PP_000SK6J.1

Display Name: USA/PP_000SK6J.1/2018-09-20
Feriancek, Nicole M.; Breban, Mallery I.; Bourgikos, Ellie; Bransfield, Angela; Armstrong, Philip M.; Vogels, Chantal B.F.; Grubaugh, Nathan D.

Submission details

Submission ID
Yale-WNV0580
Submitting group
Grubaugh Lab
Date submitted
2024-11-06 12:51:04 UTC
Date released
2024-11-06 12:55:45 UTC

Data use terms

Data use terms
OPEN

Data Use Terms History

ChangedUserData Use Terms
2024-11-06 12:51annaparker_curatorOPEN
Data use terms URL
https://pathoplexus.org/about/terms-of-use/open-data

Sequencing

Amplicon PCR primer scheme
WNVUS1
Amplicon size
400bp
Consensus sequence software name
iVar
Consensus sequence software version
v1.3.1
Depth of coverage
10
Quality control method name
iVar trim
Quality control method version
v1.3.1
Raw sequence data processing method
iVar v1.3.1
Sequenced by - contact name
Nicole M Feriancek
Sequenced by
Grubaugh Lab, Yale University, CT, USA
Sequencing date
2024-02-19
Sequencing protocol
COVIDSeq protocol (primers switched)

Authors

Author affiliations
Grubaugh Lab, Yale University, CT, USA

INSDC

Bioproject accession
PRJEB80643
Biosample accession
SAMEA116354776
INSDC accession
OZ201732.1

Sampling

Collection device
Mosquitos trapped using Light Trap
Collection method
mosquito trapping
Purpose of sampling
surveillance for arboviruses
Sample type
pooled blended mosquitoes

Alignment states and QC metrics

Completeness
98.97%
Length
11029
Total ambiguous nucs
2
Total deleted nucs
0
Total frame shifts
0
Total inserted nucs
0
Total SNPs
87
Total stop codons
0
Total unknown nucs
112

Sample details

Collection subdivision level 1
Connecticut
Collection subdivision level 2
New Haven
Collection city
Madison
Collection country
USA
Latitude
41.359615
Longitude
-72.6516
Collection date
2018-09-20
Collection date (lower bound)
2018-09-20
Collection date (upper bound)
2018-09-20
Isolate name
M26L-9-20-Cme

Host

Host name scientific
Culiseta melanura
Host taxon id
329109
Is lab host
False

Lineage

Lineage
1A

Specimen processing

Specimen processing details
Sample consisted of 46 whole, blended mosquitoes from a given trap pooled in groups of up to 50 by species and date

Nucleotide mutations

Substitutions

  • C55T
  • A630G
  • T1368C
  • A1401G
  • T1442C
  • C1465T
  • T1939C
  • T1965C
  • A2097C
  • C2371T
  • C2466T
  • C2593T
  • C2958T
  • T3138C
  • C3504T
  • C3680T
  • C3699T
  • C3702T
    • Deletions
    None
    Insertions
    None

    Amino acid mutations

    Substitutions

    NS2A

  • NS2A:T52I
  • NS2A:L95F
  • NS2A:H119Y

    • NS3

  • NS3:S334T

    • NS4B

  • NS4B:S14I

    • NS5

  • NS5:R422K

    • env

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