80 Syn. Frame shift 60 Missense In frame indel Splice site Other non syn. Syn. 40 Non syn. Nonsense 20

# mutations/Mb 0 15% STK11 313 54% TP53 169 30% KRAS 17% KEAP1 13% EGFR 8% BRAF 4% CDKN2A 3% NFE2L2 2% POTEM 2% U2AF1 2% EMG1 1% ZNF595 6% RBM10 8% FSTL5 6% OR4A5 6% OR5D13 6% RB1 4% REG1B 6% LRRIQ3 6% OR4C16 6% RGS7 7% WDR49 7% POTEG 4% MUC7 4% TAS2R1 3% KIAA0408 4% FERD3L 3% CTNNB1 5% OR5W2 17% ZNF804A 4% OR8K5 4% LDB2 5% GABRG2 21% COL11A1 2% HBG2 3% DIO2 4% ZNF492 5% PIK3CA 6% OR5F1 5% TBX22 9% TMTC1 12% CDH12 6% REG3A 4% CMKLR1 6% OR2T4 6% ELTD1 17% CDH10 3% PPP3CA 10% EPHA6 2% VWC2 3% LUM 3% OR51G2 5% EDIL3 7% TRHDE 5% OR5T3 2% APCS 3% PNLIP 6% SATB2 1% SNRPD3 6% FOLH1 3% CPXCR1 3% DCAF8L2 8% NLRP14 4% KRTAP24-1 5% PYHIN1 6% FAM71B 2% LCE1F 8% ADAMTS2 4% OR4C3 3% TCEAL5 3% OR51A7 163 21% NAV3 6% OR5L1 3% SELE 4% OR8I2 11% SNTG1 3% PRB2 4% SPATA18 6% ZBBX 3% DUSP22 10% ADAMTS16 3% OR2A2 7% C7 7% ZNF676 10% ASTN2 2% OR4C12 4% NPFFR2 15% NRXN1 3% PRIM2 1% S100A7 4% ITGBL1 5% OR8H2 3% MS4A4A 5% SERPINB3 0% RPS16 2% RALYL 4% ZNF98 1% KRTAP21-2 5% INHBA 3% CD1A 3% OR2A5 1% TSLP 3% CFHR3 6% ZIC4 3% DLX5 4% C1orf94 2% MAGEB2 2% LCE2B 5% IL1RAPL1 6% POSTN 1% GOLGA6C 2% KRTAP5-10 3% HAPLN1 5% PSG11 2% KRTAP27-1 2% ATXN3L 8% SMARCA4 3% SGCZ 2% SPANXN2 1% IFNA6 4% MPPED2 1% ZNF268 3% RPL10L 6% SLITRK6 1% KRTAP19-6 1% KRTAP6-2 2% LSP1 17% TNR 3% ZWINT 6% OR4A16 3% HOXA1 4% OR8H3 5% PSG2 2% RIT1 2% AKR1B15 5% ZSWIM2 4% WDR64 6% SETD2 4% OR2B11 4% CD5L 2% ANKRD7 5% NRG3 1% SNX24 4% UGT2B28 2% OR5K3 7% SLITRK4 5% CDH17 3% BCKDHB 2% CD96 5% OR5J2 8% NLRP5 10% GPR158 2% C14orf177 3% OR4L1 1% CMTM5 4% DRD2 5% DLGAP3 3% PHF14 3% ZFYVE28 1% B2M 5% CNBD1 4% ANTXR1 6% EPHA7 2% VSTM2A 100 150 100 50 0 80 0.5 2.0 3.5 # mutations 60 -log10(q-value) 40 Allelic 20 fraction 0 100 double_null indel+null 80 A->(C/G) 60 flip % *Cp(A/C/T)->(A/T) 40 *CpG->(A/T) 20 0 LUAD-05-4395-TP LUAD-73-4670-TP LUAD-97-8179-TP LUAD-55-8299-TP LUAD-99-8025-TP LUAD-50-5939-TP LUAD-44-6779-TP LUAD-05-5425-TP LUAD-75-5146-TP LUAD-55-7913-TP LUAD-55-7574-TP LUAD-44-8120-TP LUAD-05-4432-TP LUAD-49-4487-TP LUAD-86-8280-TP LUAD-55-1596-TP LUAD-78-7535-TP LUAD-44-6144-TP LUAD-35-3615-TP LUAD-78-7166-TP LUAD-44-7671-TP LUAD-44-6776-TP LUAD-67-3774-TP LUAD-J2-8194-TP LUAD-55-8203-TP LUAD-55-8508-TP LUAD-05-4417-TP LUAD-86-7713-TP LUAD-86-8359-TP LUAD-80-5608-TP LUAD-55-8615-TP LUAD-99-8032-TP LUAD-50-5932-TP LUAD-78-7161-TP LUAD-49-4507-TP LUAD-91-6849-TP LUAD-49-4486-TP LUAD-50-5072-TP LUAD-05-4422-TP LUAD-75-7031-TP LUAD-55-8094-TP LUAD-99-8033-TP LUAD-55-8302-TP LUAD-95-7039-TP LUAD-93-8067-TP LUAD-49-4505-TP LUAD-05-4433-TP LUAD-78-7145-TP LUAD-55-7907-TP LUAD-55-8616-TP LUAD-95-7562-TP LUAD-44-8117-TP LUAD-17-Z022-TP LUAD-97-7938-TP LUAD-44-6777-TP LUAD-69-7980-TP LUAD-99-8028-TP LUAD-91-6836-TP LUAD-95-7567-TP LUAD-99-7458-TP LUAD-17-Z042-TP LUAD-05-4415-TP LUAD-86-8056-TP LUAD-05-4427-TP LUAD-97-7554-TP LUAD-55-7911-TP LUAD-44-6145-TP LUAD-55-7910-TP LUAD-69-7974-TP LUAD-64-5778-TP LUAD-17-Z017-TP LUAD-55-7576-TP LUAD-55-8514-TP LUAD-44-7661-TP LUAD-64-5775-TP LUAD-44-2668-TP LUAD-69-7978-TP LUAD-55-7283-TP LUAD-17-Z037-TP LUAD-83-5908-TP LUAD-55-7726-TP LUAD-78-7540-TP LUAD-17-Z020-TP LUAD-55-8506-TP LUAD-17-Z026-TP LUAD-95-7947-TP LUAD-67-3771-TP LUAD-73-4666-TP LUAD-44-7667-TP LUAD-55-8620-TP LUAD-91-6848-TP LUAD-17-Z030-TP LUAD-95-7043-TP LUAD-86-8358-TP LUAD-55-8510-TP LUAD-44-7660-TP LUAD-44-7669-TP LUAD-73-4676-TP LUAD-53-7624-TP LUAD-78-7154-TP LUAD-49-4514-TP LUAD-49-4488-TP LUAD-55-7995-TP LUAD-44-6778-TP LUAD-05-4384-TP LUAD-55-8085-TP LUAD-17-Z001-TP LUAD-55-1594-TP LUAD-50-5068-TP LUAD-78-7149-TP LUAD-05-4382-TP LUAD-05-4410-TP LUAD-69-7765-TP LUAD-78-7155-TP LUAD-78-7147-TP LUAD-44-6147-TP LUAD-97-8172-TP LUAD-50-5944-TP LUAD-55-7570-TP LUAD-05-5423-TP LUAD-55-8096-TP LUAD-50-5066-TP LUAD-67-3770-TP LUAD-50-6595-TP LUAD-62-8394-TP LUAD-86-8055-TP LUAD-55-7573-TP LUAD-49-4490-TP LUAD-64-1681-TP LUAD-86-8075-TP LUAD-17-Z047-TP LUAD-50-5930-TP LUAD-44-3918-TP LUAD-44-6774-TP LUAD-50-6594-TP LUAD-78-8662-TP LUAD-05-5428-TP LUAD-55-8092-TP LUAD-55-6979-TP LUAD-44-2662-TP LUAD-44-2666-TP LUAD-44-7662-TP LUAD-55-8089-TP LUAD-17-Z062-TP LUAD-55-8205-TP LUAD-17-Z057-TP LUAD-44-5645-TP LUAD-38-4625-TP LUAD-97-8547-TP LUAD-05-4426-TP LUAD-17-Z015-TP LUAD-17-Z023-TP LUAD-78-7220-TP LUAD-17-Z049-TP LUAD-91-6840-TP LUAD-55-7727-TP LUAD-50-8460-TP LUAD-55-7994-TP LUAD-55-8301-TP LUAD-05-4424-TP LUAD-75-6214-TP LUAD-55-8208-TP LUAD-97-7937-TP LUAD-78-7146-TP LUAD-05-4398-TP LUAD-38-6178-TP LUAD-35-5375-TP LUAD-55-8507-TP LUAD-64-1677-TP LUAD-44-5644-TP LUAD-44-2659-TP LUAD-44-3396-TP LUAD-17-Z031-TP LUAD-86-6851-TP LUAD-35-4122-TP LUAD-50-6590-TP LUAD-78-8640-TP LUAD-17-Z055-TP LUAD-50-5933-TP LUAD-97-7553-TP LUAD-50-5049-TP LUAD-50-5045-TP LUAD-86-8073-TP LUAD-50-6593-TP LUAD-17-Z056-TP LUAD-17-Z009-TP LUAD-17-Z045-TP LUAD-44-7670-TP LUAD-50-6592-TP LUAD-55-6969-TP LUAD-95-7944-TP LUAD-73-7499-TP LUAD-17-Z028-TP LUAD-17-Z044-TP LUAD-69-8255-TP LUAD-55-8621-TP LUAD-50-5931-TP LUAD-05-4430-TP LUAD-53-7626-TP LUAD-55-1592-TP LUAD-75-5125-TP LUAD-78-7536-TP LUAD-64-1678-TP LUAD-49-6767-TP LUAD-86-8279-TP LUAD-86-8673-TP LUAD-78-7150-TP LUAD-35-4123-TP LUAD-38-4632-TP LUAD-62-8399-TP LUAD-95-8039-TP LUAD-64-1679-TP LUAD-55-6985-TP LUAD-86-7954-TP LUAD-17-Z003-TP LUAD-17-Z007-TP LUAD-55-7724-TP LUAD-05-4420-TP LUAD-86-7701-TP LUAD-95-8494-TP LUAD-91-6831-TP LUAD-44-6775-TP LUAD-17-Z052-TP LUAD-55-8204-TP LUAD-17-Z021-TP LUAD-55-8614-TP LUAD-05-4405-TP LUAD-17-Z005-TP LUAD-86-7711-TP LUAD-55-7227-TP LUAD-17-Z053-TP LUAD-75-5147-TP LUAD-86-8074-TP LUAD-97-8175-TP LUAD-17-Z027-TP LUAD-75-6207-TP LUAD-62-8402-TP LUAD-91-6847-TP LUAD-50-6673-TP LUAD-17-Z061-TP LUAD-38-4630-TP LUAD-69-7760-TP LUAD-78-7143-TP LUAD-55-8619-TP LUAD-73-7498-TP LUAD-05-4418-TP LUAD-86-8674-TP LUAD-50-5051-TP LUAD-97-8176-TP LUAD-69-8253-TP LUAD-73-4677-TP LUAD-75-6206-TP LUAD-62-8398-TP LUAD-75-7027-TP LUAD-55-7815-TP LUAD-78-7167-TP LUAD-50-5941-TP LUAD-78-7539-TP LUAD-05-4249-TP LUAD-17-Z033-TP LUAD-55-6975-TP LUAD-97-7941-TP LUAD-05-4403-TP LUAD-05-4390-TP LUAD-55-1595-TP LUAD-78-8655-TP LUAD-91-6828-TP LUAD-44-7659-TP LUAD-55-7281-TP LUAD-78-7148-TP LUAD-69-8254-TP LUAD-55-8090-TP LUAD-67-4679-TP LUAD-55-7914-TP LUAD-49-4510-TP LUAD-55-8207-TP LUAD-55-7728-TP LUAD-05-4250-TP LUAD-86-8076-TP LUAD-55-8097-TP LUAD-75-5126-TP LUAD-17-Z010-TP LUAD-64-5774-TP LUAD-38-4626-TP LUAD-17-Z060-TP LUAD-55-7284-TP LUAD-73-4659-TP LUAD-55-7725-TP LUAD-17-Z014-TP LUAD-49-6761-TP LUAD-69-7973-TP LUAD-50-8459-TP LUAD-55-6970-TP LUAD-NJ-A4YI-TP LUAD-73-4662-TP LUAD-67-3773-TP LUAD-17-Z036-TP LUAD-86-8054-TP LUAD-44-7672-TP LUAD-64-5815-TP LUAD-17-Z050-TP LUAD-93-7347-TP LUAD-55-6642-TP LUAD-50-8457-TP LUAD-55-8512-TP LUAD-05-4244-TP LUAD-62-A471-TP LUAD-44-A479-TP LUAD-NJ-A4YF-TP LUAD-NJ-A55R-TP LUAD-NJ-A4YP-TP LUAD-62-A46S-TP LUAD-NJ-A55O-TP LUAD-95-A4VP-TP LUAD-62-A470-TP LUAD-62-A46P-TP LUAD-MP-A4T4-TP LUAD-93-A4JO-TP LUAD-MP-A4TI-TP LUAD-62-A46R-TP LUAD-53-A4EZ-TP LUAD-55-A4DF-TP LUAD-62-A46O-TP LUAD-55-A48Z-TP LUAD-93-A4JP-TP LUAD-44-A4SU-TP LUAD-MP-A4T9-TP LUAD-55-A491-TP LUAD-69-A59K-TP LUAD-55-A48X-TP LUAD-L4-A4E5-TP LUAD-93-A4JN-TP LUAD-86-A4P7-TP LUAD-55-A493-TP LUAD-44-A4SS-TP LUAD-55-A4DG-TP LUAD-97-A4LX-TP LUAD-J2-A4AD-TP LUAD-91-A4BC-TP LUAD-O1-A52J-TP LUAD-62-A46U-TP LUAD-44-A47G-TP LUAD-L9-A444-TP LUAD-62-A46Y-TP LUAD-MP-A4T7-TP LUAD-55-A490-TP LUAD-44-A47A-TP LUAD-86-A4JF-TP LUAD-95-A4VN-TP LUAD-L9-A443-TP LUAD-55-A494-TP LUAD-95-A4VK-TP LUAD-44-A47F-TP LUAD-97-A4M0-TP LUAD-86-A456-TP LUAD-MP-A4T8-TP LUAD-J2-A4AG-TP LUAD-NJ-A4YG-TP LUAD-97-A4M5-TP LUAD-55-A492-TP LUAD-NJ-A4YQ-TP LUAD-97-A4M3-TP LUAD-97-A4M7-TP LUAD-97-A4M1-TP LUAD-62-A472-TP LUAD-62-A46V-TP LUAD-91-A4BD-TP LUAD-L4-A4E6-TP LUAD-55-A48Y-TP LUAD-44-A47B-TP LUAD-NJ-A55A-TP LUAD-MP-A4T2-TP LUAD-J2-A4AE-TP LUAD-93-A4JQ-TP LUAD-97-A4M6-TP LUAD-97-A4M2-TP LUAD-MP-A4T6-TP LUAD-38-A44F-TP LUAD-86-A4P8-TP LUAD-MP-A4TF-TP LUAD-MP-A4TE-TP LUAD-MP-A4TH-TP LUAD-MP-A4TK-TP LUAD-MN-A4N5-TP LUAD-MN-A4N1-TP LUAD-MN-A4N4-TP LUAD-MP-A4TA-TP LUAD-MP-A4TC-TP LUAD-MP-A4SV-TP LUAD-MP-A4SY-TP LUAD-MP-A4TD-TP LUAD-MP-A5C7-TP LUAD-MP-A4SW-TP