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PPD_000SQPC.1

Display Name: USA/PPD_000SQPC.1/2016-06-22
Grubaugh, N.; Matteson, N.; Gangavarupa, K.; Barker, C.; Wheeler, S.; Fang, Y.; Coffey, L.; Reisen, W.; Andersen, K.

Submission details

Submission ID
OQ721781.1
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
OQ721781.1
NCBI release date
2023-08-02
NCBI update date
2023-08-02

Alignment and QC metrics

Completeness
93.41%
Length
10302
Total ambiguous nucs
0
Total deleted nucs
0
Total frame shifts
0
Total inserted nucs
0
Total SNPs
80
Total stop codons
0
Total unknown nucs
0

Sample details

Earliest release date
2023-08-02
Collection subdivision level 1
Sacramento, California
Collection country
USA
Collection date
2016-06-22
Collection date (lower bound)
2016-06-22
Collection date (upper bound)
2016-06-22

Host

Host name scientific
Euphagus cyanocephalus
Host taxon id
84817

Lineage

Lineage
1A

Nucleotide mutations

Mutations called relative to the NC_009942.1 reference

Substitutions

  • G177A
  • C292T
  • A630G
  • C660T
  • C762T
  • T1442C
  • C1465T
  • A1527G
  • A1791G
  • T1980C
  • C2080T
  • A2205G
  • T2259C
  • C2448T
  • C2466T
  • C2652T
  • C2961T
  • C3159T
    • Deletions
    None
    Insertions
    None

    Amino acid mutations

    Mutations called relative to the NC_009942.1 reference

    Substitutions

    2K

  • 2K:S19G

    • NS4B

  • NS4B:F119L

    • NS5

  • NS5:T25N

    • env

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

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