PP_000RDZ5.2

Display Name: Pakistan/PP_000RDZ5.2/2023-09-25
Umair, M.; Haider, S. A.; Jamal, Z.; Ammar, M.; Hakim, R.; Ali, Q.; Salman, M.

Submission details

Submission ID
OR964929.1.L/OR964940.1.M/OR964918.1.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
99.81%
Frame shifts L
RdRp:792-795(nt:2450-2461)
Length L
12122
Total ambiguous nucs L
0
Total deleted nucs L
5
Total frame shifts L
1
Total inserted nucs L
35
Total SNPs L
1616
Total unknown nucs L
7

Alignment states and QC metrics M

Completeness M
98.29%
Frame shifts M
GPC:724-1685(nt:2262-5147)
Length M
5324
Total ambiguous nucs M
0
Total deleted nucs M
9
Total frame shifts M
1
Total inserted nucs M
11
Total SNPs M
1011
Total unknown nucs M
48

Alignment states and QC metrics S

Completeness S
96.95%
Length S
1630
Total ambiguous nucs S
0
Total deleted nucs S
1
Total frame shifts S
0
Total inserted nucs S
2
Total SNPs S
219
Total unknown nucs S
8

Sample details

Collection country
Pakistan
Collection date
2023-09-25
Isolate name
CCHF/NIHPAK-9/2023

Host

Host name scientific
Homo sapiens
Host taxon id
9606

INSDC

INSDC accession L
OR964929.1
INSDC accession M
OR964940.1
INSDC accession S
OR964918.1
NCBI release date
2023-12-26

Nucleotide mutations

Substitutions

L

  • L:G23T
  • L:A35G
  • L:G43T
  • L:C48T
  • L:T49C
  • L:C63G
  • L:C64T
  • L:T65C
  • L:T66C
  • L:T68C
  • L:G69A
  • L:G71C
  • L:G88A
  • L:G93A
  • L:A109G
  • L:C117A
  • L:A124G
  • L:T131A

    • M

  • M:G50T
  • M:A51G
  • M:G56A
  • M:A57C
  • M:A70G
  • M:T71A
  • M:T72C
  • M:G76T
  • M:A80G
  • M:T83C
  • M:C85T
  • M:T86C
  • M:A90G
  • M:T91C
  • M:C92T
  • M:A93G
  • M:T98C
  • M:T100C

    • S

  • S:A50G
  • S:G54A
  • S:G76A
  • S:T79C
  • S:A85G
  • S:T88C
  • S:G91A
  • S:T106C
  • S:A109G
  • S:A118G
  • S:A121G
  • S:C142A
  • S:T144A
  • S:C145T
  • S:A148G
  • S:C166T
  • S:G169A
  • S:G171A
    • Deletions
    L:2449, L:11980, L:11981, L:12076, L:12083, M:162-164, M:5253-5257, M:5268, S:1532
    Insertions
    ins_S:1545:T, ins_S:1574:T, ins_M:158:CTG, ins_M:5170:G, ins_M:5264:T, ins_M:2915:A, ins_M:5249:GTTG, ins_M:2261:A, ins_L:12096:GTTC, ins_L:12101:CGT, ins_L:12108:TTTC, ins_L:12064:GATTAACCT, ins_L:11977:A, ins_L:12054:TAAAATTTT, ins_L:11973:A, ins_L:2461:G, ins_L:58:T, ins_L:11915:AA

    Amino acid mutations

    Substitutions

    GPC

  • GPC:M1V
  • GPC:I3T
  • GPC:S4L
  • GPC:M6V
  • GPC:I9V
  • GPC:L10F
  • GPC:L12M
  • GPC:C15W
  • GPC:G16S
  • GPC:L17P
  • GPC:E19G
  • GPC:S23L
  • GPC:H24S
  • GPC:R28Q
  • GPC:H29Y
  • GPC:K31S
  • GPC:D33S
  • GPC:T34I

    • NP

  • NP:F30Y
  • NP:S39N
  • NP:V83A
  • NP:S109N
  • NP:D116E
  • NP:T124S
  • NP:G125N
  • NP:D199E
  • NP:V205I
  • NP:I246V
  • NP:S301G
  • NP:A307V
  • NP:E322D
  • NP:Q405L
  • NP:V436I
  • NP:A450S

    • 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:E203D
  • RdRp:S205P
  • RdRp:N206Y
  • RdRp:V214I
  • RdRp:I223V
    • Deletions
    GPC:131-133
    Insertions
    ins_GPC:136:EA, ins_GPC:138:I