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_000LNJ2.1

Display Name: USA/LOC_000LNJ2.1/2016-08-04
Feriancek, N. M.; Breban, M. I.; Bourgikos, E.; Bransfield, A.; Armstrong, P. M.; Vogels, C. B.; Grubaugh, N. D.

Submission details

Submission ID
OZ201812.1
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2024-12-23 19:43:09 UTC
Date released
2024-12-23 19:51:20 UTC

Data use terms

Data use terms
OPEN

Data Use Terms History

ChangedUserData Use Terms
2024-12-23 19:43insdc_ingest_userOPEN
Data use terms URL
https://#TODO-MVP/open

Authors

Author affiliations
Yale School of Public Health, New Haven, CT

INSDC

Bioproject accession
PRJEB80643
Biosample accession
SAMEA116354239
INSDC accession
OZ201812.1
NCBI release date
2024-11-07
NCBI update date
2024-11-08

Alignment states and QC metrics

Completeness
98.96%
Length
11028
Total ambiguous nucs
3
Total deleted nucs
1
Total frame shifts
0
Total inserted nucs
0
Total SNPs
89
Total stop codons
0
Total unknown nucs
112

Sample details

Earliest release date
2024-11-07
Collection subdivision level 1
Connecticut
Collection country
USA
Collection date
2016-08-04
Collection date (lower bound)
2016-08-04
Collection date (upper bound)
2016-08-04
Isolate name
SM88G-8-4-Cxp-4

Host

Host name scientific
Culex pipiens
Host taxon id
7175

Lineage

Lineage
1A

Nucleotide mutations

Substitutions

  • C340T
  • C435T
  • C456T
  • C474T
  • T585C
  • A630G
  • T928C
  • C1050T
  • T1442C
  • C1465T
  • G1662A
  • T1681C
  • C1750T
  • C2109T
  • C2304T
  • C2466T
  • A2640G
  • T2880C
    • Deletions
    10897
    Insertions
    None

    Amino acid mutations

    Substitutions

    NS2A

  • NS2A:R188K

    • NS4B

  • NS4B:I240M

    • NS5

  • NS5:K76R
  • NS5:S844T

    • env

  • env:V159A
  • env:L167F

    • prM

  • prM:F155L
    • Deletions
    None
    Insertions
    None