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Fig. 1 | BMC Biology

Fig. 1

From: Patterns of cross-contamination in a multispecies population genomic project: detection, quantification, impact, and solutions

Fig. 1

Detection of within-species contamination through homo-quartet analysis. Each multicolored square represents a quartet, that is, read counts for states A (green), C (yellow), G (blue), and T (orange) at a specific position in a specific individual, zeros being omitted. A fictive dataset of four individuals (Ind 1 to Ind 4 ) and five positions (Pos 1 to Pos 5 ) is shown. At all five positions, the quartet for individual Ind1 is a homo-quartet (thick borders): the major state has more than 40 reads, and the minor state has exactly one read. Positions Pos1 and Pos2 are monoallelic: the major state represents more than 95% of reads across the four individuals. These two positions inform on the contamination-free error pattern. Positions Pos3, Pos4, and Pos5 are biallelic: besides the major state, another allele segregates in the sample. At Pos3 the Ind1, the minor state (G) differs from the other segregating allele (C); this error cannot result from within-species contamination. At Pos4 and Pos5, the Ind1 minor state is identical to the other segregating allele (T), potentially reflecting allele leakage between individuals, as indicated by red arrows. The proportions of these different types of position inform on the prevalence of within-species contamination

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