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-AL-3466-01A-01D-1190-01	TCGA-AL-3467-01A-01D-1190-01	TCGA-AL-3468-01A-02D-1348-01	TCGA-AL-3471-01A-02D-1348-01	TCGA-AL-3472-01A-01D-1190-01	TCGA-AL-3473-01A-01D-1190-01	TCGA-B1-5398-01A-02D-1588-01	TCGA-B3-3925-01A-02D-1348-01	TCGA-B3-3926-01A-02D-1348-01	TCGA-B3-4103-01A-02D-1348-01	TCGA-B3-4104-01A-02D-1348-01	TCGA-B9-4113-01A-01D-1190-01	TCGA-B9-4114-01A-01D-1190-01	TCGA-B9-4115-01A-01D-1549-01	TCGA-B9-4116-01A-02D-1348-01	TCGA-B9-4117-01A-02D-1348-01	TCGA-B9-4617-01A-01D-1190-01	TCGA-B9-5155-01A-01D-1588-01	TCGA-B9-5156-01A-01D-1588-01	TCGA-BQ-5875-01A-11D-1588-01	TCGA-BQ-5876-01A-11D-1588-01	TCGA-BQ-5877-01A-11D-1588-01	TCGA-BQ-5878-01A-11D-1588-01	TCGA-BQ-5879-01A-11D-1588-01	TCGA-BQ-5880-01A-11D-1588-01	TCGA-BQ-5881-01A-11D-1588-01	TCGA-BQ-5882-01A-11D-1588-01	TCGA-BQ-5883-01A-11D-1588-01	TCGA-BQ-5884-01A-11D-1588-01	TCGA-BQ-5885-01A-11D-1588-01	TCGA-BQ-5886-01A-11D-1588-01	TCGA-BQ-5888-01A-11D-1588-01	TCGA-BQ-5889-01A-11D-1588-01	TCGA-BQ-5890-01A-11D-1588-01	TCGA-BQ-5891-01A-11D-1588-01	TCGA-BQ-5892-01A-11D-1588-01	TCGA-BQ-5893-01A-11D-1588-01	TCGA-BQ-5894-01A-11D-1588-01	TCGA-DW-5560-01A-01D-1588-01	TCGA-DW-5561-01A-01D-1588-01	TCGA-EV-5901-01A-11D-1588-01	TCGA-EV-5902-01A-11D-1588-01	TCGA-EV-5903-01A-11D-1588-01	
Deletion Peak 1	1p36.32 	chr1:1-28297496(probes 1:12567)                  	chr1:1-6612726(probes 1:1957)                     	chr1:1-28211570(probes 1:12524)                  	0.12387	  0.12387		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	1	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	1	0	1	0	0	0	0	1	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	
Deletion Peak 2	1p31.1  	chr1:70675808-71304028(probes 38238:38663)      	chr1:71190214-71288166(probes 38590:38653)      	chr1:71186897-71244462(probes 38586:38624)      	0.12387	  0.12662		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	1	0	0	0	0	0	1	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	
Deletion Peak 3	2q37.2  	chr2:217430650-242951149(probes 249665:264003)	chr2:232874651-239782968(probes 258629:262899)	chr2:225021303-242951149(probes 254342:264003)	0.12387	  0.12387		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	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	
Deletion Peak 4	5q35.3  	chr5:172937971-177517373(probes 583416:585551)	chr5:176481175-176664472(probes 585276:585359)	chr5:176583221-176586251(probes 585318:585319)	0.19928	  0.20652		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	0	0	0	0	0	0	0	0	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	0	0	0	0	0	0	0	0	
Deletion Peak 5	9p21.3  	chr9:21545227-22438737(probes 871718:872303)    	chr9:21949052-22001391(probes 871978:872019)    	chr9:21521537-24384829(probes 871707:873472)    	0.075334	 0.075334		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	1	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	
Deletion Peak 6	9q21.13 	chr9:76751178-77699761(probes 886639:887333)    	chr9:76785266-76953119(probes 886660:886766)    	chr9:76805659-76995000(probes 886672:886797)    	0.13175	  0.13175		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	0	0	0	0	0	0	0	0	1	0	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	
Deletion Peak 7	13q21.31	chr13:1-69613124(probes 1165160:1197005)       	chr13:63205516-63322365(probes 1193323:1193324)	chr13:63205533-63323282(probes 1193324:1193325)	0.13175	  0.13175		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	1	0	0	0	0	0	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	
Deletion Peak 8	16q23.1 	chr16:75872277-88827254(probes 1349541:1359605)	chr16:76686559-77804527(probes 1350466:1351672)	chr16:77355589-77355931(probes 1351070:1351071)	0.20652	  0.20652		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	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	
Deletion Peak 9	18q23   	chr18:72302240-72667805(probes 1443623:1443859)	chr18:72368996-72401730(probes 1443661:1443682)	chr18:72383939-72388919(probes 1443672:1443673)	0.1382	   0.1337		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	1	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	
Deletion Peak 1 - CN values	1p36.32 	chr1:1-28297496(probes 1:12567)                  	chr1:1-6612726(probes 1:1957)                     	chr1:1-28211570(probes 1:12524)                  	0.12387	  0.12387		Actual Copy Change Given	-0.53104	-0.17752	-0.13057	-0.10203	-0.045635	-0.084015	-0.017529	-0.01849	-0.85551	-0.038306	-0.010941	-0.033541	-0.050235	-0.099188	-0.43262	-0.039665	-0.14011	-0.03749	-0.05725	-0.39745	0.0055529	-0.64067	0.026233	-0.13005	-0.0041546	-0.025072	-0.61624	-0.020493	-0.029584	-0.71568	0.0208	-0.39028	-0.0067813	-0.6564	-0.098945	-0.12082	-0.02603	-0.27502	-0.00055444	-0.021784	-0.046012	-0.088904	-0.023155	
Deletion Peak 2 - CN values	1p31.1  	chr1:70675808-71304028(probes 38238:38663)      	chr1:71190214-71288166(probes 38590:38653)      	chr1:71186897-71244462(probes 38586:38624)      	0.12387	  0.12662		Actual Copy Change Given	1.4037	-0.086518	-0.055364	-0.022744	-0.0037395	0.0069435	-0.0024938	-0.0045695	-0.85161	0.0012481	-0.027983	-0.0010556	-0.005814	-0.8353	-0.16421	-0.025893	-0.069842	-0.018216	-0.005261	-0.37508	-0.0037395	-0.68624	0.0049969	0.011539	-0.0019399	0.0037465	-0.59107	-0.0064486	-0.014228	0.010712	0.0030894	0.004171	-0.0024938	-0.017529	-0.026988	-0.045635	-0.013402	-0.2755	-0.0019399	0.023566	-0.018078	-0.024251	-0.010922	
Deletion Peak 3 - CN values	2q37.2  	chr2:217430650-242951149(probes 249665:264003)	chr2:232874651-239782968(probes 258629:262899)	chr2:225021303-242951149(probes 254342:264003)	0.12387	  0.12387		Actual Copy Change Given	0.93386	-0.044009	-0.059269	0.83078	-0.0067813	-0.014661	-0.0079885	0	0.025952	-0.0044247	-0.2407	-0.033269	-0.0092666	-0.046239	0.018663	-0.68435	-0.074395	-0.0033243	-0.049459	-0.031543	-0.0013858	0.011121	-0.84843	0.018383	-0.0015243	-0.0053992	0.018243	0	-0.0048461	0.60739	0.02052	0.0045085	0.00027728	0.012291	-0.075478	0.1592	0.6148	0.25243	-0.0050351	0.77176	-0.026125	-0.063527	-0.0016629	
Deletion Peak 4 - CN values	5q35.3  	chr5:172937971-177517373(probes 583416:585551)	chr5:176481175-176664472(probes 585276:585359)	chr5:176583221-176586251(probes 585318:585319)	0.19928	  0.20652		Actual Copy Change Given	3.9459	-0.00027724	-0.062769	-0.085988	-0.0059522	0.30185	0.32028	-0.006505	0.032986	-0.023557	-0.97371	-0.084528	-0.059942	-0.041222	-0.0166	0.54171	-0.1114	-0.0076101	0	-0.0022654	0.011539	0.023005	0.0054139	-0.70496	0.00458	-0.012438	0.021052	0.0014434	-0.051316	0.00028602	0.024305	-0.013257	-0.10224	0.52223	1.4699	0.77064	-0.02384	-0.26639	-0.0096806	-0.0083005	-0.031496	0.95263	-0.023703	
Deletion Peak 5 - CN values	9p21.3  	chr9:21545227-22438737(probes 871718:872303)    	chr9:21949052-22001391(probes 871978:872019)    	chr9:21521537-24384829(probes 871707:873472)    	0.075334	 0.075334		Actual Copy Change Given	-0.99548	0.031999	-0.0055375	-0.0048461	0.025812	0.026061	0.0093098	0.0022193	-0.84803	-0.0033243	0.66124	0.0068825	0.00083195	0.004238	-0.67085	-0.032723	-0.0095165	0.013353	0.0081959	-0.0014371	-0.0053992	-1.0929	0.0027745	-0.72218	-0.0008316	0.0036076	0.023286	0.0058877	0.0024969	0.004172	-0.0046708	-0.35942	-0.14168	0.0029133	-0.012713	-0.020412	0.0073609	-0.029164	0.00013863	0.00597	0.0070826	0.015727	0.0058309	
Deletion Peak 6 - CN values	9q21.13 	chr9:76751178-77699761(probes 886639:887333)    	chr9:76785266-76953119(probes 886660:886766)    	chr9:76805659-76995000(probes 886672:886797)    	0.13175	  0.13175		Actual Copy Change Given	-0.016154	0.012655	-0.012162	-0.03286	0.015028	0.011818	-0.014532	0.0041632	-0.83397	0.0071303	-1.5	0.0013868	-0.00698	0.0024329	0.004719	-0.030449	-0.029112	-0.0084385	-0.010094	-0.0054047	-0.0038779	0.0013868	0.0026357	-0.73064	-0.0066432	-0.0094046	0.013074	-0.0068631	-0.0024938	-0.0015156	0.0040615	-0.37188	-0.14322	-0.010784	-0.033814	-0.020001	-0.010098	-0.031386	0.00013863	-0.0036011	-0.0087146	0.00458	-0.0013858	
Deletion Peak 7 - CN values	13q21.31	chr13:1-69613124(probes 1165160:1197005)       	chr13:63205516-63322365(probes 1193323:1193324)	chr13:63205533-63323282(probes 1193324:1193325)	0.13175	  0.13175		Actual Copy Change Given	-0.023233	0.023706	-0.005814	0.019643	0.032281	0.059794	0.34453	0.0076392	-0.85198	0	-0.033318	0.016985	0.035806	-0.8403	0.051672	1.1162	0.9337	0.017684	0.010006	-0.3639	-0.027945	-0.029989	0.0043021	-0.71764	0.00055459	0.0015255	-0.58402	0.013549	0.017404	0.20428	-0.0062774	0.023714	-0.015879	-0.013264	0.028903	-0.019782	0.0043021	-0.2886	0.0063871	0.80247	0.0054139	0.044148	0.56774	
Deletion Peak 8 - CN values	16q23.1 	chr16:75872277-88827254(probes 1349541:1359605)	chr16:76686559-77804527(probes 1350466:1351672)	chr16:77355589-77355931(probes 1351070:1351071)	0.20652	  0.20652		Actual Copy Change Given	0.42957	0.018103	0.53485	0.73948	-0.028081	-0.038034	0.3145	-0.0088526	0.028341	1.4082	-0.025346	-0.051316	0.53309	-0.018691	-0.039529	0.50203	0.79049	0.75261	0.5259	0.70301	0.0087528	0.063652	0.020763	0.022024	0.27395	0.59728	-0.36386	-0.023169	-0.014503	-0.031487	0.6049	0.0023659	-0.0060904	-0.0055375	1.4016	-0.014503	-0.61595	0.036202	-0.0040162	-0.011473	-0.019726	0.91743	0.54753	
Deletion Peak 9 - CN values	18q23   	chr18:72302240-72667805(probes 1443623:1443859)	chr18:72368996-72401730(probes 1443661:1443682)	chr18:72383939-72388919(probes 1443672:1443673)	0.1382	   0.1337		Actual Copy Change Given	0.069382	-0.010922	-0.035857	-0.062454	-0.0047079	0.021463	0.059508	0.028763	-0.21552	0.74347	0.042166	0.0049615	0.016146	-0.046416	-0.69859	-0.034768	-0.014477	0.78755	0.04344	0.014002	0.0063871	-0.65622	0.020063	-0.7554	-0.0013858	0.018943	-0.5944	0.0043588	0.024127	0.010433	0.009765	0.028489	0.016006	0.019503	-0.049849	-0.033814	0.010006	-0.25009	0.86731	0.012516	0.019806	0.0093098	-0.57279	
