PP_000RE4V.2

Display Name: France/PP_000RE4V.2/2023-01-01
Picard, C.; Baize, S.

Submission details

Submission ID
PP067063.1.L/PP067076.1.M/PP067048.1.S
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2024-09-26 15:01:57 UTC
Date released
2024-09-26 15:22:15 UTC

Data use terms

Data use terms
OPEN

Data Use Terms History

ChangedUserData Use Terms
2024-08-27 12:11insdc_ingest_userOPEN
Data use terms URL
https://pathoplexus.org/about/terms-of-use/open-data

Authors

Author affiliations
Institut Pasteur, Virology

Alignment and QC metrics L

Completeness L
97.77%
Length L
11838
Total ambiguous nucs L
0
Total deleted nucs L
0
Total frame shifts L
0
Total inserted nucs L
0
Total SNPs L
243
Total unknown nucs L
0

Alignment and QC metrics M

Completeness M
80.79%
Length M
4335
Total ambiguous nucs M
0
Total deleted nucs M
0
Total frame shifts M
0
Total inserted nucs M
0
Total SNPs M
373
Total unknown nucs M
0

Alignment and QC metrics S

Completeness S
86.66%
Length S
1449
Total ambiguous nucs S
0
Total deleted nucs S
0
Total frame shifts S
0
Total inserted nucs S
0
Total SNPs S
107
Total unknown nucs S
0

Sample details

Earliest release date
2024-01-21
Collection country
France
Collection date
2023
Collection date (lower bound)
2023-01-01
Collection date (upper bound)
2023-12-31
Isolate name
12AG9

Host

Host name scientific
Hyalomma marginatum
Host taxon id
34627

INSDC

INSDC accession L
PP067063.1
INSDC accession M
PP067076.1
INSDC accession S
PP067048.1
NCBI release date
2024-01-21

Nucleotide mutations

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

Substitutions

L

  • L:G93A
  • L:A220G
  • L:T254A
  • L:A298G
  • L:C313T
  • L:T340C
  • L:T550A
  • L:G553A
  • L:C568T
  • L:G619A
  • L:C673T
  • L:C727T
  • L:A745G
  • L:G766A
  • L:T781C
  • L:T790C
  • L:C829T
  • L:A859G

    • M

  • M:G818A
  • M:A833G
  • M:A840G
  • M:T860C
  • M:T866C
  • M:T872C
  • M:T887C
  • M:G890C
  • M:T897C
  • M:A899T
  • M:G908A
  • M:A911T
  • M:T938C
  • M:A941G
  • M:G944A
  • M:A955G
  • M:T968C
  • M:C983T

    • S

  • S:G67A
  • S:G99A
  • S:G100A
  • S:C178A
  • S:G189A
  • S:T199C
  • S:G202A
  • S:G229A
  • S:C235T
  • S:A247G
  • S:G271A
  • S:C295T
  • S:A298G
  • S:A322G
  • S:A327G
  • S:G346A
  • S:A358C
  • S:C370T
    • Deletions
    None
    Insertions
    None

    Amino acid mutations

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

    Substitutions

    GPC

  • GPC:K250E
  • GPC:Q273H
  • GPC:K288R
  • GPC:T298A
  • GPC:K302E
  • GPC:P334H
  • GPC:G336K
  • GPC:L337P
  • GPC:E341K
  • GPC:I377V
  • GPC:V385A
  • GPC:V433L
  • GPC:I445A
  • GPC:A448T
  • GPC:Y455H
  • GPC:V459T
  • GPC:D484G
  • GPC:A511V

    • NP

  • NP:R15K
  • NP:R45K
  • NP:K91R
  • NP:T124A
  • NP:G125N
  • NP:L179Q
  • NP:H195R
  • NP:I246V
  • NP:S301G
  • NP:T418I
  • NP:K428R
  • NP:V436I

    • RdRp

  • RdRp:S6N
  • RdRp:Y60N
  • RdRp:I223M
  • RdRp:I261M
  • RdRp:I505T
  • RdRp:T767A
  • RdRp:R770K
  • RdRp:I783V
  • RdRp:K809R
  • RdRp:G812E
  • RdRp:T876S
  • RdRp:D993N
  • RdRp:G1029S
  • RdRp:A1038T
  • RdRp:G1047E
  • RdRp:H1161N
  • RdRp:D1173N
  • RdRp:V1228I
    • Deletions
    None
    Insertions
    None

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