PP_000RDUF.2

Display Name: Pakistan/PP_000RDUF.2/2023-05-01
Umair, M.; Haider, S. A.; Jamal, Z.; Ammar, M.; Hakim, R.; Ali, Q.; Salman, M.

Submission details

Submission ID
OR964924.1.L/OR964935.1.M/OR964913.1.S
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2024-09-26 15:01:57 UTC
Date released
2024-09-26 15:22:15 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
National Institute of Health, Department of Virology

Alignment states and QC metrics L

Completeness L
99.86%
Frame shifts L
RdRp:792-795(nt:2450-2461)
Length L
12134
Total ambiguous nucs L
0
Total deleted nucs L
10
Total frame shifts L
1
Total inserted nucs L
52
Total SNPs L
1636
Total unknown nucs L
1

Alignment states and QC metrics M

Completeness M
97.07%
Length M
5336
Total ambiguous nucs M
0
Total deleted nucs M
0
Total frame shifts M
0
Total inserted nucs M
1
Total SNPs M
990
Total unknown nucs M
126

Alignment states and QC metrics S

Completeness S
98.98%
Length S
1656
Total ambiguous nucs S
0
Total deleted nucs S
0
Total frame shifts S
0
Total inserted nucs S
1
Total SNPs S
211
Total unknown nucs S
0

Sample details

Collection country
Pakistan
Collection date
2023-05-01
Isolate name
CCHF/NIHPAK-30/2023

Host

Host name scientific
Homo sapiens
Host taxon id
9606

INSDC

INSDC accession L
OR964924.1
INSDC accession M
OR964935.1
INSDC accession S
OR964913.1
NCBI release date
2023-12-26

Nucleotide mutations

Substitutions

L

  • L:G23T
  • L:A35G
  • L:G43T
  • L:T49C
  • L:C63G
  • L:C64T
  • L:T65C
  • L:T66C
  • L:T68C
  • L:G69A
  • L:G71C
  • L:C85T
  • L:G88A
  • L:G93A
  • L:A109G
  • L:C117A
  • L:A124G
  • L:T131A

    • M

  • M:G50T
  • M:G56A
  • M:A57C
  • 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:A108C
  • M:A112G

    • S

  • S:T48C
  • S:G54A
  • S:A55G
  • S:A61G
  • S:C64T
  • S:G67A
  • S:A85G
  • S:G91A
  • S:G99A
  • S:T157C
  • S:C166T
  • S:C178A
  • S:C187T
  • S:G190A
  • S:G196A
  • S:A209G
  • S:C214T
  • S:C217T
    • Deletions
    L:2449, L:11920-11924, L:12058, L:12059, L:12076, L:12083
    Insertions
    ins_S:1577:A, ins_M:5171:C, ins_L:12108:TGTGGGGG, ins_L:12098:TCATGTCCGTTTTATT, ins_L:58:T, ins_L:11917:CATTATC, ins_L:12064:GGTTAACCT, ins_L:12054:TACAATTTCT, ins_L:2461:G

    Amino acid mutations

    Substitutions

    GPC

  • GPC:H2Y
  • GPC:I3T
  • GPC:S4P
  • GPC:M6L
  • GPC:Y7C
  • GPC:I9V
  • GPC:Q13K
  • GPC:C15W
  • GPC:G16S
  • GPC:E19G
  • GPC:T20A
  • GPC:S23P
  • GPC:H24S
  • GPC:R28Q
  • GPC:N30S
  • GPC:K31N
  • GPC:T32A
  • GPC:D33S

    • NP

  • NP:R15K
  • NP:S52G
  • NP:S65A
  • 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:A14D
  • RdRp:S19T
  • RdRp:Y60N
  • RdRp:R63H
  • RdRp:S67V
  • RdRp:R80K
  • RdRp:V82I
  • RdRp:L94Q
  • RdRp:I114V
  • RdRp:T163A
  • RdRp:A168T
  • RdRp:M172V
  • RdRp:R174K
  • RdRp:S205P
  • RdRp:N206C
  • RdRp:I223V
  • RdRp:N236S
    • Deletions
    None
    Insertions
    None