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Genome-wide Analysis of Aminoacylation Charging Levels of tRNA Using Microarrays
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Low-level contamination confounds population genomic analysis.

Audrey K Ward1, Eduardo F C Scopel2, Brent Shuman3

  • 1Department of Genetics, University of Georgia, 120 E. Green St., Athens, GA 30602, United States.

G3 (Bethesda, Md.)
|January 30, 2026
PubMed
Summary
This summary is machine-generated.

Intra-species genome contamination can be detected using B-allele frequency plots. Even low levels of contamination can significantly alter phylogenetic analyses and lead to misidentification of genetic hybrids.

Keywords:
BAF plotscross-contaminationheterozygosityphylogenomicpopulation genomicspopulation structuresingle nucleotide polymorphism (SNP) calls

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Area of Science:

  • Genomics
  • Bioinformatics
  • Population Genetics

Background:

  • Genome sequence contamination poses a challenge in biological research.
  • Previous studies primarily addressed inter-species contamination or prokaryotic genomes.
  • Intra-species contamination, especially in eukaryotes, remains less explored.

Purpose of the Study:

  • To investigate the prevalence and impact of intra-species genome contamination.
  • To develop and validate a method for detecting such contamination.
  • To assess the effects of contamination on downstream genomic analyses.

Main Methods:

  • Analyzed 1,298 Saccharomyces cerevisiae genome sequences for contamination.
  • Mapped short-read genome data to reference genomes.
  • Visualized single nucleotide differences to identify secondary allele frequencies.
  • Used in silico contaminated data to validate detection methods.
  • Evaluated contamination effects on admixture and phylogenetic analyses in two fungal species.

Main Results:

  • Identified at least 5% contamination in 8 out of 1,298 Saccharomyces cerevisiae genomes.
  • Contamination rates varied significantly between sequencing centers and studies.
  • Secondary allele frequency plots effectively identified contamination with as little as 5% B-allele frequency.
  • Contamination levels of 5-10% distorted phylogenetic tree topologies and suggested false admixture.

Conclusions:

  • Intra-species genome contamination is detectable using B-allele frequency plots.
  • Standard base calling pipelines may not reveal superficial contamination.
  • Even low levels of contamination can critically impact phylogenetic and admixture analyses.
  • Recommends B-allele frequency plots as a standard screening tool for genome resequencing data.