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-5887-01A-11D-1959-01	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-BQ-7044-01A-11D-1959-01	TCGA-BQ-7045-01A-31D-1959-01	TCGA-BQ-7046-01A-11D-1959-01	TCGA-BQ-7048-01A-11D-1959-01	TCGA-BQ-7049-01A-11D-1959-01	TCGA-BQ-7050-01A-11D-1959-01	TCGA-BQ-7051-01A-12D-1959-01	TCGA-BQ-7053-01A-11D-1959-01	TCGA-BQ-7055-01A-11D-1959-01	TCGA-BQ-7056-01A-11D-1959-01	TCGA-BQ-7058-01A-11D-1959-01	TCGA-BQ-7059-01A-11D-1959-01	TCGA-BQ-7060-01A-11D-1959-01	TCGA-BQ-7061-01A-11D-1959-01	TCGA-BQ-7062-01A-11D-1959-01	TCGA-DW-5560-01A-01D-1588-01	TCGA-DW-5561-01A-01D-1588-01	TCGA-DZ-6131-01A-11D-1959-01	TCGA-DZ-6132-01A-11D-1959-01	TCGA-DZ-6133-01A-11D-1959-01	TCGA-DZ-6134-01A-11D-1959-01	TCGA-DZ-6135-01A-11D-1959-01	TCGA-EV-5901-01A-11D-1588-01	TCGA-EV-5902-01A-11D-1588-01	TCGA-EV-5903-01A-11D-1588-01	TCGA-G7-6789-01A-11D-1959-01	TCGA-G7-6790-01A-11D-1959-01	TCGA-G7-6792-01A-21D-1959-01	TCGA-G7-6793-01A-11D-1959-01	TCGA-G7-6795-01A-11D-1959-01	TCGA-G7-6796-01A-11D-1959-01	TCGA-G7-6797-01A-11D-1959-01	TCGA-GL-6846-01A-11D-1959-01	TCGA-HE-7128-01A-11D-1959-01	TCGA-HE-7129-01A-11D-1959-01	TCGA-HE-7130-01A-11D-1959-01	
Deletion Peak 1	1p36.31	chr1:1-8925111(probes 1:3449)                     	chr1:6154447-6281666(probes 1941:1981)            	chr1:1-6974986(probes 1:2304)                     	0.02879	    0.02879		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	0	1	0	1	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	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	
Deletion Peak 2	2q37.2 	chr2:229039385-243199373(probes 252822:260562)	chr2:236401743-236766331(probes 257016:257243)	chr2:234467827-243199373(probes 255596:260562)	0.02879	    0.02879		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	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	
Deletion Peak 3	4q32.1 	chr4:1-191154276(probes 366990:469783)          	chr4:157666630-157895679(probes 453531:453653)	chr4:157786226-157786771(probes 453593:453594)	0.13468	          1		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	0	0	0	0	0	1	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	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	
Deletion Peak 4	4q32.1 	chr4:101108133-178352218(probes 422338:464928)	chr4:157666630-157895679(probes 453531:453653)	chr4:157786226-157786771(probes 453593:453594)	0.13468	    0.13468		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	0	0	0	0	0	1	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	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	
Deletion Peak 5	5q12.1 	chr5:58260298-60047770(probes 500877:501946)    	chr5:59780948-59787985(probes 501820:501821)    	chr5:59165898-59920953(probes 501541:501890)    	0.029846	   0.029846		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	0	0	0	0	0	0	1	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	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	
Deletion Peak 6	9p21.3 	chr9:21865498-22448737(probes 843262:843626)    	chr9:21959052-21997722(probes 843313:843326)    	chr9:21420139-22934248(probes 842988:843927)    	4.8772e-08	 4.8772e-08		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	2	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	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	2	
Deletion Peak 1 - CN values	1p36.31	chr1:1-8925111(probes 1:3449)                     	chr1:6154447-6281666(probes 1941:1981)            	chr1:1-6974986(probes 1:2304)                     	0.02879	    0.02879		Actual Copy Change Given	-0.49476	-0.12448	-0.041845	-0.00041585	-0.029175	0.0040243	0.030451	-0.019177	-0.84472	-0.049081	0.012097	0.0062481	-0.0079747	-0.00053602	-0.63842	-0.027493	-0.06677	-0.0099172	-0.0078863	-0.40574	-0.016647	-0.68887	-0.0019757	-0.016194	0.0020634	-0.021832	-0.62966	-0.00037066	0.032877	-0.67274	-0.021965	-0.040632	-0.42702	0.010146	-0.68861	-0.1189	-0.16489	-0.0123	-0.30898	-0.83397	-0.019589	-0.018628	-0.067001	-0.0023979	0.012591	-0.080541	-0.019288	-0.71286	0.013632	-0.030404	-0.0011389	-0.026011	0.027778	-0.0078614	-0.008896	0.010902	-0.017529	0.0019418	-0.0017853	-0.0054505	0	-0.0016629	-1.0132	-0.0039179	-0.025893	0.00045452	-0.0047828	-0.070536	0.00041593	0.015308	-0.87221	-0.0098185	-0.00806	-0.011473	1.1401	
Deletion Peak 2 - CN values	2q37.2 	chr2:229039385-243199373(probes 252822:260562)	chr2:236401743-236766331(probes 257016:257243)	chr2:234467827-243199373(probes 255596:260562)	0.02879	    0.02879		Actual Copy Change Given	0.83116	-0.02678	0.01177	0.82823	-0.0016303	0.0058309	0.0022193	0.020903	0.04741	0.044934	-0.19149	0.020903	0.018383	0.0095044	0.008169	-0.67315	0.060941	0.020063	0.015447	0.030909	-0.0092672	0.041648	-0.89361	0.021597	0.026141	0.019363	0.0078427	0.004428	0.020094	0.71867	0.01639	0.094688	0.0008789	0.0027745	0.024829	0.029588	0.17761	0.64469	0.24691	-0.0044312	0.013492	0.51943	-0.0021278	-0.0019455	0.014684	0.0083351	0.028836	0.01638	-0.0054268	0.0044411	0.010812	0.0082076	-0.01218	0.0040742	0.023847	0.77126	0.0049969	0	0.77986	0.007704	-0.00151	0.010842	0.0023581	0.017264	0.87528	0.64181	0.021387	-0.0053992	0.57987	0.0012481	0.00076951	0.010424	0.0024611	0.027357	-0.87471	
Deletion Peak 3 - CN values	4q32.1 	chr4:1-191154276(probes 366990:469783)          	chr4:157666630-157895679(probes 453531:453653)	chr4:157786226-157786771(probes 453593:453594)	0.13468	          1		Actual Copy Change Given	-0.10829	0.017124	0.0010524	-0.0067453	0.00050249	-0.0042388	-0.013127	0.011121	-0.78322	0.020699	-0.079016	-0.0039223	0.59255	-0.0015243	-0.016593	-0.035583	0.012498	-0.0012473	0.0017719	0.0069216	-0.84731	-0.017321	-0.0040006	-0.041255	-0.00084868	-0.0040276	-0.59208	-0.0013866	-0.015836	-0.020961	0.0017684	-0.022486	0.010842	-0.0035659	-0.0033243	0.013319	0.16791	-0.0097288	-0.29436	-0.01409	-0.0012473	0.0026357	0.0047973	0.00091325	-0.002004	0.024829	0.0046524	-0.0057206	-0.0020672	0.016006	0.00075125	0.0039355	-0.026441	0.011689	0.0042216	-0.044881	-0.36283	0.0011093	-0.0133	0.0050505	-0.0019951	-0.00066053	0.05067	0.0058309	0.51429	-0.0091514	-0.00085527	0.011679	0.62151	-0.011931	-0.0019399	-0.0049844	0.00060117	-0.0089192	-0.74621	
Deletion Peak 4 - CN values	4q32.1 	chr4:101108133-178352218(probes 422338:464928)	chr4:157666630-157895679(probes 453531:453653)	chr4:157786226-157786771(probes 453593:453594)	0.13468	    0.13468		Actual Copy Change Given	-0.10829	0.017124	0.0010524	-0.0067453	0.00050249	-0.0042388	-0.013127	0.011121	-0.78322	0.020699	-0.079016	-0.0039223	0.59255	-0.0015243	-0.016593	-0.035583	0.012498	-0.0012473	0.0017719	0.0069216	-0.84731	-0.017321	-0.0040006	-0.041255	-0.00084868	-0.0040276	-0.59208	-0.0013866	-0.015836	-0.020961	0.0017684	-0.022486	0.010842	-0.0035659	-0.0033243	0.013319	0.16791	-0.0097288	-0.29436	-0.01409	-0.0012473	0.0026357	0.0047973	0.00091325	-0.002004	0.024829	0.0046524	-0.0057206	-0.0020672	0.016006	0.00075125	0.0039355	-0.026441	0.011689	0.0042216	-0.044881	-0.36283	0.0011093	-0.0133	0.0050505	-0.0019951	-0.00066053	0.05067	0.0058309	0.51429	-0.0091514	-0.00085527	0.011679	0.62151	-0.011931	-0.0019399	-0.0049844	0.00060117	-0.0089192	-0.74621	
Deletion Peak 5 - CN values	5q12.1 	chr5:58260298-60047770(probes 500877:501946)    	chr5:59780948-59787985(probes 501820:501821)    	chr5:59165898-59920953(probes 501541:501890)    	0.029846	   0.029846		Actual Copy Change Given	-0.54973	0	-0.0038779	-0.032128	0.00022518	0.13698	0.35055	0	0.07785	0.00021366	-0.0031258	-0.005814	-0.0157	-0.0045695	-0.011086	0.54027	-0.0013858	-0.0039334	-0.005449	-0.00077705	0.01888	0.0039324	-0.012395	-0.77657	-0.006587	-0.0033243	0.072839	0.00017281	-0.0044633	-0.012576	-0.0014833	0.099562	0.0045322	-0.0042539	-0.058936	1.6754	0.16371	-0.0018014	-0.30556	-0.0078104	0.0012481	-0.0020784	0.0011986	0.00027728	-0.0010344	0.0054139	0.0023663	0.0003709	-0.0071958	0.012595	-0.00016884	0	0.031155	0.005578	0.0016642	-0.040591	-1.459	-0.0015243	-0.016138	-0.0014598	-0.0018014	0.00041593	1.1299	0	0.46519	-0.0046694	0.000963	-0.014246	-0.010784	-0.00097017	-0.0011087	-0.0083005	0.26541	-0.011529	-0.3463	
Deletion Peak 6 - CN values	9p21.3 	chr9:21865498-22448737(probes 843262:843626)    	chr9:21959052-21997722(probes 843313:843326)    	chr9:21420139-22934248(probes 842988:843927)    	4.8772e-08	 4.8772e-08		Actual Copy Change Given	-1.5	0.0114	-0.0033243	0.0037465	0.021271	0.0085718	0.0022193	0.0089356	-0.80509	-0.0039413	0.67458	0.0080567	-0.008245	0.0061581	-0.68439	-0.023668	-0.0030475	-0.0070576	-0.0019399	0.00088251	0	-1.2004	0.0020394	-0.75932	-0.0043099	0.00097064	0.049824	-0.0052834	-0.010246	0.0027745	-0.004604	-0.059285	-0.41146	-0.15745	0.0048579	-0.02384	-0.0059786	0.010146	-0.022316	0.021559	0.013213	-0.00055444	-0.13651	-0.00028328	0.0027102	-0.021647	0.0053473	0.022819	-1.5	0.10424	0.0021891	-0.0026277	0.00055459	0	-0.012851	0	-1.4664	0.0027745	0.0014029	0.0010353	0.0022193	0.0022193	-0.017495	0.0073609	-0.03245	0.002952	-0.0011611	-0.55547	0.0055529	-0.40307	0.0083351	0.0038854	-0.0007288	0.0094389	-1.5	
