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_000L289.1

Display Name: USA/LOC_000L289.1/2015-09-03
Grubaugh, N.; Matteson, N.; Gangavarupa, K.; Gurfield, N.; Grewal, S.; Tuncap, J.; Andersen, K.

Submission details

Submission ID
OQ721804.1
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
OQ721804.1
NCBI release date
2023-08-02
NCBI update date
2023-08-02

Alignment states and QC metrics

Completeness
88.96%
Length
10302
Total ambiguous nucs
0
Total deleted nucs
0
Total frame shifts
0
Total inserted nucs
0
Total SNPs
83
Total stop codons
0
Total unknown nucs
491

Sample details

Earliest release date
2023-08-02
Collection subdivision level 1
San Diego, California
Collection country
USA
Collection date
2015-09-03
Collection date (lower bound)
2015-09-03
Collection date (upper bound)
2015-09-03

Host

Host name scientific
Corvus brachyrhynchos
Host taxon id
85066

Lineage

Lineage
1A

Nucleotide mutations

Substitutions

  • A630G
  • C660T
  • G780A
  • T850C
  • G1098A
  • G1185A
  • A1320G
  • T1442C
  • C1465T
  • C1470T
  • G1485A
  • C1773T
  • C1974T
  • C2466T
  • C2574T
  • A2847G
  • T3093C
  • T3399C
    • Deletions
    None
    Insertions
    None

    Amino acid mutations

    Substitutions

    NS1

  • NS1:Q349H

    • NS2A

  • NS2A:I37V
  • NS2A:I39L

    • NS4A

  • NS4A:A85T
  • NS4A:K124R

    • NS5

  • NS5:N306S
  • NS5:K314R
  • NS5:A860T

    • env

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