MDT-AP-1386/primary/A11858_4_lanes_dupsFlagged.bam.pileup_CNVs
MDT-AP-1386_primary	TTC34	1	2620700	2630752	6	gain
MDT-AP-1386_primary	AL137798.3	1	16934748	16956288	6	gain
MDT-AP-1386_primary	NBPF1	1	16934748	16956288	6	gain
MDT-AP-1386_primary	CROCCP2	1	16934748	16956288	6	gain
MDT-AP-1386_primary	AL137798.2	1	16934748	16956288	6	gain
MDT-AP-1386_primary	ESPNP	1	17020908	17052500	5	gain
MDT-AP-1386_primary	AL021920.2	1	17020908	17052500	5	gain
MDT-AP-1386_primary	PDE4DIP	1	144945532	145092004	7	gain
MDT-AP-1386_primary	7SK.266	1	144945532	145092004	7	gain
MDT-AP-1386_primary	SEC22B	1	145099184	145117852	7	gain
MDT-AP-1386_primary	SEC22B	1	145096312	145099184	5	gain
MDT-AP-1386_primary	BX322613.2	10	42354820	42402208	18	gain
MDT-AP-1386_primary	BX322613.3	10	42354820	42402208	18	gain
MDT-AP-1386_primary	BX322613.1	10	42354820	42402208	18	gain
MDT-AP-1386_primary	RP11-38L15.3	10	46964380	47011768	5	gain
MDT-AP-1386_primary	SYT15	10	46964380	47011768	5	gain
MDT-AP-1386_primary	GPRIN2	10	46964380	47011768	5	gain
MDT-AP-1386_primary	XXyac-YR14BB7.1	10	46964380	47011768	5	gain
MDT-AP-1386_primary	XXyac-YR14BB7.1	10	47011768	47149624	5	gain
MDT-AP-1386_primary	PPYR1	10	47011768	47149624	5	gain
MDT-AP-1386_primary	RP11-314P12.2	10	47011768	47149624	5	gain
MDT-AP-1386_primary	RP11-314P12.3	10	47011768	47149624	5	gain
MDT-AP-1386_primary	DHX32	10	127577112	127587164	8	gain
MDT-AP-1386_primary	U2.26	10	127577112	127587164	8	gain
MDT-AP-1386_primary	FANK1	10	127577112	127587164	8	gain
MDT-AP-1386_primary	BET1L	11	189552	195296	6	gain
MDT-AP-1386_primary	SCGB1C1	11	189552	195296	6	gain
MDT-AP-1386_primary	MUC6	11	1015252	1018124	7	gain
MDT-AP-1386_primary	CACNA1C	12	2363656	2366528	5	gain
MDT-AP-1386_primary	TAS2R14	12	11225212	11245316	0	loss
MDT-AP-1386_primary	TAS2R46	12	11225212	11245316	0	loss
MDT-AP-1386_primary	TAS2R43	12	11225212	11245316	0	loss
MDT-AP-1386_primary	ZIC2	13	100630572	100634880	0	loss
MDT-AP-1386_primary	HEATR4	14	74001388	74022928	0	loss
MDT-AP-1386_primary	ACOT1	14	74001388	74022928	0	loss
MDT-AP-1386_primary	AB019440.1	14	106535404	106561252	0	loss
MDT-AP-1386_primary	AB019440.4	14	106535404	106561252	0	loss
MDT-AP-1386_primary	AB019440.5	14	106535404	106561252	0	loss
MDT-AP-1386_primary	AB019440.22	14	106535404	106561252	0	loss
MDT-AP-1386_primary	snoU13.388	15	20547724	20570700	7	gain
MDT-AP-1386_primary	HERC2P3	15	20593676	20853592	7	gain
MDT-AP-1386_primary	AC131280.1	15	20593676	20853592	7	gain
MDT-AP-1386_primary	GOLGA6L6	15	20593676	20853592	7	gain
MDT-AP-1386_primary	GOLGA8C	15	20593676	20853592	7	gain
MDT-AP-1386_primary	AC131280.4	15	20593676	20853592	7	gain
MDT-AP-1386_primary	AC131280.2	15	20593676	20853592	7	gain
MDT-AP-1386_primary	AC131280.3	15	20593676	20853592	7	gain
MDT-AP-1386_primary	IGF1R	15	99190264	99193136	0	loss
MDT-AP-1386_primary	KCNJ12	17	21303060	21320292	6	gain
MDT-AP-1386_primary	AC018696.4	2	91760400	91819276	11	gain
MDT-AP-1386_primary	AC116050.1	2	91760400	91819276	11	gain
MDT-AP-1386_primary	ANKRD30BL	2	133000884	133023860	5	gain
MDT-AP-1386_primary	5_8S_rRNA.5	2	133000884	133023860	5	gain
MDT-AP-1386_primary	MIR663B	2	133000884	133023860	5	gain
MDT-AP-1386_primary	CDC27P1	2	133000884	133023860	5	gain
MDT-AP-1386_primary	AC009299.4	2	162134452	162140196	27	gain
MDT-AP-1386_primary	BAGE2	21	11039968	11186440	9	gain
MDT-AP-1386_primary	VN1R7P	21	11039968	11186440	9	gain
MDT-AP-1386_primary	EIF3FP1	21	11039968	11186440	9	gain
MDT-AP-1386_primary	SLC25A18	22	18057700	18060572	0	loss
MDT-AP-1386_primary	ROBO2	3	75981632	75994556	5	gain
MDT-AP-1386_primary	Z95704.4	4	27284	68928	10	gain
MDT-AP-1386_primary	Z95704.2	4	27284	68928	10	gain
MDT-AP-1386_primary	ZNF595	4	27284	68928	10	gain
MDT-AP-1386_primary	Z95704.1	4	27284	68928	10	gain
MDT-AP-1386_primary	UGT2B28	4	70132804	70231888	0	loss
MDT-AP-1386_primary	RP11-618I10.4	4	70132804	70231888	0	loss
MDT-AP-1386_primary	RP11-618I10.2	4	70132804	70231888	0	loss
MDT-AP-1386_primary	GALNTL6	4	172987740	172993484	0	loss
MDT-AP-1386_primary	RP11-462G22.1	4	190539968	190680696	7	gain
MDT-AP-1386_primary	U1.61	4	190539968	190680696	7	gain
MDT-AP-1386_primary	HLA-DRB5	6	32453600	32541196	0	loss
MDT-AP-1386_primary	U1.110	6	32453600	32541196	0	loss
MDT-AP-1386_primary	HLA-DRB6	6	32453600	32541196	0	loss
MDT-AP-1386_primary	AL713966.1	6	32453600	32541196	0	loss
MDT-AP-1386_primary	PRIM2	6	57371072	57529032	6	gain
MDT-AP-1386_primary	CNTNAP2	7	148071704	148076012	0	loss
MDT-AP-1386_primary	MLL3	7	152098248	152114044	11	gain
MDT-AP-1386_primary	Y_RNA.859	7	152098248	152114044	11	gain
MDT-AP-1386_primary	ERICH1	8	594504	600248	0	loss
MDT-AP-1386_primary	AC090691.3	8	594504	600248	0	loss
MDT-AP-1386_primary	RP11-764K9.2	9	68412476	68425400	25	gain
MDT-AP-1386/relapse/A10068_A11859_dupsFlagged.bam.pileup_CNVs
MDT-AP-1386_relapse	RP11-169K16.8	1	16150554	16156350	0	loss
MDT-AP-1386_relapse	AL137798.3	1	16931565	16948953	7	gain
MDT-AP-1386_relapse	AL137798.3	1	16954749	17054730	5	gain
MDT-AP-1386_relapse	NBPF1	1	16931565	16948953	7	gain
MDT-AP-1386_relapse	CROCCP2	1	16931565	16948953	7	gain
MDT-AP-1386_relapse	CROCCP2	1	16954749	17054730	5	gain
MDT-AP-1386_relapse	AL137798.2	1	16931565	16948953	7	gain
MDT-AP-1386_relapse	RP5-1182A14.3	1	16954749	17054730	5	gain
MDT-AP-1386_relapse	RNU1-3	1	16954749	17054730	5	gain
MDT-AP-1386_relapse	AL137798.1	1	16954749	17054730	5	gain
MDT-AP-1386_relapse	RP1-163M9.6	1	16954749	17054730	5	gain
MDT-AP-1386_relapse	AL021920.1	1	16954749	17054730	5	gain
MDT-AP-1386_relapse	ESPNP	1	16954749	17054730	5	gain
MDT-AP-1386_relapse	AL021920.2	1	16954749	17054730	5	gain
MDT-AP-1386_relapse	PDE4DIP	1	144986940	145092717	8	gain
MDT-AP-1386_relapse	7SK.266	1	144986940	145092717	8	gain
MDT-AP-1386_relapse	SEC22B	1	145097064	145292679	7	gain
MDT-AP-1386_relapse	AL359758.1	1	145097064	145292679	7	gain
MDT-AP-1386_relapse	U6.306	1	145097064	145292679	7	gain
MDT-AP-1386_relapse	NOTCH2NL	1	145097064	145292679	7	gain
MDT-AP-1386_relapse	RP11-458D21.5	1	145097064	145292679	7	gain
MDT-AP-1386_relapse	AL592307.1	1	145097064	145292679	7	gain
MDT-AP-1386_relapse	NBPF10	1	145097064	145292679	7	gain
MDT-AP-1386_relapse	RNU1-5	1	149220918	149228163	5	gain
MDT-AP-1386_relapse	BX322613.2	10	42355719	42402087	22	gain
MDT-AP-1386_relapse	BX322613.3	10	42355719	42402087	22	gain
MDT-AP-1386_relapse	BX322613.1	10	42355719	42402087	22	gain
MDT-AP-1386_relapse	RP11-38L15.3	10	46964988	47007009	5	gain
MDT-AP-1386_relapse	SYT15	10	46964988	47007009	5	gain
MDT-AP-1386_relapse	GPRIN2	10	46964988	47007009	5	gain
MDT-AP-1386_relapse	XXyac-YR14BB7.1	10	47007009	47149011	5	gain
MDT-AP-1386_relapse	PPYR1	10	47007009	47149011	5	gain
MDT-AP-1386_relapse	RP11-314P12.2	10	47007009	47149011	5	gain
MDT-AP-1386_relapse	RP11-314P12.3	10	47007009	47149011	5	gain
MDT-AP-1386_relapse	DHX32	10	127574307	127587348	7	gain
MDT-AP-1386_relapse	U2.26	10	127574307	127587348	7	gain
MDT-AP-1386_relapse	FANK1	10	127574307	127587348	7	gain
MDT-AP-1386_relapse	BET1L	11	189819	195615	5	gain
MDT-AP-1386_relapse	SCGB1C1	11	189819	195615	5	gain
MDT-AP-1386_relapse	PHRF1	11	583947	586845	5	gain
MDT-AP-1386_relapse	MUC6	11	1015749	1018647	7	gain
MDT-AP-1386_relapse	TAS2R14	12	11226852	11247138	0	loss
MDT-AP-1386_relapse	TAS2R46	12	11226852	11247138	0	loss
MDT-AP-1386_relapse	TAS2R43	12	11226852	11247138	0	loss
MDT-AP-1386_relapse	snoU13.388	15	20549718	20567106	7	gain
MDT-AP-1386_relapse	HERC2P3	15	20591739	20854008	7	gain
MDT-AP-1386_relapse	AC131280.1	15	20591739	20854008	7	gain
MDT-AP-1386_relapse	GOLGA6L6	15	20591739	20854008	7	gain
MDT-AP-1386_relapse	GOLGA8C	15	20591739	20854008	7	gain
MDT-AP-1386_relapse	AC131280.4	15	20591739	20854008	7	gain
MDT-AP-1386_relapse	AC131280.2	15	20591739	20854008	7	gain
MDT-AP-1386_relapse	AC131280.3	15	20591739	20854008	7	gain
MDT-AP-1386_relapse	U6.948	15	20854008	21940758	6	gain
MDT-AP-1386_relapse	AC012414.2	15	20854008	21940758	6	gain
MDT-AP-1386_relapse	AC012414.1	15	20854008	21940758	6	gain
MDT-AP-1386_relapse	U6.950	15	20854008	21940758	6	gain
MDT-AP-1386_relapse	AC126335.1	15	20854008	21940758	6	gain
MDT-AP-1386_relapse	AC126335.3	15	20854008	21940758	6	gain
MDT-AP-1386_relapse	AC126335.2	15	20854008	21940758	6	gain
MDT-AP-1386_relapse	AC068446.1	15	20854008	21940758	6	gain
MDT-AP-1386_relapse	RP11-2F9.1	15	22431969	22491378	5	gain
MDT-AP-1386_relapse	VSIG6	15	22431969	22491378	5	gain
MDT-AP-1386_relapse	CNTNAP4	16	76539078	76544874	0	loss
MDT-AP-1386_relapse	MAP2K3	17	21207564	21211911	6	gain
MDT-AP-1386_relapse	KCNJ12	17	21303198	21320586	6	gain
MDT-AP-1386_relapse	AC018696.4	2	91759374	91820232	12	gain
MDT-AP-1386_relapse	AC116050.1	2	91759374	91820232	12	gain
MDT-AP-1386_relapse	ANKRD30BL	2	133003710	133023996	6	gain
MDT-AP-1386_relapse	5_8S_rRNA.5	2	133003710	133023996	6	gain
MDT-AP-1386_relapse	MIR663B	2	133003710	133023996	6	gain
MDT-AP-1386_relapse	CDC27P1	2	133003710	133023996	6	gain
MDT-AP-1386_relapse	AC009299.4	2	162134406	162140202	25	gain
MDT-AP-1386_relapse	SIRPB1	20	1563471	1593900	0	loss
MDT-AP-1386_relapse	C20orf112	20	31170888	31173786	0	loss
MDT-AP-1386_relapse	RP11-410N8.4	20	31170888	31173786	0	loss
MDT-AP-1386_relapse	RP11-410N8.1	20	31170888	31173786	0	loss
MDT-AP-1386_relapse	RP5-991B18.1	20	47130174	47133072	9	gain
MDT-AP-1386_relapse	AF254982.1	21	10795050	10800846	6	gain
MDT-AP-1386_relapse	BAGE2	21	11039931	11090646	14	gain
MDT-AP-1386_relapse	VN1R7P	21	11132667	11181933	7	gain
MDT-AP-1386_relapse	EIF3FP1	21	11132667	11181933	7	gain
MDT-AP-1386_relapse	RP1-199H16.5	22	39038958	39041856	6	gain
MDT-AP-1386_relapse	Z95704.4	4	27531	69552	10	gain
MDT-AP-1386_relapse	Z95704.2	4	27531	69552	10	gain
MDT-AP-1386_relapse	ZNF595	4	27531	69552	10	gain
MDT-AP-1386_relapse	Z95704.1	4	27531	69552	10	gain
MDT-AP-1386_relapse	RP11-1281K21.3	4	49213836	49221081	5	gain
MDT-AP-1386_relapse	UGT2B28	4	70133049	70231581	0	loss
MDT-AP-1386_relapse	RP11-618I10.4	4	70133049	70231581	0	loss
MDT-AP-1386_relapse	RP11-618I10.2	4	70133049	70231581	0	loss
MDT-AP-1386_relapse	RP11-462G22.1	4	190539153	190684053	7	gain
MDT-AP-1386_relapse	U1.61	4	190539153	190684053	7	gain
MDT-AP-1386_relapse	HLA-DRB5	6	32454702	32541642	0	loss
MDT-AP-1386_relapse	U1.110	6	32454702	32541642	0	loss
MDT-AP-1386_relapse	HLA-DRB6	6	32454702	32541642	0	loss
MDT-AP-1386_relapse	AL713966.1	6	32454702	32541642	0	loss
MDT-AP-1386_relapse	PRIM2	6	57368808	57532545	6	gain
MDT-AP-1386_relapse	C6orf35	6	157730895	157735242	6	gain
MDT-AP-1386_relapse	MLL3	7	152098632	152113122	11	gain
MDT-AP-1386_relapse	Y_RNA.859	7	152098632	152113122	11	gain
MDT-AP-1386_relapse	ERICH1	8	594090	599886	0	loss
MDT-AP-1386_relapse	AC090691.3	8	594090	599886	0	loss
MDT-AP-1386_relapse	CSMD1	8	4122405	4125303	0	loss
MDT-AP-1386_relapse	RP11-764K9.2	9	68413086	68426127	26	gain
MDT-AP-1386_relapse	AL353763.1	9	68995584	69002829	6	gain
MDT-AP-1386_relapse	MIR1299	9	68995584	69002829	6	gain
MDT-AP-1388/primary/A11851_5_lanes_dupsFlagged.bam.pileup_CNVs
MDT-AP-1388_primary	AL137798.3	1	16931052	17054780	6	gain
MDT-AP-1388_primary	NBPF1	1	16931052	17054780	6	gain
MDT-AP-1388_primary	CROCCP2	1	16931052	17054780	6	gain
MDT-AP-1388_primary	AL137798.2	1	16931052	17054780	6	gain
MDT-AP-1388_primary	RP5-1182A14.3	1	16931052	17054780	6	gain
MDT-AP-1388_primary	RNU1-3	1	16931052	17054780	6	gain
MDT-AP-1388_primary	AL137798.1	1	16931052	17054780	6	gain
MDT-AP-1388_primary	RP1-163M9.6	1	16931052	17054780	6	gain
MDT-AP-1388_primary	AL021920.1	1	16931052	17054780	6	gain
MDT-AP-1388_primary	ESPNP	1	16931052	17054780	6	gain
MDT-AP-1388_primary	AL021920.2	1	16931052	17054780	6	gain
MDT-AP-1388_primary	PDE4DIP	1	144986720	145092170	6	gain
MDT-AP-1388_primary	7SK.266	1	144986720	145092170	6	gain
MDT-AP-1388_primary	SEC22B	1	145097794	145291822	6	gain
MDT-AP-1388_primary	AL359758.1	1	145097794	145291822	6	gain
MDT-AP-1388_primary	U6.306	1	145097794	145291822	6	gain
MDT-AP-1388_primary	NOTCH2NL	1	145097794	145291822	6	gain
MDT-AP-1388_primary	RP11-458D21.5	1	145097794	145291822	6	gain
MDT-AP-1388_primary	AL592307.1	1	145097794	145291822	6	gain
MDT-AP-1388_primary	NBPF10	1	145097794	145291822	6	gain
MDT-AP-1388_primary	RP11-744H18.1	1	149033188	149040218	9	gain
MDT-AP-1388_primary	BX322613.2	10	42355750	42402148	26	gain
MDT-AP-1388_primary	BX322613.3	10	42355750	42402148	26	gain
MDT-AP-1388_primary	BX322613.1	10	42355750	42402148	26	gain
MDT-AP-1388_primary	DHX32	10	127574816	127586064	6	gain
MDT-AP-1388_primary	U2.26	10	127574816	127586064	6	gain
MDT-AP-1388_primary	FANK1	10	127574816	127586064	6	gain
MDT-AP-1388_primary	MUC6	11	1016538	1019350	9	gain
MDT-AP-1388_primary	AB019440.1	14	106778670	106805384	5	gain
MDT-AP-1388_primary	AB019439.4	14	106778670	106805384	5	gain
MDT-AP-1388_primary	AB019439.32	14	106778670	106805384	5	gain
MDT-AP-1388_primary	AB019439.23	14	106778670	106805384	5	gain
MDT-AP-1388_primary	AB019439.5	14	106778670	106805384	5	gain
MDT-AP-1388_primary	AB019439.26	14	106778670	106805384	5	gain
MDT-AP-1388_primary	AB019439.27	14	106778670	106805384	5	gain
MDT-AP-1388_primary	AB019439.13	14	106778670	106805384	5	gain
MDT-AP-1388_primary	CES1P1	16	55798516	55822418	0	loss
MDT-AP-1388_primary	PDPR	16	70183302	70197362	6	gain
MDT-AP-1388_primary	AC009060.2	16	70183302	70197362	6	gain
MDT-AP-1388_primary	KCNJ12	17	21302306	21330426	6	gain
MDT-AP-1388_primary	AC018696.4	2	91759778	91820236	11	gain
MDT-AP-1388_primary	AC116050.1	2	91759778	91820236	11	gain
MDT-AP-1388_primary	ANKRD30BL	2	132982292	133023066	6	gain
MDT-AP-1388_primary	5_8S_rRNA.5	2	132982292	133023066	6	gain
MDT-AP-1388_primary	MIR663B	2	132982292	133023066	6	gain
MDT-AP-1388_primary	CDC27P1	2	132982292	133023066	6	gain
MDT-AP-1388_primary	AC009299.4	2	162134296	162139920	19	gain
MDT-AP-1388_primary	AL441988.1	20	29637074	29649728	5	gain
MDT-AP-1388_primary	MLLT10P1	20	29637074	29649728	5	gain
MDT-AP-1388_primary	RP11-348I14.4	20	29637074	29649728	5	gain
MDT-AP-1388_primary	AF254982.1	21	10724968	10861350	9	gain
MDT-AP-1388_primary	BAGE2	21	11039912	11127084	9	gain
MDT-AP-1388_primary	GSTT1	22	24347702	24394100	0	loss
MDT-AP-1388_primary	AP000351.6	22	24347702	24394100	0	loss
MDT-AP-1388_primary	AP000351.7	22	24347702	24394100	0	loss
MDT-AP-1388_primary	AP000351.1	22	24347702	24394100	0	loss
MDT-AP-1388_primary	AP000351.2	22	24347702	24394100	0	loss
MDT-AP-1388_primary	AP000351.8	22	24347702	24394100	0	loss
MDT-AP-1388_primary	AP000351.9	22	24347702	24394100	0	loss
MDT-AP-1388_primary	AP000351.10	22	24347702	24394100	0	loss
MDT-AP-1388_primary	GSTTP2	22	24347702	24394100	0	loss
MDT-AP-1388_primary	RP1-199H16.5	22	39038996	39041808	8	gain
MDT-AP-1388_primary	SENP5	3	196623476	196626288	18	gain
MDT-AP-1388_primary	Z95704.4	4	28120	68894	10	gain
MDT-AP-1388_primary	Z95704.2	4	68894	74518	10	gain
MDT-AP-1388_primary	Z95704.2	4	28120	68894	10	gain
MDT-AP-1388_primary	ZNF595	4	68894	74518	10	gain
MDT-AP-1388_primary	ZNF595	4	28120	68894	10	gain
MDT-AP-1388_primary	Z95704.1	4	28120	68894	10	gain
MDT-AP-1388_primary	RP11-462G22.1	4	190539714	190684532	7	gain
MDT-AP-1388_primary	U1.61	4	190539714	190684532	7	gain
MDT-AP-1388_primary	PRIM2	6	57369018	57575700	6	gain
MDT-AP-1388_primary	C6orf35	6	157730704	157736328	6	gain
MDT-AP-1388_primary	RP11-715L17.1	7	61527966	61980698	5	gain
MDT-AP-1388_primary	MLL3	7	152098268	152113734	7	gain
MDT-AP-1388_primary	Y_RNA.859	7	152098268	152113734	7	gain
MDT-AP-1388_primary	CSMD1	8	3783546	3790576	0	loss
MDT-AP-1388_primary	AL391380.1	X	134808686	134818528	5	gain
MDT-AP-1388_primary	RP11-432N13.4	X	134808686	134818528	5	gain
MDT-AP-1388/relapse/A11860_3_lanes_dupsFlagged.bam.pileup_CNVs
MDT-AP-1388_relapse	TTC34	1	2620640	2631063	5	gain
MDT-AP-1388_relapse	AL137798.3	1	16931419	16964177	7	gain
MDT-AP-1388_relapse	NBPF1	1	16931419	16964177	7	gain
MDT-AP-1388_relapse	CROCCP2	1	16931419	16964177	7	gain
MDT-AP-1388_relapse	AL137798.2	1	16931419	16964177	7	gain
MDT-AP-1388_relapse	ESPNP	1	17020759	17055006	6	gain
MDT-AP-1388_relapse	AL021920.2	1	17020759	17055006	6	gain
MDT-AP-1388_relapse	PDE4DIP	1	144986908	145092627	6	gain
MDT-AP-1388_relapse	7SK.266	1	144986908	145092627	6	gain
MDT-AP-1388_relapse	SEC22B	1	145097094	145292153	7	gain
MDT-AP-1388_relapse	AL359758.1	1	145097094	145292153	7	gain
MDT-AP-1388_relapse	U6.306	1	145097094	145292153	7	gain
MDT-AP-1388_relapse	NOTCH2NL	1	145097094	145292153	7	gain
MDT-AP-1388_relapse	RP11-458D21.5	1	145097094	145292153	7	gain
MDT-AP-1388_relapse	AL592307.1	1	145097094	145292153	7	gain
MDT-AP-1388_relapse	NBPF10	1	145097094	145292153	7	gain
MDT-AP-1388_relapse	BX322613.2	10	42356094	42402253	13	gain
MDT-AP-1388_relapse	BX322613.3	10	42356094	42402253	13	gain
MDT-AP-1388_relapse	BX322613.1	10	42356094	42402253	13	gain
MDT-AP-1388_relapse	DHX32	10	127574542	127586454	7	gain
MDT-AP-1388_relapse	U2.26	10	127574542	127586454	7	gain
MDT-AP-1388_relapse	FANK1	10	127574542	127586454	7	gain
MDT-AP-1388_relapse	BET1L	11	190592	195059	5	gain
MDT-AP-1388_relapse	SCGB1C1	11	190592	195059	5	gain
MDT-AP-1388_relapse	MUC6	11	1015498	1018476	7	gain
MDT-AP-1388_relapse	KIAA0391	14	35604968	35615391	0	loss
MDT-AP-1388_relapse	RP11-173D9.1	14	35604968	35615391	0	loss
MDT-AP-1388_relapse	AB019439.13	14	106801503	106807459	7	gain
MDT-AP-1388_relapse	CES1P1	16	55798786	55822610	0	loss
MDT-AP-1388_relapse	PDPR	16	70184015	70195927	5	gain
MDT-AP-1388_relapse	AC009060.2	16	70184015	70195927	5	gain
MDT-AP-1388_relapse	MAP2K3	17	21192937	21212294	5	gain
MDT-AP-1388_relapse	KCNJ12	17	21303123	21320991	7	gain
MDT-AP-1388_relapse	AC018696.4	2	91759625	91820674	11	gain
MDT-AP-1388_relapse	AC116050.1	2	91759625	91820674	11	gain
MDT-AP-1388_relapse	ANKRD30BL	2	133001947	133022793	5	gain
MDT-AP-1388_relapse	5_8S_rRNA.5	2	133001947	133022793	5	gain
MDT-AP-1388_relapse	MIR663B	2	133001947	133022793	5	gain
MDT-AP-1388_relapse	CDC27P1	2	133001947	133022793	5	gain
MDT-AP-1388_relapse	AC009299.4	2	162134232	162140188	14	gain
MDT-AP-1388_relapse	AF254982.1	21	10774404	10874167	5	gain
MDT-AP-1388_relapse	IGHV1OR21-1	21	10774404	10874167	5	gain
MDT-AP-1388_relapse	AF254982.2	21	10774404	10874167	5	gain
MDT-AP-1388_relapse	BAGE2	21	11040935	11133253	8	gain
MDT-AP-1388_relapse	VN1R7P	21	11140698	11186857	8	gain
MDT-AP-1388_relapse	EIF3FP1	21	11140698	11186857	8	gain
MDT-AP-1388_relapse	DDTL	22	24312392	24392798	0	loss
MDT-AP-1388_relapse	DDT	22	24312392	24392798	0	loss
MDT-AP-1388_relapse	AP000351.3	22	24312392	24392798	0	loss
MDT-AP-1388_relapse	GSTT2	22	24312392	24392798	0	loss
MDT-AP-1388_relapse	AP000351.4	22	24312392	24392798	0	loss
MDT-AP-1388_relapse	GSTT1	22	24312392	24392798	0	loss
MDT-AP-1388_relapse	GSTTP1	22	24312392	24392798	0	loss
MDT-AP-1388_relapse	AP000351.6	22	24312392	24392798	0	loss
MDT-AP-1388_relapse	AP000351.7	22	24312392	24392798	0	loss
MDT-AP-1388_relapse	AP000351.1	22	24312392	24392798	0	loss
MDT-AP-1388_relapse	AP000351.2	22	24312392	24392798	0	loss
MDT-AP-1388_relapse	AP000351.8	22	24312392	24392798	0	loss
MDT-AP-1388_relapse	AP000351.9	22	24312392	24392798	0	loss
MDT-AP-1388_relapse	AP000351.10	22	24312392	24392798	0	loss
MDT-AP-1388_relapse	GSTTP2	22	24312392	24392798	0	loss
MDT-AP-1388_relapse	Z95704.4	4	28291	68494	13	gain
MDT-AP-1388_relapse	Z95704.2	4	28291	68494	13	gain
MDT-AP-1388_relapse	ZNF595	4	28291	68494	13	gain
MDT-AP-1388_relapse	Z95704.1	4	28291	68494	13	gain
MDT-AP-1388_relapse	AC118282.4	4	49148912	49221873	9	gain
MDT-AP-1388_relapse	AC118282.3	4	49148912	49221873	9	gain
MDT-AP-1388_relapse	AC118282.2	4	49148912	49221873	9	gain
MDT-AP-1388_relapse	AC118282.1	4	49148912	49221873	9	gain
MDT-AP-1388_relapse	RP11-1281K21.2	4	49148912	49221873	9	gain
MDT-AP-1388_relapse	RP11-1281K21.3	4	49148912	49221873	9	gain
MDT-AP-1388_relapse	RP11-462G22.1	4	190536907	190681340	8	gain
MDT-AP-1388_relapse	U1.61	4	190536907	190681340	8	gain
MDT-AP-1388_relapse	PRIM2	6	57368192	57575163	5	gain
MDT-AP-1388_relapse	MLL3	7	152098372	152113262	7	gain
MDT-AP-1388_relapse	Y_RNA.859	7	152098372	152113262	7	gain
MDT-AP-1388_relapse	RP11-764K9.3	9	68412105	68425506	24	gain
MDT-AP-1388_relapse	RP11-764K9.2	9	68412105	68425506	24	gain
MDT-AP-1390/primary/A11861_4_lanes_dupsFlagged.bam.pileup_CNVs
MDT-AP-1390_primary	AL137798.3	1	16934720	17054400	7	gain
MDT-AP-1390_primary	NBPF1	1	16934720	17054400	7	gain
MDT-AP-1390_primary	CROCCP2	1	16934720	17054400	7	gain
MDT-AP-1390_primary	AL137798.2	1	16934720	17054400	7	gain
MDT-AP-1390_primary	RP5-1182A14.3	1	16934720	17054400	7	gain
MDT-AP-1390_primary	RNU1-3	1	16934720	17054400	7	gain
MDT-AP-1390_primary	AL137798.1	1	16934720	17054400	7	gain
MDT-AP-1390_primary	RP1-163M9.6	1	16934720	17054400	7	gain
MDT-AP-1390_primary	AL021920.1	1	16934720	17054400	7	gain
MDT-AP-1390_primary	ESPNP	1	16934720	17054400	7	gain
MDT-AP-1390_primary	AL021920.2	1	16934720	17054400	7	gain
MDT-AP-1390_primary	AL583842.1	1	121351440	145117440	6	gain
MDT-AP-1390_primary	AL583842.1	1	121351440	145117440	6	gain
MDT-AP-1390_primary	AL583842.2	1	121351440	145117440	6	gain
MDT-AP-1390_primary	AL583842.3	1	121351440	145117440	6	gain
MDT-AP-1390_primary	AL583842.6	1	121351440	145117440	6	gain
MDT-AP-1390_primary	AL583842.3	1	121351440	145117440	6	gain
MDT-AP-1390_primary	AL583842.2	1	121351440	145117440	6	gain
MDT-AP-1390_primary	AL583842.4	1	121351440	145117440	6	gain
MDT-AP-1390_primary	AL583842.5	1	121351440	145117440	6	gain
MDT-AP-1390_primary	AL583842.7	1	121351440	145117440	6	gain
MDT-AP-1390_primary	AL583842.8	1	121351440	145117440	6	gain
MDT-AP-1390_primary	RP11-423O2.3	1	121351440	145117440	6	gain
MDT-AP-1390_primary	RP11-423O2.2	1	121351440	145117440	6	gain
MDT-AP-1390_primary	RP11-423O2.1	1	121351440	145117440	6	gain
MDT-AP-1390_primary	RP11-423O2.4	1	121351440	145117440	6	gain
MDT-AP-1390_primary	RP11-423O2.5	1	121351440	145117440	6	gain
MDT-AP-1390_primary	RP11-423O2.6	1	121351440	145117440	6	gain
MDT-AP-1390_primary	RP11-423O2.7	1	121351440	145117440	6	gain
MDT-AP-1390_primary	BX571672.2	1	121351440	145117440	6	gain
MDT-AP-1390_primary	BX571672.1	1	121351440	145117440	6	gain
MDT-AP-1390_primary	BX571672.4	1	121351440	145117440	6	gain
MDT-AP-1390_primary	BX571672.3	1	121351440	145117440	6	gain
MDT-AP-1390_primary	BX571672.5	1	121351440	145117440	6	gain
MDT-AP-1390_primary	BX571672.6	1	121351440	145117440	6	gain
MDT-AP-1390_primary	BX571672.7	1	121351440	145117440	6	gain
MDT-AP-1390_primary	BX571672.8	1	121351440	145117440	6	gain
MDT-AP-1390_primary	BX004987.1	1	121351440	145117440	6	gain
MDT-AP-1390_primary	BX004987.2	1	121351440	145117440	6	gain
MDT-AP-1390_primary	BX004987.3	1	121351440	145117440	6	gain
MDT-AP-1390_primary	BX004987.4	1	121351440	145117440	6	gain
MDT-AP-1390_primary	BX004987.5	1	121351440	145117440	6	gain
MDT-AP-1390_primary	BX004987.1	1	121351440	145117440	6	gain
MDT-AP-1390_primary	BX004987.2	1	121351440	145117440	6	gain
MDT-AP-1390_primary	BX004987.6	1	121351440	145117440	6	gain
MDT-AP-1390_primary	BX004987.7	1	121351440	145117440	6	gain
MDT-AP-1390_primary	RNU1-10P	1	121351440	145117440	6	gain
MDT-AP-1390_primary	BX284650.1	1	121351440	145117440	6	gain
MDT-AP-1390_primary	U1.115	1	121351440	145117440	6	gain
MDT-AP-1390_primary	RNU1-13P	1	121351440	145117440	6	gain
MDT-AP-1390_primary	BX284650.2	1	121351440	145117440	6	gain
MDT-AP-1390_primary	U1.71	1	121351440	145117440	6	gain
MDT-AP-1390_primary	BX284650.3	1	121351440	145117440	6	gain
MDT-AP-1390_primary	BX284650.4	1	121351440	145117440	6	gain
MDT-AP-1390_primary	PPIAL4G	1	121351440	145117440	6	gain
MDT-AP-1390_primary	AL109844.1	1	121351440	145117440	6	gain
MDT-AP-1390_primary	FAM72D	1	121351440	145117440	6	gain
MDT-AP-1390_primary	SRGAP2P2	1	121351440	145117440	6	gain
MDT-AP-1390_primary	RP11-289H16.1	1	121351440	145117440	6	gain
MDT-AP-1390_primary	AL592284.1	1	121351440	145117440	6	gain
MDT-AP-1390_primary	RP3-377D14.1	1	121351440	145117440	6	gain
MDT-AP-1390_primary	BX248398.1	1	121351440	145117440	6	gain
MDT-AP-1390_primary	U1.81	1	121351440	145117440	6	gain
MDT-AP-1390_primary	PPIAL4B	1	121351440	145117440	6	gain
MDT-AP-1390_primary	AL592284.1	1	121351440	145117440	6	gain
MDT-AP-1390_primary	U1.75	1	121351440	145117440	6	gain
MDT-AP-1390_primary	U1.50	1	121351440	145117440	6	gain
MDT-AP-1390_primary	NBPF8	1	121351440	145117440	6	gain
MDT-AP-1390_primary	AL592284.3	1	121351440	145117440	6	gain
MDT-AP-1390_primary	CR589902.1	1	121351440	145117440	6	gain
MDT-AP-1390_primary	WI2-1896O14.1	1	121351440	145117440	6	gain
MDT-AP-1390_primary	NBPF9	1	121351440	145117440	6	gain
MDT-AP-1390_primary	RP4-791M13.3	1	121351440	145117440	6	gain
MDT-AP-1390_primary	PDE4DIP	1	121351440	145117440	6	gain
MDT-AP-1390_primary	RP4-791M13.4	1	121351440	145117440	6	gain
MDT-AP-1390_primary	RP4-791M13.5	1	121351440	145117440	6	gain
MDT-AP-1390_primary	U2.35	1	121351440	145117440	6	gain
MDT-AP-1390_primary	7SK.266	1	121351440	145117440	6	gain
MDT-AP-1390_primary	SEC22B	1	121351440	145117440	6	gain
MDT-AP-1390_primary	BX322613.2	10	42355840	42402080	18	gain
MDT-AP-1390_primary	BX322613.3	10	42355840	42402080	18	gain
MDT-AP-1390_primary	BX322613.1	10	42355840	42402080	18	gain
MDT-AP-1390_primary	DHX32	10	127577520	127585680	7	gain
MDT-AP-1390_primary	U2.26	10	127577520	127585680	7	gain
MDT-AP-1390_primary	FANK1	10	127577520	127585680	7	gain
MDT-AP-1390_primary	BET1L	11	190400	195840	5	gain
MDT-AP-1390_primary	SCGB1C1	11	190400	195840	5	gain
MDT-AP-1390_primary	MUC6	11	1015920	1018640	9	gain
MDT-AP-1390_primary	AB019440.1	14	106783120	106807600	11	gain
MDT-AP-1390_primary	AB019439.32	14	106783120	106807600	11	gain
MDT-AP-1390_primary	AB019439.23	14	106783120	106807600	11	gain
MDT-AP-1390_primary	AB019439.5	14	106783120	106807600	11	gain
MDT-AP-1390_primary	AB019439.26	14	106783120	106807600	11	gain
MDT-AP-1390_primary	AB019439.27	14	106783120	106807600	11	gain
MDT-AP-1390_primary	AB019439.13	14	106783120	106807600	11	gain
MDT-AP-1390_primary	AC126603.1	15	20477520	21940880	6	gain
MDT-AP-1390_primary	snoU13.388	15	20477520	21940880	6	gain
MDT-AP-1390_primary	HERC2P3	15	20477520	21940880	6	gain
MDT-AP-1390_primary	AC131280.1	15	20477520	21940880	6	gain
MDT-AP-1390_primary	GOLGA6L6	15	20477520	21940880	6	gain
MDT-AP-1390_primary	GOLGA8C	15	20477520	21940880	6	gain
MDT-AP-1390_primary	AC131280.4	15	20477520	21940880	6	gain
MDT-AP-1390_primary	AC131280.2	15	20477520	21940880	6	gain
MDT-AP-1390_primary	AC131280.3	15	20477520	21940880	6	gain
MDT-AP-1390_primary	U6.948	15	20477520	21940880	6	gain
MDT-AP-1390_primary	AC012414.2	15	20477520	21940880	6	gain
MDT-AP-1390_primary	AC012414.1	15	20477520	21940880	6	gain
MDT-AP-1390_primary	U6.950	15	20477520	21940880	6	gain
MDT-AP-1390_primary	AC126335.1	15	20477520	21940880	6	gain
MDT-AP-1390_primary	AC126335.3	15	20477520	21940880	6	gain
MDT-AP-1390_primary	AC126335.2	15	20477520	21940880	6	gain
MDT-AP-1390_primary	AC068446.1	15	20477520	21940880	6	gain
MDT-AP-1390_primary	AC007353.2	16	34466480	34757520	6	gain
MDT-AP-1390_primary	AC007353.1	16	34466480	34757520	6	gain
MDT-AP-1390_primary	AC018558.1	16	34466480	34757520	6	gain
MDT-AP-1390_primary	MAP2K3	17	21192880	21252720	6	gain
MDT-AP-1390_primary	KCNJ12	17	21303040	21330240	7	gain
MDT-AP-1390_primary	KIAA1267	17	44167360	44350960	5	gain
MDT-AP-1390_primary	U7.136	17	44167360	44350960	5	gain
MDT-AP-1390_primary	AC217773.1	17	44167360	44350960	5	gain
MDT-AP-1390_primary	Y_RNA.751	17	44167360	44350960	5	gain
MDT-AP-1390_primary	RBFOX3	17	77363600	77393520	6	gain
MDT-AP-1390_primary	SOCS6	18	67997280	68005440	5	gain
MDT-AP-1390_primary	CDC42EP3	2	37958960	38002480	6	gain
MDT-AP-1390_primary	AC006369.3	2	37958960	38002480	6	gain
MDT-AP-1390_primary	AC018696.4	2	91759200	91820400	11	gain
MDT-AP-1390_primary	AC116050.1	2	91759200	91820400	11	gain
MDT-AP-1390_primary	ANKRD30BL	2	133001200	133028400	5	gain
MDT-AP-1390_primary	5_8S_rRNA.5	2	133001200	133028400	5	gain
MDT-AP-1390_primary	MIR663B	2	133001200	133028400	5	gain
MDT-AP-1390_primary	CDC27P1	2	133001200	133028400	5	gain
MDT-AP-1390_primary	AL441988.1	20	29635760	29649360	6	gain
MDT-AP-1390_primary	MLLT10P1	20	29635760	29649360	6	gain
MDT-AP-1390_primary	RP11-348I14.4	20	29635760	29649360	6	gain
MDT-AP-1390_primary	AL109840.2	20	57464080	57468160	0	loss
MDT-AP-1390_primary	GNAS	20	57464080	57468160	0	loss
MDT-AP-1390_primary	CR392039.1	21	9826000	10726320	17	gain
MDT-AP-1390_primary	CR392039.3	21	9826000	10726320	17	gain
MDT-AP-1390_primary	CR392039.2	21	9826000	10726320	17	gain
MDT-AP-1390_primary	CR381653.2	21	9826000	10726320	17	gain
MDT-AP-1390_primary	CR381653.3	21	9826000	10726320	17	gain
MDT-AP-1390_primary	CR381653.1	21	9826000	10726320	17	gain
MDT-AP-1390_primary	SNORA70.20	21	9826000	10726320	17	gain
MDT-AP-1390_primary	CR382285.1	21	9826000	10726320	17	gain
MDT-AP-1390_primary	CR382287.1	21	9826000	10726320	17	gain
MDT-AP-1390_primary	BAGE2	21	11040480	11127520	8	gain
MDT-AP-1390_primary	VN1R7P	21	11142480	11181920	10	gain
MDT-AP-1390_primary	EIF3FP1	21	11142480	11181920	10	gain
MDT-AP-1390_primary	GSTT1	22	24346720	24394320	0	loss
MDT-AP-1390_primary	GSTTP1	22	24346720	24394320	0	loss
MDT-AP-1390_primary	AP000351.6	22	24346720	24394320	0	loss
MDT-AP-1390_primary	AP000351.7	22	24346720	24394320	0	loss
MDT-AP-1390_primary	AP000351.1	22	24346720	24394320	0	loss
MDT-AP-1390_primary	AP000351.2	22	24346720	24394320	0	loss
MDT-AP-1390_primary	AP000351.8	22	24346720	24394320	0	loss
MDT-AP-1390_primary	AP000351.9	22	24346720	24394320	0	loss
MDT-AP-1390_primary	AP000351.10	22	24346720	24394320	0	loss
MDT-AP-1390_primary	GSTTP2	22	24346720	24394320	0	loss
MDT-AP-1390_primary	CLASP2	3	33611040	34745280	28	gain
MDT-AP-1390_primary	AC112220.2	3	33611040	34745280	28	gain
MDT-AP-1390_primary	AC112220.1	3	33611040	34745280	28	gain
MDT-AP-1390_primary	PDCD6IP	3	33611040	34745280	28	gain
MDT-AP-1390_primary	AC018359.1	3	33611040	34745280	28	gain
MDT-AP-1390_primary	AC123023.1	3	33611040	34745280	28	gain
MDT-AP-1390_primary	AC018359.3	3	33611040	34745280	28	gain
MDT-AP-1390_primary	FECHP1	3	34745280	39872480	29	gain
MDT-AP-1390_primary	KRT8P18	3	34745280	39872480	29	gain
MDT-AP-1390_primary	U6.799	3	34745280	39872480	29	gain
MDT-AP-1390_primary	ARPP21	3	34745280	39872480	29	gain
MDT-AP-1390_primary	RP11-380G10.1	3	34745280	39872480	29	gain
MDT-AP-1390_primary	MIR128-2	3	34745280	39872480	29	gain
MDT-AP-1390_primary	AC104308.2	3	34745280	39872480	29	gain
MDT-AP-1390_primary	AC105901.1	3	34745280	39872480	29	gain
MDT-AP-1390_primary	STAC	3	34745280	39872480	29	gain
MDT-AP-1390_primary	NBPF21P	3	34745280	39872480	29	gain
MDT-AP-1390_primary	7SK.53	3	34745280	39872480	29	gain
MDT-AP-1390_primary	DCLK3	3	34745280	39872480	29	gain
MDT-AP-1390_primary	HSPD1P6	3	34745280	39872480	29	gain
MDT-AP-1390_primary	AC105749.5	3	34745280	39872480	29	gain
MDT-AP-1390_primary	TRANK1	3	34745280	39872480	29	gain
MDT-AP-1390_primary	AC011816.1	3	34745280	39872480	29	gain
MDT-AP-1390_primary	RNU6ATAC4P	3	34745280	39872480	29	gain
MDT-AP-1390_primary	AC011816.3	3	34745280	39872480	29	gain
MDT-AP-1390_primary	EPM2AIP1	3	34745280	39872480	29	gain
MDT-AP-1390_primary	MLH1	3	34745280	39872480	29	gain
MDT-AP-1390_primary	AC011816.4	3	34745280	39872480	29	gain
MDT-AP-1390_primary	LRRFIP2	3	34745280	39872480	29	gain
MDT-AP-1390_primary	Y_RNA.447	3	34745280	39872480	29	gain
MDT-AP-1390_primary	UBE2D3P2	3	34745280	39872480	29	gain
MDT-AP-1390_primary	U6.42	3	34745280	39872480	29	gain
MDT-AP-1390_primary	AC126118.1	3	34745280	39872480	29	gain
MDT-AP-1390_primary	AC097359.2	3	34745280	39872480	29	gain
MDT-AP-1390_primary	snoU13.312	3	34745280	39872480	29	gain
MDT-AP-1390_primary	AC097359.1	3	34745280	39872480	29	gain
MDT-AP-1390_primary	GOLGA4	3	34745280	39872480	29	gain
MDT-AP-1390_primary	AC097359.2	3	34745280	39872480	29	gain
MDT-AP-1390_primary	5S_rRNA.262	3	34745280	39872480	29	gain
MDT-AP-1390_primary	AC097359.3	3	34745280	39872480	29	gain
MDT-AP-1390_primary	C3orf35	3	34745280	39872480	29	gain
MDT-AP-1390_primary	ITGA9	3	34745280	39872480	29	gain
MDT-AP-1390_primary	RNU7-73P	3	34745280	39872480	29	gain
MDT-AP-1390_primary	AC093415.3	3	34745280	39872480	29	gain
MDT-AP-1390_primary	AC093415.4	3	34745280	39872480	29	gain
MDT-AP-1390_primary	AC093415.2	3	34745280	39872480	29	gain
MDT-AP-1390_primary	AC093415.5	3	34745280	39872480	29	gain
MDT-AP-1390_primary	CTDSPL	3	34745280	39872480	29	gain
MDT-AP-1390_primary	MIR26A1	3	34745280	39872480	29	gain
MDT-AP-1390_primary	VILL	3	34745280	39872480	29	gain
MDT-AP-1390_primary	PLCD1	3	34745280	39872480	29	gain
MDT-AP-1390_primary	Y_RNA.184	3	34745280	39872480	29	gain
MDT-AP-1390_primary	DLEC1	3	34745280	39872480	29	gain
MDT-AP-1390_primary	AC144536.4	3	34745280	39872480	29	gain
MDT-AP-1390_primary	AP006309.4	3	34745280	39872480	29	gain
MDT-AP-1390_primary	ACAA1	3	34745280	39872480	29	gain
MDT-AP-1390_primary	Y_RNA.359	3	34745280	39872480	29	gain
MDT-AP-1390_primary	MYD88	3	34745280	39872480	29	gain
MDT-AP-1390_primary	OXSR1	3	34745280	39872480	29	gain
MDT-AP-1390_primary	SLC22A13	3	34745280	39872480	29	gain
MDT-AP-1390_primary	RP11-815I22.1	3	34745280	39872480	29	gain
MDT-AP-1390_primary	SLC22A14	3	34745280	39872480	29	gain
MDT-AP-1390_primary	U6.34	3	34745280	39872480	29	gain
MDT-AP-1390_primary	RP11-213K17.1	3	34745280	39872480	29	gain
MDT-AP-1390_primary	XYLB	3	34745280	39872480	29	gain
MDT-AP-1390_primary	RP11-216F19.1	3	34745280	39872480	29	gain
MDT-AP-1390_primary	ACVR2B	3	34745280	39872480	29	gain
MDT-AP-1390_primary	EXOG	3	34745280	39872480	29	gain
MDT-AP-1390_primary	Y_RNA.656	3	34745280	39872480	29	gain
MDT-AP-1390_primary	RP11-660I20.1	3	34745280	39872480	29	gain
MDT-AP-1390_primary	RP11-660I20.4	3	34745280	39872480	29	gain
MDT-AP-1390_primary	SCN5A	3	34745280	39872480	29	gain
MDT-AP-1390_primary	SCN10A	3	34745280	39872480	29	gain
MDT-AP-1390_primary	AC116038.2	3	34745280	39872480	29	gain
MDT-AP-1390_primary	RP11-134J21.1	3	34745280	39872480	29	gain
MDT-AP-1390_primary	SCN11A	3	34745280	39872480	29	gain
MDT-AP-1390_primary	AC116038.1	3	34745280	39872480	29	gain
MDT-AP-1390_primary	U6.426	3	34745280	39872480	29	gain
MDT-AP-1390_primary	AC123903.2	3	34745280	39872480	29	gain
MDT-AP-1390_primary	AC123903.1	3	34745280	39872480	29	gain
MDT-AP-1390_primary	WDR48	3	34745280	39872480	29	gain
MDT-AP-1390_primary	GORASP1	3	34745280	39872480	29	gain
MDT-AP-1390_primary	TTC21A	3	34745280	39872480	29	gain
MDT-AP-1390_primary	CSRNP1	3	34745280	39872480	29	gain
MDT-AP-1390_primary	XIRP1	3	34745280	39872480	29	gain
MDT-AP-1390_primary	RP11-331G2.4	3	34745280	39872480	29	gain
MDT-AP-1390_primary	CX3CR1	3	34745280	39872480	29	gain
MDT-AP-1390_primary	CCR8	3	34745280	39872480	29	gain
MDT-AP-1390_primary	RP11-241K18.1	3	34745280	39872480	29	gain
MDT-AP-1390_primary	RP11-241K18.2	3	34745280	39872480	29	gain
MDT-AP-1390_primary	AC104850.1	3	34745280	39872480	29	gain
MDT-AP-1390_primary	EEF1A1P24	3	34745280	39872480	29	gain
MDT-AP-1390_primary	SLC25A38	3	34745280	39872480	29	gain
MDT-AP-1390_primary	RPSA	3	34745280	39872480	29	gain
MDT-AP-1390_primary	SNORA6	3	34745280	39872480	29	gain
MDT-AP-1390_primary	SNORA62.4	3	34745280	39872480	29	gain
MDT-AP-1390_primary	MOBP	3	34745280	39872480	29	gain
MDT-AP-1390_primary	RP11-420K5.1	3	34745280	39872480	29	gain
MDT-AP-1390_primary	AC104163.1	3	34745280	39872480	29	gain
MDT-AP-1390_primary	MYRIP	3	34745280	39872480	29	gain
MDT-AP-1390_primary	Z95704.4	4	27200	69360	13	gain
MDT-AP-1390_primary	Z95704.2	4	27200	69360	13	gain
MDT-AP-1390_primary	ZNF595	4	27200	69360	13	gain
MDT-AP-1390_primary	Z95704.1	4	27200	69360	13	gain
MDT-AP-1390_primary	RP11-462G22.1	4	190540080	190684240	7	gain
MDT-AP-1390_primary	U1.61	4	190540080	190684240	7	gain
MDT-AP-1390_primary	HLA-DRB5	6	32455040	32497200	0	loss
MDT-AP-1390_primary	PRIM2	6	57368880	57575600	5	gain
MDT-AP-1390_primary	RP11-715L17.1	7	61527760	61846000	5	gain
MDT-AP-1390_primary	MLL3	7	152098320	152113280	12	gain
MDT-AP-1390_primary	Y_RNA.859	7	152098320	152113280	12	gain
MDT-AP-1390/relapse/A11852_3_lanes_dupsFlagged.bam.pileup_CNVs
MDT-AP-1390_relapse	AL137798.3	1	16931592	17051391	6	gain
MDT-AP-1390_relapse	NBPF1	1	16931592	17051391	6	gain
MDT-AP-1390_relapse	CROCCP2	1	16931592	17051391	6	gain
MDT-AP-1390_relapse	AL137798.2	1	16931592	17051391	6	gain
MDT-AP-1390_relapse	RP5-1182A14.3	1	16931592	17051391	6	gain
MDT-AP-1390_relapse	RNU1-3	1	16931592	17051391	6	gain
MDT-AP-1390_relapse	AL137798.1	1	16931592	17051391	6	gain
MDT-AP-1390_relapse	RP1-163M9.6	1	16931592	17051391	6	gain
MDT-AP-1390_relapse	AL021920.1	1	16931592	17051391	6	gain
MDT-AP-1390_relapse	ESPNP	1	16931592	17051391	6	gain
MDT-AP-1390_relapse	PDE4DIP	1	144985707	145093113	7	gain
MDT-AP-1390_relapse	7SK.266	1	144985707	145093113	7	gain
MDT-AP-1390_relapse	SEC22B	1	145097244	145292778	7	gain
MDT-AP-1390_relapse	AL359758.1	1	145097244	145292778	7	gain
MDT-AP-1390_relapse	U6.306	1	145097244	145292778	7	gain
MDT-AP-1390_relapse	NOTCH2NL	1	145097244	145292778	7	gain
MDT-AP-1390_relapse	RP11-458D21.5	1	145097244	145292778	7	gain
MDT-AP-1390_relapse	AL592307.1	1	145097244	145292778	7	gain
MDT-AP-1390_relapse	NBPF10	1	145097244	145292778	7	gain
MDT-AP-1390_relapse	BX322613.2	10	42355143	42401961	22	gain
MDT-AP-1390_relapse	BX322613.3	10	42355143	42401961	22	gain
MDT-AP-1390_relapse	BX322613.1	10	42355143	42401961	22	gain
MDT-AP-1390_relapse	DHX32	10	127574919	127585935	8	gain
MDT-AP-1390_relapse	U2.26	10	127574919	127585935	8	gain
MDT-AP-1390_relapse	FANK1	10	127574919	127585935	8	gain
MDT-AP-1390_relapse	MUC6	11	1016226	1018980	8	gain
MDT-AP-1390_relapse	PPP1CA	11	67185207	67187961	5	gain
MDT-AP-1390_relapse	CARNS1	11	67185207	67187961	5	gain
MDT-AP-1390_relapse	FAM55A	11	114419061	114424569	5	gain
MDT-AP-1390_relapse	TAS2R14	12	11225304	11250090	0	loss
MDT-AP-1390_relapse	TAS2R46	12	11225304	11250090	0	loss
MDT-AP-1390_relapse	TAS2R43	12	11225304	11250090	0	loss
MDT-AP-1390_relapse	AB019440.1	14	106784973	106807005	10	gain
MDT-AP-1390_relapse	AB019439.32	14	106784973	106807005	10	gain
MDT-AP-1390_relapse	AB019439.23	14	106784973	106807005	10	gain
MDT-AP-1390_relapse	AB019439.5	14	106784973	106807005	10	gain
MDT-AP-1390_relapse	AB019439.26	14	106784973	106807005	10	gain
MDT-AP-1390_relapse	AB019439.27	14	106784973	106807005	10	gain
MDT-AP-1390_relapse	AB019439.13	14	106784973	106807005	10	gain
MDT-AP-1390_relapse	AC126603.1	15	20477367	21941118	7	gain
MDT-AP-1390_relapse	snoU13.388	15	20477367	21941118	7	gain
MDT-AP-1390_relapse	HERC2P3	15	20477367	21941118	7	gain
MDT-AP-1390_relapse	AC131280.1	15	20477367	21941118	7	gain
MDT-AP-1390_relapse	GOLGA6L6	15	20477367	21941118	7	gain
MDT-AP-1390_relapse	GOLGA8C	15	20477367	21941118	7	gain
MDT-AP-1390_relapse	AC131280.4	15	20477367	21941118	7	gain
MDT-AP-1390_relapse	AC131280.2	15	20477367	21941118	7	gain
MDT-AP-1390_relapse	AC131280.3	15	20477367	21941118	7	gain
MDT-AP-1390_relapse	U6.948	15	20477367	21941118	7	gain
MDT-AP-1390_relapse	AC012414.2	15	20477367	21941118	7	gain
MDT-AP-1390_relapse	AC012414.1	15	20477367	21941118	7	gain
MDT-AP-1390_relapse	U6.950	15	20477367	21941118	7	gain
MDT-AP-1390_relapse	AC126335.1	15	20477367	21941118	7	gain
MDT-AP-1390_relapse	AC126335.3	15	20477367	21941118	7	gain
MDT-AP-1390_relapse	AC126335.2	15	20477367	21941118	7	gain
MDT-AP-1390_relapse	AC068446.1	15	20477367	21941118	7	gain
MDT-AP-1390_relapse	AP3S2	15	90400050	90409689	5	gain
MDT-AP-1390_relapse	RP11-233C13.1	15	90400050	90409689	5	gain
MDT-AP-1390_relapse	CES1P1	16	55798794	55822203	0	loss
MDT-AP-1390_relapse	KCNJ12	17	21303567	21320091	5	gain
MDT-AP-1390_relapse	KIAA1267	17	44167275	44357301	5	gain
MDT-AP-1390_relapse	U7.136	17	44167275	44357301	5	gain
MDT-AP-1390_relapse	AC217773.1	17	44167275	44357301	5	gain
MDT-AP-1390_relapse	Y_RNA.751	17	44167275	44357301	5	gain
MDT-AP-1390_relapse	RBFOX3	17	77365368	77392908	5	gain
MDT-AP-1390_relapse	CDC42EP3	2	37958382	38002446	6	gain
MDT-AP-1390_relapse	AC006369.3	2	37958382	38002446	6	gain
MDT-AP-1390_relapse	AC018696.4	2	91759149	91819737	12	gain
MDT-AP-1390_relapse	AC116050.1	2	91759149	91819737	12	gain
MDT-AP-1390_relapse	RP4-610C12.1	20	29595861	29649564	6	gain
MDT-AP-1390_relapse	FRG1B	20	29595861	29649564	6	gain
MDT-AP-1390_relapse	AL441988.1	20	29595861	29649564	6	gain
MDT-AP-1390_relapse	MLLT10P1	20	29595861	29649564	6	gain
MDT-AP-1390_relapse	RP11-348I14.4	20	29595861	29649564	6	gain
MDT-AP-1390_relapse	AL109840.2	20	57463587	57467718	0	loss
MDT-AP-1390_relapse	GNAS	20	57463587	57467718	0	loss
MDT-AP-1390_relapse	RP1-309F20.3	20	57463587	57467718	0	loss
MDT-AP-1390_relapse	AF254982.1	21	10780533	10874169	6	gain
MDT-AP-1390_relapse	IGHV1OR21-1	21	10780533	10874169	6	gain
MDT-AP-1390_relapse	AF254982.2	21	10780533	10874169	6	gain
MDT-AP-1390_relapse	BAGE2	21	11040786	11133045	10	gain
MDT-AP-1390_relapse	VN1R7P	21	11133045	11186748	12	gain
MDT-AP-1390_relapse	EIF3FP1	21	11133045	11186748	12	gain
MDT-AP-1390_relapse	GSTT1	22	24346737	24394932	0	loss
MDT-AP-1390_relapse	GSTTP1	22	24346737	24394932	0	loss
MDT-AP-1390_relapse	AP000351.6	22	24346737	24394932	0	loss
MDT-AP-1390_relapse	AP000351.7	22	24346737	24394932	0	loss
MDT-AP-1390_relapse	AP000351.1	22	24346737	24394932	0	loss
MDT-AP-1390_relapse	AP000351.2	22	24346737	24394932	0	loss
MDT-AP-1390_relapse	AP000351.8	22	24346737	24394932	0	loss
MDT-AP-1390_relapse	AP000351.9	22	24346737	24394932	0	loss
MDT-AP-1390_relapse	AP000351.10	22	24346737	24394932	0	loss
MDT-AP-1390_relapse	GSTTP2	22	24346737	24394932	0	loss
MDT-AP-1390_relapse	ROBO2	3	75981483	75999384	5	gain
MDT-AP-1390_relapse	Z95704.4	4	27540	68850	10	gain
MDT-AP-1390_relapse	Z95704.2	4	27540	68850	10	gain
MDT-AP-1390_relapse	ZNF595	4	27540	68850	10	gain
MDT-AP-1390_relapse	Z95704.1	4	27540	68850	10	gain
MDT-AP-1390_relapse	RP11-462G22.1	4	190539621	190684206	8	gain
MDT-AP-1390_relapse	U1.61	4	190539621	190684206	8	gain
MDT-AP-1390_relapse	HLA-DRB5	6	32454513	32497200	0	loss
MDT-AP-1390_relapse	PRIM2	6	57368574	57532437	6	gain
MDT-AP-1390_relapse	RP11-715L17.1	7	61528491	61846578	8	gain
MDT-AP-1390_relapse	MLL3	7	152097912	152114436	16	gain
MDT-AP-1390_relapse	Y_RNA.859	7	152097912	152114436	16	gain
MDT-AP-1390_relapse	C9orf66	9	203796	225828	5	gain
MDT-AP-1390_relapse	DOCK8	9	203796	225828	5	gain
MDT-AP-1394/primary/A06705_9_lanes_dupsFlagged.bam.pileup_CNVs
MDT-AP-1394_primary	RNU1-1	1	16832109	17269833	5	gain
MDT-AP-1394_primary	RP4-798A10.4	1	16832109	17269833	5	gain
MDT-AP-1394_primary	RP4-798A10.5	1	16832109	17269833	5	gain
MDT-AP-1394_primary	RP5-875O13.1	1	16832109	17269833	5	gain
MDT-AP-1394_primary	U1.113	1	16832109	17269833	5	gain
MDT-AP-1394_primary	AL355149.1	1	16832109	17269833	5	gain
MDT-AP-1394_primary	AL137798.3	1	16832109	17269833	5	gain
MDT-AP-1394_primary	TRNAG36	1	16832109	17269833	5	gain
MDT-AP-1394_primary	RP5-875O13.6	1	16832109	17269833	5	gain
MDT-AP-1394_primary	AL355149.2	1	16832109	17269833	5	gain
MDT-AP-1394_primary	NBPF1	1	16832109	17269833	5	gain
MDT-AP-1394_primary	CROCCP2	1	16832109	17269833	5	gain
MDT-AP-1394_primary	AL137798.2	1	16832109	17269833	5	gain
MDT-AP-1394_primary	RP5-1182A14.3	1	16832109	17269833	5	gain
MDT-AP-1394_primary	RNU1-3	1	16832109	17269833	5	gain
MDT-AP-1394_primary	AL137798.1	1	16832109	17269833	5	gain
MDT-AP-1394_primary	RP1-163M9.6	1	16832109	17269833	5	gain
MDT-AP-1394_primary	AL021920.1	1	16832109	17269833	5	gain
MDT-AP-1394_primary	ESPNP	1	16832109	17269833	5	gain
MDT-AP-1394_primary	AL021920.2	1	16832109	17269833	5	gain
MDT-AP-1394_primary	RNU1-4	1	16832109	17269833	5	gain
MDT-AP-1394_primary	RP1-163M9.5	1	16832109	17269833	5	gain
MDT-AP-1394_primary	MST1P9	1	16832109	17269833	5	gain
MDT-AP-1394_primary	RP11-108M9.1	1	16832109	17269833	5	gain
MDT-AP-1394_primary	BX284668.3	1	16832109	17269833	5	gain
MDT-AP-1394_primary	RP11-108M9.2	1	16832109	17269833	5	gain
MDT-AP-1394_primary	BX284668.2	1	16832109	17269833	5	gain
MDT-AP-1394_primary	BX284668.1	1	16832109	17269833	5	gain
MDT-AP-1394_primary	RP11-108M9.3	1	16832109	17269833	5	gain
MDT-AP-1394_primary	U1.9	1	16832109	17269833	5	gain
MDT-AP-1394_primary	RP11-108M9.4	1	16832109	17269833	5	gain
MDT-AP-1394_primary	RP11-108M9.5	1	16832109	17269833	5	gain
MDT-AP-1394_primary	CROCC	1	16832109	17269833	5	gain
MDT-AP-1394_primary	RNU1-2	1	16832109	17269833	5	gain
MDT-AP-1394_primary	DDAH1	1	85980342	86004660	6	gain
MDT-AP-1394_primary	AMY2B	1	104104007	104159398	5	gain
MDT-AP-1394_primary	ACTG1P4	1	104104007	104159398	5	gain
MDT-AP-1394_primary	AMY2A	1	104104007	104159398	5	gain
MDT-AP-1394_primary	PDE4DIP	1	144906909	145291944	9	gain
MDT-AP-1394_primary	U2.35	1	144906909	145291944	9	gain
MDT-AP-1394_primary	7SK.266	1	144906909	145291944	9	gain
MDT-AP-1394_primary	SEC22B	1	144906909	145291944	9	gain
MDT-AP-1394_primary	AL359758.1	1	144906909	145291944	9	gain
MDT-AP-1394_primary	U6.306	1	144906909	145291944	9	gain
MDT-AP-1394_primary	NOTCH2NL	1	144906909	145291944	9	gain
MDT-AP-1394_primary	RP11-458D21.5	1	144906909	145291944	9	gain
MDT-AP-1394_primary	AL592307.1	1	144906909	145291944	9	gain
MDT-AP-1394_primary	NBPF10	1	144906909	145291944	9	gain
MDT-AP-1394_primary	RNU1-5	1	149220652	149239566	6	gain
MDT-AP-1394_primary	RP11-403I13.5	1	149220652	149239566	6	gain
MDT-AP-1394_primary	RP11-403I13.4	1	149220652	149239566	6	gain
MDT-AP-1394_primary	CFHR3	1	196739375	196796117	0	loss
MDT-AP-1394_primary	CFHR1	1	196739375	196796117	0	loss
MDT-AP-1394_primary	CFHR2	1	196739375	196796117	0	loss
MDT-AP-1394_primary	BX322613.2	10	42355201	42401135	38	gain
MDT-AP-1394_primary	BX322613.3	10	42355201	42401135	38	gain
MDT-AP-1394_primary	BX322613.1	10	42355201	42401135	38	gain
MDT-AP-1394_primary	RP11-38L15.3	10	46964813	47148549	5	gain
MDT-AP-1394_primary	SYT15	10	46964813	47148549	5	gain
MDT-AP-1394_primary	GPRIN2	10	46964813	47148549	5	gain
MDT-AP-1394_primary	XXyac-YR14BB7.1	10	46964813	47148549	5	gain
MDT-AP-1394_primary	PPYR1	10	46964813	47148549	5	gain
MDT-AP-1394_primary	RP11-314P12.2	10	46964813	47148549	5	gain
MDT-AP-1394_primary	RP11-314P12.3	10	46964813	47148549	5	gain
MDT-AP-1394_primary	DHX32	10	127574930	127595195	6	gain
MDT-AP-1394_primary	U2.26	10	127574930	127595195	6	gain
MDT-AP-1394_primary	FANK1	10	127574930	127595195	6	gain
MDT-AP-1394_primary	BET1L	11	189140	195895	5	gain
MDT-AP-1394_primary	SCGB1C1	11	189140	195895	5	gain
MDT-AP-1394_primary	MUC6	11	1015952	1018654	8	gain
MDT-AP-1394_primary	snoU13.388	15	20547359	21941591	10	gain
MDT-AP-1394_primary	HERC2P3	15	20547359	21941591	10	gain
MDT-AP-1394_primary	AC131280.1	15	20547359	21941591	10	gain
MDT-AP-1394_primary	GOLGA6L6	15	20547359	21941591	10	gain
MDT-AP-1394_primary	GOLGA8C	15	20547359	21941591	10	gain
MDT-AP-1394_primary	AC131280.4	15	20547359	21941591	10	gain
MDT-AP-1394_primary	AC131280.2	15	20547359	21941591	10	gain
MDT-AP-1394_primary	AC131280.3	15	20547359	21941591	10	gain
MDT-AP-1394_primary	U6.948	15	20547359	21941591	10	gain
MDT-AP-1394_primary	AC012414.2	15	20547359	21941591	10	gain
MDT-AP-1394_primary	AC012414.1	15	20547359	21941591	10	gain
MDT-AP-1394_primary	U6.950	15	20547359	21941591	10	gain
MDT-AP-1394_primary	AC126335.1	15	20547359	21941591	10	gain
MDT-AP-1394_primary	AC126335.3	15	20547359	21941591	10	gain
MDT-AP-1394_primary	AC126335.2	15	20547359	21941591	10	gain
MDT-AP-1394_primary	AC068446.1	15	20547359	21941591	10	gain
MDT-AP-1394_primary	AC068446.2	15	20547359	21941591	10	gain
MDT-AP-1394_primary	AC134980.2	15	22298255	22336083	6	gain
MDT-AP-1394_primary	AC134980.3	15	22298255	22336083	6	gain
MDT-AP-1394_primary	AC134980.1	15	22298255	22336083	6	gain
MDT-AP-1394_primary	RP11-2F9.1	15	22384719	22542786	6	gain
MDT-AP-1394_primary	VSIG6	15	22384719	22542786	6	gain
MDT-AP-1394_primary	MIR1268	15	22384719	22542786	6	gain
MDT-AP-1394_primary	5_8S_rRNA.2	16	33965491	33996564	12	gain
MDT-AP-1394_primary	RPH3AL	17	163471	166173	5	gain
MDT-AP-1394_primary	KCNJ12	17	21302568	21320131	6	gain
MDT-AP-1394_primary	ARHGEF18	19	7514262	7516964	5	gain
MDT-AP-1394_primary	AC018696.4	2	91759920	91819364	14	gain
MDT-AP-1394_primary	AC116050.1	2	91759920	91819364	14	gain
MDT-AP-1394_primary	ANKRD30BL	2	132996493	133023513	5	gain
MDT-AP-1394_primary	5_8S_rRNA.5	2	132996493	133023513	5	gain
MDT-AP-1394_primary	MIR663B	2	132996493	133023513	5	gain
MDT-AP-1394_primary	CDC27P1	2	132996493	133023513	5	gain
MDT-AP-1394_primary	AF254982.1	21	10722887	10860689	7	gain
MDT-AP-1394_primary	BAGE2	21	11040372	11137644	8	gain
MDT-AP-1394_primary	Z95704.4	4	28371	68901	8	gain
MDT-AP-1394_primary	Z95704.2	4	28371	68901	8	gain
MDT-AP-1394_primary	ZNF595	4	28371	68901	8	gain
MDT-AP-1394_primary	Z95704.1	4	28371	68901	8	gain
MDT-AP-1394_primary	RP11-462G22.1	4	190539636	190684193	7	gain
MDT-AP-1394_primary	U1.61	4	190539636	190684193	7	gain
MDT-AP-1394_primary	ZDHHC11B	5	748454	778176	5	gain
MDT-AP-1394_primary	ZDHHC11	5	748454	778176	5	gain
MDT-AP-1394_primary	CTD-2589H19.4	5	748454	778176	5	gain
MDT-AP-1394_primary	HLA-DRB5	6	32455073	32496954	0	loss
MDT-AP-1394_primary	PRIM2	6	57371566	57566110	6	gain
MDT-AP-1394_primary	ISPD	7	16436266	16440319	5	gain
MDT-AP-1394_primary	MLL3	7	152098282	152113143	10	gain
MDT-AP-1394_primary	Y_RNA.859	7	152098282	152113143	10	gain
MDT-AP-1394_primary	AL772363.1	9	140776902	140785008	5	gain
MDT-AP-1394_primary	CACNA1B	9	140776902	140785008	5	gain
MDT-AP-1394_primary	RP11-954J6.3	X	154789474	154797580	0	loss
MDT-AP-1394_primary	TMLHE	X	154789474	154797580	0	loss
MDT-AP-1394/relapse/A06708_10_lanes_dupsFlagged.bam.pileup_CNVs
MDT-AP-1394_relapse	AL137798.3	1	16934824	17052480	5	gain
MDT-AP-1394_relapse	NBPF1	1	16934824	17052480	5	gain
MDT-AP-1394_relapse	CROCCP2	1	16934824	17052480	5	gain
MDT-AP-1394_relapse	AL137798.2	1	16934824	17052480	5	gain
MDT-AP-1394_relapse	RP5-1182A14.3	1	16934824	17052480	5	gain
MDT-AP-1394_relapse	RNU1-3	1	16934824	17052480	5	gain
MDT-AP-1394_relapse	AL137798.1	1	16934824	17052480	5	gain
MDT-AP-1394_relapse	RP1-163M9.6	1	16934824	17052480	5	gain
MDT-AP-1394_relapse	AL021920.1	1	16934824	17052480	5	gain
MDT-AP-1394_relapse	ESPNP	1	16934824	17052480	5	gain
MDT-AP-1394_relapse	AL021920.2	1	16934824	17052480	5	gain
MDT-AP-1394_relapse	PDE4DIP	1	144985808	145092768	8	gain
MDT-AP-1394_relapse	7SK.266	1	144985808	145092768	8	gain
MDT-AP-1394_relapse	SEC22B	1	145097352	145117216	7	gain
MDT-AP-1394_relapse	DMBT1	10	124345584	124351696	0	loss
MDT-AP-1394_relapse	DHX32	10	127577304	127586472	7	gain
MDT-AP-1394_relapse	U2.26	10	127577304	127586472	7	gain
MDT-AP-1394_relapse	FANK1	10	127577304	127586472	7	gain
MDT-AP-1394_relapse	OR4C11	11	55365552	55452648	0	loss
MDT-AP-1394_relapse	OR4P4	11	55365552	55452648	0	loss
MDT-AP-1394_relapse	OR4S2	11	55365552	55452648	0	loss
MDT-AP-1394_relapse	OR4C6	11	55365552	55452648	0	loss
MDT-AP-1394_relapse	OR4V1P	11	55365552	55452648	0	loss
MDT-AP-1394_relapse	OR4P1P	11	55365552	55452648	0	loss
MDT-AP-1394_relapse	RP11-674C21.9	11	55365552	55452648	0	loss
MDT-AP-1394_relapse	FAM55A	11	114419696	114473176	5	gain
MDT-AP-1394_relapse	FAM55D	11	114419696	114473176	5	gain
MDT-AP-1394_relapse	AB019440.1	14	106717048	106726216	5	gain
MDT-AP-1394_relapse	AB019439.17	14	106717048	106726216	5	gain
MDT-AP-1394_relapse	AB019439.30	14	106717048	106726216	5	gain
MDT-AP-1394_relapse	IGHV@	14	106717048	106726216	5	gain
MDT-AP-1394_relapse	AC126603.1	15	20476728	21932912	7	gain
MDT-AP-1394_relapse	snoU13.388	15	20476728	21932912	7	gain
MDT-AP-1394_relapse	HERC2P3	15	20476728	21932912	7	gain
MDT-AP-1394_relapse	AC131280.1	15	20476728	21932912	7	gain
MDT-AP-1394_relapse	GOLGA6L6	15	20476728	21932912	7	gain
MDT-AP-1394_relapse	GOLGA8C	15	20476728	21932912	7	gain
MDT-AP-1394_relapse	AC131280.4	15	20476728	21932912	7	gain
MDT-AP-1394_relapse	AC131280.2	15	20476728	21932912	7	gain
MDT-AP-1394_relapse	AC131280.3	15	20476728	21932912	7	gain
MDT-AP-1394_relapse	U6.948	15	20476728	21932912	7	gain
MDT-AP-1394_relapse	AC012414.2	15	20476728	21932912	7	gain
MDT-AP-1394_relapse	AC012414.1	15	20476728	21932912	7	gain
MDT-AP-1394_relapse	U6.950	15	20476728	21932912	7	gain
MDT-AP-1394_relapse	AC126335.1	15	20476728	21932912	7	gain
MDT-AP-1394_relapse	AC126335.3	15	20476728	21932912	7	gain
MDT-AP-1394_relapse	AC126335.2	15	20476728	21932912	7	gain
MDT-AP-1394_relapse	MAP2K3	17	21193360	21252952	7	gain
MDT-AP-1394_relapse	KCNJ12	17	21303376	21327824	9	gain
MDT-AP-1394_relapse	AC018696.4	2	91759456	91820576	13	gain
MDT-AP-1394_relapse	AC116050.1	2	91759456	91820576	13	gain
MDT-AP-1394_relapse	ANKRD30BL	2	133001704	133023096	6	gain
MDT-AP-1394_relapse	5_8S_rRNA.5	2	133001704	133023096	6	gain
MDT-AP-1394_relapse	MIR663B	2	133001704	133023096	6	gain
MDT-AP-1394_relapse	CDC27P1	2	133001704	133023096	6	gain
MDT-AP-1394_relapse	SIRPB1	20	1563144	1593704	0	loss
MDT-AP-1394_relapse	AL441988.1	20	29637088	29649312	9	gain
MDT-AP-1394_relapse	MLLT10P1	20	29637088	29649312	9	gain
MDT-AP-1394_relapse	RP11-348I14.4	20	29637088	29649312	9	gain
MDT-AP-1394_relapse	AF254982.1	21	10725032	10861024	7	gain
MDT-AP-1394_relapse	AF254982.3	21	10873248	11133008	7	gain
MDT-AP-1394_relapse	TPTE	21	10873248	11133008	7	gain
MDT-AP-1394_relapse	CYCSP41	21	10873248	11133008	7	gain
MDT-AP-1394_relapse	BAGE2	21	10873248	11133008	7	gain
MDT-AP-1394_relapse	ROBO2	3	75993552	75996608	5	gain
MDT-AP-1394_relapse	AC069513.3	3	195418976	195448008	5	gain
MDT-AP-1394_relapse	MIR570	3	195418976	195448008	5	gain
MDT-AP-1394_relapse	MUC20	3	195418976	195448008	5	gain
MDT-AP-1394_relapse	Z95704.4	4	27504	68760	10	gain
MDT-AP-1394_relapse	Z95704.2	4	27504	68760	10	gain
MDT-AP-1394_relapse	ZNF595	4	27504	68760	10	gain
MDT-AP-1394_relapse	Z95704.1	4	27504	68760	10	gain
MDT-AP-1394_relapse	LRPAP1	4	3534264	3635112	5	gain
MDT-AP-1394_relapse	RP11-529E10.8	4	3534264	3635112	5	gain
MDT-AP-1394_relapse	RP3-368B9.1	4	3534264	3635112	5	gain
MDT-AP-1394_relapse	RP3-368B9.2	4	3534264	3635112	5	gain
MDT-AP-1394_relapse	RP11-462G22.1	4	190540072	190680648	7	gain
MDT-AP-1394_relapse	U1.61	4	190540072	190680648	7	gain
MDT-AP-1394_relapse	ZDHHC11B	5	756360	822064	5	gain
MDT-AP-1394_relapse	ZDHHC11	5	756360	822064	5	gain
MDT-AP-1394_relapse	CTD-2589H19.4	5	756360	822064	5	gain
MDT-AP-1394_relapse	AC026740.1	5	756360	822064	5	gain
MDT-AP-1394_relapse	CTD-2198K18.1	5	756360	822064	5	gain
MDT-AP-1394_relapse	HLA-DRB5	6	32454720	32541816	0	loss
MDT-AP-1394_relapse	U1.110	6	32454720	32541816	0	loss
MDT-AP-1394_relapse	HLA-DRB6	6	32454720	32541816	0	loss
MDT-AP-1394_relapse	AL713966.1	6	32454720	32541816	0	loss
MDT-AP-1394_relapse	PRIM2	6	57368760	57576568	6	gain
MDT-AP-1394_relapse	snoU13.460	6	157710992	157735440	5	gain
MDT-AP-1394_relapse	C6orf35	6	157710992	157735440	5	gain
MDT-AP-1394_relapse	RP11-96F3.2	6	157710992	157735440	5	gain
MDT-AP-1394_relapse	MLL3	7	152098648	152113928	7	gain
MDT-AP-1394_relapse	Y_RNA.859	7	152098648	152113928	7	gain
MDT-AP-1394_relapse	RP11-124B13.1	8	5968368	5972952	0	loss