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_00000LT.1

Uganda/coinfection-preview-005/2024-03-05
Alice Preview & Bob Example

Loculus Preview Laboratory; Example Public Health Institute

Sample details

Collection date
2024-03-05
Earliest release date
2026-06-18
Sampling location
Uganda (Central Region)
Collection city
Kampala
Collection site
Mulago National Referral Hospital
Isolate name
coinfection-preview-005

Data use terms

Data use terms
OPEN

Data use terms history

ChangedUserData use terms
2026-06-18 16:21testuserOPEN
Data use terms URL

Sampling

Sample type
clinical sample
Purpose of sampling
Diagnostic testing

Sequencing

Purpose of sequencing
Co-infection view preview data
Sequenced by
Loculus Preview Laboratory
Sequenced by - contact name
Alice Preview
Sequenced by - contact email
preview-data@loculus.org

Submission details

Submission ID
west-nile-coinfection-005
Version comment
Synthetic co-infection preview seed data derived from public example sequences
Submitting group
Date submitted
2026-06-18 16:21:23 UTC
Date released
2026-06-18 16:21:28 UTC

Lineage

Lineage
1A

Files

Annotations

Alignment and QC

Length
10302 (93.4%)
Total SNPs
92
Amino Acid Mutations from founder clade
  • 2K:L15M
  • NS1:I236V
  • NS2A:R188K
  • NS2B:A103V
  • NS3:T249P
  • NS3:I356T
  • NS4A:V85A
  • NS5:K45R
  • NS5:V49I
  • NS5:T93S
  • NS5:K177R
  • NS5:K314R
  • capsid:K10R
  • capsid:K104R
  • env:K93R
  • env:G106R
  • env:T126I
  • env:I159A
Variant
True

Nucleotide mutations

Mutations called relative to the NC_009942.1 reference

Substitutions

  • A125G
  • C340T
  • A407G
  • C435T
  • A630G
  • C871T
  • T891C
  • C969T
  • C1065T
  • C1170T
  • G1282A
  • T1442C
  • C1465T
  • G1662A
  • C1707T
  • C1750T
  • T1998C
  • G2031A
Deletions
N/A
Insertions
N/A

Amino acid substitutions

Substitutions called relative to the NC_009942.1 reference

Substitutions

NS1

  • NS1:I236V

NS2A

  • NS2A:R188K

NS5

  • NS5:K45R
  • NS5:V49I
  • NS5:T93S
  • NS5:K314R

capsid

  • capsid:K10R
  • capsid:K104R

env

  • env:G106R
  • env:V159A
  • env:L167F
Deletions
N/A
Insertions
N/A