MIP and mitochondrial genotypes.

(A) MIP genotype expressed as VAF. The number of reads supporting the variant and the number of reads covering the variant site are shown for each MIP–tumour combination. MIP probe sequences are shown, “N” within the MIP probe sequence denotes the 5-bp UMI. (B) Tumour genotypes across the MIP panel. N, genotypes that could not be determined. MIP probe sequences are shown, “N” within the MIP probe sequence denotes the 5-bp UMI. (C) Contaminating read threshold, determined empirically for each tumour, used in genotype calling (see Methods). (D) Mitochondrial (mtDNA) genotypes. Numerals “1” and “0” represent variant presence and absence, respectively. (E) mtDNA haplotype nomenclature. DFT1 mtDNAs are arranged into 36 haplotype groups, based on the presence of haplogroup-defining variants. Haplotypes falling within defined groups acquiring additional variants are named hierarchically with letters and numbers, as shown. Haplogroups DFT1_18 and DFT1_30, as well as haplogroups DFT1_22 and DFT1_29, are each defined by the same variant (10620T>A and 16143G>A, respectively). The single DFT2 haplotype is also listed. DFT1_0 and DFT2_0 are identical to the reference genome. Small insertions and deletions (indels) are not included. (XLSX)