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PPD_000SM4L.1

Display Name: USA/PPD_000SM4L.1/2008-07-24
Grubaugh, N.; Matteson, N.; Gangavarupa, K.; Barker, C.; Wheeler, S.; Fang, Y.; Coffey, L.; Reisen, W.; Andersen, K.

Submission details

Submission ID
OQ721660.1
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2025-04-02 07:54:11 UTC
Date released
2025-04-02 08:12:13 UTC

Data use terms

Data use terms
OPEN

Data Use Terms History

ChangedUserData Use Terms
2025-04-02 07:54insdc_ingest_userOPEN
Data use terms URL
https://pathoplexus.org/about/terms-of-use/open-data

Authors

Author affiliations
The Scripps Research Institute, Department of Immunology and Microbiology

INSDC

Bioproject accession
PRJNA472981
INSDC accession
OQ721660.1
NCBI release date
2023-08-02
NCBI update date
2023-08-02

Alignment and QC metrics

Completeness
92.27%
Length
10302
Total ambiguous nucs
0
Total deleted nucs
0
Total frame shifts
0
Total inserted nucs
0
Total SNPs
57
Total stop codons
0
Total unknown nucs
126

Sample details

Earliest release date
2023-08-02
Collection subdivision level 1
Sacramento, California
Collection country
USA
Collection date
2008-07-24
Collection date (lower bound)
2008-07-24
Collection date (upper bound)
2008-07-24

Host

Host name scientific
Culex tarsalis
Host taxon id
7177

Lineage

Lineage
1A

Nucleotide mutations

Mutations called relative to the NC_009942.1 reference

Substitutions

  • C519T
  • A630G
  • C660T
  • G780A
  • C1118T
  • T1442C
  • C1465T
  • C2466T
  • T2572C
  • A3092T
  • C3283T
  • C3570T
  • C3646T
  • C4107T
  • A4146G
  • C4272T
  • T4542C
  • G4573A
    • Deletions
    None
    Insertions
    None

    Amino acid mutations

    Mutations called relative to the NC_009942.1 reference

    Substitutions

    2K

  • 2K:S19G

    • NS1

  • NS1:Y35H
  • NS1:D208V
  • NS1:R272W

    • NS2B

  • NS2B:V119I

    • NS3

  • NS3:S467L

    • NS5

  • NS5:V258A

    • env

  • env:A51V
  • env:V159A
  • env:L167F
    • Deletions
    None
    Insertions
    None

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