Fig. 5: LOH and aneuploidy caused by genome-wide SCRaMbLE in diploids.

a Workflow of copy number variation analysis. Reads with or without loxPsym sites were mapped to the upstream/downstream regions of each loxPsym site. The copy number of the upstream/downstream regions for a certain loxPsym site were deduced based on read alignment. Reads from corresponding chromosomes are indicated by the same color (blue or gray). Different rectangle colors indicate four distinct situations deduced from read mapping: blue indicates loxPsym is present and not rearranged, white indicates absence of loxPsym, orange with dash lines indicates loss of loxPsym-containing sequence and half blue with half orange squares indicate rearrangement. Structural variation was deduced using copy number calculation of loxPsym flanking sequences. b Copy number variation of 2 kb upstream/downstream regions of the loxPsym sequence in the nine diploid strains. Chromosomes lacking rearrangements were shown in Supplementary Fig. 13. c Three different types of chrVIII polymorphism detected in the nine strains. d Two types of non-reciprocal translocation observed between loxPsym sites IV-9 and X-5 or IV-1 and XIII-7. e A translocation occurred between two loxPsym sites, IV-1 and VI-2, and a duplication of the region upstream of VI-2 was inserted at loxPsym site IV-1. Reads revealed that the upstream sequences (U) of VI-2 were connected to the downstream sequences (D) of IV-1.