PP_000R9NX.2

Display Name: Pakistan/PP_000R9NX.2/2022-06-01
Umair, M.; Rehman, Z.; Salman, M.; Ikram, A.; Haider, S. A.; Ammar, M.; Ali, Q.; Hakim, R.; Ansari, S.

Submission details

Submission ID
OP345196.1.L/OP345195.1.M/OP345194.1.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 15:20:44 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 and QC metrics L

Completeness L
97.77%
Frame shifts L
RdRp:792-795(nt:2450-2461)
Length L
11838
Total ambiguous nucs L
0
Total deleted nucs L
1
Total frame shifts L
1
Total inserted nucs L
1
Total SNPs L
1555
Total unknown nucs L
0

Alignment and QC metrics M

Completeness M
94.37%
Length M
5055
Total ambiguous nucs M
0
Total deleted nucs M
9
Total frame shifts M
0
Total inserted nucs M
0
Total SNPs M
620
Total unknown nucs M
0

Alignment and QC metrics S

Completeness S
86.66%
Length S
1449
Total ambiguous nucs S
0
Total deleted nucs S
0
Total frame shifts S
0
Total inserted nucs S
0
Total SNPs S
165
Total unknown nucs S
0

Sample details

Earliest release date
2022-10-02
Collection country
Pakistan
Collection date
2022-06
Collection date (lower bound)
2022-06-01
Collection date (upper bound)
2022-06-30
Isolate name
NIH-04

Host

Host name scientific
Homo sapiens
Host taxon id
9606

INSDC

INSDC accession L
OP345196.1
INSDC accession M
OP345195.1
INSDC accession S
OP345194.1
NCBI release date
2022-10-02

Nucleotide mutations

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

Substitutions

L

  • L:C85T
  • L:G88A
  • L:G93A
  • L:A109G
  • L:C117A
  • L:A124G
  • L:T131A
  • L:T139C
  • L:C148T
  • L:T151C
  • L:T154C
  • L:T160C
  • L:G190A
  • L:C208T
  • L:T229C
  • L:T250C
  • L:T253C
  • L:T254A

    • M

  • M:A107G
  • M:A117G
  • M:C119T
  • M:C120T
  • M:T122C
  • M:A128G
  • M:G131A
  • M:T137C
  • M:G143A
  • M:A146G
  • M:G147A
  • M:C153A
  • M:T155C
  • M:T159C
  • M:A169G
  • M:A170G
  • M:A174G
  • M:G175A

    • S

  • S:G67A
  • S:T79C
  • S:A81G
  • S:G99A
  • 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
  • S:C235T
    • Deletions
    L:2449, M:5145-5153
    Insertions
    ins_L:2461:G

    Amino acid mutations

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

    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:R15K
  • 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: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:N236S
  • RdRp:D264N
    • Deletions
    None
    Insertions
    None

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