This is a demonstration environment. It may contain non-accurate test data and should not be used for real-world applications. Data will be deleted regularly.

LOC_000YNYJ.1

Display Name: France/LOC_000YNYJ.1/2024
M. Gasparine

Sample details

Collection date
2024
Collection date (lower bound)
2024-01-01
Collection date (upper bound)
2024-12-31
Earliest release date
2025-08-10
Collection country
France
Isolate name
ECH

Data use terms

Data use terms
OPEN

Data use terms history

ChangedUserData use terms
2025-10-22 14:40insdc_ingest_userOPEN
Data use terms URL

Authors

Author affiliations
University of Corsica, Unite des Virus Emergents

INSDC

NCBI release date
2025-08-10
INSDC accession L

Host

Host taxon id
Host name scientific
Ixodoidea

Alignment and QC metrics L

Length L
10857
Total SNPs L
669
Total inserted nucs L
82
Total deleted nucs L
92
Total ambiguous nucs L
0
Total unknown nucs L
309
Total frame shifts L
26
Frame shifts L
RdRp:497-590(nt:1563-1846),RdRp:596-617(nt:1862-1926),RdRp:648-657(nt:2016-2046),RdRp:734-797(nt:2274-2467),RdRp:817-1073(nt:2525-3294),RdRp:1098-1107(nt:3368-3397),RdRp:1115-1121(nt:3417-3439),RdRp:1130-1139(nt:3464-3492),RdRp:1162-1168(nt:3558-3580),RdRp:1173-1178(nt:3593-3608),RdRp:1189-1204(nt:3640-3688),RdRp:1216-1269(nt:3722-3883),RdRp:1285-1311(nt:3927-4009),...
Completeness L
87.20%

Submission details

Submission ID
PV976881.1.L
Submitting group
Date submitted
2025-10-22 14:40:13 UTC
Date released
2025-10-22 14:46:33 UTC

Files

Annotations

Nucleotide mutations

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

Substitutions

L

  • L:G1321C
  • L:A1375G
  • L:G1408A
  • L:T1420C
  • L:C1435T
  • L:G1448C
  • L:C1495T
  • L:T1590C
  • L:T1732C
  • L:C1743T
  • L:G1756C
  • L:G1797A
  • L:G1817C
  • L:T1877C
  • L:A1879G
  • L:G1980C
  • L:C2006T
  • L:G2041A
    • Deletions
    L:1562, L:1604, L:1927, L:2015, L:2273, L:2288, L:2468, L:2524, L:2894, L:3295, L:3364-3367, L:3416, L:3440, L:3441, L:3463, L:3476, L:3493, L:3557, L:3812-3814, L:3884-3890, L:3926, L:4010, L:4011, L:4043, L:4061, L:4117, L:4130-4133, L:5045, L:7277, L:7438, L:8696, L:8920, L:8954, L:8955, L:8981, L:9422, L:9443, L:10328, L:10640, L:10641, L:10675, L:10676, L:10769-10772, L:10787,...
    Insertions
    ins_L:1657:C, ins_L:1846:C, ins_L:1861:A, ins_L:2046:G, ins_L:3397:G, ins_L:3580:G, ins_L:3592:TA, ins_L:3608:C, ins_L:3639:CAGA, ins_L:3670:G, ins_L:3688:C, ins_L:3721:T, ins_L:4159:GA, ins_L:4180:C, ins_L:4201:G, ins_L:4250:C, ins_L:4954:AG, ins_L:8650:A, ins_L:8896:GA, ins_L:10690:AG, ins_L:10702:TC, ins_L:10718:G, ins_L:10960:G, ins_L:10998:GC, ins_L:11026:T, ins_L:11041:TGA,...

    Amino acid mutations

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

    Substitutions

    RdRp

  • RdRp:Q415H
  • RdRp:D458H
  • RdRp:R635P
  • RdRp:K673E
  • RdRp:D693N
  • RdRp:S695Q
  • RdRp:R704K
  • RdRp:S724P
  • RdRp:E804K
  • RdRp:K809R
  • RdRp:G812E
  • RdRp:Q815E
  • RdRp:C1079R
  • RdRp:R1081T
  • RdRp:V1087M
  • RdRp:C1091Y
  • RdRp:E1092G
  • RdRp:N1093E
    • Deletions
    RdRp:496, RdRp:647, RdRp:733, RdRp:798, RdRp:1095-1097, RdRp:1114, RdRp:1122, RdRp:1161, RdRp:1270-1272, RdRp:1284, RdRp:1312-1314, RdRp:1323, RdRp:1352, RdRp:1353, RdRp:1657, RdRp:2874, RdRp:3116, RdRp:3123, RdRp:3534, RdRp:3571, RdRp:3593, RdRp:3600, RdRp:3629, RdRp:3897, RdRp:3898
    Insertions
    ins_RdRp:1178:Q, ins_RdRp:1187:YR, ins_RdRp:1391:A, ins_RdRp:3655:E*

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