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Updated: Jan 10, 2026

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Variant Calling in the Goldilocks Zone: How Reference Genome Choice and Read Mapping Stringency Impact Heterozygosity

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Summary

Choosing the right reference genome and mapping method is crucial for accurate population genomics. A closely related reference genome and the Bowtie 2 --end-to-end method minimize bias and improve variant calls in oak studies.

Keywords:
QuercusBWABowtie 2SNP‐callingWGSreference mapping

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Area of Science:

  • Genomics
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Advancements in sequencing enable population and phylogenomic studies on non-model organisms.
  • Selecting appropriate reference genomes and mapping strategies is critical for comparative genomics.

Purpose of the Study:

  • To evaluate the impact of reference genome choice and mapping methods on data accuracy and bias in oak population genomics.
  • To determine the optimal combination of reference genome and mapping strategy for reliable variant calling.

Main Methods:

  • Mapping short-read resequencing data from oak samples to four Quercus reference genomes.
  • Utilizing three mapping methods: Bowtie 2 --end-to-end (global), Bowtie 2 --local (local), and BWA-MEM (local).
  • Analyzing read mapping accuracy, efficiency, missing data, heterozygosity, and inferred phylogenies.

Main Results:

  • Genetic distance between reference and sample genomes, along with mapping method, significantly influenced heterozygosity and phylogenetic inference.
  • Global alignment (Bowtie 2 --end-to-end) showed decreased heterozygosity with increased genetic distance.
  • Distantly related reference genomes led to reduced base pair recovery and skewed heterozygosity estimates and phylogenies.

Conclusions:

  • Using a closely related, non-conspecific reference genome minimizes reference bias.
  • The Bowtie 2 --end-to-end mapping method reduces mismapping, leading to more accurate variant calls.
  • Optimal reference genome and mapping method selection is essential for robust population genomic analyses.