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-CH-5743-01A-21D-1572-02	TCGA-CH-5744-01A-11D-1572-02	TCGA-CH-5745-01A-11D-1572-02	TCGA-CH-5746-01A-11D-1572-02	TCGA-CH-5750-01A-11D-1572-02	TCGA-CH-5751-01A-11D-1572-02	TCGA-CH-5754-01A-11D-1572-02	TCGA-CH-5762-01A-11D-1572-02	TCGA-CH-5763-01A-11D-1572-02	TCGA-CH-5765-01A-11D-1572-02	TCGA-CH-5766-01A-11D-1572-02	TCGA-CH-5768-01A-11D-1572-02	TCGA-CH-5769-01A-11D-1572-02	TCGA-G9-6348-01A-11D-1784-02	TCGA-G9-6494-01A-11D-1784-02	
Amplification Peak 1	8q24.13	chr8:93935184-146364022(probes 665:677)	chr8:108263899-146364022(probes 666:677)	chr8:108263899-146364022(probes 666:677)	0.04721	 0.04721		0: t<0.3; 1: 0.3<t< 0.9; 2: t>0.9	0	0	0	0	0	2	2	1	0	0	0	0	0	0	1	
Deletion Peak 1	3q26.31	chr3:171086049-198022430(probes 222:250)	chr3:173006255-177803511(probes 223:232)	chr3:173006255-179264551(probes 223:235)	0.10139	 0.10139		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	
Deletion Peak 2	6q21   	chr6:81745283-127847770(probes 477:506)  	chr6:83177876-123272695(probes 478:503)  	chr6:83177876-127847770(probes 478:506)  	0.10139	 0.10139		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	
Deletion Peak 3	13q14.2	chr13:37890423-95333015(probes 1006:1022)	chr13:38379701-81142770(probes 1007:1018)	chr13:38379701-95333014(probes 1007:1021)	0.10139	 0.10139		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	0	0	0	0	0	0	1	0	0	1	0	1	0	0	0	
Amplification Peak 1 - CN values	8q24.13	chr8:93935184-146364022(probes 665:677)	chr8:108263899-146364022(probes 666:677)	chr8:108263899-146364022(probes 666:677)	0.04721	 0.04721		Actual Copy Change Given	-0.0052464	0.0060175	0.0060579	-0.0028426	0.0047548	1.7144	0.94494	0.38385	-0.017294	0.004299	0.0051289	-0.095413	0.0023282	0.01345	0.58362	
Deletion Peak 1 - CN values	3q26.31	chr3:171086049-198022430(probes 222:250)	chr3:173006255-177803511(probes 223:232)	chr3:173006255-179264551(probes 223:235)	0.10139	 0.10139		Actual Copy Change Given	0.0056686	0	0.0086656	0.010473	0	0.29323	0.93328	0.016298	0.00017577	-0.3802	0.03295	-0.6844	-0.0015381	0.0010286	0.017311	
Deletion Peak 2 - CN values	6q21   	chr6:81745283-127847770(probes 477:506)  	chr6:83177876-123272695(probes 478:503)  	chr6:83177876-127847770(probes 478:506)  	0.10139	 0.10139		Actual Copy Change Given	6.5443e-06	-0.23149	0.017146	0.0042857	0.0085686	0.18551	-0.61118	-0.0068782	-0.019341	-0.010418	-0.5323	-0.1684	0.00074916	-0.00086391	-0.030642	
Deletion Peak 3 - CN values	13q14.2	chr13:37890423-95333015(probes 1006:1022)	chr13:38379701-81142770(probes 1007:1018)	chr13:38379701-95333014(probes 1007:1021)	0.10139	 0.10139		Actual Copy Change Given	0.00066792	0.0088557	0.01619	0.0067026	-0.027795	-0.19368	-0.52725	-0.26671	-0.0041676	-0.74379	0.010748	-0.69931	-0.0015944	-0.27932	-0.14966	
