Panel (A) shows the base calls for positions on scaffold 70 for six nuclei (four nuclei of mating type M-1 and two of M-2, as indicated in the top row). Each base call was assigned to a mating type class (green or yellow) in Chen et al. (2018a) based on an unspecified criterion. Variation between nuclei of the same mating type (e.g. variation among nuclei 2, 21, 22, and 24) is interpreted as recombination. We used their Illumina reads to show the ratio of reads supporting alternative nucleotides for each position. For example, in strain 4, mating-type 1, nucleus 2, position 100454, in Chen et al. the base was called as a G with a mating type ‘green’, and 51 of 52 reads matched G. However, for nucleus 21, only 85 of 151 reads supported an A at that position, while the other 66 supported a G. Panel (B) shows the alignment of the region shown in (A) with its best BLAST hit region on scaffold 3570. Heterozygous sites in the mapped reads of the dikaryon are indicated in bold, with the two alternate and reference bases shown slightly above/below. Gray boxes surround those sites included in (A). Note that both regions are heterozygous at the same aligned sites, and with the same alternate base for each heterozygous site. Graphic of (A) modified from Figure 3 of Chen et al. (2018a), with the addition of nuclei 21 and 24.