PP_00110PJ.1

Display Name: Senegal/PP_00110PJ.1/2022-08
O. Sene

Sample details

Collection date
2022-08
Collection date (lower bound)
2022-08-01
Collection date (upper bound)
2022-08-31
Collection country
Senegal

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

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

Host

Host taxon ID
Host name - scientific
Hyalomma marginatum

Alignment and QC metrics L

Length L
12157
Total SNPs L
300
Total inserted nucs L
52
Total deleted nucs L
0
Total ambiguous nucs L
0
Total unknown nucs L
0
Total frame shifts L
0
Completeness L
99.98%

Alignment and QC metrics M

Length M
5368
Total SNPs M
139
Total inserted nucs M
2
Total deleted nucs M
0
Total ambiguous nucs M
0
Total unknown nucs M
0
Total frame shifts M
0
Completeness M
100.00%

Alignment and QC metrics S

Length S
1673
Total SNPs S
133
Total inserted nucs S
1
Total deleted nucs S
0
Total ambiguous nucs S
0
Total unknown nucs S
0
Total frame shifts S
0
Completeness S
100.00%

Submission details

Submission ID
PP916049.1.L/PP894742.1.M/PP894739.1.S
Submitting group
Date submitted
2025-01-22 09:24:35 UTC
Date released
2025-01-22 09:25:07 UTC
Earliest release date
2025-01-18

Nucleotide mutations

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

Substitutions

L

  • L:T10C
  • L:T62C
  • L:T65C
  • L:T70C
  • L:C75T
  • L:G93A
  • L:C94T
  • L:G130T
  • L:T151C
  • L:C244T
  • L:T254A
  • L:G286A
  • L:A298G
  • L:C313T
  • L:T340C
  • L:C343T
  • L:T382C
  • L:A409G

    • M

  • M:T68C
  • M:A70G
  • M:C194T
  • M:C217T
  • M:T259C
  • M:C269T
  • M:T301C
  • M:C320T
  • M:T360C
  • M:A377G
  • M:T385C
  • M:C426T
  • M:C428T
  • M:C431T
  • M:G456A
  • M:C460T
  • M:A484G
  • M:C581T

    • 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_L:12093:ACCATTCATTTCA, ins_L:12096:TCATCGTCATCGTTATTATCTTGGGGTGTGGGGGGAACG, ins_M:9:GA, 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:P42L
  • GPC:L56P
  • GPC:L70S
  • GPC:S90P
  • GPC:V98A
  • GPC:P112S
  • GPC:A122T
  • GPC:P123L
  • GPC:N131S
  • GPC:S171P
  • GPC:Q191R
  • GPC:L216P
  • GPC:P226L
  • GPC:H238S
  • GPC:K250E
  • GPC:Q273H
  • GPC:G336R
  • GPC:D484N

    • 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

    Report an issue with this sequence or metadata

    Create GitHub issue