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_000Q39Y.1

Pakistan/LOC_000Q39Y.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
202000302_732018|Pakistan|2018

Data use terms

Data use terms
OPEN

Data use terms history

ChangedUserData use terms
2026-05-09 06:41insdc_ingest_userOPEN
Data use terms URL

INSDC

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

Host

Host

Submission details

Submission ID
OM162111.1.L/OM162112.1.S
Submitting group
Date submitted
2026-05-09 06:41:32 UTC
Date released
2026-05-09 06:49:26 UTC

Clade & Lineage

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

Files

Annotations

Alignment and QC

Total SNPs L segment
1565
Total inserted nucs L segment
30
Total deleted nucs L segment
1
Total ambiguous nucs L segment
19
Total unknown nucs L segment
590
Length L segment
12114 (94.8%)
Total SNPs S segment
188
Length S segment
1537 (85.1%)

Nucleotide mutations

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

Substitutions

L segment

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

S segment

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

L segment

12034
Insertions

L segment

ins_58:T, ins_684:GNN, ins_3102:TACTAGNNN, ins_11982:GC, ins_12054:TACAATTT, ins_12083:ACTATTC

Amino acid substitutions

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

Substitutions

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:N236S
  • RdRp:K275R
  • RdRp:I279V
  • RdRp:R302K
  • RdRp:M303L
Deletions
N/A
Insertions

RdRp

ins_RdRp:227:X, ins_RdRp:1007:VTT

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