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-CS-4938-01B-11D-1891-02	TCGA-CS-4941-01A-01D-1465-02	TCGA-CS-4944-01A-01D-1465-02	TCGA-CS-5396-01A-02D-1465-02	TCGA-CS-6186-01A-12D-2022-02	TCGA-CS-6290-01A-11D-1703-02	TCGA-DB-5273-01A-01D-1465-02	TCGA-DB-5276-01A-01D-1465-02	TCGA-DB-5279-01A-01D-1465-02	TCGA-DB-5280-01A-01D-1465-02	TCGA-DH-5143-01A-01D-1465-02	TCGA-DU-5847-01A-11D-1703-02	TCGA-DU-5849-01A-11D-1703-02	TCGA-DU-5852-01A-11D-1703-02	TCGA-DU-5854-01A-11D-1703-02	TCGA-DU-5872-01A-11D-1703-02	TCGA-DU-6392-01A-11D-1703-02	TCGA-DU-6399-01A-12D-1703-02	TCGA-DU-6402-01A-11D-1703-02	TCGA-DU-6403-01A-11D-1703-02	TCGA-DU-6405-01A-11D-1703-02	TCGA-DU-6408-01A-11D-1703-02	TCGA-DU-6542-01A-11D-1891-02	TCGA-DU-7006-01A-11D-2022-02	TCGA-DU-7007-01A-11D-2022-02	TCGA-DU-7008-01A-11D-2022-02	TCGA-DU-7010-01A-11D-2022-02	TCGA-DU-7018-01A-11D-2022-02	TCGA-DU-7290-01A-11D-2022-02	TCGA-DU-7292-01A-11D-2022-02	TCGA-DU-7294-01A-11D-2022-02	TCGA-E1-5303-01A-01D-1465-02	TCGA-E1-5305-01A-01D-1891-02	TCGA-E1-5307-01A-01D-1891-02	TCGA-FG-5963-01A-11D-1703-02	TCGA-FG-6688-01A-11D-1891-02	TCGA-FG-6689-01A-11D-1891-02	TCGA-FG-6690-01A-11D-1891-02	TCGA-FG-6691-01A-11D-1891-02	TCGA-FG-6692-01A-11D-1891-02	TCGA-FG-7636-01A-11D-2088-02	TCGA-FN-7833-01A-11D-2088-02	TCGA-HT-7468-01A-11D-2022-02	TCGA-HT-7472-01A-11D-2022-02	TCGA-HT-7473-01A-11D-2022-02	TCGA-HT-7475-01A-11D-2022-02	TCGA-HT-7476-01A-11D-2022-02	TCGA-HT-7481-01A-11D-2022-02	TCGA-HT-7601-01A-11D-2088-02	TCGA-HT-7604-01A-11D-2088-02	TCGA-HW-7489-01A-11D-2022-02	TCGA-HW-7495-01A-11D-2022-02	
Amplification Peak 1	1q32.1 	chr1:203146460-205225922(probes 123:134)	chr1:203198850-204787405(probes 124:131)	chr1:203198850-212612545(probes 124:136)	0.023697	   0.023697		0: t<0.3; 1: 0.3<t< 0.9; 2: t>0.9	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	0	0	0	0	1	0	1	2	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	
Amplification Peak 2	7p11.2 	chr7:55200240-55340844(probes 1124:1133)  	chr7:55220592-55299013(probes 1125:1132)  	chr7:54074235-56476291(probes 1103:1149)  	1.0942e-12	 1.0942e-12		0: t<0.3; 1: 0.3<t< 0.9; 2: t>0.9	0	2	0	0	1	0	0	0	0	0	0	0	0	2	2	0	1	0	1	2	2	0	0	1	0	0	0	0	0	2	0	0	0	0	0	2	0	0	1	2	0	0	0	0	1	0	0	0	0	0	0	0	
Amplification Peak 3	12q14.1	chr12:57622487-58850360(probes 2023:2038)	chr12:58103614-58532341(probes 2026:2037)	chr12:58103614-58871666(probes 2026:2040)	0.1577	     0.1577		0: t<0.3; 1: 0.3<t< 0.9; 2: t>0.9	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	2	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	
Deletion Peak 1	2q37.3	chr2:231497683-243199373(probes 333:359)	chr2:239012517-243199373(probes 348:359)	chr2:232615596-243199373(probes 335:359)	0.096327	   0.096327		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	1	0	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	
Deletion Peak 2	9p21.3	chr9:21238775-23878121(probes 1483:1499)  	chr9:21807670-22414457(probes 1487:1496)  	chr9:20036102-30793104(probes 1469:1529)  	3.2826e-12	 3.2826e-12		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	2	0	2	1	0	0	1	1	1	1	0	1	2	0	0	0	1	0	1	0	0	0	0	1	0	0	0	0	1	1	0	0	0	0	1	1	0	0	0	0	0	
Amplification Peak 1 - CN values	1q32.1 	chr1:203146460-205225922(probes 123:134)	chr1:203198850-204787405(probes 124:131)	chr1:203198850-212612545(probes 124:136)	0.023697	   0.023697		Actual Copy Change Given	-0.009189	0.4747	-0.030259	2.6796e-05	0.00072756	0	0.00049171	-0.0019946	0.002462	0.00011393	0.0032531	0.0041464	0.010473	0.0091402	0.00055475	-0.0057277	0.34932	0.0041559	0.00026736	1.2401	0.031421	0	0.20092	-0.089881	0.027649	-0.013693	0.82743	0.0047714	0.51919	6	-0.021297	0.00017994	-0.033455	0	0.0089292	6	-0.026858	0.00019998	0	0.0015751	-0.040739	-0.0033228	-0.00074636	0.0084756	0.0011573	0.64796	0.011403	0.001742	0.016016	0	0.00086789	0.0026221	
Amplification Peak 2 - CN values	7p11.2 	chr7:55200240-55340844(probes 1124:1133)  	chr7:55220592-55299013(probes 1125:1132)  	chr7:54074235-56476291(probes 1103:1149)  	1.0942e-12	 1.0942e-12		Actual Copy Change Given	0.0053677	6	0.18494	0.17461	0.84143	-0.0041118	0	0.011091	0.0029366	0.008153	0.043218	-0.0060351	-0.012996	6	6	-0.0109	0.80233	-0.0025384	0.63397	6	6	0.018005	0.037309	0.74699	0.026474	0.048248	0.016765	0.019237	0.00075597	6	0.033168	0	0.0041421	0.031674	0.013819	6	0.0073003	0	0.75413	6	0.023166	-0.0016172	0.0009269	0.019148	0.76874	0.0042372	-0.0028635	0	0.013563	0.05557	0.0095361	-0.0031929	
Amplification Peak 3 - CN values	12q14.1	chr12:57622487-58850360(probes 2023:2038)	chr12:58103614-58532341(probes 2026:2037)	chr12:58103614-58871666(probes 2026:2040)	0.1577	     0.1577		Actual Copy Change Given	0.0021361	2.0636	-0.00090788	0.0019167	-0.028148	-0.071176	-0.061173	-0.0029297	-0.45214	0	-0.023442	0	0.0067204	0.0042605	0	0	-0.0047513	-0.011978	-0.0035961	6	-0.00070233	0.0027838	-0.35124	0.016185	-0.39527	-0.11255	2.9124	0.0081413	0.0034707	0.00043857	-0.0012814	0.001072	0.33145	0.027003	0.021337	-0.009719	-0.57135	-0.15738	0.0011008	-0.003009	0.20575	0	0.00014237	-0.035013	-0.0033529	0.0020729	0	-0.0037557	-0.0036634	-0.08122	0	-0.00034287	
Deletion Peak 1 - CN values	2q37.3	chr2:231497683-243199373(probes 333:359)	chr2:239012517-243199373(probes 348:359)	chr2:232615596-243199373(probes 335:359)	0.096327	   0.096327		Actual Copy Change Given	0.0015394	-0.015358	0.00038575	-0.021124	0.025735	0.041349	0.0036872	-0.0027465	0.0030475	0.0073265	-0.0038773	0.00098461	-0.0070661	0.015409	0.0011883	0.0084256	0.016095	0.0017266	0	0	-0.36955	-0.28656	-0.31008	0.049987	-0.81246	-0.63657	-0.017468	-0.034492	0.00041923	-0.0026023	0.0042564	0.0010874	0.0080378	0.063661	0.011393	0.00634	0.0019976	-0.010883	0.0047659	0.0097177	-0.011444	0.013094	-0.00068077	0.011852	-0.74359	0	0.0075234	0.00081155	-0.65466	-0.0014708	-0.030801	0.0014662	
Deletion Peak 2 - CN values	9p21.3	chr9:21238775-23878121(probes 1483:1499)  	chr9:21807670-22414457(probes 1487:1496)  	chr9:20036102-30793104(probes 1469:1529)  	3.2826e-12	 3.2826e-12		Actual Copy Change Given	-0.0026922	-0.014056	0	-0.19545	-0.24277	-0.0049614	0.0011972	-0.064564	-0.45177	-0.0065986	-0.005355	-1.5	0.0054823	-1.5	-1.0205	-0.027663	0	-0.44508	-1.2518	-0.72809	-1.2811	0.012373	-0.39965	-1.3971	-0.29781	0	1.1933	-0.37909	-0.052887	-1.2934	-0.0037296	-0.012267	-0.051142	-0.16181	-0.79977	-0.00099733	0.00091825	-0.14084	0.0045947	-0.81458	-0.5032	-0.0060537	-0.0030748	-0.0093766	-0.0010515	-0.82963	-0.80847	-0.012529	-0.0089047	-0.010058	-0.036845	0.0029182	
