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_000P0GP.1

Display Name: Pakistan/LOC_000P0GP.1/2018
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
OM162111.1.L/OM162112.1.S
Submitting group
Date submitted
2025-06-03 04:35:40 UTC
Date released
2025-06-03 04:39:38 UTC

Data use terms

Data use terms
OPEN

Data Use Terms History

ChangedUserData Use Terms
2025-06-03 04:35insdc_ingest_userOPEN
Data use terms URL

Authors

Author affiliations
CDC, NCEZID-VSPB

Alignment and QC metrics L

Completeness L
94.79%
Frame shifts L
RdRp:792-795(nt:2450-2461)
Length L
12114
Total ambiguous nucs L
19
Total deleted nucs L
6
Total frame shifts L
1
Total inserted nucs L
34
Total SNPs L
1552
Total unknown nucs L
590

Alignment and QC metrics S

Completeness S
94.26%
Length S
1537
Total ambiguous nucs S
0
Total deleted nucs S
41
Total frame shifts S
0
Total inserted nucs S
2
Total SNPs S
182
Total unknown nucs S
0

Sample details

Earliest release date
2024-07-26
Collection country
Pakistan
Collection date
2018
Collection date (lower bound)
2018-01-01
Collection date (upper bound)
2018-12-31
Isolate name
202000302_732018|Pakistan|2018

Host

Host name scientific
Homo sapiens
Host taxon id

INSDC

INSDC accession L
INSDC accession S
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:G32A
  • L:A35G
  • L:G43T
  • L:T49C
  • L:C63G
  • L:C64T
  • L:T65C
  • L:T66C
  • L:T68C
  • L:G69A
  • L:G71T
  • L:C85T
  • L:G88A
  • L:G93A
  • L:A109G
  • L:C117A
  • L:A124G

    • S

  • S:A50G
  • S:G54A
  • 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
    • Deletions
    L:2449, L:12034, L:12070-12072, L:12099, S:1530, S:1531, S:1551-1579, S:1584-1593
    Insertions
    ins_S:1538:TA, ins_L:11982:GC, ins_L:58:T, ins_L:12054:TACAATTT, ins_L:2461:G, ins_L:12083:ACTATTC, ins_L:12064:GGT, ins_L:3102:TACTAGNNN, ins_L:684:GNN

    Amino acid mutations

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

    Substitutions

    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: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:N236S
  • RdRp:K275R
  • RdRp:I279V
  • RdRp:R302K
  • RdRp:M303L
    • Deletions
    None
    Insertions
    ins_RdRp:227:X, ins_RdRp:1007:VTT

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