Fig. 3.

Haplotype assignment by read subtraction and mapping process. a Illumina reads from Pgt21-0 were mapped to the Ug99 genome assembly at high stringency. Unmapped reads derived from divergent regions of the B haplotype were retained and then mapped to the Pgt21-0 genome assembly. Read coverage of individual contigs with the original and subtracted reads were compared to designate haplotypes as either A or B. b The same process was followed with reads from Ug99 subtracted against the Pgt21-0 reference to designate the A and C haplotypes. c Pie chart showing proportion and total sizes of contigs assigned to haplotypes A, B or C or unassigned in Pgt21-0 and Ug99 assemblies. d BUSCO analysis to assess completeness of haplotype genome assemblies. Bars represent the percentage of total BUSCOs as depicted by the colour key