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January 22nd, 2025
Version: 1
Department of Plant Biology, University of Georgia, 2502 Miller Plant Sciences, Athens GA 30602, U.S.A
genomics
biorxiv

Low level contamination confounds population genomic analysis

Ward, A.•Scopel, E. F. C.•Shuman, B.•Momany, M.•Bensasson, D.

Genome sequence contamination has a variety of causes and can originate from within or between species. Previous research focused primarily on cross-species contamination or on prokaryotes. This paper visualizes B-allele frequency to test for intra-species contamination, and measures its effects on phylogenetic and admixture analysis in two fungal species. Using a standard base calling pipeline, we found that contaminated genomes superficially appeared to produce good quality genome data. Yet as little as 5-10% genome contamination was enough to change phylogenetic tree topologies and make contaminated strains appear as hybrids between lineages (genetically admixed). We recommend the use of B-allele frequency plots to screen genome resequencing data for intra-species contamination.

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