Effects of Different SNP Calling and Sequence Mapping Choices on the Inference of Genetic Architecture Underlying Migration Tendency

Genome-wide association studies with identification of biologically relevant genes rely on correct mapping of sequence variation. Here, we re-analysed RADseq data from two migration types of brown trout (<i>Salmo trutta</i>) from Koutajoki and Oulujoki watersheds by replacing the originally applied Atlantic salmon (<i>Salmo salar</i>) reference genome with the later published brown trout reference genome and by testing three 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 the number of called SNPs varied between the used bioinformatic pipelines and reference genomes and was surprisingly lower with the conspecific reference genome. While only two SNP outliers were found by all the alternative methods, several other outlier SNPs related to migration differences among the populations were identified. These findings confirm that the choice of the reference genome is not critical for the inference of population structures but can improve the reliability of candidate gene identification in brown trout.