PPD_001RTB1.1

Display Name: Tajikistan/PPD_001RTB1.1/2023-07-12

J. D'Addiego, M. Mullojanova, T. Hikmatov, F. Tishkova & R. Hewson

Sample details

Collection date

2023-07-12

Country

Tajikistan

Isolate name

CCHFV_K.Sh.21

Data use terms

Changed	User	Data use terms
2025-09-17 10:51	insdc_ingest_user	OPEN

OPEN

Data use terms URL

https://pathoplexus.org/about/terms-of-use/open-data

Authors

Author affiliations

UK Health Security Agency, Research & Evaluation

INSDC

INSDC accession L

PV390622.1

INSDC accession M

PV390615.1

INSDC accession S

PV390604.1

NCBI release date

2025-04-05

Host

Host taxon ID

9606

Host name - scientific

Homo sapiens

Alignment and QC metrics L

Length L

12131

# of SNPs L

1577

# of inserted bases L

# of deleted bases L

# of ambiguous bases L

# of unknown bases L

# of frame shifts L

Completeness L

99.58%

Alignment and QC metrics S

Length S

1673

# of SNPs S

215

# of inserted bases S

# of deleted bases S

# of ambiguous bases S

# of unknown bases S

# of frame shifts S

Completeness S

99.88%

Alignment and QC metrics M

Length M

5311

# of SNPs M

1011

# of inserted bases M

# of deleted bases M

# of ambiguous bases M

# of unknown bases M

# of frame shifts M

Frame shifts M

GPC:38-45(nt:204-227),GPC:164-168(nt:582-595)

Completeness M

98.57%

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

2025-09-17 10:51:39 UTC

Date released

2025-09-17 11:10:15 UTC

Earliest 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_L:66:CC, ins_L:11922:T, ins_L:11924:GTGTG, ins_L:11987:T, ins_L:11993:CG, ins_L:11995:G, ins_L:12044:TCTATTTTAGTTCA, ins_L:12055:CAT, ins_L:12062:C, ins_L:12085:TCATTTAC, ins_L:12095:AGTTTGAT, ins_L:12102:AGGGTG, ins_L:12108:GAA, ins_M:203:GT, ins_M:227:T, ins_M:263:CTT, ins_M:581:GCAAA, ins_M:5171:C, ins_S:1584:AAC, ins_S:1612:C

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:57:L, ins_GPC:68:VN

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