GS_00DDLM0.1

Display Name: USA/GS_00DDLM0.1/2025-04-03
USDA Swine Surveillance, A.; Lin, K.; Dohrn, C.

Submission details

Submission ID
PV579099.1.seg4/PV579100.1.seg6
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2025-04-30 18:09:49 UTC
Date released
2025-04-30 18:10:16 UTC

Authors

Author affiliations
Iowa State University Veterinary Diagnostic Lab, Bioinformatics

Clade

Clade HA
6

Alignment states and QC metrics seg4

Completeness seg4
97.09%
Length seg4
1695
Total ambiguous nucs seg4
0
Total deleted nucs seg4
6
Total frame shifts seg4
0
Total inserted nucs seg4
0
Total SNPs seg4
275
Total unknown nucs seg4
0

Sample details

Collection country
USA
Collection subdivision level 1
Texas
Collection date
2025-04-03
Isolate name
A02858512

Host

Host name scientific
Sus scrofa
Host taxon id
9823

INSDC

INSDC accession seg4
PV579099.1
INSDC accession seg6
PV579100.1
NCBI release date
2025-04-29

Alignment states and QC metrics seg6

Length seg6
1410

INSDC seg4

Subtype seg4
H1

INSDC seg6

Subtype seg6
N1

Nucleotide mutations

Mutations called relative to the NC_026438.1, NC_026435.1, NC_026437.1, CY121680.1, NC_026436.1, MW626056.1, NC_026431.1 & NC_026432.1 references

Substitutions

seg4

  • seg4:A35G
  • seg4:G36T
  • seg4:A38G
  • seg4:T41C
  • seg4:C42T
  • seg4:T48C
  • seg4:T54C
  • seg4:T78A
  • seg4:A110T
  • seg4:C113T
  • seg4:A119T
  • seg4:C122T
  • seg4:A128G
  • seg4:C129T
  • seg4:A134G
  • seg4:T161C
  • seg4:G179A
  • seg4:C185T
    • Deletions
    seg4:450-455
    Insertions
    None

    Amino acid mutations

    Mutations called relative to the NC_026438.1, NC_026435.1, NC_026437.1, CY121680.1, NC_026436.1, MW626056.1, NC_026431.1 & NC_026432.1 references

    Substitutions

    HA1

  • HA1:L3I
  • HA1:R45G
  • HA1:V47K
  • HA1:A48S
  • HA1:H51Y
  • HA1:I61L
  • HA1:S69P
  • HA1:L70I
  • HA1:S71L
  • HA1:A73V
  • HA1:P83S
  • HA1:S84N
  • HA1:D94S
  • HA1:I96T
  • HA1:D97N
  • HA1:R113K
  • HA1:K119T
  • HA1:T120E

    • HA2

  • HA2:E29D
  • HA2:L38Q
  • HA2:N43R
  • HA2:E47G
  • HA2:H72N
  • HA2:K75R
  • HA2:K82R
  • HA2:Y110F
  • HA2:S124N
  • HA2:K127R
  • HA2:D158N
  • HA2:P160L
  • HA2:A166S
  • HA2:E179D
  • HA2:I183V
  • HA2:L199I
  • HA2:V200L
  • HA2:I206L

    • SigPep

  • SigPep:V6L
  • SigPep:Y10H
  • SigPep:F12L
    • Deletions
    HA1:126, HA1:127
    Insertions
    None