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PPD_0013ZD2.1

Display Name: Senegal/PPD_0013ZD2.1/2022-08
O. Sene

Submission details

Submission ID
PP894725.1.M/PP894733.1.S
Submitting group
Date submitted
2025-07-16 15:07:50 UTC
Date released
2025-07-16 15:23:10 UTC

Data use terms

Data use terms
OPEN

Data Use Terms History

ChangedUserData Use Terms
2025-07-16 15:07insdc_ingest_userOPEN
Data use terms URL

Authors

Author affiliations
Institut Pasteur, Dakar, Virology

Alignment and QC metrics M

Completeness M
98.81%
Length M
5252
Total ambiguous nucs M
0
Total deleted nucs M
50
Total frame shifts M
0
Total inserted nucs M
0
Total SNPs M
149
Total unknown nucs M
0

Alignment and QC metrics S

Completeness S
98.98%
Length S
1656
Total ambiguous nucs S
0
Total deleted nucs S
0
Total frame shifts S
0
Total inserted nucs S
1
Total SNPs S
132
Total unknown nucs S
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
Isolate name
SH401971

Host

Host name - scientific
Homo sapiens
Host taxon ID

INSDC

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

Nucleotide mutations

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

Substitutions

M

  • M:T68C
  • M:A70G
  • M:C194T
  • M:C217T
  • M:T259C
  • M:C269T
  • M:T301C
  • M:C320T
  • M:T360C
  • M:A377G
  • M:T385C
  • M:C404T
  • M:T406C
  • M:C410T
  • M:C412A
  • M:G414A
  • M:C426T
  • M:C428T

    • 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
    M:5271-5320
    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:P42L
  • GPC:L56P
  • GPC:L70S
  • GPC:S90P
  • GPC:V98A
  • GPC:L105S
  • GPC:A107E
  • 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
    • Deletions
    None
    Insertions
    None

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