Plant material Four sets of A. thaliana materials were analysed in this study, including MA16 and MA32 lines, HPG1 accessions, and rtel1-1 mutants (Supplementary Table 1). The MA16 lines (two lines, samples A and B) were derived from a trans-generational mutation accumulation experiment, originating from a single Col-0 mother plant (Nottingham Arabidopsis Stock Centre ID
PPCG cohort, WGS and variant calling We used data from the PPCG consortium of primary prostate cancer samples from a total of 1,001 prostate cancer donors with 1,172 tumour samples. Informed ethical consent was obtained at clinical follow-up, and was consistent with local research ethics and International Cancer Genome Consortium (ICGC) guidelines (https://icgc.org/). Ethical approval
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Pangenome reference The pangenome reference used in this study is a sequence graph augmented with phased small variants. It is stored in two data files: a sequence graph in reference rGFA format16 containing the structural variants and a supplementary phased VCF33 file containing small variants. The rGFA sequence graph is constructed first from haplotype assemblies,
