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_000Q2R0.1

Pakistan/LOC_000Q2R0.1/2019
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
2019
Earliest release date
2024-07-26
Sampling location
Pakistan
Isolate name
202000282_652019|Pakistan|2019

Data use terms

Data use terms
OPEN

Data use terms history

ChangedUserData use terms
2026-05-14 12:58insdc_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
OM162060.1.L/OM162061.1.M/OM162062.1.S
Submitting group
Date submitted
2026-05-14 12:58:49 UTC
Date released
2026-05-14 13:07:55 UTC

Clade & Lineage

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

Files

Annotations

Alignment and QC

Total SNPs S segment
213
Total inserted nucs S segment
3
Total deleted nucs S segment
2
Length S segment
1646 (91.1%)
Total SNPs L segment
1648
Total inserted nucs L segment
46
Total ambiguous nucs L segment
1
Length L segment
12142 (99.9%)
Total SNPs M segment
40
Length M segment
5340 (97.9%)

Nucleotide mutations

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

Substitutions

L segment

  • G23T
  • G32A
  • A35G
  • G43T
  • T49C
  • C63G
  • C64T
  • T65C
  • T66C
  • T68C
  • G69A
  • G71T
  • C85T
  • G88A
  • G93A
  • A109G
  • C117A
  • A124G

M segment

  • A236G
  • C245A
  • A251G
  • C288T
  • T326C
  • A372G
  • A508G
  • G529A
  • C576T
  • G634A
  • C645T
  • C720T
  • C780T
  • C817T
  • G836A
  • A888G
  • T1000C
  • G1069A

S segment

  • T16A
  • C31G
  • T63C
  • A65G
  • A84G
  • A93G
  • A98T
  • A102G
  • C150T
  • G153A
  • T156C
  • T166C
  • A173G
  • G174A
  • G180A
  • A186G
  • C192T
  • C201T
Deletions

S segment

1627, 1628
Insertions

L segment

ins_58:T, ins_11917:CA, ins_12054:TACAATTT, ins_12083:ACTATTC, ins_12108:TTTATTATTTCTGGGGTGTGGGGGGAAC

S segment

ins_0:CAY

Amino acid substitutions

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

Substitutions

GPC

  • GPC:T50A
  • GPC:P53T
  • GPC:T55A
  • GPC:A67V
  • GPC:S80P
  • GPC:E95G
  • GPC:P163L
  • GPC:P186L
  • GPC:S211L
  • GPC:S231F
  • GPC:D250N
  • GPC:K267R
  • GPC:T348A
  • GPC:I432V
  • GPC:I449V
  • GPC:F482L
  • GPC:N966S
  • GPC:N1586D

NP

  • NP:N9S
  • NP:Y20F
  • NP:K45R
  • NP:V83A
  • NP:D116E
  • NP:A124S
  • NP:Q179L
  • NP:D199E
  • NP:R270K
  • NP:A307V
  • NP:E322D
  • NP:Q405L

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:V214I
  • RdRp:I223V
  • RdRp:N236S
Deletions
N/A
Insertions
N/A

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