This is a demonstration environment. It may contain non-accurate test data and should not be used for real-world applications. Data will be deleted regularly.

LOC_000L27B.1

Display Name: USA/LOC_000L27B.1/2015-01-01
Grubaugh, N.; Matteson, N.; Gangavarupa, K.; Bradway, D.; Wolking, B.; Francis, M.; Andersen, K.

Submission details

Submission ID
OQ721803.1
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2024-12-29 12:39:12 UTC
Date released
2024-12-29 12:46:26 UTC

Data use terms

Data use terms
OPEN

Data Use Terms History

ChangedUserData Use Terms
2024-12-29 12:39insdc_ingest_userOPEN
Data use terms URL
https://#TODO-MVP/open

Authors

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

INSDC

Bioproject accession
PRJNA472981
INSDC accession
OQ721803.1
NCBI release date
2023-08-02
NCBI update date
2023-08-02

Alignment states 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
73
Total stop codons
0
Total unknown nucs
0

Sample details

Earliest release date
2023-08-02
Collection subdivision level 1
Kittitas, Washington
Collection country
USA
Collection date
2015-01-01
Collection date (lower bound)
2015-01-01
Collection date (upper bound)
2015-01-01

Host

Host name scientific
Corvidae
Host taxon id
28725

Lineage

Lineage
1A

Nucleotide mutations

Substitutions

  • G198T
  • A324T
  • C600T
  • A630G
  • C660T
  • G792A
  • T923C
  • A1097G
  • A1320G
  • C1326T
  • A1333G
  • T1442C
  • C1465T
  • C1974T
  • T2103C
  • C2448T
  • C2466T
  • G2661A
    • Deletions
    None
    Insertions
    None

    Amino acid mutations

    Substitutions

    NS2A

  • NS2A:L55I

    • NS4A

  • NS4A:R41K
  • NS4A:A85T

    • NS4B

  • NS4B:V91I
  • NS4B:S94P

    • NS5

  • NS5:K314R
  • NS5:N419K
  • NS5:I520V

    • capsid

  • capsid:M34I

    • env

  • env:K44R
  • env:T123A
  • env:V159A
  • env:L167F

    • prM

  • prM:V153A
    • Deletions
    None
    Insertions
    None