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_000LX6J.1

Kenya/LOC_000LX6J.1/2023-12-10
T. Wanjiru, S. Langat, H. Koka, S. Yalwala, G. Kerich, J. Ambale, J. Johnson, E. Garges, R. Haynes, G. Kellar, J. Eads & F. Eyase

Jomo Kenyatta University of Science and Technology, Biochemistry

Sample details

Collection date
2023-12-10
Earliest release date
2026-02-07
Sampling location
Kenya (Kilifi)
Isolate name
MAL/S9/44235

Data use terms

Data use terms
OPEN
Data use terms URL

INSDC

NCBI release date
2026-02-07
NCBI update date
2026-03-10
INSDC accession

Host

Host

Submission details

Submission ID
PX619831.1
Submitting group
Date submitted
2026-10-02 14:56:18 UTC
Date released
2026-10-02 15:10:07 UTC

Lineage

Lineage
1A

Files

Annotations

Alignment and QC

Total SNPs
274
Total inserted nucs
40
Total ambiguous nucs
3
Total unknown nucs
4130
Total frame shifts
1
Frame shifts
NS4B:27-33(nt:6992-7014)
Length
11012 (62%)
Amino Acid Mutations from founder clade
  • 2K:L15M
  • NS4A:H40L
  • NS4B:E249D
  • NS5:K177R
  • env:K93R
  • env:H395Y
Variant
True

Nucleotide mutations

Mutations called relative to the NC_009942.1 reference

Substitutions
  • G186A
  • T195A
  • T234C
  • G354A
  • T367C
  • C483T
  • G492A
  • G495T
  • C519T
  • C561T
  • C562T
  • C600T
  • T606C
  • A630G
  • T639C
  • T666C
  • C672T
  • A744T
Deletions
N/A
Insertions
ins_6991:NN, ins_7014:N, ins_10424:CACAAGCATGTATATAGGTATAGNNNNNNNNNNNNN, ins_10462:N

Amino acid substitutions

Substitutions called relative to the NC_009942.1 reference

Substitutions

NS4A

  • NS4A:H40L
  • NS4A:A85V

NS4B

  • NS4B:E249D

env

  • env:I126T
  • env:V159I
  • env:L167F
  • env:H395Y
Deletions
N/A
Insertions

NS4B

ins_NS4B:33:X

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