PP_000RDVD.2

Display Name: Pakistan/PP_000RDVD.2/2023-07-14
Umair, M.; Haider, S. A.; Jamal, Z.; Ammar, M.; Hakim, R.; Ali, Q.; Salman, M.

Submission details

Submission ID
OR964925.1.L/OR964936.1.M/OR964914.1.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
97.47%
Frame shifts L
RdRp:792-795(nt:2450-2461)
Length L
12098
Total ambiguous nucs L
0
Total deleted nucs L
12
Total frame shifts L
1
Total inserted nucs L
29
Total SNPs L
1455
Total unknown nucs L
279

Alignment states and QC metrics M

Completeness M
91.09%
Length M
5136
Total ambiguous nucs M
0
Total deleted nucs M
0
Total frame shifts M
0
Total inserted nucs M
0
Total SNPs M
564
Total unknown nucs M
248

Alignment states and QC metrics S

Completeness S
95.04%
Length S
1598
Total ambiguous nucs S
0
Total deleted nucs S
4
Total frame shifts S
0
Total inserted nucs S
5
Total SNPs S
201
Total unknown nucs S
8

Sample details

Collection country
Pakistan
Collection date
2023-07-14
Isolate name
CCHF/NIHPAK-116/2023

Host

Host name scientific
Homo sapiens
Host taxon id
9606

INSDC

INSDC accession L
OR964925.1
INSDC accession M
OR964936.1
INSDC accession S
OR964914.1
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:A69G
  • M:C82T
  • M:C85T
  • M:T86C
  • M:A107G
  • M:A117G
  • M:C119T
  • M:C120T
  • M:T122C
  • M:C126T
  • M:A128G
  • M:G131A
  • M:T137C
  • M:G143A
  • M:A146G
  • M:G147A
  • M:C153A
  • M:T155C

    • S

  • S:A50G
  • S:G54A
  • S:G67A
  • S:T79C
  • S:A81G
  • S:A109G
  • S:A118G
  • S:C166T
  • S:G169A
  • S:T172C
  • S:C178A
  • S:T182C
  • S:G190A
  • S:G196A
  • S:T199C
  • S:C208T
  • S:C217T
  • S:G229A
    • Deletions
    L:2449, L:11920-11924, L:11981, L:11982, L:12034, L:12076, L:12083, L:12099, S:1541-1543, S:1618
    Insertions
    ins_S:1532:CCA, ins_S:1584:C, ins_S:1613:G, ins_L:58:T, ins_L:11917:CATTATC, ins_L:12064:GGTTAACCT, ins_L:11977:A, ins_L:12054:TACAATTTT, ins_L:11973:A, ins_L:2461:G

    Amino acid mutations

    Substitutions

    GPC

  • GPC:I9V
  • GPC:L10F
  • GPC:E19K
  • GPC:H21N
  • GPC:S23P
  • GPC:E26G
  • GPC:R28E
  • GPC:K31N
  • GPC:D33H
  • GPC:T34V
  • GPC:G39D
  • GPC:N41S
  • GPC:P42Q
  • GPC:S44P
  • GPC:S53P
  • GPC:I54V
  • GPC:L56P
  • GPC:T64S

    • NP

  • NP:N9S
  • NP:V83A
  • NP:D116E
  • NP:T124S
  • NP:G125N
  • NP:H195R
  • NP:D199E
  • NP:I246V
  • NP:R270K
  • NP:S301G
  • NP:A307V
  • NP:E322D
  • NP:Q405L
  • NP:K428R
  • NP:V436I

    • RdRp

  • RdRp:S6N
  • RdRp:A14D
  • RdRp:S19T
  • RdRp:Y60N
  • RdRp:R63H
  • RdRp:S67V
  • RdRp:R80K
  • RdRp:V82I
  • RdRp:I114V
  • RdRp:T163A
  • RdRp:A168T
  • RdRp:M172V
  • RdRp:R174K
  • RdRp:S205P
  • RdRp:N206Y
  • RdRp:I223V
  • RdRp:K275R
  • RdRp:I279V
    • Deletions
    None
    Insertions
    None