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bioRxiv · 10.1101/2025.01.17.633387

Low level contamination confounds population genomic analysis

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

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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Ward, A., Scopel, E. F. C., Shuman, B., Momany, M., Bensasson, D.. 2025-01-22. Low level contamination confounds population genomic analysis. https://doi.org/10.1101/2025.01.17.633387

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