PP_0010Z00.1

Display Name: Senegal/PP_0010Z00.1/2022-01-01
Sene, O.

Submission details

Submission ID
PP845328.1.L
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2025-01-21 09:55:39 UTC
Date released
2025-01-21 09:56:11 UTC

Data use terms

Data use terms
OPEN

Data Use Terms History

ChangedUserData Use Terms
2025-01-21 09:55insdc_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
99.88%
Length L
12157
Total ambiguous nucs L
12
Total deleted nucs L
0
Total frame shifts L
0
Total inserted nucs L
52
Total SNPs L
288
Total unknown nucs L
0

Sample details

Earliest release date
2025-01-15
Collection country
Senegal
Collection date
2022
Collection date (lower bound)
2022-01-01
Collection date (upper bound)
2022-12-31
Isolate name
SH402092

Host

Host name scientific
Homo sapiens
Host taxon id
9606

INSDC

INSDC accession L
PP845328.1
NCBI release date
2025-01-15

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:T550G
  • L:G553A
    • 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

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