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Categorization results by method. Number of reads categorized to the A-genome (a) and to the D-genome (b). Reads from three allotetraploid cotton species--AD3(blue), AD4(red), and AD5(green)--were categorized by PolyDog, PolyCat using the A-genome as reference, PolyCat using the D-genome as reference, and the full reference method.
