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_000M10Q.1

Display Name: USA/LOC_000M10Q.1/2006-07-31
N. Grubaugh, Y. Fang, N. L. Matteson, K. Gangavarapu, L. Coffey, C. Barker & K. Andersen

Sample details

Collection date
2006-07-31
Collection date (lower bound)
2006-07-31
Collection date (upper bound)
2006-07-31
Earliest release date
2019-01-20
Collection country
USA
Collection subdivision level 1
Bakersfield,California

Data use terms

Data use terms
OPEN

Data use terms history

ChangedUserData use terms
2025-12-17 18:35insdc_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 californica

Alignment and QC metrics

Length
10302
Total SNPs
55
Total inserted nucs
0
Total deleted nucs
0
Total ambiguous nucs
0
Total unknown nucs
0
Total frame shifts
0
Completeness
93.41%
Total stop codons
0

Submission details

Submission ID
MH507829.1
Submitting group
Date submitted
2025-12-17 18:34:57 UTC
Date released
2025-12-17 18:46:57 UTC

Lineage

Lineage
1A

Files

Annotations

Nucleotide mutations

Mutations called relative to the NC_009942.1 reference

Substitutions

  • G451A
  • A630G
  • C660T
  • C693T
  • T1290C
  • A1320G
  • T1442C
  • C1465T
  • T1890G
  • C1953T
  • T1971C
  • C1974T
  • C2466T
  • A2589G
  • G2631T
  • C2792T
  • T3399C
  • C3693T
    • Deletions
    None
    Insertions
    None

    Amino acid mutations

    Mutations called relative to the NC_009942.1 reference

    Substitutions

    NS1

  • NS1:T108M

    • NS2B

  • NS2B:T34A

    • NS4A

  • NS4A:A85T

    • NS5

  • NS5:R26K
  • NS5:K314R

    • capsid

  • capsid:A119T

    • env

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

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