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_000P9YF.1

Display Name: Pakistan/LOC_000P9YF.1/2017-10-13
A. Zohaib, M. Saqib, M. A. Athar, M. H. Hussain, A. U. Sial, M. H. Tayyab, M. Batool, H. Sadia, Z. Taj, U. Tahir, M. Y. Jakhrani, J. Tayyab, M. A. Kakar, M. F. Shahid, T. Yaqub, J. Zhang, Q. Wu, F. Deng, V. M. Corman, S. Shen, I. Khan, Z. L. Shi, A.-U.-R. Sial, F. Ahmed, S. Faiz, M. Furqan, S. Shu & Z.-L. Shi

Sample details

Collection date
2017-10-13
Collection date (lower bound)
2017-10-13
Collection date (upper bound)
2017-10-13
Earliest release date
2020-03-31
Collection country
Pakistan

Data use terms

Data use terms
OPEN

Data use terms history

ChangedUserData use terms
2025-11-27 12:22insdc_ingest_userOPEN
Data use terms URL

Authors

Author affiliations
Wuhan Institute of Virology, Key Lab of Special Pathogens

INSDC

NCBI release date
2020-03-31
INSDC accession L
INSDC accession M
INSDC accession S

Alignment and QC metrics L

Length L
12149
Total SNPs L
1640
Total inserted nucs L
55
Total deleted nucs L
0
Total ambiguous nucs L
0
Total unknown nucs L
0
Total frame shifts L
0
Completeness L
99.88%
Total stop codons L
0

Alignment and QC metrics M

Length M
5339
Total SNPs M
665
Total inserted nucs M
0
Total deleted nucs M
0
Total ambiguous nucs M
0
Total unknown nucs M
0
Total frame shifts M
0
Completeness M
99.50%
Total stop codons M
0

Alignment and QC metrics S

Length S
1633
Total SNPs S
217
Total inserted nucs S
1
Total deleted nucs S
0
Total ambiguous nucs S
0
Total unknown nucs S
0
Total frame shifts S
0
Completeness S
97.61%
Total stop codons S
0

Submission details

Submission ID
MN135944.1.L/MN135943.1.M/MN135942.1.S
Submitting group
Date submitted
2025-11-27 12:22:07 UTC
Date released
2025-11-27 12:26:21 UTC

Lineage

Segment S Lineage
IV.1

Files

Annotations

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:T47C
  • 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

    • M

  • M:G60A
  • M:A78T
  • M:C82T
  • M:C85T
  • M:T86C
  • M:A107G
  • M:A117G
  • M:C119T
  • M:C120T
  • M:T122C
  • M:C126T
  • M:A128G
  • M:T137C
  • M:G143A
  • M:A146G
  • M:G147A
  • M:G149A
  • M:C153A

    • S

  • S:A50G
  • S:G54A
  • S:G67A
  • S:T79C
  • S:C82T
  • S:G99A
  • S:G100A
  • S:A109G
  • S:A118G
  • S:C142T
  • S:T144A
  • S:C154A
  • S:T163C
  • S:C166T
  • S:G169A
  • S:T172C
  • S:C178A
  • S:T182C
    • Deletions
    None
    Insertions
    ins_L:58:T, ins_L:11917:CA, ins_L:12054:TACAATTTT, ins_L:12083:ACTATTC, ins_L:12096:GCTCATGTCCGTTTTA, ins_L:12108:TGTGGGGGGAACGATTTCTT, ins_S:1577:A

    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:T60A

    • NP

  • NP:R15K
  • NP:F30Y
  • NP:V83A
  • NP:D116E
  • NP:T124S
  • NP:G125N
  • NP:H195R
  • NP:D199E
  • NP:I246V
  • NP:R270K
  • NP:S301G
  • NP:A307V
  • 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:K275R
  • RdRp:I279V
    • Deletions
    None
    Insertions
    None

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