Fig. 6.

Summary of physical linkage of genome scaffolds and inferred haplotype combinations at each scaffold. Only the 20 largest scaffolds are shown and representative isolates carrying CCNVs and their scaffolds showing copy number variations were arranged to highlight physical linkage. See Additional file 7 for details. A and B denote homologous haplotypes at each individual scaffold. In other words, A on one scaffold does not necessarily link to A on the other scaffold. Inferred haplotype combinations are shown when those are deviated from a heterozygous disomic haplotype combination, AB. AAB, AA and A denote three copies of a DNA segment (i.e. trisomy), cnLOH, and copy deletion (i.e. monosomy), respectively. AB + X indicates a mixture of AB disomy and monosomy with an unknown haplotype. Likewise, AB + XXX indicates a mixture of AB disomy and trisomy with an unknown haplotype combination. HK in CCNV type indicates a heterokaryon. Scaffolds 5, 8, 14, 15, and 20 are likely physically linked, whereas each of scaffold 9 and 10 do not link to any of the 31 largest scaffolds in the current assembly