PP_0015FXD.1

Display Name: Tajikistan/PP_0015FXD.1/2023-07-12
D'Addiego, J.; Mullojanova, M.; Hikmatov, T.; Tishkova, F.; Hewson, R.

Submission details

Submission ID
PV390622.1.L/PV390615.1.M/PV390604.1.S
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2025-04-06 03:03:08 UTC
Date released
2025-04-06 03:03:40 UTC

Data use terms

Data use terms
OPEN

Data Use Terms History

ChangedUserData Use Terms
2025-04-06 03:03insdc_ingest_userOPEN
Data use terms URL
https://pathoplexus.org/about/terms-of-use/open-data

Authors

Author affiliations
UK Health Security Agency, Research & Evaluation

Alignment and QC metrics L

Completeness L
99.58%
Length L
12131
Total ambiguous nucs L
27
Total deleted nucs L
9
Total frame shifts L
0
Total inserted nucs L
55
Total SNPs L
1577
Total unknown nucs L
1

Alignment and QC metrics M

Completeness M
98.57%
Frame shifts M
GPC:38-45(nt:204-227),GPC:164-168(nt:582-595)
Length M
5311
Total ambiguous nucs M
16
Total deleted nucs M
11
Total frame shifts M
2
Total inserted nucs M
12
Total SNPs M
1011
Total unknown nucs M
5

Alignment and QC metrics S

Completeness S
99.88%
Length S
1673
Total ambiguous nucs S
2
Total deleted nucs S
3
Total frame shifts S
0
Total inserted nucs S
4
Total SNPs S
215
Total unknown nucs S
0

Sample details

Earliest release date
2025-04-05
Collection country
Tajikistan
Collection date
2023-07-12
Collection date (lower bound)
2023-07-12
Collection date (upper bound)
2023-07-12
Isolate name
CCHFV_K.Sh.21

Host

Host name scientific
Homo sapiens
Host taxon id
9606

INSDC

INSDC accession L
PV390622.1
INSDC accession M
PV390615.1
INSDC accession S
PV390604.1
NCBI release date
2025-04-05

Nucleotide mutations

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

Substitutions

L

  • L:A35G
  • L:G43C
  • L:C48T
  • L:T49C
  • L:C59T
  • L:C64T
  • L:T65G
  • L:G71T
  • L:A72T
  • L:C85T
  • L:G93A
  • L:C105T
  • L:A109G
  • L:G112A
  • L:T121C
  • L:T131A
  • L:C136T
  • L:C148T

    • M

  • M:A51G
  • M:A70G
  • M:T71A
  • M:A80G
  • M:T83C
  • M:G84T
  • M:C85T
  • M:T86C
  • M:C92T
  • M:C96T
  • M:T98C
  • M:T100C
  • M:T102C
  • M:T105C
  • M:A108T
  • M:A112G
  • M:A116T
  • M:A117G

    • S

  • S:T48C
  • S:G54A
  • S:A61G
  • S:C64T
  • S:G67A
  • S:T79C
  • S:A81G
  • S:G99A
  • S:A118G
  • S:C142T
  • S:T157C
  • S:C166T
  • S:C178A
  • S:T182C
  • S:G190A
  • S:G196A
  • S:C214T
  • S:C217T
    • Deletions
    L:11932-11935, L:11974-11978, M:189-191, M:271-273, M:596-600, S:1575, S:1576, S:1617
    Insertions
    ins_S:1584:AAC, ins_S:1612:C, ins_M:203:GT, ins_M:227:T, ins_M:263:CTT, ins_M:5171:C, ins_M:581:GCAAA, ins_L:11987:T, ins_L:12044:TCTATTTTAGTTCA, ins_L:11922:T, ins_L:12108:GAA, ins_L:12062:C, ins_L:12085:TCATTTAC, ins_L:11995:G, ins_L:12102:AGGGTG, ins_L:11993:CG, ins_L:12095:AGTTTGAT, ins_L:66:CC, ins_L:11924:GTGTG, ins_L:12055:CAT

    Amino acid mutations

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

    Substitutions

    GPC

  • GPC:H2Y
  • GPC:I3T
  • GPC:S4P
  • GPC:M6L
  • GPC:Y7C
  • GPC:I9V
  • GPC:Q13K
  • GPC:C15W
  • GPC:G16S
  • GPC:L17S
  • GPC:G18E
  • GPC:E19G
  • GPC:S23L
  • GPC:H24S
  • GPC:E26G
  • GPC:R28Q
  • GPC:N30S
  • GPC:K31N

    • NP

  • NP:N9S
  • NP:R15K
  • NP:D116E
  • NP:T124A
  • NP:G125N
  • NP:N150H
  • NP:H195R
  • NP:D199E
  • NP:I246V
  • NP:R270K
  • NP:S275N
  • NP:S301G
  • NP:V436I

    • RdRp

  • RdRp:S6N
  • RdRp:T10I
  • RdRp:S19T
  • RdRp:Y60N
  • RdRp:R63H
  • RdRp:S67V
  • RdRp:R80K
  • RdRp:V82I
  • RdRp:L90I
  • RdRp:I114V
  • RdRp:I157M
  • RdRp:T163A
  • RdRp:A168T
  • RdRp:M172V
  • RdRp:R174K
  • RdRp:S205P
  • RdRp:N206Y
  • RdRp:K275R
    • Deletions
    GPC:61-63, GPC:169, GPC:170
    Insertions
    ins_GPC:68:VN, ins_GPC:57:L

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