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_000LW4P.1

Display Name: USA/LOC_000LW4P.1/2015-11-10
N. Grubaugh, S. Grewal, N. L. Matteson, K. Gangavarapu, N. Gurfield & K. Andersen

Sample details

Collection date
2015-11-10
Collection date (lower bound)
2015-11-10
Collection date (upper bound)
2015-11-10
Earliest release date
2019-01-20
Collection country
USA
Collection subdivision level 1
Carlsbad,California

Data use terms

Data use terms
OPEN

Data use terms history

ChangedUserData use terms
2025-10-13 08:43insdc_ingest_userOPEN
Data use terms URL

Authors

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

INSDC

NCBI release date
2019-01-20
NCBI update date
2019-01-20
INSDC accession
Bioproject accession

Host

Host taxon id
Host name scientific
Aphelocoma

Alignment and QC metrics

Length
10302
Total SNPs
76
Total inserted nucs
0
Total deleted nucs
0
Total ambiguous nucs
0
Total unknown nucs
2
Total frame shifts
0
Completeness
93.39%
Total stop codons
0

Submission details

Submission ID
MH507697.1
Submitting group
Date submitted
2025-10-13 08:43:05 UTC
Date released
2025-10-13 08:58:03 UTC

Lineage

Lineage
1A

Files

Annotations

Nucleotide mutations

Mutations called relative to the NC_009942.1 reference

Substitutions

  • A630G
  • C660T
  • T850C
  • G1098A
  • G1185A
  • A1320G
  • T1442C
  • C1465T
  • C1470T
  • G1485A
  • C1773T
  • C1974T
  • C2466T
  • A2847G
  • T3093C
  • T3399C
  • A3516C
  • A3634G
    • Deletions
    None
    Insertions
    None

    Amino acid mutations

    Mutations called relative to the NC_009942.1 reference

    Substitutions

    NS1

  • NS1:Q349H

    • NS2A

  • NS2A:I37V
  • NS2A:I39L

    • NS3

  • NS3:I209V

    • NS4A

  • NS4A:A85T
  • NS4A:K124R

    • NS5

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

    • env

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

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