PP_000RE2Z.3

Display Name: France/PP_000RE2Z.3/2023-01-01
Piorkowski, G.; Kiwan, P.; Masse, S.; Ayhan, N.; Charrel, R.; de Lamballerie, X.; Falchi, A.

Submission details

Submission ID
PP025040.1.L/PP025039.1.M/PP025038.1.S
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2024-10-29 17:10:51 UTC
Date released
2024-10-29 17:16:10 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
IHU mediterranee, UMR190 Unite des Virus Emergents U1207

Alignment states and QC metrics L

Completeness L
91.96%
Length L
11246
Total ambiguous nucs L
0
Total deleted nucs L
7
Total frame shifts L
0
Total inserted nucs L
0
Total SNPs L
228
Total unknown nucs L
119

Alignment states and QC metrics M

Completeness M
89.64%
Frame shifts M
GPC:63-70(nt:278-300),GPC:86-106(nt:348-408),GPC:126-130(nt:468-482),GPC:1686(nt:5147)
Length M
5075
Total ambiguous nucs M
0
Total deleted nucs M
155
Total frame shifts M
4
Total inserted nucs M
75
Total SNPs M
1155
Total unknown nucs M
345

Alignment states and QC metrics S

Completeness S
61.30%
Length S
1498
Total ambiguous nucs S
0
Total deleted nucs S
39
Total frame shifts S
0
Total inserted nucs S
17
Total SNPs S
177
Total unknown nucs S
495

Sample details

Collection country
France
Collection date
2023-01-01
Isolate name
1207

Host

Host name scientific
Ixodoidea
Host taxon id
297308

INSDC

INSDC accession L
PP025040.1
INSDC accession M
PP025039.1
INSDC accession S
PP025038.1
NCBI release date
2024-06-25

Nucleotide mutations

Substitutions

L

  • L:A859T
  • L:A901G
  • L:C904T
  • L:G951A
  • L:G961A
  • L:C1015T
  • L:C1016T
  • L:C1019T
  • L:A1120G
  • L:G1174A
  • L:C1240T
  • L:A1338G
  • L:A1354T
  • L:T1420C
  • L:C1495T
  • L:A1501G
  • L:C1549T
  • L:A1555G

    • M

  • M:A203T
  • M:C204G
  • M:G208C
  • M:T209A
  • M:T212A
  • M:G243A
  • M:T246A
  • M:G248C
  • M:T253A
  • M:T254C
  • M:T259C
  • M:T260G
  • M:C263T
  • M:C280A
  • M:C283G
  • M:A284G
  • M:A285T
  • M:T296A

    • S

  • S:C160T
  • S:T163C
  • S:C166T
  • S:G171A
  • S:T172C
  • S:T175G
  • S:C178G
  • S:T181C
  • S:T182C
  • S:G184T
  • S:G196A
  • S:T199C
  • S:C208T
  • S:A209G
  • S:C214A
  • S:G229A
  • S:G232A
  • S:C235T
    • Deletions
    L:12026-12032, M:214-231, M:249-251, M:264-277, M:291, M:292, M:301-305, M:363-365, M:379-386, M:472, M:483, M:555-569, M:5146, M:5153-5178, M:5187-5192, M:5198, M:5199, M:5223-5230, M:5277-5295, M:5306-5309, M:5331-5349, S:1543-1546, S:1564-1572, S:1592-1594, S:1599, S:1608-1611, S:1646-1663
    Insertions
    ins_S:1550:AA, ins_S:1554:T, ins_S:1530:TGTG, ins_S:1533:C, ins_S:1580:A, ins_S:1506:C, ins_S:1512:GTTTTTT, ins_M:347:GAAAT, ins_M:5217:AT, ins_M:5261:GCACCTT, ins_M:5209:AATATT, ins_M:236:CCG, ins_M:403:GCAGGA, ins_M:408:AACCCAAGCACCACGGCTG, ins_M:5244:CA, ins_M:5323:ATG, ins_M:467:TTAGA, ins_M:432:ACACCACAT, ins_M:5242:CTA, ins_M:356:TT, ins_M:454:ACT

    Amino acid mutations

    Substitutions

    GPC

  • GPC:L17A
  • GPC:G18A
  • GPC:H21V
  • GPC:V76S
  • GPC:Y77S
  • GPC:S79D
  • GPC:P81Q
  • GPC:I82T
  • GPC:T84N
  • GPC:G85R
  • GPC:A107N
  • GPC:G119S
  • GPC:T124I
  • GPC:V125L
  • GPC:T135G
  • GPC:P136T
  • GPC:D141T
  • GPC:T142A

    • NP

  • NP:S39N
  • NP:S52G
  • NP:F73Y
  • NP:A100T
  • NP:T124A
  • NP:G125N
  • NP:A154S
  • NP:H195K
  • NP:V198I
  • NP:D199E
  • NP:I220V
  • NP:T420S

    • RdRp

  • RdRp:R292Q
  • RdRp:H314Y
  • RdRp:N421S
  • RdRp:I505T
  • RdRp:C648R
  • RdRp:R764K
  • RdRp:L765P
  • RdRp:T767A
  • RdRp:D771E
  • RdRp:E776K
  • RdRp:K809R
  • RdRp:G812E
  • RdRp:T876S
  • RdRp:R896S
  • RdRp:G1047E
  • RdRp:V1228I
  • RdRp:N1367D
  • RdRp:P1660T
    • Deletions
    GPC:22-62, GPC:71, GPC:108-111, GPC:115, GPC:122, GPC:131, GPC:155-159
    Insertions
    ins_GPC:61:IN, ins_GPC:119:GASTPSNTTSNKPDVNSL