:V99I
  • NA:H100Y
  • NA:H155Y
  • NA:T188I
  • NA:M258I
  • NA:L269M
  • NA:E287D
  • NA:T289M
  • NP

  • NP:Y52H
  • NP:V105M
  • NP:I119V
  • NP:M136L
  • NP:A353V
  • NP:S450N
  • NP:S451A
  • 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
  • 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
  • Deletions
    HA:344
    Insertions
    None