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_000PE15.1

Display Name: Russia/LOC_000PE15.1/2021
Volynkina, A.; Zhirova, A.; Lisitskaya, Y.; Dedkov, V.; Dolgova, A.; Gladkih, A.

Submission details

Submission ID
PV126634.1.L/PV126633.1.M/PV126632.1.S
Submitting group
Date submitted
2025-04-18 08:49:47 UTC
Date released
2025-04-18 08:54:38 UTC

Data use terms

Data use terms
OPEN

Data Use Terms History

ChangedUserData Use Terms
2025-04-18 08:49insdc_ingest_userOPEN
Data use terms URL

Authors

Author affiliations
St. Petersburg Scientific Research Institute of Epidemiology and Microbiology named after Pasteur, Department of Epidemiology

Alignment and QC metrics L

Completeness L
97.77%
Frame shifts L
RdRp:772-774(nt:2390-2398),RdRp:779(nt:2409-2412),RdRp:3899-3904(nt:11771-11788)
Length L
11838
Total ambiguous nucs L
0
Total deleted nucs L
16
Total frame shifts L
3
Total inserted nucs L
16
Total SNPs L
2444
Total unknown nucs L
0

Alignment and QC metrics M

Completeness M
95.66%
Frame shifts M
GPC:17-19(nt:141-149),GPC:36-51(nt:198-245),GPC:58-60(nt:263-272),GPC:87-93(nt:350-369),GPC:126-133(nt:467-491),GPC:168-171(nt:594-603),GPC:192-194(nt:664-674),GPC:205-206(nt:703-710)
Length M
5061
Total ambiguous nucs M
0
Total deleted nucs M
157
Total frame shifts M
8
Total inserted nucs M
85
Total SNPs M
1258
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
253
Total unknown nucs S
0

Sample details

Earliest release date
2025-03-05
Collection country
Russia
Collection date
2021
Collection date (lower bound)
2021-01-01
Collection date (upper bound)
2021-12-31
Isolate name
622-STV-TI-2021

Host

Host name scientific
Ixodoidea
Host taxon id

INSDC

INSDC accession L
INSDC accession M
INSDC accession S
NCBI release date
2025-03-05

Nucleotide mutations

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

Substitutions

L

  • L:C82G
  • L:C85T
  • L:T86C
  • L:G88A
  • L:C94T
  • L:C100T
  • L:A109G
  • L:G112A
  • L:A113G
  • L:T115G
  • L:A124G
  • L:A126T
  • L:T131A
  • L:C133T
  • L:A135G
  • L:T139G
  • L:T151C
  • L:T154C

    • M

  • M:T15A
  • M:C18A
  • M:A42T
  • M:C43T
  • M:T44C
  • M:A101G
  • M:C103T
  • M:T106G
  • M:A107T
  • M:A108T
  • M:T109G
  • M:G110T
  • M:A112G
  • M:A116C
  • M:G124A
  • M:T127A
  • M:G131A
  • M:G136T

    • S

  • S:C70T
  • S:A72T
  • S:T79C
  • S:A81G
  • S:C82T
  • S:A85G
  • S:G91A
  • S:G99A
  • S:G112A
  • S:C115T
  • S:A121G
  • S:G123T
  • S:T127C
  • S:A130G
  • S:C154T
  • S:T157C
  • S:T163C
  • S:G171A
    • Deletions
    L:1571-1573, L:2369-2374, L:2408, L:2423-2425, L:11777-11779, M:21-36, M:48-57, M:61-97, M:150, M:228-233, M:246-250, M:273-279, M:318-326, M:342-349, M:358-362, M:370-392, M:405-410, M:423-425, M:465, M:466, M:582-584, M:663, M:675-679, M:699-702, M:2636-2641
    Insertions
    ins_M:484:AGCCCGGGGGCGCT, ins_M:140:C, ins_M:194:TCATCC, ins_M:603:TG, ins_M:593:CCTC, ins_M:491:GGACTCACACACCCCCAAGATCC, ins_M:197:CTCA, ins_M:212:C, ins_M:480:AATCAGCTCT, ins_M:710:ACCAGCAAGT, ins_M:262:ATCC, ins_M:2623:TGAAAC, ins_L:1567:GAA, ins_L:11770:T, ins_L:11788:GT, ins_L:2412:GTCG, ins_L:2389:TCTG, ins_L:2398:TG

    Amino acid mutations

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

    Substitutions

    GPC

  • GPC:Y7L
  • GPC:C11Y
  • GPC:L12Q
  • GPC:C15L
  • GPC:G16D
  • GPC:H21N
  • GPC:S23V
  • GPC:E26N
  • GPC:T27I
  • GPC:R28T
  • GPC:H29Y
  • GPC:T32N
  • GPC:D33N
  • GPC:M35S
  • GPC:L56P
  • GPC:D57E
  • GPC:T64S
  • GPC:P66L

    • NP

  • NP:E6V
  • NP:N9S
  • NP:R15K
  • NP:G23V
  • NP:S39N
  • NP:R45K
  • NP:A100T
  • NP:T124A
  • NP:G125S
  • NP:N150S
  • NP:A154S
  • NP:S165P
  • NP:G185S
  • NP:H195R
  • NP:D199E
  • NP:D248E
  • NP:K251R
  • NP:E255D

    • RdRp

  • RdRp:D2E
  • RdRp:I13V
  • RdRp:Y17F
  • RdRp:S19T
  • RdRp:N20S
  • RdRp:Y60H
  • RdRp:S67V
  • RdRp:Y72F
  • RdRp:Q74L
  • RdRp:R80K
  • RdRp:S85D
  • RdRp:L90I
  • RdRp:L94M
  • RdRp:G113N
  • RdRp:I114V
  • RdRp:D135E
  • RdRp:T163N
  • RdRp:A168T
    • Deletions
    GPC:20, GPC:52, GPC:53, GPC:61-63, GPC:84-86, GPC:94-100, GPC:125, GPC:167, GPC:172-183, GPC:191, GPC:195, GPC:196, GPC:203, GPC:204, RdRp:771, RdRp:778
    Insertions
    ins_RdRp:763:NTNS, ins_GPC:7:CCC, ins_GPC:161:ESSTKL, ins_GPC:152:ASTEIEQTSASA, ins_GPC:75:TPLFIX, ins_GPC:193:XDSN

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