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_000PZKH.1

Display Name: Senegal/LOC_000PZKH.1/2022-08
O. Sene, S. N. Sagne, D. Ngom, M. Bocoum, M. K. Diallo, A. Khoule, E. T. Faye, S. M. Diop, I. Diallo, C. Loucoubar, M. Diallo, N. Dia, Y. Sall, B. Diop, M. Ndiaye, A. A. Sall, M. Weidmann, M. M. Diagne, M. Fall, O. Faye, E. Simon-Loriere, D. Diallo, M. A. Barry & G. Fall

Sample details

Collection date
2022-08
Collection date (lower bound)
2022-08-01
Collection date (upper bound)
2022-08-31
Earliest release date
2025-01-18
Collection country
Senegal
Isolate name
ARD401180

Data use terms

Data use terms
OPEN

Data use terms history

ChangedUserData use terms
2026-02-10 15:18insdc_ingest_userOPEN
Data use terms URL

Authors

Author affiliations
Institut Pasteur, Dakar, Virology

INSDC

NCBI release date
2025-01-18
INSDC accession L
INSDC accession M
INSDC accession S

Host

Host taxon id
Host name scientific
Rhipicephalus senegalensis

Alignment and QC metrics L

Length L
12090
Total SNPs L
294
Total inserted nucs L
0
Total deleted nucs L
0
Total ambiguous nucs L
0
Total unknown nucs L
0
Total frame shifts L
0
Completeness L
99.85%
Total stop codons L
0

Alignment and QC metrics M

Length M
5092
Total SNPs M
645
Total inserted nucs M
0
Total deleted nucs M
0
Total ambiguous nucs M
0
Total unknown nucs M
0
Total frame shifts M
0
Completeness M
93.31%
Total stop codons M
0

Alignment and QC metrics S

Length S
1569
Total SNPs S
19
Total inserted nucs S
0
Total deleted nucs S
0
Total ambiguous nucs S
1
Total unknown nucs S
0
Total frame shifts S
0
Completeness S
86.82%
Total stop codons S
0

Submission details

Submission ID
PP894721.1.L/PP894745.1.M/PP894740.1.S
Submitting group
Date submitted
2026-02-10 15:18:07 UTC
Date released
2026-02-10 15:22:07 UTC

Files

Annotations

Nucleotide mutations

Mutations called relative to the NC_005301.3, MH396653.1 & OL774851.1 references

Substitutions

L

  • L:A40G
  • L:T65C
  • L:T70C
  • L:G93A
  • L:G130T
  • L:T151C
  • L:C244T
  • L:T254A
  • L:A280G
  • L:T292C
  • L:A298G
  • L:C313T
  • L:T340C
  • L:A409G
  • L:C427T
  • L:A460G
  • L:T550G
  • L:G553A

    • M

  • M:T78C
  • M:T81C
  • M:C82T
  • M:G103A
  • M:G113A
  • M:T115C
  • M:T116C
  • M:C118T
  • M:T122C
  • M:G124A
  • M:A127G
  • M:C133T
  • M:A139G
  • M:G142A
  • M:A143G
  • M:A149C
  • M:C151T
  • M:C155T

    • S

  • S:T16A
  • S:A98T
  • S:T165C
  • S:A311G
  • S:C327T
  • S:G330A
  • S:C573T
  • S:G765A
  • S:G822A
  • S:T912C
  • S:A945C
  • S:A969T
  • S:C1035T
  • S:A1182T
  • S:C1296T
  • S:T1368C
  • S:G1428A
  • S:C1574T
  • S:T1576C
    • Deletions
    None
    Insertions
    None

    Amino acid mutations

    Mutations called relative to the NC_005301.3, MH396653.1 & OL774851.1 references

    Substitutions

    GPC

  • GPC:V9I
  • GPC:F10L
  • GPC:K19E
  • GPC:N21H
  • GPC:P23S
  • GPC:G26E
  • GPC:E28R
  • GPC:H29R
  • GPC:N31K
  • GPC:H33D
  • GPC:V34T
  • GPC:D39G
  • GPC:S41N
  • GPC:Q42L
  • GPC:P44S
  • GPC:P53S
  • GPC:V54I
  • GPC:S64T

    • NP

  • NP:Y20F
  • NP:K91R

    • RdRp

  • RdRp:S6N
  • RdRp:Y60N
  • RdRp:I505T
  • RdRp:T767A
  • RdRp:K809R
  • RdRp:G812E
  • RdRp:T876S
  • RdRp:A1038T
  • RdRp:G1047E
  • RdRp:V1228I
  • RdRp:N1367D
  • RdRp:N1514S
  • RdRp:M1647L
  • RdRp:P1660T
  • RdRp:T1675N
  • RdRp:R1676K
  • RdRp:I1949V
  • RdRp:I1996V
    • Deletions
    None
    Insertions
    None

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