This is a demonstration environment. It may contain non-accurate test data and should not be used for real-world applications. Data will be deleted regularly.

LOC_000P3AY.1

Display Name: Pakistan/LOC_000P3AY.1/2019
Umair, M.; Rehman, Z.; Whitmer, S.; Mobley, M.; Fahim, A.; Ikram, A.; Salman, M.; Montgomery, J. M.; Klena, J. D.; Khurshid, A.; Talundzic, E.; Montgomery, J.; Klena, J.

Submission details

Submission ID
OM162091.1.L/OM162092.1.S
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2025-03-11 18:18:53 UTC
Date released
2025-03-11 18:22:52 UTC

Data use terms

Data use terms
OPEN

Data Use Terms History

ChangedUserData Use Terms
2025-03-11 18:18insdc_ingest_userOPEN
Data use terms URL
https://#TODO-MVP/open

Authors

Author affiliations
CDC, NCEZID-VSPB

Alignment and QC metrics L

Completeness L
99.87%
Frame shifts L
RdRp:792-795(nt:2450-2461)
Length L
12139
Total ambiguous nucs L
0
Total deleted nucs L
10
Total frame shifts L
1
Total inserted nucs L
57
Total SNPs L
1593
Total unknown nucs L
0

Alignment and QC metrics S

Completeness S
98.09%
Length S
1625
Total ambiguous nucs S
0
Total deleted nucs S
16
Total frame shifts S
0
Total inserted nucs S
1
Total SNPs S
204
Total unknown nucs S
0

Sample details

Earliest release date
2024-07-26
Collection country
Pakistan
Collection date
2019
Collection date (lower bound)
2019-01-01
Collection date (upper bound)
2019-12-31
Isolate name
202000293_2792019|Pakistan|2019

Host

Host name scientific
Homo sapiens
Host taxon id
9606

INSDC

INSDC accession L
OM162091.1
INSDC accession S
OM162092.1
NCBI release date
2024-07-26

Nucleotide mutations

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

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

    • S

  • S:T48C
  • S:G54A
  • S:A61G
  • S:C64T
  • S:G67A
  • S:G99A
  • S:A118G
  • S:C142T
  • S:T157C
  • S:C166T
  • S:G169A
  • S:C178A
  • S:T182C
  • S:T199C
  • S:C217T
  • S:G229A
  • S:C235T
  • S:T250A
    • Deletions
    L:2449, L:11920-11924, L:11981, L:11982, L:12068, L:12069, S:1611, S:1612, S:1617-1624, S:1634-1639
    Insertions
    ins_S:1577:A, ins_L:12083:A, ins_L:12064:GG, ins_L:11977:A, ins_L:12054:TACAATTTT, ins_L:11973:A, ins_L:12108:TGTGGGGGGAAC, ins_L:11917:CATTATC, ins_L:12098:TCATGTCCGTTTTATT, ins_L:12085:ATTCAA, ins_L:58:T, ins_L:2461:G

    Amino acid mutations

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

    Substitutions

    NP

  • 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: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

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