Red lines show SNPs per kilobase, normalized by coverage, within WO-1, and blue lines show SNPs per kilobase between WO-1 and SC5314. Although both copies of chromosome 5 have rearranged at the MRS (yellow box) in WO-1, we show this as a single chromosome to allow a haploid reference for polymorphism. Relative to SC5314, chromosomes 1, 4 and 6 have the opposite orientation (Supplementary Fig. 6). Chr, chromosome; sc, supercontig; kb, kilobase.