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_000L3ND.1

Display Name: USA/LOC_000L3ND.1/2005-08-03
Grubaugh, N.; Matteson, N.; Gangavarupa, K.; Barker, C.; Wheeler, S.; Fang, Y.; Coffey, L.; Reisen, W.; Andersen, K.

Submission details

Submission ID
OQ721851.1
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
OQ721851.1
NCBI release date
2023-08-02
NCBI update date
2023-08-02

Alignment states and QC metrics

Completeness
91.60%
Length
10302
Total ambiguous nucs
0
Total deleted nucs
0
Total frame shifts
0
Total inserted nucs
0
Total SNPs
49
Total stop codons
0
Total unknown nucs
199

Sample details

Earliest release date
2023-08-02
Collection subdivision level 1
Yolo, California
Collection country
USA
Collection date
2005-08-03
Collection date (lower bound)
2005-08-03
Collection date (upper bound)
2005-08-03

Host

Host name scientific
Corvus brachyrhynchos
Host taxon id
85066

Lineage

Lineage
1A

Nucleotide mutations

Substitutions

  • A149G
  • A630G
  • C660T
  • T1236C
  • C1246A
  • T1442C
  • C1465T
  • A2191G
  • C2466T
  • T3186C
  • C3570T
  • C4107T
  • A4146G
  • C4272T
  • T4542C
  • C4803T
  • C4827T
  • T4928C
    • Deletions
    None
    Insertions
    None

    Amino acid mutations

    Substitutions

    2K

  • 2K:S19G

    • NS3

  • NS3:V106A
  • NS3:T436A

    • NS4B

  • NS4B:T221A

    • capsid

  • capsid:K18R

    • env

  • env:Q94K
  • env:V159A
  • env:L167F
  • env:T409A
    • Deletions
    None
    Insertions
    None