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Data and code: Effects of different SNP calling and sequence mapping choices on the inference of genetic architecture underlying migration tendency

Mottola, Giovanna12

Published May 27, 2026 on Dryad. https://doi.org/10.5061/dryad.v6wwpzh9f

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Abstract

Genome-wide association studies with identification of biologically relevant genes rely on correct mapping of sequence variation. Here, we re-analysed RAD-Seq data from two life-history types of brown trout (Salmo trutta) from River Koutajoki and River Oulujoki by replacing the originally applied Atlantic salmon (Salmo salar) reference genome with the later published brown trout reference genome, and by testing two alternative bioinformatic pipelines for identifying single nucleotide polymorphisms (SNPs). As expected, the results from population genomics and outlier analyses largely confirmed the original patterns of population structure and divergence, although SNP detection success varied between the used bioinformatic pipelines and reference genomes. While only two SNP outliers were found by all the alternative methods, several other outlier candidate SNPs related to migration, growth, and other biologically significant traits were identified. These findings confirm that the choice of the reference genome is not critical for basic population genomics but can improve the ability to detect functionally relevant genomic variation explaining migratory patterns in brown trout.