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PolyCat performance. Reads from three allotetraploid cotton species--AD3(blue), AD4(red), and AD5(green)--were mapped by GSNAP with SNP-tolerant mapping and categorized by PolyCat using either the A-genome or D-genome reference sequence. The total number of mapped reads in each case is shown (Aref-mapped and Dref-mapped), as well as the number of reads categorized to the A (Aref-A and Dref-A) and D genomes (Aref-D and Dref-D).
