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_000Q3FL.1

Pakistan/LOC_000Q3FL.1/2018
M. Umair, Z. Rehman, S. Whitmer, M. Mobley, A. Fahim, A. Ikram, M. Salman, J. M. Montgomery, J. D. Klena, A. Khurshid, E. Talundzic, J. Montgomery & J. Klena

CDC, NCEZID-VSPB

Sample details

Collection date
2018
Earliest release date
2024-07-26
Sampling location
Pakistan
Isolate name
202000304_562018|Pakistan|2018

Data use terms

Data use terms
OPEN

Data use terms history

ChangedUserData use terms
2026-05-11 10:16insdc_ingest_userOPEN
Data use terms URL

INSDC

NCBI release date
2024-07-26
INSDC accession L segment
INSDC accession M segment
INSDC accession S segment

Host

Host

Submission details

Submission ID
OM162113.1.L/OM162114.1.M/OM162115.1.S
Submitting group
Date submitted
2026-05-11 10:16:46 UTC
Date released
2026-05-11 10:23:28 UTC

Clade & Lineage

Closest reference L segment
singleReference (variant)
Closest reference M segment
M (MH396653.1) (variant)
Closest reference S segment
S1 (OL774851.1) (variant)

Files

Annotations

Alignment and QC

Total SNPs L segment
1649
Total inserted nucs L segment
47
Length L segment
12155 (100%)
Total SNPs S segment
216
Total inserted nucs S segment
9
Length S segment
1621 (89.3%)
Total SNPs M segment
114
Total inserted nucs M segment
1
Total ambiguous nucs M segment
1
Length M segment
5350 (98%)

Nucleotide mutations

Mutations called relative to the NC_005301.3, MH396653.1 & OL774851.1 references

Substitutions

L segment

  • T10C
  • G23T
  • A35G
  • G43T
  • T47C
  • T49C
  • C63G
  • C64T
  • T65C
  • T66C
  • T68C
  • G69A
  • G71C
  • C85T
  • G88A
  • G93A
  • A109G
  • C117A

M segment

  • G56A
  • G65A
  • A74T
  • C77T
  • A127G
  • G145A
  • G166A
  • T242C
  • A244G
  • A266G
  • T270C
  • T278A
  • G355A
  • C375T
  • G394A
  • A416G
  • G440A
  • C450T

S segment

  • T16A
  • C31G
  • T63C
  • C66T
  • A93G
  • A98T
  • A102G
  • C126T
  • T128A
  • C138A
  • T147C
  • C150T
  • G153A
  • T156C
  • T166C
  • A173G
  • G174A
  • T177C
Deletions
N/A
Insertions

L segment

ins_0:G, ins_58:T, ins_11917:CA, ins_12054:TACAATTTT, ins_12083:ACTATTC, ins_12108:TTTATTATTTCTGGGGTGTGGGGGAMG

M segment

ins_0:C

S segment

ins_0:GAAACACGT

Amino acid substitutions

Substitutions called relative to the NC_005301.3, MH396653.1 & OL774851.1 references

Substitutions

GPC

  • GPC:T60A
  • GPC:V61A
  • GPC:S64T
  • GPC:P96L
  • GPC:T110A
  • GPC:G118R
  • GPC:P121L
  • GPC:S131N
  • GPC:Y144H
  • GPC:G167D
  • GPC:T180A
  • GPC:L208I
  • GPC:H210Q
  • GPC:S211L
  • GPC:P220S
  • GPC:S231Y
  • GPC:I239P
  • GPC:T348A

NP

  • NP:Y20F
  • NP:F30Y
  • NP:K45R
  • NP:V83A
  • NP:D116E
  • NP:A124S
  • NP:Q179L
  • NP:D199E
  • NP:R270K
  • NP:A307V
  • NP:Q405L
  • NP:R428K

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
N/A
Insertions
N/A

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