4 Syn. Frame shift Missense In frame indel 3 Syn. Splice site Other non syn. Non syn. 2 Nonsense 1

# mutations/Mb 0 78 21% EGFR 69 20% TP53 69 23% PTEN 32 11% PIK3R1 7% RB1 9% NF1 5% IDH1 29 9% SPTA1 9% PIK3CA 3% GABRA6 37 8% FLG 3% RPL5 4% KEL 3% RIMS2 29 8% PCLO 3% RBM47 5% TCHH 3% SEMA3C 2% OR8K3 2% PRB2 7% RYR2 2% TPTE2 3% LZTR1 2% DCAF12L2 2% PSPH 3% PDGFRA 2% SPRYD5 2% LRFN5 52 12% MUC16 2% CALN1 2% HCN1 2% KIF2B 6% MUC17 2% AZGP1 2% AFM 2% OR5D13 2% SULT1B1 2% SEMG1 2% DRD5 2% OR5D18 2% TRPV6 2% POM121L12 3% COL1A2 2% LRRC55 2% OR4D5 3% CNTNAP2 2% WNT2 2% GABRA1 1% OR5W2 2% SLC1A6 3% DOCK5 6% HMCN1 2% UGT2A3 3% STAG2 1% CDKN2C 2% REN 2% CDC27 2% WBSCR17 2% GRM3 2% KLF17 1% FOXG1 2% UGT2B28 2% SLCO6A1 1% HIST1H2BE 1% AP3S1 2% PROKR2 2% DSG3 1% QKI 1% TAS2R41 2% PCDHA3 2% PAN3 3% HEATR7B2 4% COL6A3 2% CYP3A5 1% ANO9 1% PLCXD3 1% OR5D16 2% NOX4 1% KLK6 2% TMPRSS6 1% PODNL1 1% OR5AR1 2% CALCR 2% PCDHA1 2% ADCY5 1% TGFA 2% GABRB2 2% ADAMTS16 1% POTEH 1% OR52M1 3% BCOR 1% TMEM229B 2% TSHZ2 1% PSG1 2% FGD5 2% CDH18 1% KDELC2 1% TREML2 1% FOXR2 2% ADAM29 1% SERPINB4 1% OR13C5 1% OR5A1 2% DPP10 2% KPRP 1% LUM 1% GNAT3 2% PCDH19 1% OR5M3 1% ALPPL2 1% MSL3 1% GLT1D1 2% ABCB1 1% TRAT1 2% ELTD1 1% MAGEB4 100 25 20 15 10 5 0 80 0.5 2.0 3.5 # mutations 60 -log10(q-value) 40 Allelic 20 fraction 0 100 double_null indel+null 80 C->G 60 A->(C/G) % C->(A/T) 40 A->T 20 0 GBM-06-0743-TP GBM-02-0003-TP GBM-32-1970-TP GBM-19-2625-TP GBM-06-2563-TP GBM-06-2567-TP GBM-06-0876-TP GBM-14-0813-TP GBM-28-5207-TP GBM-32-1991-TP GBM-76-4927-TP GBM-06-0157-TP GBM-06-0155-TP GBM-06-0649-TP GBM-06-0749-TP GBM-14-1395-TP GBM-76-6191-TP GBM-28-5209-TP GBM-06-2561-TP GBM-06-1804-TP GBM-06-0881-TP GBM-76-6661-TP GBM-14-1456-TP GBM-14-0790-TP GBM-06-6695-TP GBM-76-6656-TP GBM-26-5139-TP GBM-06-0750-TP GBM-81-5911-TP GBM-14-1034-TP GBM-27-2528-TP GBM-06-5413-TP GBM-06-0879-TP GBM-15-0742-TP GBM-19-1790-TP GBM-06-0154-TP GBM-06-0158-TP GBM-06-0211-TP GBM-76-4926-TP GBM-28-1747-TP GBM-06-0137-TP GBM-06-0650-TP GBM-06-0142-TP GBM-14-1829-TP GBM-06-2557-TP GBM-14-1823-TP GBM-12-3652-TP GBM-14-0786-TP GBM-06-5856-TP GBM-06-0174-TP GBM-27-1831-TP GBM-81-5910-TP GBM-12-3650-TP GBM-14-0789-TP GBM-06-0747-TP GBM-06-6700-TP GBM-19-2624-TP GBM-06-0878-TP GBM-16-1045-TP GBM-06-2565-TP GBM-76-6662-TP GBM-32-2634-TP GBM-06-0184-TP GBM-76-6286-TP GBM-06-5858-TP GBM-76-6283-TP GBM-27-1838-TP GBM-06-0875-TP GBM-06-0195-TP GBM-27-2519-TP GBM-76-4925-TP GBM-16-0846-TP GBM-76-6664-TP GBM-19-2629-TP GBM-06-0128-TP GBM-15-1444-TP GBM-76-4929-TP GBM-74-6573-TP GBM-06-6698-TP GBM-76-6663-TP GBM-32-2491-TP GBM-06-0130-TP GBM-06-2569-TP GBM-26-5133-TP GBM-06-5417-TP GBM-06-0221-TP GBM-32-4208-TP GBM-27-2521-TP GBM-14-4157-TP GBM-26-1442-TP GBM-41-5651-TP GBM-06-2559-TP GBM-06-0238-TP GBM-02-2485-TP GBM-76-6193-TP GBM-06-6694-TP GBM-41-2575-TP GBM-06-2558-TP GBM-06-0744-TP GBM-28-5219-TP GBM-32-4210-TP GBM-27-1836-TP GBM-12-0619-TP GBM-06-0237-TP GBM-06-0189-TP GBM-14-0817-TP GBM-28-5216-TP GBM-26-5136-TP GBM-14-0871-TP GBM-14-1825-TP GBM-06-0190-TP GBM-76-6657-TP GBM-26-6174-TP GBM-19-5955-TP GBM-32-4213-TP GBM-06-0192-TP GBM-41-4097-TP GBM-06-5412-TP GBM-06-0939-TP GBM-32-5222-TP GBM-12-1597-TP GBM-12-0618-TP GBM-06-0166-TP GBM-76-4931-TP GBM-06-0124-TP GBM-16-0861-TP GBM-28-2510-TP GBM-27-1834-TP GBM-06-0216-TP GBM-06-0188-TP GBM-06-0644-TP GBM-76-6192-TP GBM-06-5418-TP GBM-27-1837-TP GBM-28-1753-TP GBM-19-5952-TP GBM-06-0125-TP GBM-02-2470-TP GBM-41-2573-TP GBM-76-4934-TP GBM-32-1977-TP GBM-76-4935-TP GBM-06-0168-TP GBM-02-0055-TP GBM-26-5132-TP GBM-19-5959-TP GBM-74-6577-TP GBM-32-1982-TP GBM-41-2571-TP GBM-06-0882-TP GBM-74-6575-TP GBM-06-2562-TP GBM-06-0129-TP GBM-19-5947-TP GBM-06-0877-TP GBM-28-2513-TP GBM-76-6280-TP GBM-06-6388-TP GBM-41-3915-TP GBM-19-5951-TP GBM-12-0688-TP GBM-02-0033-TP GBM-32-2632-TP GBM-19-2623-TP GBM-06-0213-TP GBM-06-0140-TP GBM-27-2524-TP GBM-06-0214-TP GBM-06-5410-TP GBM-41-3392-TP GBM-14-1043-TP GBM-06-0119-TP GBM-28-6450-TP GBM-28-2502-TP GBM-19-5953-TP GBM-32-1986-TP GBM-41-6646-TP GBM-32-1980-TP GBM-28-5208-TP GBM-32-2494-TP GBM-06-2570-TP GBM-02-2483-TP GBM-06-6389-TP GBM-06-6701-TP GBM-06-6391-TP GBM-06-0210-TP GBM-27-1835-TP GBM-32-4211-TP GBM-06-0185-TP GBM-26-5135-TP GBM-28-5213-TP GBM-19-5954-TP GBM-02-0047-TP GBM-12-5301-TP GBM-41-2572-TP GBM-06-0171-TP GBM-74-6578-TP GBM-32-1979-TP GBM-16-1048-TP GBM-27-2527-TP GBM-06-5414-TP GBM-06-6390-TP GBM-27-2526-TP GBM-19-2620-TP GBM-02-2486-TP GBM-06-5411-TP GBM-28-5211-TP GBM-76-4928-TP GBM-12-0615-TP GBM-28-5214-TP GBM-06-0152-TP GBM-06-5408-TP GBM-06-5415-TP GBM-76-6282-TP GBM-06-0173-TP GBM-12-3649-TP GBM-06-6697-TP GBM-26-5134-TP GBM-14-0781-TP GBM-28-2501-TP GBM-06-0169-TP GBM-06-6699-TP GBM-06-0122-TP GBM-19-2619-TP GBM-28-2514-TP GBM-26-1439-TP GBM-19-5960-TP GBM-06-0646-TP GBM-26-6173-TP GBM-06-0240-TP GBM-06-0145-TP GBM-14-0787-TP GBM-14-0862-TP GBM-32-4209-TP GBM-06-0141-TP GBM-28-5204-TP GBM-19-1390-TP GBM-19-2631-TP GBM-06-0686-TP GBM-41-3393-TP GBM-12-5295-TP GBM-06-0209-TP GBM-14-0740-TP GBM-12-0821-TP GBM-76-6660-TP GBM-27-2523-TP GBM-28-5218-TP GBM-12-0692-TP GBM-14-2554-TP GBM-28-2509-TP GBM-27-1830-TP GBM-32-2495-TP GBM-14-1450-TP GBM-12-3653-TP GBM-06-0745-TP GBM-76-4932-TP GBM-06-5859-TP GBM-06-0151-TP GBM-06-0126-TP GBM-19-4068-TP GBM-06-0645-TP GBM-32-2615-TP GBM-28-5220-TP GBM-06-6693-TP GBM-06-0648-TP GBM-28-5215-TP GBM-06-0241-TP GBM-27-1832-TP GBM-32-2498-TP GBM-12-0616-TP GBM-87-5896-TP GBM-19-5950-TP GBM-06-0219-TP GBM-27-2518-TP GBM-06-0167-TP GBM-27-1833-TP GBM-14-3476-TP GBM-32-2638-TP GBM-06-2564-TP GBM-76-6285-TP GBM-19-5958-TP GBM-74-6584-TP GBM-12-5299-TP GBM-32-4719-TP GBM-06-1806-TP GBM-06-0132-TP GBM-28-2499-TP GBM-08-0386-TP GBM-06-0165-TP GBM-06-0139-TP GBM-06-0178-TP