PP_001102T.1

Display Name: Senegal/PP_001102T.1/2022-08-01
Sene, O.

Submission details

Submission ID
PP894720.1.L
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2025-01-22 09:24:35 UTC
Date released
2025-01-22 09:25:07 UTC

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
https://pathoplexus.org/about/terms-of-use/open-data

Authors

Author affiliations
Institut Pasteur, Dakar, Virology

Alignment and QC metrics L

Completeness L
99.68%
Length L
12121
Total ambiguous nucs L
0
Total deleted nucs L
0
Total frame shifts L
0
Total inserted nucs L
52
Total SNPs L
298
Total unknown nucs L
0

Sample details

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

Host

Host name scientific
Rhipicephalus sulcatus
Host taxon id
669938

INSDC

INSDC accession L
PP894720.1
NCBI 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:A50G
  • 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
  • L:C427T
    • Deletions
    None
    Insertions
    ins_L:12093:ACCATTCATTTCA, ins_L:12096:TCATCGTCATCGTTATTATCTTGGGGTGTGGGGGGAACG

    Amino acid mutations

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

    Substitutions

    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