Unique Name	Descriptor	Wide Peak Limits	Peak Limits	Region Limits	q values	Residual q values after removing segments shared with higher peaks	Broad or Focal	Amplitude Threshold	TCGA-BJ-A0YZ-01A-11D-A10T-01	TCGA-BJ-A0Z0-01A-11D-A10T-01	TCGA-BJ-A0Z2-01A-11D-A10T-01	TCGA-BJ-A0Z3-01A-11D-A13V-01	TCGA-BJ-A0Z5-01A-11D-A10T-01	TCGA-BJ-A0Z9-01A-11D-A10T-01	TCGA-BJ-A0ZA-01A-11D-A10T-01	TCGA-BJ-A0ZB-01A-11D-A10T-01	TCGA-BJ-A0ZC-01A-12D-A13V-01	TCGA-BJ-A0ZE-01A-11D-A10T-01	TCGA-BJ-A0ZG-01A-11D-A10T-01	TCGA-BJ-A0ZH-01A-11D-A10T-01	TCGA-BJ-A0ZJ-01A-11D-A10T-01	TCGA-BJ-A18Y-01A-11D-A13V-01	TCGA-BJ-A18Z-01A-21D-A13V-01	TCGA-BJ-A190-01A-11D-A13V-01	TCGA-BJ-A191-01A-11D-A13V-01	TCGA-BJ-A192-01A-31D-A13V-01	TCGA-BJ-A28R-01A-11D-A16M-01	TCGA-BJ-A28T-01A-11D-A16M-01	TCGA-BJ-A28W-01A-11D-A16M-01	TCGA-BJ-A28Z-01A-11D-A16M-01	TCGA-BJ-A291-01A-11D-A16M-01	TCGA-CE-A13K-01A-11D-A10T-01	TCGA-CE-A27D-01A-11D-A16M-01	TCGA-DE-A0Y2-01A-11D-A10T-01	TCGA-DE-A0Y3-01B-11D-A10T-01	TCGA-DJ-A13M-01A-11D-A10T-01	TCGA-DJ-A13O-01A-11D-A10T-01	TCGA-DJ-A13P-01A-11D-A10T-01	TCGA-DJ-A13R-01A-11D-A10T-01	TCGA-DJ-A13S-01A-11D-A10T-01	TCGA-DJ-A13T-01A-11D-A10T-01	TCGA-DJ-A13U-01A-11D-A10T-01	TCGA-DJ-A13V-01A-11D-A10T-01	TCGA-DJ-A13W-01A-11D-A10T-01	TCGA-DJ-A13X-01A-11D-A10T-01	TCGA-DJ-A1QD-01A-11D-A14V-01	TCGA-DJ-A1QE-01A-21D-A14V-01	TCGA-DJ-A1QF-01A-12D-A14V-01	TCGA-DJ-A1QG-01A-11D-A14V-01	TCGA-DJ-A1QH-01A-21D-A14V-01	TCGA-DJ-A1QI-01A-11D-A14V-01	TCGA-DJ-A1QL-01A-11D-A14V-01	TCGA-DJ-A1QM-01A-11D-A14V-01	TCGA-DJ-A1QN-01A-11D-A14V-01	TCGA-DJ-A1QO-01A-11D-A14V-01	TCGA-DJ-A1QQ-01A-11D-A14V-01	TCGA-DO-A1JZ-01A-11D-A13V-01	TCGA-DO-A1K0-01A-11D-A13V-01	TCGA-E8-A242-01A-21D-A16M-01	TCGA-EM-A1CS-01A-11D-A13V-01	TCGA-EM-A1CT-01A-11D-A13V-01	TCGA-EM-A1CU-01A-11D-A13V-01	TCGA-EM-A1CV-01A-11D-A13V-01	TCGA-EM-A1CW-01A-21D-A13V-01	TCGA-EM-A1YA-01A-11D-A14V-01	TCGA-EM-A1YB-01A-11D-A14V-01	TCGA-EM-A1YC-01A-11D-A14V-01	TCGA-EM-A1YD-01A-11D-A14V-01	TCGA-EM-A1YE-01A-11D-A14V-01	TCGA-ET-A25G-01A-11D-A16M-01	TCGA-ET-A25I-01A-11D-A16M-01	TCGA-ET-A25J-01A-11D-A16M-01	TCGA-ET-A25K-01A-11D-A16M-01	TCGA-ET-A25L-01A-11D-A16M-01	TCGA-ET-A25M-01A-11D-A16M-01	TCGA-ET-A25N-01A-11D-A16M-01	TCGA-ET-A25O-01A-11D-A16M-01	TCGA-ET-A25P-01A-11D-A16M-01	TCGA-ET-A25R-01A-11D-A16M-01	TCGA-FE-A22Z-01A-11D-A16M-01	TCGA-FE-A230-01A-11D-A14V-01	TCGA-FE-A231-01A-11D-A14V-01	TCGA-FE-A232-01A-11D-A14V-01	TCGA-FE-A233-01A-11D-A14V-01	TCGA-FE-A234-01A-11D-A14V-01	TCGA-FE-A235-01A-11D-A16M-01	TCGA-FE-A236-01A-11D-A16M-01	TCGA-FE-A237-01A-11D-A16M-01	TCGA-FE-A238-01A-11D-A16M-01	TCGA-FE-A239-01A-11D-A16M-01	TCGA-FE-A23A-01A-11D-A16M-01	TCGA-GE-A2C6-01A-11D-A16M-01	TCGA-H2-A26U-01A-11D-A16M-01	
Amplification Peak 1	11p15.4 	chr11:3376079-3481387(probes 1009354:1009371)    	chr11:3378320-3480109(probes 1009355:1009370)    	chr11:3378320-3486513(probes 1009355:1009373)    	0.15982	   0.15982		0: t<0.3; 1: 0.3<t< 0.9; 2: t>0.9	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	1	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	
Amplification Peak 2	13q14.11	chr13:42429589-42688912(probes 1181609:1181623)	chr13:42431633-42688374(probes 1181610:1181622)	chr13:42431633-42690039(probes 1181610:1181625)	0.0091372	 0.0091372		0: t<0.3; 1: 0.3<t< 0.9; 2: t>0.9	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	
Deletion Peak 1	7q22.3  	chr7:106587765-116611362(probes 743514:749009)	chr7:107006014-107054657(probes 743698:743725)	chr7:107034215-107037624(probes 743712:743713)	0.21628	 0.21628		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	
Deletion Peak 2	9q33.1  	chr9:1-140273252(probes 855388:926615)           	chr9:118227042-119219406(probes 914769:915613)	chr9:118750539-118752153(probes 915192:915193)	0.22496	 0.22496		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	
Deletion Peak 3	10q21.2 	chr10:42596299-93781320(probes 952959:981873)  	chr10:61216681-61338957(probes 961993:962090)  	chr10:61277911-61280043(probes 962042:962043)  	0.21628	 0.21628		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	
Deletion Peak 4	10q23.1 	chr10:82289828-94825202(probes 974312:982329)  	chr10:87343879-88124236(probes 977827:978382)  	chr10:87730796-87734377(probes 978105:978106)  	0.21628	 0.21628		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	
Deletion Peak 5	13q12.12	chr13:23794594-24082673(probes 1168830:1169017)	chr13:23892059-23985809(probes 1168882:1168963)	chr13:23941131-23943119(probes 1168923:1168924)	0.21628	 0.21628		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	
Deletion Peak 6	19p13.3 	chr19:5774904-5865624(probes 1446501:1446529)    	chr19:5781288-5825102(probes 1446502:1446524)    	chr19:5782108-5833868(probes 1446504:1446525)    	0.21628	 0.21628		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	
Amplification Peak 1 - CN values	11p15.4 	chr11:3376079-3481387(probes 1009354:1009371)    	chr11:3378320-3480109(probes 1009355:1009370)    	chr11:3378320-3486513(probes 1009355:1009373)    	0.15982	   0.15982		Actual Copy Change Given	-0.016337	-0.024265	-0.047531	0.65295	-0.028491	-0.025756	0.026935	-0.076545	0.0098669	0.051829	-0.020275	-0.051284	-0.039394	0.0089233	0.096224	-0.4983	0.021183	0.024408	0.023426	0.027216	0.0073609	-0.033814	0.036653	0.022585	-0.039801	-0.10026	-0.0084385	-0.070001	0.015727	-0.042517	-0.02416	0.00055459	-0.0185	0.003409	-0.080141	-0.050235	-0.015191	0.011074	0.00597	0.016845	-0.027261	-0.028901	0	-0.0096806	-0.0016629	-0.036674	0.0114	-0.0040217	0.0076392	-0.013677	0.026935	0.61843	0.016705	0.47615	-0.015329	0.019223	0.027497	-0.045364	0.62861	-0.0077482	0.020063	-0.023155	-0.046312	-0.0077482	-0.0033243	0.80267	0.63299	-0.044555	-0.041419	0.048546	-0.16853	0.012516	0.027778	-0.061689	0.0026357	0.033972	0.047694	0.045141	0.020713	-0.02603	-0.056577	-0.93843	-0.093006	0.12756	-0.063166	
Amplification Peak 2 - CN values	13q14.11	chr13:42429589-42688912(probes 1181609:1181623)	chr13:42431633-42688374(probes 1181610:1181622)	chr13:42431633-42690039(probes 1181610:1181625)	0.0091372	 0.0091372		Actual Copy Change Given	-0.058237	-0.002508	-0.0069195	-0.0055373	0.019923	-0.010094	-0.0056757	0.0076392	0.73644	0.00056873	-0.022195	0.010876	-0.014366	0.0039166	-0.035731	0.015727	0.017963	-0.013402	0	0	0.0022193	0	0.0058309	-0.050641	0.0044558	1.6693	0.038145	0.003191	0.00027728	-0.75239	-0.013999	0.003191	0.018234	-0.016515	0.023426	0.015331	0.0056919	0.0036992	-0.0081624	-0.0031859	0.0013868	0.01189	-0.012851	-0.043331	1.3219	-0.46398	-0.00069303	-0.030136	0	0.017124	-0.0060904	-0.019177	0.0037465	-0.0088344	-0.0037395	-0.011749	-0.013756	-0.66247	-0.0084385	0.44528	0.0044411	0.00458	0.0090312	0.0097276	-0.0041546	-0.01106	-0.0077482	0.00027293	0.002926	-0.0094046	0.010006	-0.0040445	0.001803	0.011679	-0.0085766	0.0027745	-0.006505	-0.91455	0.00050491	0.0063871	-0.010508	-0.90881	0.0098669	-0.077878	-0.0066432	
Deletion Peak 1 - CN values	7q22.3  	chr7:106587765-116611362(probes 743514:749009)	chr7:107006014-107054657(probes 743698:743725)	chr7:107034215-107037624(probes 743712:743713)	0.21628	 0.21628		Actual Copy Change Given	0.066611	0.016213	0.029888	0.01447	0.019618	0.022164	0.0097276	0.0097111	-0.0057713	-0.028887	0.0070826	0.0085078	0.018523	0.0033611	0.022294	0.50494	0.0063871	0.73682	-0.028075	-0.03286	0.0015255	0.0040243	-0.025307	-0.0022168	0.00083195	0.035383	0.0015255	-0.0024938	0.0020805	0.01167	0.012747	-0.0055375	-0.01286	0.016086	0.0036076	-0.015604	0.00041593	-0.016338	0.0069435	-0.0096806	-0.00041585	0.0056919	0.013353	0.0030522	-0.007472	0.012655	-0.019452	-0.014646	-0.017165	-0.015466	-0.013402	0.018383	-0.00013862	0.019319	0.0049969	-0.0084385	0.0063871	0.015308	1.2889	0.45734	-0.012438	-0.01037	-0.0089906	-0.0083005	-0.014916	0.018663	0.011261	0.015583	-0.0034501	0.0040243	0.018767	0.0041632	-0.013264	0.021323	-0.011473	-0.021647	0.0027745	-0.92612	-0.0039274	-0.0013858	0.015866	-0.014916	-0.0060904	0.01433	0.039195	
Deletion Peak 2 - CN values	9q33.1  	chr9:1-140273252(probes 855388:926615)           	chr9:118227042-119219406(probes 914769:915613)	chr9:118750539-118752153(probes 915192:915193)	0.22496	 0.22496		Actual Copy Change Given	0.0060633	-0.0073481	-0.034139	-0.0031859	-0.024388	-0.0038779	-0.0018014	0.054233	0.0037465	0.032155	-0.0091697	-0.033781	0.001556	-0.0033552	0.030159	0.01419	-0.0040989	0.044999	-0.97046	-0.025775	-0.0013858	-0.056577	-0.0015243	0.0049969	0.82549	-0.036265	-0.019177	-0.0022168	-0.022504	-0.0017862	-0.0058853	0	0.003876	0.031172	-0.0024938	-0.010646	-0.0024938	0.0042548	-0.019589	0	-0.019863	-0.024251	0.0056919	-0.00097017	0.0051359	-0.024524	0.022725	0.011255	0.011958	-0.0047079	0.0013868	0.0016642	0.011624	0.00027728	-0.0034627	0.0063871	-0.00035699	-0.67536	-0.0048461	0.42873	-0.33202	-0.0045695	-0.0098185	-0.0029091	0.0055529	-0.045906	-0.00069303	0.040181	-0.011461	0.00041593	-0.035849	-0.0008316	0.0033299	-0.89442	0.0056919	0.0024969	0.0114	0.017124	-0.0044808	-0.028491	-0.023364	-0.0029091	-0.0099565	0.045424	-0.0060904	
Deletion Peak 3 - CN values	10q21.2 	chr10:42596299-93781320(probes 952959:981873)  	chr10:61216681-61338957(probes 961993:962090)  	chr10:61277911-61280043(probes 962042:962043)  	0.21628	 0.21628		Actual Copy Change Given	-0.0043383	0.011246	-0.017254	-0.0067813	0.02511	0.011261	-0.0056757	0.0049969	-0.6857	-0.0099424	-0.00027724	0.013665	0.010842	0.0093411	-0.018728	-0.50857	0.023706	-0.007472	0.006109	0.0020805	0.0037465	0.0013868	0.018243	-0.011378	0.0094491	0.033972	0.033127	0.02525	-0.0045695	-0.0015243	-0.001365	-0.00027724	0.0062386	-0.01836	0.021323	-0.011887	0.0022193	0.0092624	-0.0048461	-0.0013858	0.0041632	0.0052749	0.0090312	0.0041841	-0.016292	0.0081959	0.012244	-0.023571	-0.86947	0.026233	-0.016979	0.0072365	-0.00013862	0.00597	-0.0054041	-0.0042929	0.0058389	0.016425	0.6594	0.0063871	0.01447	0.010564	0.0048579	0.0029133	7.0686e-05	-0.0055375	0.0040243	0.0058266	0.0098796	-0.00013862	-0.013953	-0.0083005	0.0075	0.021323	0.0079175	-0.0008316	0.011261	-0.0036011	0.0014758	0.019223	0	-0.013264	-0.010922	-0.022744	0.028341	
Deletion Peak 4 - CN values	10q23.1 	chr10:82289828-94825202(probes 974312:982329)  	chr10:87343879-88124236(probes 977827:978382)  	chr10:87730796-87734377(probes 978105:978106)  	0.21628	 0.21628		Actual Copy Change Given	0.0057853	-0.91808	-0.017254	0.00097064	-0.014228	-0.016051	-0.00069303	0.00027728	-0.67857	0.02344	0.0012481	-0.010337	-0.0040162	0.010316	0.015717	-0.51969	-0.00097017	0.023005	0.006109	-0.0027707	0.015308	0.008846	0.010842	0.0086135	-0.0049844	-0.026577	-0.024114	-0.0085766	-0.0045695	-0.0023553	-0.0062756	0.0041632	-0.0030569	0.0064221	-0.017116	0.024408	-0.0020784	0.018196	0.0073609	0.00458	0.010564	-0.017431	0.013911	-0.0015243	-0.0096583	-0.012438	0.016705	-0.0071509	0.0086135	0.00055459	0.018943	0.0052749	0.0066653	-0.0019399	-0.010922	0.0092755	0.0058389	-0.0259	0.6605	-0.01106	-0.71871	0.0094433	0.013632	-0.0031859	0.0075	0.0086564	0.0041632	-0.0081668	0.0097403	0.00013863	-0.024388	-0.0025433	0.0013868	-0.03286	0.0029133	-0.011335	0.015587	0.019643	0.0060592	-0.005261	-0.017941	0.0034687	-0.010922	0.0375	-0.010508	
Deletion Peak 5 - CN values	13q12.12	chr13:23794594-24082673(probes 1168830:1169017)	chr13:23892059-23985809(probes 1168882:1168963)	chr13:23941131-23943119(probes 1168923:1168924)	0.21628	 0.21628		Actual Copy Change Given	-0.058237	-0.01066	-0.0069195	-0.0055373	0.001803	-0.024935	-0.0036011	-0.010232	0.011818	0.00056873	0.0019418	-0.0055043	0.00041593	0.0039166	0.0056819	0.015727	0.017963	0.0012481	0.014749	0.0076392	-0.0094046	-0.016292	0.0058309	-0.024935	0.0044558	-0.00069303	-0.027398	0.003191	-0.00097017	-0.76098	-0.0066901	0.0013772	-0.0031953	-0.008498	0.0056919	0.015331	-0.0045695	0.013724	-0.0020784	0.011679	-0.21299	-0.0015243	-0.0078863	-0.043331	-0.028081	-0.0038779	0.0068044	-0.016572	0	0.017124	0.023566	-0.019951	0.0063871	0.0013868	-0.0037395	0.0063871	0.0054139	-0.66827	0.0049969	0.43556	0.022164	0.0098669	-0.017391	0.0040243	-0.0012473	-0.01106	-0.0016629	-0.0062329	-0.034937	-0.00013862	-0.015054	0.048404	0.001803	0.011679	-0.0007359	0.0027745	-0.006505	0.0011093	0.00050491	0.015308	-0.010232	-0.93024	0.0098669	-0.056038	-0.0066432	
Deletion Peak 6 - CN values	19p13.3 	chr19:5774904-5865624(probes 1446501:1446529)    	chr19:5781288-5825102(probes 1446502:1446524)    	chr19:5782108-5833868(probes 1446504:1446525)    	0.21628	 0.21628		Actual Copy Change Given	-0.31135	-0.077758	-0.046265	-0.015466	-0.0029091	0.041317	0.094782	-0.00013862	0.015028	0.11889	0.0041632	0.0015589	0.060079	0.0064184	0.11168	0.07815	0.013353	-0.72897	0.075271	0.067948	-0.0067703	-0.050506	-0.018078	0.013772	-0.030131	-0.072808	-0.038578	-0.019601	-0.0085766	0.011679	0.047929	0.023005	-0.0067907	0.062948	-0.024661	-0.038714	-0.014641	0.0010621	0.0029133	0.037076	-0.021921	-0.055499	0.023286	0.0016642	0.016146	-0.058731	0.058367	0.012231	0.065942	-0.014916	0.031999	0.076029	0.027778	0.0030522	0.00013863	0.046275	0.015727	-0.046583	0.68291	0.0098669	0.049114	-0.026562	-0.038034	0.0020805	0.031859	-0.098418	0.00097064	-0.032318	-0.037478	0.067232	0.024548	0.025531	-0.0081624	-0.027945	0.022304	0.006109	0.054091	0.050819	-0.95749	-0.011198	-0.00069303	-0.049559	-0.048207	0.10512	-0.054013	
