PP_001T5YA.1

Display Name: Kenya/PP_001T5YA.1/2018-02-15
A. W. Lambisia, C. Lewa, M. Mutunga, R. Cheruiyot, D. Okanda, T. Makori, G. Githinji, J. D. Nokes & C. Agoti

Sample details

Collection date
2018-02-15
Country
Kenya
Admin level 1
Kilifi
Isolate name
Kilifi/RSVA/HF20100_15/02/2018

Data use terms

Data use terms
OPEN

Data use terms history

ChangedUserData use terms
2025-05-22 14:42insdc_ingest_userOPEN
Data use terms URL

Lineage

Lineage
A.D.4

Authors

Author affiliations
KEMRI-Wellcome Trust, Epidemiology and Demography

INSDC

INSDC accession
NCBI release date
2023-04-15
NCBI update date
2025-01-14

Host

Host taxon ID
Host name - scientific
Homo sapiens

Alignment and QC metrics

Length
14779
Completeness
96.93%
# of SNPs
168
# of inserted bases
1
# of deleted bases
1
# of ambiguous bases
0
# of unknown bases
22
# of frame shifts
0
# of stop codons
0

Submission details

Submission ID
OQ595330.2
Submitting group
Date submitted
2025-05-22 14:41:42 UTC
Date released
2025-05-22 15:04:05 UTC
Earliest release date
2023-04-15

Nucleotide mutations

Mutations called relative to the PP109421.1 reference

Substitutions

  • T276C
  • C378T
  • T697C
  • C982T
  • A1009G
  • C1012T
  • G1050A
  • A1091G
  • T1215A
  • C1257T
  • C1293T
  • T1359C
  • T1701C
  • C1788T
  • C1806T
  • T2165C
  • A2392G
  • T2481C
    • Deletions
    4592
    Insertions
    ins_3184:N

    Amino acid mutations

    Mutations called relative to the PP109421.1 reference

    Substitutions

    F

  • F:K68E
  • F:T122A

    • G

  • G:A57T
  • G:P71L
  • G:H90Y
  • G:L101F
  • G:I134K
  • G:P206Q
  • G:G224E
  • G:T231A
  • G:S243I
  • G:N251D
  • G:K262E
  • G:I265L
  • G:P276L
  • G:D284G
  • G:Y304H
  • G:E308K
  • G:L310P
  • G:T320I

    • L

  • L:P171L
  • L:Q220H
  • L:R256K
  • L:V335I
  • L:Y598H
  • L:D1183N
  • L:L1438Q
  • L:G1550S
  • L:N1723S
  • L:K1726R
  • L:G1731E
  • L:A1787T

    • M

  • M:L47Q

    • M2-1

  • M2-1:S176P
  • M2-1:S182N

    • M2-2

  • M2-2:Y24C
  • M2-2:S44N

    • N

  • N:V352A

    • P

  • P:L55P
  • P:I63V
    • Deletions
    None
    Insertions
    None

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