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_000Q3UT.1

Pakistan/LOC_000Q3UT.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
202000276_202019|Pakistan|2019

Data use terms

Data use terms
OPEN

Data use terms history

ChangedUserData use terms
2026-06-12 15:19insdc_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
OM162045.1.L/OM162046.1.M/OM162047.1.S
Submitting group
Date submitted
2026-06-12 15:19:09 UTC
Date released
2026-06-12 15:23:39 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 S segment
231
Total inserted nucs S segment
16
Total deleted nucs S segment
2
Length S segment
1661 (91.2%)
Total SNPs L segment
1646
Total inserted nucs L segment
48
Length L segment
12155 (100%)
Total SNPs M segment
1026
Total inserted nucs M segment
4
Length M segment
5346 (97.9%)

Nucleotide mutations

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

Substitutions

L segment

  • T10C
  • G23T
  • A35G
  • G43C
  • T49C
  • C63G
  • C64T
  • T65C
  • T66C
  • G69A
  • G71T
  • G88A
  • G93A
  • A109G
  • A124G
  • T131A
  • C148T
  • T151C

M segment

  • G46T
  • A47G
  • G52A
  • A53C
  • G65A
  • A66G
  • T67A
  • A76G
  • T78C
  • G80T
  • T81C
  • C82A
  • C88T
  • C92T
  • T94C
  • T96C
  • T98C
  • T101C

S segment

  • T16A
  • C31G
  • T33C
  • A62C
  • T63C
  • C66T
  • A84G
  • T90C
  • A98T
  • A102G
  • A132G
  • C150T
  • G153A
  • T156C
  • T166C
  • A173G
  • G174A
  • A186G
Deletions

S segment

1604, 1605
Insertions

L segment

ins_58:T, ins_11930:AA, ins_12083:TAATATCCTGCTATTC, ins_12108:TTTAGTTTTATTATTTCCAGGGTGTGGGG

M segment

ins_0:CTC, ins_5165:A

S segment

ins_0:SCTCAAAGAAACACGT

Amino acid substitutions

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

Substitutions

GPC

  • GPC:H2Y
  • GPC:I3T
  • GPC:S4P
  • GPC:M6L
  • GPC:Y7C
  • GPC:F10L
  • GPC:L12S
  • GPC:C15W
  • GPC:G16S
  • GPC:L17S
  • GPC:G18E
  • GPC:K19G
  • GPC:N21H
  • GPC:P23L
  • GPC:H24S
  • GPC:G26E
  • GPC:E28Q
  • GPC:N30G

NP

  • NP:N8T
  • NP:Y20F
  • NP:K45R
  • NP:V83A
  • NP:D116E
  • NP:A124S
  • NP:Q179L
  • NP:D199E
  • NP:R270K
  • NP:A307V
  • NP:E322D
  • NP:Q405L
  • NP:R428K

RdRp

  • RdRp:S6N
  • RdRp:S19T
  • RdRp:N52H
  • RdRp:Y60N
  • RdRp:R63H
  • RdRp:S67V
  • RdRp:R80K
  • RdRp:V82I
  • RdRp:I114V
  • RdRp:T163V
  • RdRp:A168T
  • RdRp:M172V
  • RdRp:R174K
  • RdRp:S205P
  • RdRp:N206Y
  • RdRp:K275R
  • RdRp:I279V
  • RdRp:S498G
Deletions
N/A
Insertions
N/A

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