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_000L03M.1

Display Name: USA/LOC_000L03M.1/2017-08-03
Grubaugh, N.; Matteson, N.; Gangavarupa, K.; Barker, C.; Wheeler, S.; Fang, Y.; Coffey, L.; Reisen, W.; Andersen, K.

Submission details

Submission ID
OQ721732.1
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
OQ721732.1
NCBI release date
2023-08-02
NCBI update date
2023-08-02

Alignment states and QC metrics

Completeness
91.50%
Length
10302
Total ambiguous nucs
0
Total deleted nucs
0
Total frame shifts
0
Total inserted nucs
0
Total SNPs
104
Total stop codons
0
Total unknown nucs
210

Sample details

Earliest release date
2023-08-02
Collection subdivision level 1
Sacramento, California
Collection country
USA
Collection date
2017-08-03
Collection date (lower bound)
2017-08-03
Collection date (upper bound)
2017-08-03

Lineage

Lineage
1A

Nucleotide mutations

Substitutions

  • T158C
  • T477C
  • A630G
  • C660T
  • C732T
  • T891C
  • C1356T
  • T1442C
  • G1455A
  • C1465T
  • A1566G
  • C1569T
  • T1971C
  • T2250C
  • T2280C
  • C2454T
  • G2742A
  • T3160C
    • Deletions
    None
    Insertions
    None

    Amino acid mutations

    Substitutions

    2K

  • 2K:S19G

    • NS2B

  • NS2B:T34S

    • NS3

  • NS3:I162M
  • NS3:E529D

    • NS4B

  • NS4B:V126I

    • NS5

  • NS5:D438Y

    • capsid

  • capsid:M21T

    • env

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