PP_001103R.2

Display Name: Senegal/PP_001103R.2/2022-08
O. Sene

Sample details

Collection date
2022-08
Country
Senegal
Isolate name
ARD401180

Data use terms

Data use terms
OPEN

Data use terms history

ChangedUserData use terms
2025-01-22 09:24insdc_ingest_userOPEN
Data use terms URL

Authors

Author affiliations
Institut Pasteur, Dakar, Virology

INSDC

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

Host

Host taxon ID
Host name - scientific
Rhipicephalus senegalensis

Alignment and QC metrics L

Length L
12090
Completeness L
99.85%
# of SNPs L
294
# of inserted bases L
0
# of deleted bases L
0
# of ambiguous bases L
0
# of unknown bases L
0
# of frame shifts L
0
# of stop codons L
0

Alignment and QC metrics M

Length M
5092
Completeness M
94.89%
# of SNPs M
135
# of inserted bases M
0
# of deleted bases M
0
# of ambiguous bases M
0
# of unknown bases M
0
# of frame shifts M
0
# of stop codons M
0

Alignment and QC metrics S

Length S
1569
Completeness S
93.72%
# of SNPs S
126
# of inserted bases S
1
# of deleted bases S
0
# of ambiguous bases S
1
# of unknown bases S
0
# of frame shifts S
0
# of stop codons S
0

Submission details

Submission ID
PP894721.1.L/PP894745.1.M/PP894740.1.S
Submitting group
Date submitted
2025-05-28 14:40:10 UTC
Date released
2025-05-28 14:40:38 UTC
Earliest release date
2025-01-18

Lineage

Segment S Lineage
III

Nucleotide mutations

Mutations called relative to the NC_005301.3, NC_005300.2 & NC_005302.1 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:A178G
  • M:A203G
  • M:C217T
  • M:G236A
  • M:T259C
  • M:C269T
  • M:T301C
  • M:C320T
  • M:T360C
  • M:A377G
  • M:T385C
  • M:C404T
  • M:T406C
  • M:C410T
  • M:G414A
  • M:C426T
  • M:C428T
  • M:C431T

    • S

  • S:G47C
  • S:A50G
  • S:G54A
  • S:G67A
  • S:G99A
  • S:G100A
  • S:C178A
  • S:T181C
  • S:G189A
  • S:T199C
  • S:G202A
  • S:G229A
  • S:C235T
  • S:A247G
  • S:G271A
  • S:C295T
  • S:A298G
  • S:A322G
    • Deletions
    None
    Insertions
    ins_S:1577:A

    Amino acid mutations

    Mutations called relative to the NC_005301.3, NC_005300.2 & NC_005302.1 references

    Substitutions

    GPC

  • GPC:H29R
  • GPC:P42L
  • GPC:L56P
  • GPC:L70S
  • GPC:S90P
  • GPC:V98A
  • GPC:L105S
  • GPC:G108S
  • GPC:P112S
  • GPC:A122T
  • GPC:P123L
  • GPC:N131S
  • GPC:S171P
  • GPC:Q191R
  • GPC:L216P
  • GPC:P226L
  • GPC:H238S
  • GPC:K250E

    • NP

  • NP:R15K
  • NP:R45K
  • NP:K91R
  • NP:T124A
  • NP:G125N
  • NP:L179Q
  • NP:H195R
  • NP:I246V
  • NP:S301G
  • NP:K428R
  • NP:V436I

    • 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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