sample	event	source	type	chromosome1	bp1	chromosome2	bp2	split_reads	disc_reads	genotype	id	length.Kb.	position	configuration	allele_frequency	log2.cnv.	microhomology	inserted_seq	consensus	contig_sequence	mechanism	bp1_locus	bp2_locus	affected_genes	status	notes	snp_freq
A373R11	13	novobreak	DEL	2R	6153193	2R	6153589	5	0	somatic_tumour	14	0.4	2R:6153193-6153589	5to3	0.05	0	GCCTCCGT	-	TTTATCGATAAAATTCTTAAAAACTGATCAATTTTACTTATTGATATAACAAGGTATGTAACTAGATATGAAATATCGAACTGGTTCCATAGCCTCCGTCAAGTGGCTGCTTTCACGAACGCCAATGCATTTTAGTGCCTAATTTCCAATAAATCACTGCCGTCGTTGACTTATAAGCTCCTTAAAGA	CTGATCAATTTTACTTATTGATATAACAAGGTATGTAACTAGATATGAAATATCGAACTGGTTCCATAGCCTCCGTCAAGTGGCTGCTTTCACGAACGCCAATGCATTTTAG	Alt-EJ	tRNA:Asn-GTT-1-2, tRNA	EcR, intron	EcR, tRNA:Asn-GTT-1-2	NA	mh:8; ins:0; tup:0; tdown:0	0
A373R11	16	lumpy	BND	2R	13505400	2R	13505470	1	4	somatic_tumour	2075_1	0.1	2R:13505400-13505470	5to5	0.04	0	CGCAA	-	-	CGGCGGCCGCAAGAATCGCGGGTTTCAGGAGCGCATTTGGCGCAACCGCCGATCTTTTTCGCCCGCCCGCACAGTACTCCGCATGTCCACCGG	Alt-EJ	mars, exon	mars, exon	mars	NA	mh:5; ins:0; tup:0; tdown:0	0
A373R11	18	Control-Freec	DEL	2R	19515550	2R	19535125	-	-	somatic_tumour	-	19.6	2R:19515550-19535125	Heterozygous deletion	0.31	-0.53	-	-	-	-	-	intergenic	sm, intron	sm	NA	snp_su:0; snp_op:0	0
A373R11	26	Control-Freec	DUP	3L	21427375	3L	21433900	-	-	somatic_tumour	-	6.5	3L:21427375-21433900	Heterozygous duplication	0.42	0.59	-	-	-	-	-	barc, intron	Aef1, exon_1	barc, CG33288, Aef1	NA	snp_su:0; snp_op:0	0
A373R11	28	Control-Freec	DUP	3R	5733300	3R	5795650	-	-	somatic_tumour	-	62.4	3R:5733300-5795650	Heterozygous duplication	0.2	0.21	-	-	-	-	-	intergenic	CG10979, exon_3	CG10979	TRUE	low FC; snp_su:24; snp_op:12; snp_ratio:2.0	10.65
A373R11	29	Control-Freec	DUP	3R	18283050	3R	18292475	-	-	somatic_tumour	-	9.4	3R:18283050-18292475	Heterozygous duplication	0.38	0.51	-	-	-	-	-	CG14312, 3UTR	l(3)05822, intron	CG14312, CG8064, CG7131, l(3)05822	NA	snp_su:11; snp_op:6; snp_ratio:1.83	12.65
A373R11	37	delly	DEL	X	3146220	X	3148372	31	29	somatic_tumour	DEL00000033	2.2	X:3146220-3148372	5to3	0.92	-2.14	-	-	GATTTGCACTATATTATATATCTGTTGGATTTGTGGCATTTGTCTATTTTCTTGCAGCCTTCAGTCTGCGGTCTCCAGTCTGCAGTTTTTTTTTTCGGCCTGCAGTCTTCT	-	-	N, intron	N, intron	N	NA	snp_su:0; snp_op:0	0
A373R11	37	lumpy	DEL	X	3146220	X	3148372	31	29	somatic_tumour	5904	2.2	X:3146220-3148372	5to3	0.92	-2.14	-	-	-	-	-	N, intron	N, intron	N	NA	snp_su:0; snp_op:0	0
A373R11	37	novobreak	DEL	X	3146220	X	3148372	31	29	somatic_tumour	58	2.2	X:3146220-3148372	5to3	0.92	-2.14	-	-	CAAAAGTTGGAAAGATATCGAATGTTTGCAGATTTGCACTATATTATATATCTGTTGGATTTGTGGCATTTGTCTATTTTCTTGCAGCCTTCAGTCTGCGGTCTCCAGTCTGCAGTTTTTTTTTTCGGCCTGCAGTCTTCTCTGCTGCGAATCGTATCAAAACGGGCTCGTTGTCGAGCGACATTCCTGGCAAATCGGTTTGAACCTAAACGAGAGTCTGGGAGTCTCTGGTTCGTGCCTTTAGCC	-	-	N, intron	N, intron	N	NA	snp_su:0; snp_op:0	0
A373R11	38	novobreak	BND	X	4954265	X	4954391	8	2	somatic_tumour	60	0.1	X:4954265-4954391	5to5	0.13	0	-	-	GCTCTTGCTTGGGTTTTTCTATCGCCTCCTGGAGAACCACATGCACGTCATGGGTGCTGCTGCTGCAGCTGGCCACGGAAGTTAAGCCAAAGGGTAGCAATGACGATGAAGAAGACGAAGAAGACGATGACGACGACGACGATGACCAG	-	-	Ptp4E, exon	Ptp4E, exon	Ptp4E	NA	-	0
A373R11	39	novobreak	BND	X	9302146	X	9302259	5	1	somatic_tumour	61	0.1	X:9302146-9302259	5to5	0.16	0	GCTGCAGCTGGCC	-	AATCCATGGCCATGCATCTCGGGCAGCACCGCCGGCAGGTGGGCGGCAATGGAGCCACCATGGGCATGGGCATGGGAGTGGGAGTGGGCATGGGCATGAATCACTACGGCGGTGGCTA	GGAGAACCACATGCACGTCATGGGTGCTGCTGCTGCAGCTGGCCACGGAAGTTAAGCCAAAGGGTAGCAATGACGATGAAGAAGACGAAGAAGACGATGACGACGAC	Alt-EJ	lz, exon	lz, exon	lz	NA	mh:13; ins:0; tup:0; tdown:0	0
A373R11	40	novobreak	BND	X	10498521	X	10498657	3	0	somatic_tumour	64	0.1	X:10498521-10498657	5to5	0.04	0	GTGGGCGGCA	-	AGACATTCGCCAAGCGATTGTCGCCGGAGGGCGAGTGTAAGGACACGCTGTCCTCGCAGGGATCCTCTTCTAACGATAGTCGCTGGCCGCCGGCGTAGTAACCTCCACGAATTTTCCATTACCATTACCAACCGTCGGTCCACTACCGCCGCCACCTCCGTTCTCCATCGAGAAGGTAACCGTGGTGGTTACCGTAAAATTGCCATTGGCACTTCCATTCTGATCCGGAGAATGGGGCTTTGACC	AATCCATGGCCATGCATCTCGGGCAGCACCGCCGGCAGGTGGGCGGCAATGGAGCCACCATGGGCATGGGCATGGGAGTGGGAGTGGGCATGGGCATGAATCACTACG	Alt-EJ	spri, exon_6	spri, exon_6	spri	NA	mh:10; ins:0; tup:0; tdown:0	0
A373R11	41	novobreak	TRA	X	12265734	3R	29465597	8	0	somatic_tumour	65	17199.9	X:12265734 3R:29465597	5to5	0.23	0	-	-	TTTTTTTTTTTTTTTTTTTTTTGGCTTTTCCATGGTGGTGACTTTCCGTTGCACTTGCAGCTGCAGGAATCCGAAAACCGGGGACATGCCGTCTAATTCAATT	-	-	Ten-a, intron	Ptp99A, intron	Ten-a, Ptp99A	NA	-	0
A373R11	43	novobreak	BND	X	17769397	X	17769504	5	0	somatic_tumour	71	0.1	X:17769397-17769504	5to5	0.09	0	-	-	GGATGGTGGCCACTGTACTGGCGACGGCCGCCACGCAAATGGCCGCTGTGAATGCTAGCAATGCGTTCGCCAATCTAACGGGACTGAGTGCGGCGGCGCTGCGAAACGTGAGTGCCGCCC	-	-	unc-4, exon_1	unc-4, exon_1	unc-4	NA	-	0
A373R13	2	novobreak	TRA	2L	553722	2R	10934808	9	0	somatic_tumour	3	10381.1	2L:553722 2R:10934808	5to3	0.16	0	-	-	GTGTAACTTATTGCAAATATATTTGTTATAAGGTGTTGTATTAAGTTAGGCGATGTTATGATATTATTGTATGGTATACTTGTTGAATCCTTTTTTTTTCTCAGTGCGCACACGTATATTTATATCTCAAAGTTCTCAATCAAAACGAACAAGTTACGTATTTGTATAACTTGTATTTGTATTTCACAAGACTGCTTAAATTGCTGCTTATATTGTATAC	-	NHEJ	intergenic	intergenic	-	NA	mh:0; ins:0; tup:0; tdown:0	0
A373R13	12	novobreak	TRA	2L	3115500	3R	13703238	5	0	somatic_tumour	13	10587.7	2L:3115500 3R:13703238	3to3	0.07	0	-	TTAC	CCAATATTTTCCATCCATGTACAATGGACGAAGCTGAGCGTAAACATTTCAACAACTCTTCCAATGTTACCCAGCTGCTTGAGAAAGCGCAGATCCGCATCCGCCGGAGCCAAGGC	CCAATATTTTCCATCCATGTACAATGGACGAAGCTGAGCGTAAACATTTCAACAACTCTTCCAATGTTACCCAGCTGCTTGAGAAAGCGCAGATCCGCATCCGCCGGAGCCAAGGC	NHEJ	toc, intron	Adgf-D, exon	toc, Adgf-D	NA	mh:0; ins:4; tup:3; tdown:2	0
A373R13	14	novobreak	TRA	2L	3771067	3L	24121078	3	0	somatic_tumour	17	20350	2L:3771067 3L:24121078	14:14_314	0.04	0	-	-	TTTTAATAGTTCTTGGGCCTACTTGTAGCGGTGGTGGCGTAGCCTCAAAGACAATAGCAGTGAAGCAGTCAACATACACTTCATCGCTATCGTTGATAGGCTGGTAGTTCCCTGTTTATTGTTATGCCTTTTTAGTGGGGGTGTATTTTGT	-	-	intergenic	Snap25, intron	Snap25	NA	bp2_INE-1_Helitron=2	0
A373R13	21	novobreak	TRA	2L	5313800	X	12654753	3	0	somatic_tumour	27	7341	2L:5313800 X:12654753	5to3	0.06	0	GGAAAAGGAAGGC	-	GCCGTAGCCCGCTCCCGGTGCTCGTATGCATTGAGGGATTCGCGGAAAAGGAAGGCAAAACAAATTCCGGAGAGCAGAAAGAGAGGTGGAAAAGAAAGTGTTGAGAAAGGGATGACAGCAAAAAG	GCCGTAGCCCGCTCCCGGTGCTCGTATGCATTGAGGGATTCGCGGAAAAGGAAGGCAAAACAAATTCCGGAGAGCAGAAAGAGAGGTGGAAAAGAAAGTGT	Alt-EJ	CG14024, exon_2	CkIalpha, exon_1	CG14024, CkIalpha	NA	mh:13; ins:0; tup:0; tdown:0	0
A373R13	29	novobreak	TRA	2L	6068689	Tomelloso	31531	3	0	somatic_tumour	35	6037.2	2L:6068689 Tomelloso:31531	29:24_29_30	0.09	0	AT	-	CACCACAGCCAGTTTGTTCTGCCACCGCTCCATGCCGTCTTGTGAATGAGGAGCTGATGCAAGTAAGAAGCTCGCATCGGAAACTCGGGAGCAGTTTCATGGCTTCTTGGTTCGCAATTGAGGTTAATCTCCAACGGTCAAATTCACAAGAAGCTGTTTGAATTCTATACACATTGTGTGTTTGCACCGGCCATGATACAATTGCGAAGC	GTTCGCAATTGAGGTTAATCTCCAACGGTCAAATTCACAAGAAGCTGTTTGAATTCTATACACATTGTGTGTTTGCACCGGCCATGATACAATTGCGAAGC	Alt-EJ	intergenic	intergenic	-	NA	bp1_Tomelloso_2; mh:2; ins:0; tup:0; tdown:0	0
A373R13	29	novobreak	TRA	2L	6110188	Tomelloso	35464	3	0	somatic_tumour	36	6074.7	2L:6110188 Tomelloso:35464	30:24_29_30	0.11	0	T	-	ACACATATCCCAGCAATCTACACTACCAGTTCTTTAGTTGTGTGAAAGAAAGCAGATCCCACGATGCTGATTGGATTAGTACGCGACTCGGTTATGCAGTGCTTCTCCCTCACTACGTGCTAGCAGAAATAAATTGAGTGCCCATTGTGGGGTGTTGGTCGGTATACCC	GATTGGATTAGTACGCGACTCGGTTATGCAGTGCTTCTCCCTCACTACGTGCTAGCAGAAATAAATTGAGTGCCCATTGTGGGGTGTTGGTCGGTATACCC	Alt-EJ	stai, exon_3	intergenic	stai	NA	mh:1; ins:0; tup:0; tdown:0	0
A373R13	35	novobreak	TRA	2L	7747929	3R	27519078	3	0	somatic_tumour	41	19771.1	2L:7747929 3R:27519078	5to3	0.06	0	GTTC	-	CATGGGCGTAGCTGTTTATATTGTTTTTTCCCTAGAAATTCGCTTTATGTTCCTACGATTGATTAAAAACCATGGTATCTTAAGATTGCACTCCAAAATTGAAATATTACGTTACTTTCGCTACTCATAAATGCACTTTCAGTATTTTTGG	CATGGGCGTAGCTGTTTATATTGTTTTTTCCCTAGAAATTCGCTTTATGTTCCTACGATTGATTAAAAACCATGGTATCTTAAGATTGCACTCCAAAATTG	Alt-EJ	intergenic	intergenic	-	NA	mh:4; ins:0; tup:0; tdown:0	0
A373R13	47	novobreak	TRA	2L	10991843	X	19688243	3	0	somatic_tumour	54	8696.4	2L:10991843 X:19688243	3to3	0.05	0	-	TGCGCCTAAGTGT	CTTCAGCACCCGTGGTATGCTGCGAAAGTCTTCTGCAGTGGTGCCCCAGACGGTCAACTGGAATCGGTCGATGGCCGCCACTGGCTCATTGATGAGCAGACACTTAGGCGCACGAAGTCTATGGCACTGCGGTGATCTTCCTGTTTGTGTTCCGGCTCCAGC	GCTGGAGCCGGAACACAAACAGGAAGATCACCGCAGTGCCATAGACTTCGTGCGCCTAAGTGTCTGCTCATCAATGAGCCAGTGGCGGCCATCGACCGATT	FoSTeS	CG16833, exon_4	CG14227, exon	CG16833, CG14227	NA	mh:0; ins:13; tup:4; tdown:4	0
A373R13	71	novobreak	TRA	2L	19788773	2R	18156855	5	0	somatic_tumour	80	1631.9	2L:19788773 2R:18156855	5to5	0.09	0	-	-	ACGCGACGGCGTCGGCTCGAACAGGGGTAAACAGCAATAAGACTCTCATATGCGCTACACTGGCAGCCGGCTGTATGTTTCTGCGTGGGCGGGGGAGAGCAGGGCATATAGTTTGCCGCCAGAGCTTAAACTTTAGTCTCACGCTCTCTGTGTCCCTCGTTCTCTTTCGCTAAGCGCTCTCAAC	-	-	CdGAPr, intron	lolal, exon_1	CdGAPr, lolal	NA	-	0
A373R13	74	Control-Freec	DUP	2L	21390362	2L	21393869	-	-	somatic_tumour	-	3.5	2L:21390362-21393869	75:74_75	0.44	0.74	-	-	-	-	-	nrv3, 3UTR	intergenic	nrv3	NA	snp_su:0; snp_op:0	0
A373R13	79	novobreak	TRA	2R	24570562	3R	4746260	3	0	somatic_tumour	163	19824.3	2R:24570562 3R:4746260	139:79_139	0.06	0	-	-	GTTCACTTGGCTCCAAAAAATAATGGATCTATAGAGTTCCTTAGTTTGCAAATGTGCAGTTCGTACAGCTGGGACATGCGCTCCAGAAACTCGGCGGTGCCGGGGCGCAGGCGCGTGTGGTACCACGGGGAATGTGGG	-	-	Fcp1, exon_3	tacc, 5UTR	Fcp1, tacc	NA	-	0
A373R13	113	novobreak	TRA	2R	16673460	3R	18114304	3	0	somatic_tumour	133	1440.8	2R:16673460 3R:18114304	5to3	0.05	0	-	-	GTGAAGCTCGCTGGCTGGAATAAAACAAAGCAAATGAAAAACAATGCGCAGAGATCAAAACTTTATAGACAGACGCGTTTATAGTTCCGCTGCGATGAGTATTCGTATCTTTGGCTAAATATAACCCACGCGTACTATTTATATCGTTTCA	-	-	CG30463, 3UTR	sr, intron	CG30463, sr	NA	-	0
A373R13	137	novobreak	TRA	2R	24191931	3L	14203584	2	1	somatic_tumour	160	9988.3	2R:24191931 3L:14203584	3to3	0.04	0	-	-	TCGTCAGAAAGTTGATTTGGAAACATCGGTAAAGATATCGCCGTATTGCAATTCTTGGCCATCGGCTTGTTGGTTCACTCTTAAAGGCATTGATTTGTTGAAACTTCTGGTATTGGAAAGATCACCAACTTACCTGGTGACGCACTCGATCTGCCCGTCTTTGGTTTAGGCGCTGGTAAGAGT	-	-	ocm, exon_5	CG32141, exon_1	ocm, nuf, CG32141	NA	-	0
A373R13	140	novobreak	TRA	2R	24861392	2L	17928964	7	0	somatic_tumour	164	6932.4	2R:24861392 2L:17928964	140:140_141	0.1	0	-	-	GCACGGTGCGTGGCTGTTTAAAACGCTGTTTACGACTCCGTAAGCGTGCGAGTATGTCTGTGTTAAATTGGATTCGAGTGACAATTGACAAAGGGGAGGCAAAGTTTCGGGGACCTTTGAACCCATCGAAAGTTGTCAATCAGAGGGCGATTTTCGCTGAATTTTCCAACACCCCGTGGATCATGATTCGCCGCTTAACGC	-	-	intergenic	intergenic	-	NA	-	0
A373R13	143	novobreak	BND	3L	72734	3L	76450	2	1	somatic_tumour	167	3.7	3L:72734-76450	5to5	0.04	-0.16	-	-	TTGCGCACTGAATAAGTAAAACAATCACTAACAATCTTCCGCTCAGACTTTTGTTTTCCTTTGTCTTGCATCTTTTTTGTGCTATTGTTACAACGGAATGGGGACTGTTTTTTTGTTTATGCC	-	-	CR43988, ncRNA	intergenic	CR43988	NA	-	0
A373R13	149	novobreak	TRA	3L	2245015	3R	28316834	3	0	somatic_tumour	175	26071.8	3L:2245015 3R:28316834	5to3	0.06	0	-	-	ATACGAATCCATTGCCATATTGGTCAGCTGTTTAATGGCTCTGCTTTTGACTGCGATGGGTCTGGTTAGCGACAACCTATGACAGGTTGTGTGGGTTTGTCCGGTGGC	-	-	CG32301, intron	intergenic	CG32301	NA	-	0
A373R13	153	novobreak	BND	3L	4065761	3L	9407320	2	1	somatic_tumour	179	5341.6	3L:4065761-9407320	3to3	0.03	0.04	-	-	CCGTTGCTCTGCACTCCTCAGCTGATCCGGCGGAGGTTTATCGAGGCGAGGACTAAGATCCAGGTTGTTCGGTCGACGTAGAGCCGTCACCAGATTGGACTTCTCTTCGCCCACCTTTTGGATACCGAAACGGGGAAACTACATTTCATTCTATTTATTTTCCGTTCGTGCTTGTTGTGTTGTAATTGTGTAATAC	-	-	wit, exon	CG4022, 3UTR	wit, CG4022	NA	-	0
A373R13	159	novobreak	BND	3L	4982252	3L	19898802	3	1	somatic_tumour	186	14916.5	3L:4982252-19898802	3to3	0.04	0.05	-	-	GTGAGTTGTGGAGAGGAGTGCGGAGGGATGGGAAGAGGTGGCACAGGGTCAGGGGGCAAGGGACAGGCAAAAGGAAATGCGAGGACCTCGACAACGCCTTGGCTGCCACCGGATTTCACTTCCTTTTTTTGACTTCTGGATGAGGAGGCAT	-	-	Con, intron	Su(Tpl), intron	Con, Mi-2, Su(Tpl)	NA	-	0
A373R13	178	Control-Freec	DUP	3L	10506972	3L	10513986	-	-	somatic_tumour	-	7	3L:10506972-10513986	Heterozygous duplication	0.38	0.62	-	-	-	-	-	Rbfox1, intron	Rbfox1, intron	Rbfox1	NA	snp_su:15; snp_op:15; snp_ratio:1.0	10.9
A373R13	179	novobreak	BND	3L	10815481	3L	19549419	4	2	somatic_tumour	206	8733.9	3L:10815481-19549419	3to3	0.06	0.04	-	-	CTCCAGCACCCCATTTAAAGGCCCTTCCTTCGAGGCAACACTCGCTATATAACCATCTTACCCAACGTTGACAGCATACAAAGTAACTTAAATCGAAACAATAAAGCGGATACTTTGGATGGAATGGCAGAGGCGATGGCCAAGTTTGTTATTTGCTCAACGGAAAATATTGAAGATGAGTATAAGCGCTTGGAG	-	-	CG42831, 3UTR	Ltn1, exon_5	CG42831, Ltn1	NA	bp2_opus_Gypsy=2	0
A373R13	234	novobreak	TRA	3R	7943071	2L	18464955	5	0	somatic_tumour	276	10521.9	3R:7943071 2L:18464955	5to5	0.09	0	-	-	ATTAAATTTCCATGATAAACTTCTTTTAATTTCGCCACTTTTCCACCTTTTTGCACTGGCATTCTGTTAACATCAAATAGGGTAAGTTGCCTTAATAATATTTTTTTATTTTTCTAACCTGACAAATTGCTACAAAGATTAAAATACGTCTAATAT	-	-	dsx, intron	let-7-C, ncRNA	dsx, let-7-C	NA	-	0
A373R13	235	novobreak	BND	3R	8015021	3R	25233379	2	1	somatic_tumour	278	17218.4	3R:8015021-25233379	3to3	0.03	0.04	-	-	GTCACGGTAGGTACCCAATATATTGAATAATTTTTAATTTATTATTTCGCTCCTTTGAAACAGTTTGAATGTGAGCCAAACGAAGCCACAAGAACAGGGAAAACCTGGCACGGAACTGTAC	-	-	Pbp95, intron	intergenic	Pbp95	NA	-	0
A373R13	236	novobreak	BND	3R	8222686	3R	8519520	6	0	somatic_tumour	279	296.8	3R:8222686-8519520	3to3	0.05	0.07	-	-	ATACGAATTTAATTCAAAATAATTGCACGGCATGCACAGGAGGACATGTGGAGTGCTCTCTGGCTGTGGGGCTGCTGTTGGCCCAAGACTAGTTAGTACTCTGCCTGGAAGTTGGTCAAGAAGGGGAAGTGGAGTGGAGTAGTGAGTTATAAAAGAACCTGCCAGGCTCGATTATCTCTCTCAAACTCGGTAAACATTTATAA	ACAATGAATGGATATATCTGCAGCCGACATGTGTATAACTTTAAGTTCGCTTGTCCTACCTTCAGGGTATTACAAATTCGAAAGGAATTTTGTTTATGTTTTGC	NHEJ	intergenic	CG11737, intron	CG11737	NA	mh:0; ins:0; tup:0; tdown:0	0
A373R13	251	delly	COMPLEX_BND	3R	11840838	3R	11861600	6	8	somatic_tumour	INV00000017	20.8	3R:11840838-11861600	251:251_252	0.18	0.22	-	-	CTTTTGCCAGCTGTCCCAAAACAGCAGAGTGGCGCCGACAACAATGAATGGATATATCTGCAGCCGACATGTGTATAACTTTAAGTTCGCTTGTCCTACCTTCAGGGTATTACAAATTCGAAAGGAATTTTGTTTATGTTTTGC	-	-	CG6959, intron	CG6959, intron	CG6959	NA	-	0
A373R13	251	lumpy	COMPLEX_BND	3R	11840838	3R	11861600	6	8	somatic_tumour	5253_1	20.8	3R:11840838-11861600	251:251_252	0.18	0.22	-	-	-	-	-	CG6959, intron	CG6959, intron	CG6959	NA	-	0
A373R13	251	novobreak	COMPLEX_BND	3R	11840838	3R	11861600	6	8	somatic_tumour	295	20.8	3R:11840838-11861600	251:251_252	0.18	0.22	-	-	AATGGAGCCAATGGCCATGGAACATAACAACAGAAACTACAGTAAAAGCACCCAAAACGGTTAACAAAGCAAAACATAAACAAAATTCCTTTCGAATTTGTAATACCCTGAAGGTAGGACAAGCGAACTTAAAGTTATACACATGTCGGCTGCAGATATATCCATTCATTGTTGTCGGCGCCACTCTGCTGTTTTGGGACAGCTGGCAAAAGTTGGTGGGCGAGGAATCCAATTCGGCCTGATTTTGACACCCGGCCACTGG	-	-	CG6959, intron	CG6959, intron	CG6959	NA	-	0
A373R13	255	lumpy	BND	3R	12534177	3R	19941125	7	10	somatic_tumour	6040_1	7406.9	3R:12534177-19941125	5to5	0.13	0.05	-	-	-	-	-	Octbeta3R, intron	Hs6st, intron	Octbeta3R, Hs6st	NA	bp1_roo_BEL=24	0
A373R13	255	novobreak	BND	3R	12534177	3R	19941125	7	10	somatic_tumour	298	7406.9	3R:12534177-19941125	5to5	0.13	0.05	-	-	ACATTTAACTGACACCGAAGGGGAAGAATACAAATCATTGTTGGAATTTCACGCCACGGGTTTAAAGAGAAAAATTTAACTTCATAAAATGTCCGATCTAGCTGCTGATTGCATTCATAAAACCCAACAAAGAAGCCATTTAACTTCAGCATGAACATGTCGAGAGCCAGCAATAAAAACAAGTTGAAAAATAATAATGCTCGGCAATAATTTCCATTCATA	-	-	Octbeta3R, intron	Hs6st, intron	Octbeta3R, Hs6st	NA	bp1_roo_BEL=24	0
A373R13	274	novobreak	BND	3R	17743124	3R	30214752	1	2	somatic_tumour	321	12471.6	3R:17743124-30214752	5to5	0.03	0.03	-	-	ATCTTTAGGTTTTCAACATCTGTTGACCAACATTCCACCGAGTCATCAATTAAGTCAAGTTCGAGGTATCGCGTATGTGGTCTTGTAAATACCAACCTTAACAAAGTTGCATTTGTACAATTATACTGTCAGGTTATTTTGGTATCGGGTAGCAGTAATTACCGTGAGTTTTTGGATAACACATACTTGGGGTA	-	-	TyrRII, intron	intergenic	TyrRII	NA	-	0
A373R13	280	novobreak	BND	3R	20476344	3R	27592686	2	2	somatic_tumour	327	7116.3	3R:20476344-27592686	3to3	0.05	0.03	-	-	AATCAAAAAAGAAATGAAAATGGCTTTCAGTTTCTGTGGTAAGTGAAAAACAACAAAGCAAAAGCCGTCCGGCAGCAGGCAATTAAAGCTGGCCCCTTTTGTTTAATTTTCAAATGGTACTTCAGTTGCAGTTAACTTAAAGCTGAAACCC	-	-	Gfrl, intron	CG5639, intron	Gfrl, CG5639	NA	-	0
A373R13	296	novobreak	BND	3R	27135525	3R	31630504	2	1	somatic_tumour	353	4495	3R:27135525-31630504	3to3	0.03	0.01	-	-	GGAAGCGGATGTGGAGGCGAAGGCGAAGGCAGTTGGCCTCGACAACAGCGAAAGCGGCAGCCAAGGCAGGAACATTACGAACACTGCAAAAAAAAAAATAAAAACGCTTTTCAAATGGCCAAAGCAACGGTCAGTCGGGGAAAAGTAAAAG	-	-	CG6051, intron	kek6, intron	CG6051, kek6	NA	-	0
A373R13	297	novobreak	TRA	3R	27240880	X	18343349	1	2	somatic_tumour	354	8897.5	3R:27240880 X:18343349	5to5	0.06	0	-	-	CAAAGATTTACGTAATTATCCTCGGCGAAGCTGGGAAAAATTGGCGTTGAAATATGCACAGCTCAAACAGCTACCAAATGTGCTCATCTTGCCCAGCGATCAGCGGCATTTCATCCGCTTGGTCAACGACTGCCTGGTGATCAATCCCGGCCGTGTCGCGGACAAGAAGGGTGGAACTTTCGCCCGATTCCTGG	-	-	DNApol-alpha73, exon	CG6123, intron	DNApol-alpha73, CG6123	NA	-	0
A373R13	310	Control-Freec	DEL	3R	31994361	3R	32079331	-	-	somatic_tumour	-	85	3R:31994361-32079331	Heterozygous deletion	0.35	-0.62	-	-	-	-	-	heph, intron	intergenic	heph, CR45556, CR45557, CG2053, krz, mod, Map205	NA	snp_su:127; snp_op:19; snp_ratio:6.68	20.57
A373R13	317	novobreak	TRA	Tomelloso	6209	2R	11742375	5	0	somatic_tumour	382	11736.2	Tomelloso:6209 2R:11742375	-	0.13	0	-	-	ACAGTACTCCCCTAATGCGATCGACACAACGAATTATTGACAGCATTTTGCCACCAAATGATCAAACCAATATGTTTTCTGGCTCATTTGCCATCTAGAGTTGATTTATTTTTTTTGTTAACTAGTGGACCTTGGGAATGAAAATGTTTCCTCCTCCTCCTCCTCCTCCATTGTCTC	-	-	intergenic	intergenic	-	NA	-	0
A373R13	320	novobreak	TRA	Tomelloso	76121	2L	14257152	3	0	somatic_tumour	434	14181	Tomelloso:76121 2L:14257152	-	0.08	0	-	-	GCTCTGAAGGTGTTATGCCCAAATACCGAGTAAAAAATAACAAGCAACTTTCACTTCTCTGACAAGGAAGATATGCCACATGTGCCGCGTCTCGGGTGAAGACATTGCTGTCTTGATGGCACACCACATCTGAAATAAAAGAAAATATTATT	-	-	intergenic	intergenic	-	NA	bp2_Tomelloso_2	0
A373R13	321	novobreak	TRA	Tomelloso	95382	X	7378327	3	0	somatic_tumour	443	7282.9	Tomelloso:95382 X:7378327	-	0.14	0	-	-	CAATTGAGCAACTATTCAGTCGTTTCGGCATGCACAAAATTGTTTCGAATCGAGACAATCAAATCTCACGAAATCAATTTGTGGTTAGCGGAGACTTTGAATTCAAACTCAATATGGCCGATGAGCAGAAGGTAAGTG	-	-	intergenic	CheA7a, exon_1	CR44357, CG1677, CheA7a	NA	bp2_Tomelloso_2	0
A373R13	324	novobreak	COMPLEX_BND	X	3057935	X	3299323	7	12	somatic_tumour	457	241.4	X:3057935-3299323	324:324_325_326_327_328	0.38	0.11	-	-	CTTAAAAATAATCACAAACTCTTTCGATAATCGGACTCCTGAAATTTCTTGGTGCACCCAGGCATAAATCTTGATTAACACGAGAGCGACAAACGACACTGATACACAAAAAACCAAATGAGCCGATGATAAATACAGAGTCGCGGCATTAAGATATAACAATACATCCCAAGATGGAAGACGCATAGAGGCGCCCCAGCTCGCTCTCTAAAATTTAAATGAAATTAGCGCAAGCAGCTATCGCATCGAATTAATCAAAACTTTTGAGTTATCCAATTAGCGCGCGTCGAAAAGTTTATCACCTAGCCCATAACATAACCTCAAACCTCTTAACCCCTCGTCGCCCCAATCGGATTCCCCTA	-	-	kirre, intron	dnc, intron	kirre, N, dnc	TRUE	-	0
A373R13	324	lumpy	COMPLEX_BND	X	3057935	X	3299323	7	12	somatic_tumour	7005_1	241.4	X:3057935-3299323	324:324_325_326_327_328	0.38	0.11	-	-	-	-	-	kirre, intron	dnc, intron	kirre, N, dnc	TRUE	-	0
A373R13	324	novobreak	COMPLEX_BND	X	3057935	X	3299323	7	12	somatic_tumour	458	241.4	X:3057935-3299323	324:324_325_326_327_328	0.38	0.11	-	-	GATAAATACAGAGTCGCGGCATTAAGATATAACAATACATCCCAAGATGGAAGACGCATAGAGGCGCCCCAGCTCGCTCTCTAAAATTTAAATGAAATTAGCGCAAGCAGCTATCGCATCGAATTAATCAAAACTTTTGAGTTATCCAATTAGCGCGCGTCGAAAAGTTTATCACCTAGCCCATAACATAACC	-	-	kirre, intron	dnc, intron	kirre, N, dnc	TRUE	-	0
A373R13	329	novobreak	TANDUP	X	4612489	X	4612609	6	0	somatic_tumour	460	0.1	X:4612489-4612609	3to5	0.2	0	-	-	TCATATCAAATATAAAGTAGTGTTGTTTAACGTTATTTTTGTAGGTTGAATAGTATATTCCAACAGTTTTTTTTTAGATTTTGTACAAACCCGCAATGCCCATCGCAGCACCGATACTTTTCACAAAATTCCGCAGATCCCAGATAATGTGAAACCACAATCGAGTTAGCAGAACTTGGTAGTGGTTTCACATTATCTGGGATCTGCGGAATTTTGTGAAAAGTATCGGTGCTGCGATGGGCATTGCGGGTTTGTACAAAATCTAAAAAAAAACTGTTGGAATATACTATTC	-	-	intergenic	intergenic	-	NA	bp1_copia_Copia=11; bp2_copia_Copia=10	0
A373R13	331	novobreak	TRA	X	5718128	3L	13369579	3	0	somatic_tumour	464	7651.5	X:5718128 3L:13369579	5to5	0.06	0	-	-	TCGGTATACGGGGCGTATTAGCAATATCTGCGTAACCAGCGCACCCGGATTGAGGGAAAAACTTGCCAGCCAATAGCACACATGACTCAACACACAAAATACTTGGCCAAAAAATGCTACAGCCCAGACTTCGAGGCCGGAATCGGAGGGAC	-	-	intergenic	intergenic	-	NA	-	0
A373R1	12	novobreak	TRA	2L	65533	2R	21906958	3	0	somatic_tumour	28	21841.4	2L:65533 2R:21906958	3to3	0.1	0	-	-	TGCTGGTGTAGCTGCAACATCGCTCGCTTCCGCCGCAATTCGTAGTTTGCTTGTTGTCCACTTAAAGTGCCTTAGATGAAAAAAAATCAAGGATATGTGCGCCCTGGTACCCAATTCTTACC	-	-	intergenic	Fili, intron	Fili	NA	-	0
A373R1	21	novobreak	TRA	2L	174862	3L	4661861	3	0	somatic_tumour	38	4487	2L:174862 3L:4661861	3to5	0.14	0	-	-	GTTTTTATGTCACAACCCCTTAAACCGAACCCCTCCGTGCAGCCTGCAAGCCTTACAACAGAGCATGATGGAATTTATACATAGTTGTTCTTAAATTAAAGACATATACAAA	-	NHEJ	spen, intron	axo, intron	spen, axo	NA	bp2_Dmel\F-element_LINE-like=3; mh:0; ins:0; tup:0; tdown:0	0
A373R1	30	novobreak	TRA	2L	483252	3R	30098205	2	1	somatic_tumour	55	29615	2L:483252 3R:30098205	3to3	0.09	0	-	-	CTTTTTCCACTATTGCTCAGCAAAAGAAACCAAATTATTTAATTAGAAGTGCAATATGTTTTTGAAGGTTTAATTTACGAAGAACGATCGTTAAAAGCTCACTTAAATGGAAATTCTTGACAGAGGAGAGGTG	-	-	ush, intron	sima, intron	ush, sima	NA	-	0
A373R1	33	novobreak	TRA	2L	603468	3L	302053	3	0	somatic_tumour	61	301.4	2L:603468 3L:302053	5to3	0.12	0	T	-	TGGTAATGACTTAAAAATGTATCTTACGTAAAATGTTATAATTTAAGCTCAAGTTTATAAGTTTGGTATTTAGTTGCTCGTGCAGAGGAAGGGTCTGTTCCTGTTCCCGT	CTTAAAAATGTATCTTACGTAAAATGTTATAATTTAAGCTCAAGTTTATAAGTTTGGTATTTAGTTGCTCGTGCAGAGGAAGGGTCTGTTCCTGTTCCCGT	Alt-EJ	CG13689, 3UTR	RhoGEF3, exon_4	CG13689, RhoGEF3	NA	mh:1; ins:0; tup:0; tdown:0	0
A373R1	35	novobreak	TRA	2L	666036	3R	7433241	3	0	somatic_tumour	64	6767.2	2L:666036 3R:7433241	36:35_36_1700	0.11	0	-	-	AAACGAAGCCCCGGTCGAGACAATTACGATGGAGGGGAGACCGGCGTGTAATTCAGCTAGGGGCTTTCTCCTTTCTTTTCTCGTTTTTCTTGCGGGTCAGAGACATTATGTTGTGACATTTATCAGCAACTCATGTGGGT	-	-	ds, intron	intergenic	ds	NA	-	0
A373R1	72	novobreak	TRA	2L	1621944	3R	6345586	3	0	somatic_tumour	109	4723.6	2L:1621944 3R:6345586	5to3	0.1	0	TGCCGC	-	TTTTCCCTTTGGCTGGCCACATCTCGTTGCTTGGGAAACTCGAGAAAATTAGGTTATGCCCTGTTGTTGCCGCGCCAGCTCCTCCGGGGTCAGCTCCGATTTCGGTTTCACAAGAG	TTTTCCCTTTGGCTGGCCACATCTCGTTGCTTGGGAAACTCGAGAAAATTAGGTTATGCCCTGTTGTTGCCGCGCCAGCTCCTCCGGGGTCAGCTCCGATTTCGGTTTCACAAGAG	Alt-EJ	CR44603, exon_1	SmD2, exon	CR44603, SmD2	NA	mh:6; ins:0; tup:0; tdown:0	0
A373R1	81	novobreak	TRA	2L	2029429	3L	7940911	3	0	somatic_tumour	125	5911.5	2L:2029429 3L:7940911	3to3	0.1	0	-	-	CCTTTGGCCTGGTAAATCAACGTCTATGATTAGAGCTTAATACATCTTGATAAGGTCGCCATAAATGAAGGTAGCTCGGGTTGAACTCAGTCAGAACTCAAATTATTGATAAATCAAAAGTATAACACTCACCTCCAGTTCGTTTTCATCGAAAATGCTGAGAAGGTTATCC	-	-	CG4238, intron	intergenic	CG4238	NA	-	0
A373R1	85	novobreak	BND	2L	2065379	2L	19693188	3	0	somatic_tumour	131	17627.8	2L:2065379-19693188	3to3	0.08	0	-	-	CCAGGAGCAGCAGGAGGAGCAGGAGCAGCAGGAGCAGCAGGAGCGGCAGGAGCTCGACCTCGCTTTTTATTTATTTACTTATTTATGGGCCGCGCCATCACCGCCATCCCACCGCCTCCTGGCCATAG	-	-	dpr3, intron	CG46244, intron	dpr3, Lar, CG46244	NA	bp2_Dmel\F-element_LINE-like=2	0
A373R1	88	novobreak	TRA	2L	2208673	3L	17103423	3	0	somatic_tumour	137	14894.8	2L:2208673 3L:17103423	5to5	0.08	0	CATCT	-	AGCGGATACCCCGGAGATATCCATTCCGAACTTCGGATCGAAAAAGATGTTGTACTTGCGTATTTTTTGTGTGTTGGTGGGCGAGTCTATGTGTGTGTGTGTGGAGCTTTTGTTGCGGTGCTGCAGTGCAATTTTCCCGACCCACACCCCCTCCCCTTTTG	ACACACACACACATAGACTCGCCCACCAACACACAAAAAATACGCAAGTACAACATCTTTTTCGATCCGAAGTTCGGAATGGATATCTCCGGGGTATCCGCT	Alt-EJ	CG33124, exon_2	Rbp6, intron	CG33124, Rbp6	NA	mh:5; ins:0; tup:0; tdown:0	0
A373R1	90	novobreak	BND	2L	2241903	2L	11365061	3	0	somatic_tumour	140	9123.2	2L:2241903-11365061	3to3	0.11	-0.01	-	-	GTATCGGCATCTGTATCTGTATCTAGCGAGTGTTTACCTTTGCCAATAAATTCTCTTAATTGCCGTGAAATAATCATAAAGGCTGCGTTATGAGTATGGTTTTCCGAATCCTGGGGCCACGTTTTTATGGCTGTCAGTCAGCGCGAATGCTTATCGC	-	-	intergenic	salr, intron	salr	NA	-	0
A373R1	95	novobreak	TRA	2L	2371725	2R	22139254	3	0	somatic_tumour	148	19767.5	2L:2371725 2R:22139254	95:95_96_702	0.09	0	-	-	CATTCATTGCAATTTTCGTATTCCATTGCATTCCGGTTGATAAGGAACCACCCAGTTCCGCACACTGGCGCTCTATAGTTGCATTTTCGGGCTACGATTCTCGTTTTCTTATAAATCCTATAGAACGTAGACCTTTCCGTCGTTGATTTGTATGATTGGTTATTGAATAAACAATTTATT	-	-	intergenic	CG11269, exon	a, CG11269	NA	bp1_Rt1b_R1=5	0
A373R1	103	novobreak	TRA	2L	2691227	3L	19049563	3	0	somatic_tumour	157	16358.3	2L:2691227 3L:19049563	3to3	0.11	0	-	-	CACCTGCGATACCAATTGATTAGATCACGCCCCCTCAAACTTAAATGAACCTTTCGAAAACATTTAACGAAATAAATAATCAAATTGCAACACACATATGCATATTTATAATAATTGTGTGTGTGTGTGAGTGTGTGTTCCTTTTAC	-	-	CG31690, intron	intergenic	CG31690	NA	-	0
A373R1	106	novobreak	TRA	2L	2716106	2R	24871228	3	0	somatic_tumour	162	22155.1	2L:2716106 2R:24871228	5to5	0.14	0	TAAGCTGCTGT	-	AGAGATATCCCGGCTATTGATGGCTTACGAGTAAATAATGTACAAACAGCAGCTTAGCTGGCGGTAAGCTTTAATAAACCATTCCTGAAGTTAAGTTAATTTATTTTCGTTTATAGTGGTGGCC	AATTAACTTAACTTCAGGAATGGTTTATTAAAGCTTACCGCCAGCTAAGCTGCTGTTTGTACATTATTTACTCGTAAGCCATCAATAGCCGGGATATCTCT	Alt-EJ	CG31690, intron	Atf-2, exon_1	CG31690, Atf-2	NA	mh:11; ins:0; tup:0; tdown:0	0
A373R1	110	novobreak	TRA	2L	2766399	3R	15255243	4	0	somatic_tumour	166	12488.8	2L:2766399 3R:15255243	3to5	0.15	0	-	-	ATCCCAAGGAGCACTTCCTGCCCAACGACACCAGTGCGGATCATCATTCTGATTGCGGCGGCATTCTTCTGGCTGCTTTCCCTGCTGATCTCTTCCCTGTGGTATGCCCTGATTCCGCTGAAGGAGTTCCTGGCATTCGGCGTGGTCTTCTCGGTGTGCTTCCAGG	-	-	aph-1, exon_1	CG42404, exon_4	aph-1, CG42404	NA	bp1_Dmel\Doc3-element_LINE-like=3	0
A373R1	112	Control-Freec	DUP	2L	2787990	2L	2797940	-	-	somatic_tumour	-	9.9	2L:2787990-2797940	Heterozygous duplication	0.43	0.71	-	-	-	-	-	Syt1, intron	CR43821, ncRNA	Syt1, CR43821	NA	snp_su:30; snp_op:33; snp_ratio:0.91	10.02
A373R1	115	novobreak	TRA	2L	2837516	3R	23683953	3	0	somatic_tumour	172	20846.4	2L:2837516 3R:23683953	116:115_116	0.15	0	GCG	-	GTGCTCACTTGTCCGGAGAACGTGCAGAGTCTGGCCAGAAGTGTCTACGATACCTGGGGCCAGCGCTGCAGCCGCAAAAATAAATTAGGAAATTTCATTGAGTCATTGGGATTTATGAGTTTGTTGATCCATT	AATGGATCAACAAACTCATAAATCCCAATGACTCAATGAAATTTCCTAATTTATTTTTGCGGCTGCAGCGCTGGCCCCAGGTATCGTAGACACTTCTGGCC	Alt-EJ	CG3119, exon_1	CG16710, 3UTR	CG3119, CG16710	NA	mh:3; ins:0; tup:0; tdown:0	0
A373R1	129	novobreak	TRA	2L	3145342	2R	7504368	3	0	somatic_tumour	189	4359	2L:3145342 2R:7504368	5to3	0.13	0	-	-	AGCTTATTTCGATCAGAAGAGGAACGAGTACCTGGCCAAAAGGGACGCCGTCTTCCGGCATACAGACCTACGCCCGCGGCATGCTGGCGCGCAACAAGTTCCACGCGATGCGGGATCACTACCGGGCAGTTCAGATCCAGCGTTTCGTGCGTGGTGCTTTGGCACGGCGAGCTTACCAAAAGCGGCGTCGCAACATCATCATTTGTCAAG	-	-	ND-B14.5B, exon_2	didum, exon_9	ND-B14.5B, didum	NA	-	0
A373R1	131	novobreak	TRA	2R	16697447	3L	1885675	4	1	somatic_tumour	1622	14811.8	2R:16697447 3L:1885675	1163:131_1162_1163_1673_1674	0.16	0	-	-	GATAGAACTTAAGAATCCTCTATTTTACGGTTATAGCTTTTGTAGCTCTTTAAAAATTCCGGAATGCTTTACGGCTATTCGCTGAGAAACGAACTGAATCTTTCTTGGCATTGGGAGTCTAAGATACAGACACACAGAT	-	-	CG30463, intron	Tmhs, exon_1	CG30463, Tmhs	NA	bp1_accord_Gypsy=3	0
A373R1	133	novobreak	TRA	2L	3225319	X	4453399	3	0	somatic_tumour	195	1228.1	2L:3225319 X:4453399	5to3	0.19	0	CC	-	ATGTAAATGTTTATTTGACAAGCTGTTAAAGTTCCATTGTCTTCGTTGAGTTAACAAGTCACGGAAATGACTGAGAAATAATAGTCCGAGTTTGGGTACCAACCCCAACCGCTTCATTTCATTTTTGGTTTCGGTGAAA	GAAATGACTGAGAAATAATAGTCCGAGTTTGGGTACCAACCCCAACCGCTTCATTTCATTTTTGGTTTCGGTGAAAATCCCTCAACAAGAAATAAGTAAAT	Alt-EJ	intergenic	bi, intron	CR32773, bi	NA	mh:2; ins:0; tup:0; tdown:0	0
A373R1	140	novobreak	TRA	3L	3850501	2L	17992512	7	0	somatic_tumour	2230	14142	3L:3850501 2L:17992512	1562:140_141_800_845_1562_1563	0.25	0	-	-	TTAGAAAATAACTTATTGACCATTAAGTTTTTAAAGGCTACACCCATAAGCTCTGAATTTCCAGCTTGATGCAAATGTTTTATTGAAATTTATTGCCCAACAAATTGCATAGCCACAGGGCGCTCTATTATACAC	-	-	Awh, intron	intergenic	Awh	NA	bp1_17.6_Gypsy-like=4; bp2_Rt1b_R1=5	0
A373R1	142	novobreak	TRA	2L	3399658	3L	3296613	3	0	somatic_tumour	206	103	2L:3399658 3L:3296613	3to3	0.09	0	TTGACTGGC	-	AGCCATAACTTGTGGTATGCATCTGGGGCGGACATTGATTTGACTGGCTTCATGGGCTTGGCAGTTTGGACTTCGGGCTCCGCCGGAACCTCTGGCTCTGACTCAACGGG	TTGTGGTATGCATCTGGGGCGGACATTGATTTGACTGGCTTCATGGGCTTGGCAGTTTGGACTTCGGGCTCCGCCGGAACCTCTGGCTCTGACTCAACGGG	Alt-EJ	intergenic	CG12009, exon	CG12009	NA	mh:9; ins:0; tup:0; tdown:0	0
A373R1	156	novobreak	BND	2L	3798316	2L	21842984	3	0	somatic_tumour	221	18044.7	2L:3798316-21842984	3to3	0.08	0	-	-	GGAATGTCGAGGTGACGAGGAGAGAATGGAGGATTGTGCGGAGCGATTGAATGGTCAACTTTATGGACATCGCCACGAATGCCGTTGGGATCCTTGTTGCGCTAACTATCGGCGATCGAGCGTATCGACAACTCCTTCTGTT	-	-	bark, exon_5	intergenic	bark	NA	bp2_Dmel\F-element_LINE-like=8	0
A373R1	165	novobreak	TRA	2L	4004703	3L	16251568	3	0	somatic_tumour	234	12246.9	2L:4004703 3L:16251568	3to3	0.1	0	-	-	GCAATCACTTGTTGTTTTGTTAATGTCTAGCAAAACTTTAATTCATTTTCACCAATTCTTTGCCTGCTGCTCCTCGATGTCCAGCGTGCTGCTCGTTTCGCTGGAGGCGCACGACATGGACATCAGCTCCAGACGCGACTGGTGTGCGTTGAGGCC	-	-	intergenic	CG13055, exon	CG13055	NA	-	0
A373R1	182	novobreak	TRA	2L	4687951	3L	23096651	4	0	somatic_tumour	261	18408.7	2L:4687951 3L:23096651	3to5	0.13	0	AGCA	-	CTCCGTCATAAGTACCACTCACGGGTAGCATTGCTGTCCATGAGCAAGGAGGAGAGGGAAGATGCCGGCGGCCAGCAACTGTTGGTCCAGTACACCGAGAATGAAAAGGCGGGCGAGCGCCTCATCCAGAAACTTGTTTCTCCAAACAATGTAATGCTGCTGAGCACCAAGCCCGAGCTGAAGGGTAATCCTCTGGTG	CTCCGTCATAAGTACCACTCACGGGTAGCATTGCTGTCCATGAGCAAGGAGGAGAGGGAAGATGCCGGCGGCCAGCAACTGTTGGTCCAGTACACCGAGAA	Alt-EJ	Elba3, exon	intergenic	Elba3	NA	bp2_S2_Mariner/Tc1=4; mh:4; ins:0; tup:0; tdown:0	0
A373R1	190	novobreak	TRA	2L	4800841	2R	13316186	3	0	somatic_tumour	271	8515.3	2L:4800841 2R:13316186	3to3	0.08	0	-	-	GCATTGCAAAGCATTGCAATTGTGAGTTGCTGCATCCTTCCACTAAGTGTGCATTTGTGTCCGTGAGAAGGCGTGGCACCAGTCGCGCCCCTTTGCTGACCGCTGATAAGCGCTGGCCCGTCGTTAATGATTTATAGTTGCCAAATCAGCGGACAGCTGGCGATCAAATAAACACT	-	-	Clect27, intron	intergenic	Clect27	NA	-	0
A373R1	199	novobreak	TRA	2L	4928549	3R	22460521	3	0	somatic_tumour	283	17532	2L:4928549 3R:22460521	3to3	0.1	0	-	-	TCCGATGCCCATCCGATGCCGATCCGATGCCATGCAGGCGTAGCTATAGCTACTTATTCCGATACTCATGTTGCTACTTCGTGCGGCTATTTATGTAAATGTAAGCCTAAGCGTCGCCCTCGAT	-	-	hoe1, intron	CG34376, 3UTR	hoe1, CG34376	NA	-	0
A373R1	201	novobreak	TANDUP	2L	4952655	2L	12989484	8	0	somatic_tumour	286	8036.8	2L:4952655-12989484	3to5	0.2	0	-	-	ACACATCCCTAGGTAGCTACAAGTCGAAGTTCAGTCAAGTGCATAAAAAGTGAAAAACAATAAACATCATCGGGCAGCTCCACCTTGTTGATCAGGTGCCAGAAGTCCACGTGCGGGGTGTTGATCAGCGAGATGTCGTTGTTCAGGTTGTTGG	-	-	Jon25Bii, exon	intergenic	Jon25Bii	NA	bp2_blood_Gypsy/TABOR=6	0
A373R1	204	novobreak	TRA	X	14753155	3R	17275527	3	0	somatic_tumour	4946	2522.4	X:14753155 3R:17275527	3091:204_205_3060_3091	0.11	0	-	-	GCCCAAATGTATTCGTTCAGCTCGGTTACTTATCAAATGCGCACTTTGATTTGTTGCTTACCGAGCAGAACTGAATTGGTTCTGTGAAAGGTTAAAATAGTTAAACCTTGCAATAGATTATAC	-	-	intergenic	intergenic	-	NA	-	0
A373R1	208	novobreak	TRA	2L	5077640	3R	27530506	3	0	somatic_tumour	293	22452.9	2L:5077640 3R:27530506	5to3	0.13	0	-	CTGCTTGTTG	GAGACAGCTCCAGATTTTCGCCGCCCCAAATGTCCATGCCCTCGTCGTAGGAGCCAATCTCATAGAAGTAATCCTTATCGATGGAGAACAGACCACCGGCCCTGCTTGTTGTAAAACTTTCAATATGAATTCGAGTTTAAATA	CGTCGTAGGAGCCAATCTCATAGAAGTAATCCTTATCGATGGAGAACAGACCACCGGCCCTGCTTGTTGTAAAACTTTCAATATGAATTCGAGTTTAAATA	FoSTeS	pgant5, exon_6	CG12885, intron	pgant5, CG12885	NA	mh:0; ins:10; tup:3; tdown:3	0
A373R1	212	novobreak	TRA	2L	5185983	3R	19218961	3	0	somatic_tumour	298	14033	2L:5185983 3R:19218961	3to5	0.12	0	-	-	GAAGAAAACACACGTTAGTCATATCATGCTGTGGATTCTTCGTTTATTCATAATTCTAATTTTTGCAGCTTTTCTGTGTGGTTTCGGTATTTGTTCATGGCTTTTATACGGCAATCGATCGTGTTGCTGTTGTGGCCAGGTTCCGACC	-	-	Msp300, exon	vib, intron	Msp300, vib	NA	-	0
A373R1	216	novobreak	TRA	2L	5246840	2R	18197358	4	0	somatic_tumour	302	12950.5	2L:5246840 2R:18197358	5to3	0.15	0	-	-	GCCCTGCAGGCAGCAAAAGTGCATGCGTGCACTTAACACCTTCTGCGCAAGTTTTTTAGCTGGGATCCTGGCTTTTGGCGTACCCGTTGCAACCAGGAAGTGGGGTGGATCATGGAGCCATGGCCATATAGCCCAAGCTGGGCATGAACCGTTTGGCCGGCTGGGCCCTAACTGCTGCTGCCCTGCAGCGGCGATCGTCATAGGCTGCAAAAAAAATTATATATATATTTATG	-	-	tkv, intron	intergenic	tkv	NA	-	0
A373R1	219	novobreak	TRA	2L	5311551	3L	21953089	6	0	somatic_tumour	306	16641.5	2L:5311551 3L:21953089	5to3	0.19	0	-	-	TGGAGAATCGTCGATGACATTGATAAAAATATGGTGTTAAAGCGAAAAAAAAATTCATCCAGCGAATGTTTTGGGAAAAACGTATCTAGAGTCCACAAAAGTTATAGACTTAGATCAAGACCTGTTTATAAATTTCGTTAATATATAGGTATATAT	-	NHEJ	CG14024, 3UTR	intergenic	CG14024	NA	bp1_17.6_Gypsy-like=3; bp2_hopper2_Transib=5; mh:0; ins:0; tup:0; tdown:0	0
A373R1	223	novobreak	BND	2L	5454015	2L	19145783	3	0	somatic_tumour	312	13691.8	2L:5454015-19145783	3to3	0.07	0	-	-	GAGTGGGCCAGTCGACAATAAAAAAACCAAAAAGAAACGAGAAAAGGGGGAAAATTCTTGAGGGGAGTGCCGCCAAAGAAATAAATTAATCATATTAGATTTGATAGCCAATTAACTGCCATGCAATTATTG	-	-	intergenic	brat, intron	brat	NA	-	0
A373R1	226	novobreak	TRA	2L	5529404	X	17596447	3	0	somatic_tumour	316	12067	2L:5529404 X:17596447	226:226_3125	0.13	0	-	-	GGTGTAAATTCGCTTCGTCTGAAGGGATTATTTCTTTCCTGTGTAGGCGGAGCACTTCCCGGCCGTTGATGGCAAAGAACTGAGCACGGAAAGGCTGCTGGAGATGGGCGTACGATTTCTGCCCGGCTACGAGGATCCCTATCATCATCGGGCGATGACAATGGGCGAGATTGGCTGCTTTCTGAGCCACTACAAC	-	-	CG31915, exon	CG12991, intron	Cap-D3, CG31915, CG12991	NA	-	0
A373R1	237	novobreak	TRA	2L	5777785	3R	11302926	3	0	somatic_tumour	329	5525.1	2L:5777785 3R:11302926	3to3	0.1	0	-	-	AGACAGATTGTTGGCTGCCCTAATGAAATTTCTCGTTCAATTGTTGACTTACATGATTACCACTCGGTGCTCGTAAGCATCCCACTTCCACTGAACCATCCACATCG	-	-	CG9171, intron	CR31386, ncRNA	CG9171, CR31386	NA	-	0
A373R1	243	novobreak	BND	2L	5923419	2L	5923721	4	0	somatic_tumour	335	0.3	2L:5923419-5923721	3to3	0.14	0	-	-	AATGAACAACTGGTAGAACCAAACTCGACAGGCTGAGAAATGAAAAACCCCCAGCCTCCTGTGTCTTTCGAACCTGCGAGCAGTAGCCGCCGTTGTTGGAGCTGCAACTGTTGCTGTTGCTGTTACTGTAGAAGCCGTCCATGCTGCTCACTAAAATCGTAGTGTTAAAAAAAATATAACTATTATTAC	-	NHEJ	CG9016, exon	intergenic	CG9016	NA	mh:0; ins:0; tup:0; tdown:0	0
A373R1	244	novobreak	TRA	3L	18201995	2L	5982759	3	0	somatic_tumour	2902	12219.2	3L:18201995 2L:5982759	1985:244_1903_1985_2690	0.09	0	-	-	AGCTTGAACAAAAATACTCGGATGCACATGAACTCGGGCCCAAGCCGTCGAAATTCAGGATATAAGTTTACCTAGTCAATTCTTTATTGTTGATAATGTGA	-	-	CG7320, exon	eIF-4a, 5UTR	CG7320, eIF-4a	NA	bp2_Dmel\Doc3-element_LINE-like=3	0
A373R1	253	novobreak	TRA	2L	6162141	3L	11842292	5	0	somatic_tumour	348	5680.2	2L:6162141 3L:11842292	253:253_254_3064	0.19	0	-	-	CCTTCTTTCCGTGCCTCGATTTTTTTTTTTTTTTTGCTTTTGTTTGCTAGTAATCATATTTTAATGCCCTTTAAACTATTTTCTGTTGTGAGAAAGGGGATAAGGAATTATAATTAATATGCTGATTTTTGACATGAGTGTATCTTGGCTTGATTTTGTATCTTTGTCTGACTG	-	-	intergenic	intergenic	-	NA	-	0
A373R1	258	novobreak	BND	2L	6259554	2L	17917524	2	1	somatic_tumour	353	11658	2L:6259554-17917524	3to3	0.08	0.01	-	-	GATTTATGTGTCTGCTGCAGTGCGGTTCAGACGCGACCACTTTGAAAAACTTGGCTCAACCTATCGCCAATCGGATTCATGGGCTAGCCAATGTCTGGTCTGTGTTTTGG	-	-	Ddr, intron	intergenic	Ddr	NA	-	0
A373R1	259	novobreak	BND	2L	6273754	2L	12455352	9	1	somatic_tumour	355	6181.6	2L:6273754-12455352	5to5	0.26	0	-	-	GTCTTTGGACGGACCACTTCCTTGGCCCAACAATTATTAGTTACGGTTTTGTTAGTGTTGATTAGTATTGCTTAATTTCATTGATTCCCACAGAAAAATTATATATGTGCAATAG	-	-	Ddr, intron	intergenic	Ddr	NA	-	0
A373R1	266	novobreak	TRA	2L	6469039	X	18063310	3	0	somatic_tumour	364	11594.3	2L:6469039 X:18063310	3to3	0.14	0	CGGGC	-	CCACATGCGAGGCGAGATTCTCGCCGGCGTAGGTGACGAAGGGCGAGATCTCGCAGACTTCGCCATGCACAATGCCACCGGCGCCTTCGATATACTTCTTGTGCAGGCGATGGAGGACCGAGCGGGCGTTGCGATTCTGGGTTCCGCAGACTAGAGTCTCCAGCGCC	GCACAATGCCACCGGCGCCTTCGATATACTTCTTGTGCAGGCGATGGAGGTCCGAGCGGGCGTTGCGATTCTGGGTTCCGCAGACTAGAGTCTCCAGCGCCTAGTCGTTGGG	Alt-EJ	mmy, exon	intergenic	mmy	NA	bp2_rover_Gypsy=2; mh:5; ins:0; tup:0; tdown:0	0
A373R1	269	novobreak	TRA	2L	6567403	3R	19234202	2	1	somatic_tumour	369	12666.8	2L:6567403 3R:19234202	3to3	0.11	0	GTG	-	GGATACTTCCACCCAATTGTAGGCCACTGAAATTGGATAATGACCGTGGTGACATACGTGAGTCATGGCCGTGCGCAACAAGTCCCTGGAGAATGCAGCCG	GGATACTTCCACCCAATTGTAGGCCACTGAAATTGGATAATGACCGTGGTGACATACGTGAGTCATGGCCGTGCGCAACAAGTCCCTGGAGAATGCAGCCG	Alt-EJ	intergenic	unc79, exon_22	unc79	NA	mh:3; ins:0; tup:0; tdown:0	0
A373R1	270	novobreak	TRA	2L	6582343	3R	15642669	3	0	somatic_tumour	370	9060.3	2L:6582343 3R:15642669	5to3	0.08	0	-	-	GGTACAATAAATATAATAAATCAACGAATGACAACCATAAATAAACAAACTTTACCCAAAGCCGAACCAGCACCTGCCTGAATTATCGCAACCTCTTAACTGCTGTGTTTACCTTGACCAGCCCACACGTTTTTCTCTCTACCGGGAATCC	-	-	CG11319, intron	intergenic	CG11319	NA	-	0
A373R1	275	novobreak	TRA	2L	6641134	2R	24855620	4	0	somatic_tumour	376	18214.5	2L:6641134 2R:24855620	3to5	0.15	0	-	-	CTATAATTATCCGCCGCTAATAATATTCAAATACCCCGAACATCGTAACCCACTTCCAGCATCCATGGTGACATGATCATCGACAATTGCCGGCGTCGGCATCAAACACATTGAGCGACATAGACAAATTGTCCGTCTACACAAAGTAAAAAAAAAAAAAAAATTTTAAAG	-	-	CG31635, intron	intergenic	CG31635	NA	-	0
A373R1	281	lumpy	BND	2L	6755669	2L	9204071	6	0	somatic_tumour	1137_1	2448.4	2L:6755669-9204071	5to5	0.16	0.01	GAGATCAAA	-	-	ATGCAAATTTGTTGTGGGCGAAGCAAAATTTATAGGACACAGCTGTTTTCGGGAAAGAGATCAAAAAAGAAAAAAAAAAAAAAAAAACACGTCAACGGATAACTTTCC	Alt-EJ	CG11221, 3UTR	tai, intron	CG11221, tai	NA	mh:9; ins:0; tup:0; tdown:0	0
A373R1	281	novobreak	BND	2L	6755669	2L	9204071	6	0	somatic_tumour	385	2448.4	2L:6755669-9204071	5to5	0.16	0.01	GAGATCAAA	-	GGAAAGTTATCCGTTGACGTGTTTTGTTTTTTTTTTTTCTTTTTTGATCTCTTTCCCGAAAACAGCTGTGTCCTATAAATTTTGCTTCGCCCACAACAAATTTGCAT	ATGCAAATTTGTTGTGGGCGAAGCAAAATTTATAGGACACAGCTGTTTTCGGGAAAGAGATCAAAAAAGAAAAAAAAAAAAAAAAAACACGTCAACGGATAACTTTCC	Alt-EJ	CG11221, 3UTR	tai, intron	CG11221, tai	NA	mh:9; ins:0; tup:0; tdown:0	0
A373R1	284	novobreak	TRA	2L	6896861	3L	21622111	3	0	somatic_tumour	389	14725.2	2L:6896861 3L:21622111	284:284_2069_2070	0.08	0	-	-	TGTCCGGATGCATTGACCAAGGCTATTTAAGGATGCCACGCTCTGATGCGTGGCGCAGTTAAGACCAGAGCCTGACAGCGTAAATGGTTCTTTGGTATAGGTGTGTCC	-	-	Nlg2, exon_1	CG7166, intron	Nlg2, CG7166	NA	-	0
A373R1	285	novobreak	COMPLEX_BND	2L	6904847	2L	17651652	2	1	somatic_tumour	390	10746.8	2L:6904847-17651652	285:285_1933_3048	0.07	0.01	-	-	CAATTGCAGACTAAGCCAGCTGAAGATGATAACATCATCATCATGCAGAGGAGCAGAACAACGACGCCACCGCCGCCCTCAAAGAATCCGCCGTCGAAGAGAAGTATAACTGAAATTGTTCTGCATGTTAAAT	-	-	Nlg2, exon_12	CadN, intron	Nlg2, CadN	NA	-	0
A373R1	285	novobreak	COMPLEX_TRA	3L	15675946	2L	6904318	3	0	somatic_tumour	2818	8771.6	3L:15675946 2L:6904318	1933:285_1933_3048	0.11	0	-	-	AGTCTGACTCATCCCAATCTCAGTGAGGCCCTCAATCTGGCAGTGCTCTACAATCAGCGAAGAAGCAATGCGATGCACGAGAAGCGATCCTACATTAATCTTAACAAATAAAATATATGAAAAGCAAGATATGATAA	-	-	intergenic	Nlg2, exon_10	Nlg2	NA	-	0
A373R1	285	novobreak	COMPLEX_TRA	X	11061683	2L	17652063	3	0	somatic_tumour	4874	6590.4	X:11061683 2L:17652063	3048:285_1933_3048	0.11	0	-	-	GGCTGAAAGCTGGTGGAAAAAATGACGTCGGTAACAAAGTGTTTCAAATTTGTTTACTACAAAAAGTGGATTGCTTTTTGGCCATCTAACAAAGAAAAACAGAAAAAATCCAACTTTCTGGGAACGAAGAAGCCGCAGC	-	-	intergenic	CadN, intron	CadN	NA	-	0
A373R1	291	novobreak	BND	2L	7069280	2L	15036944	2	1	somatic_tumour	399	7967.7	2L:7069280-15036944	3to3	0.08	0.01	-	-	ATTCAATCCTGGTTTTCGACTTGAAAACAGATACTTTACTGCGCCGTTTCAGAATGCTTAGCGATTCGAGTTATGGTGAAACTATATTGAAAGCTTCTCAATTGTATCGCGATCGTCCAGTGAGTC	-	-	CG11289, exon	CIAPIN1, exon_3	CG11289, yellow-c, CIAPIN1	NA	-	0
A373R1	292	novobreak	TRA	2L	7096540	3L	4603018	4	0	somatic_tumour	402	2493.5	2L:7096540 3L:4603018	5to3	0.12	0	TGCGAAC	-	ACTGCACCTGTATGTATCTGTGTATGATTGTATCTGTGCTTGTCTGTATCTGTGTGTGCGAACTTTTCCCTTGATGCATTATTAATAACTCCAGCGCAACAAGGATA	ACTGCACCTGTATGTATCTGTGTATGATTGTATCTGTGCTTGTCTGTATCTGTGTGTGCGAACTTTTCCCTTGATGCATTATTAATAACTCCAGCGCAACAAGGATA	Alt-EJ	intergenic	Src64B, intron	Src64B	NA	mh:7; ins:0; tup:0; tdown:0	0
A373R1	294	novobreak	BND	2L	7116469	2L	12408973	2	1	somatic_tumour	404	5292.5	2L:7116469-12408973	3to3	0.08	0.01	ATTTCCCACTC	-	GGCTACAAGAACTTGACATAATATTTTGATAAATTGTTTTTCATTTCACTTCCATGACATGGAGTGGGAAATGCGGCAACTACAAGGGGAAAAGCGGCAGGGCGGTGAG	CTCACCGCCCTGCCGCTTTTCCCCTTGTAGTTGCCGCATTTCCCACTCCATGTCATGGAAGTGAAATGAAAAACAATTTATCAAAATATTATGTCAAGTTCTTGTAGCC	Alt-EJ	Pvf3, intron	vir-1, intron	Pvf3, vir-1	NA	mh:11; ins:0; tup:0; tdown:0	0
A373R1	301	novobreak	TRA	2L	7331078	X	6085542	3	0	somatic_tumour	412	1245.5	2L:7331078 X:6085542	302:301_302_1734	0.18	0	-	-	TACTTCTACCACTATGACTAATGGGTGCCAAACCTGGCCCAGAGCTGTCCAAGCCGTCACTAATCGGGCTTTGCTCGGGGTATCCTCGGAGGTGGCAGAGCTGGCCGGCGGCGAGGATTGCCAG	-	-	intergenic	Mipp2, intron	raptor, Mipp2	NA	-	0
A373R1	305	novobreak	TRA	2L	7458082	3R	17006857	4	0	somatic_tumour	415	9548.8	2L:7458082 3R:17006857	5to3	0.14	0	CTGAA	-	ATTTATCATTCTGTGGAAAACAAAATAAGTTGTTCCAATTTTCTTTCCACCAATCTGTGCTACGGTTAAGTGCCGCCCTTACCTTATTGACCATCACCAGTCGCATCTCCACCAGATATGTGAAGCAACTGAATTCCGGCCTTTCAGCTGTTCCCCAGAATATCTTCCAGTTGCCATCGGCCAGGTTAGTATTGGAAAAA	GTCGCATCTCCACCAGATATGTGAAGCAACTGAATTCCGGCCTTTCAGCTGTTCCCCAGAATATCTTCCAGTTGCCATCGGCCAGGTTAGTATTGGAAAAA	Alt-EJ	Gr28b, exon_1	Irc, exon_10	Gr28b, Irc	NA	mh:5; ins:0; tup:0; tdown:0	0
A373R1	313	novobreak	TRA	2L	7807464	2R	8157412	3	0	somatic_tumour	427	349.9	2L:7807464 2R:8157412	3to3	0.1	0	GGCAG	-	TATTAGTTGGCAACAAATGCGCCCACGCCGACTTGCACACAAAACCTGACTTGCCATAATTGGATGGCAGGCCAAACGTTTCCTCGACCTTCAAAAATGTGTCCATGTTCAGGA	TATTAGTTGGCAACAAATGCGCCCACGCCGACTTGCACACAAAACCTGACTTGCCATAATTGGATGGCAGGCCAAACGTTTCCTCGACCTTCAAAAATGTGTCCATGTTCAGGA	Alt-EJ	cdc14, intron	CR30374, exon_3	cdc14, CR44068, CR30374	NA	mh:5; ins:0; tup:0; tdown:0	0
A373R1	319	novobreak	TRA	3R	28721607	3L	20665219	3	0	somatic_tumour	4359	8056.4	3R:28721607 3L:20665219	2798:319_2049_2798	0.11	0	-	-	TTTCTATCGAAGGCACCGCCGGGACAGAAACAAGGCCAAAGGACCGGCACCGCAAGCGATTTTCCTGGCCAAAGCGATTTGCAAAAGGCAACAGATTTGTGATTCGTTTCAATAACATGGAATTAAGG	-	-	htt, exon_20	intergenic	htt	NA	bp2_HMS-Beagle_Gypsy=6	0
A373R1	321	novobreak	TRA	2L	8190937	3L	14139352	3	0	somatic_tumour	438	5948.4	2L:8190937 3L:14139352	322:321_322_2626	0.09	0	-	-	CTTTGGCCCCGTGTCTGTCAATCGGCTGACGAACGGGGGCACGGAATCTGACCCTCGTCTTTGTTGGTCGAGTGTTTGATTAGTTAATAGGTCAATAACACTGGGGGTGGAAACC	-	-	CG8475, 3UTR	intergenic	CG8475	NA	bp2_opus_Gypsy=7	0
A373R1	321	novobreak	TRA	3R	20430513	3L	14115937	4	0	somatic_tumour	4006	6314.6	3R:20430513 3L:14115937	2626:321_322_2626	0.15	0	-	-	GTTTTAATTTTATGCTCAACGACTTTCGACCTGTGGGAGCGTTGAAACGGCAACTTAATCACTTTAAGATGATTGTGGTTTCCATTCTTCTGCAAATAAACCTTCTTATTTATCGTATTTC	-	-	Gfrl, intron	Sox21b, intron	Gfrl, Sox21b	NA	-	0
A373R1	324	novobreak	TRA	2L	8299956	3R	7942912	3	0	somatic_tumour	441	357	2L:8299956 3R:7942912	3to3	0.1	0	-	-	TTAGTCTCTTGTCTGATTCTTTGTATAGTCCATTGTGGCTTTAGCTCATTAGGAATCGAATAAAGATATTTTACAACAGATTGGCTGCTTAAGTATGTAATACTTCTTGTTCTAGCGACAATAAACAAAAATTAAATGCAAAGAAGAATACAAAC	GTTTGTATTCTTCTTTGCATTTAATTTTTGTTTATTGTCGCTAGAACAAGAAGTATTACATACTTAAGCAGCCAATCTGTTGTAAAATATCTTTATTCGAT	NHEJ	Btk29A, intron	dsx, intron	Btk29A, dsx	NA	mh:0; ins:0; tup:0; tdown:0	0
A373R1	341	novobreak	TRA	X	12959888	2L	6503252	3	0	somatic_tumour	4903	6456.6	X:12959888 2L:6503252	3068:341_1074_3068	0.1	0	-	-	CTATTCCGTCTCGTATCCCGCCGCTCCGGCAATGCGGGTGTATGGATTTCTTTATAGAAGTAGATATATTCACTAGGCACAAACAAAAGATGTGCACTATTCACACTTAGCATAAAGATAGTAGTTTTCTTTTTTTTGACTAGCTAATTGAAATTGGAGCATGTAGAGC	-	-	CG32642, exon_2	CG31637, intron	CG32642, CG31637	NA	-	0
A373R1	347	novobreak	TRA	2L	8839310	3L	20350987	3	0	somatic_tumour	467	11511.7	2L:8839310 3L:20350987	3to3	0.09	0	-	GATAG,CTGTC	CACAACTACGTGCGGAAGGTCGCCGAGGTGGCCACCCAGCTCTTCATCACGAACGACAAGCCCAACATTGCCGGACTCATCCTGGCTGGTAGTGCGGCAACAAGTGCAATTAGCAACCCTGGTTCGACACAATGAAGCGTGTGACCTGTC	GACAGGTCACACGCTTCATTGTGTCGAACCAGGGTTGCTAATTGCACTTGTTGCCGCACTACCAGCCAGGATGAGTCCGGCAATGTTGGGCTTGTCGTTCGCTATC	FoSTeS	intergenic	eRF1, exon_4	eRF1	NA	mh:0; ins:11; tup:3; tdown:4	0
A373R1	355	novobreak	TRA	2L	9160984	3L	10614528	3	0	somatic_tumour	476	1453.5	2L:9160984 3L:10614528	3to5	0.08	0	-	-	ACACACTTGCACACACTCGGCCAACTTAACATGCACACACTTTGCCAACAATTGTGAAACATTCTCCCAGCGCCCCACTGAGTGTGATCAGGTCAAATCTTTTGTTGTTTTACATTCGGCGGAAAAACGTTTACATAACCTTTAACT	-	-	CG32982, intron	intergenic	CG32982	NA	-	0
A373R1	359	novobreak	TRA	2L	9252716	2R	15410147	3	0	somatic_tumour	481	6157.4	2L:9252716 2R:15410147	3to3	0.09	0	CGAGCAGCTG	-	ATAGGCCAACAAACCTTCGTCATTGCGACTCCCAGTGGCGGAGGGGGCGTGGCCCTCGATGGCGCTGCCACTCATGGACATCGAGGCGAGCAGCTGTAAGCATTTAAATATTTTGACAATTCTTGTTTGTGTTCCGCCTCTCTTTCTTTTTG	GCCCTCGATGGCGCTGCCACTCATGGACATCGAGGCGAGCAGCTGTAAGCATTTAAATATTTTGACAATTCTTGTTTGTGTTCCGCCTCTCTTTCTTTTTG	Alt-EJ	borr, exon_1	CG43729, exon_2	borr, CG43729	NA	mh:10; ins:0; tup:0; tdown:0	0
A373R1	368	novobreak	COMPLEX_TRA	2L	9553073	3R	22593893	3	0	somatic_tumour	493	13040.8	2L:9553073 3R:22593893	368:368_2673	0.1	0	-	-	TCCGATGCATCCGTAAAAATGGGCGTGGGCTTGTGTTCGTGTGTGCGTCCAAGCATTGCCAAAGATGCAACAAATGCAGTTGCAGCACATGCAGCAAGCAG	-	-	jp, exon_7	Efa6, intron	jp, Efa6	NA	bp2_3S18_BEL=5	0
A373R1	368	novobreak	COMPLEX_BND	3R	22214137	3R	22598989	7	0	somatic_tumour	4092	384.9	3R:22214137-22598989	2673:368_2673	0.15	-0.01	-	-	GCTGGCTGTGACTGGAGCTGCTGCTGCTCCTCCACCCTCTGCTGCTCCTCCACCTTCTGCTGCTGCTGCTGTTGCTGCTACTGCTGTTCCCCCACCCGCCGCCCGACAGCTCCCGCAATTTTCCGCATTTCCATCGAGAAGAAAATTAAAAATAGTTTACAAGTGCCGACAGCCCAACATGCGAATAATAAT	-	-	Gld2, exon_1	Efa6, intron	SKIP, Gld2, Efa6	NA	bp2_mdg3_Gypsy/INVADER=3	0
A373R1	397	novobreak	TRA	2L	10232710	2R	25187095	8	0	somatic_tumour	532	14954.4	2L:10232710 2R:25187095	398:397_398_1479_2386	0.27	0	-	-	CTACGATCTTGCCGAGAAGCGATTCTACGAGGGTCCCCAGAAGGTAAAATCTCTAAGCAATCACAGCCATAAGTACTTAAGTTGTTAGCCAGTTGGAGGACTCAAGCACCGAGCCTTAAACTTTCTCAACTGCTGCGCATGTATTACTCAACAAATGGTGTCCTTAGT	-	-	eEF1delta, intron	CG9380, exon_2	eEF1delta, CG9380	NA	-	0
A373R1	400	novobreak	TRA	2L	10272992	3R	22714734	3	0	somatic_tumour	535	12441.7	2L:10272992 3R:22714734	3to5	0.1	0	-	-	TGGAAATCTCATCCAGCTTCCGTTTCTTCTTGCGATACTGCCGCGTTATTTTCGCCAGTCGCATACGCATACTAATGATACCTCGCATTGTCCGCAGTAATGGGATG	-	-	Utx, intron	wge, exon_5	Utx, wge	NA	-	0
A373R1	403	novobreak	TRA	2L	10370395	2R	22650212	3	0	somatic_tumour	541	12279.8	2L:10370395 2R:22650212	5to5	0.09	0	-	-	GTCGGAAACGCTTCCGACCATAAACATAAACAAATCGGTCGATGATCGGTGCGGTCATCGAGGTCGTTAACCGAGAAGTACTTGATGCACCGCAACGGCGGACGACGGG	-	-	rho-5, exon_2	intergenic	rho-5	NA	-	0
A373R1	406	novobreak	TRA	2L	775139	3R	5181428	3	0	somatic_tumour	69	4406.3	2L:775139 3R:5181428	40:40_41_132_406_2358_2359	0.08	0	-	-	TGTAGATACCCAGCTTCTCCTGACCAGCTCCCTTGGCCGCGACGATGGATAAGCCCATGCCGTTGCTGTTCTTGTGTAGCTTAAAAAGCGCGAATTTAGTCGGCAGCCAGCTCATGTGTGTGAGTGTGCG	-	-	intergenic	cno, exon_11	cno	NA	bp1_Dmel\G-element_LINE-like=2	0
A373R1	406	novobreak	TRA	3R	10500610	2R	13698093	3	0	somatic_tumour	3557	3197.5	3R:10500610 2R:13698093	2358:40_41_132_406_2358_2359	0.09	0	-	-	TGCCTTCACTTACGCACACACACCTTCGCCCGCCGTACAACGGTGCGTATGCAACCGCTGATGGAAGTGGAGATGCAGATGGATGTGGCACTGGATGTGGATGTGGATGCGGATGAGCACTGGGAGACGGTACTG	-	-	intergenic	fas, intron	fas	NA	-	0
A373R1	406	novobreak	TRA	3R	10505784	X	18303974	3	0	somatic_tumour	3559	7798.2	3R:10505784 X:18303974	2359:40_41_132_406_2358_2359	0.12	0	-	-	CACCGGGAGGAAGGAGGAAGGAGCAGGTAGTAGGTAGAGTCGGGCGGTGCGGCCGGGCCGCATCTCCGCCACGAAAGTGCGTCCCGTTTCGAGCCCAGGGG	-	-	intergenic	intergenic	-	NA	-	0
A373R1	409	novobreak	TRA	3L	12178302	2R	13922941	3	0	somatic_tumour	2663	1744.6	3L:12178302 2R:13922941	1845:409_1081_1844_1845_2960	0.08	0	-	-	GATCTTAGCTAATTCAGTGGGCAAACCAGCCTAGTCAATCAGATTTAACAGCCAAATTGAAACTTATAGAGATAAATTGAAACTGAAATCAGACGCAGCTGCACCA	-	-	CAH2, intron	shot, intron	CAH2, shot	NA	-	0
A373R1	411	novobreak	TRA	3R	15723838	X	20082047	4	0	somatic_tumour	3794	4358.2	3R:15723838 X:20082047	2507:411_683_2507	0.14	0	-	-	AAAGTCCTCGGGGATCGGAGAATCGGAGAATCGGAGGCACCCTGGCCAATGTCCGAAAGGAATCAACCGGCAGCTGGTTCCAAAAGCCAACAGTTTTGCATATTTCATATTTAGAATTTGATGCGCCACAGCGGGCTGTGCC	-	-	intergenic	intergenic	-	NA	-	0
A373R1	423	novobreak	TRA	2L	11173435	2R	11436869	3	0	somatic_tumour	573	263.4	2L:11173435 2R:11436869	3to5	0.09	0	-	-	TGTTATGATTTTTGGAATTTTGTGAGACCGCCCCCGCATGTGTCAATCTTAGCCTTTGTTTTATTGACTAAGCATACAATCCGTAGGCCTTCACTTCTCAAATAT	-	-	Ca-beta, intron	CG7777, intron	Ca-beta, CG7777	NA	-	0
A373R1	434	novobreak	BND	2L	11430408	2L	16208470	4	0	somatic_tumour	583	4778.1	2L:11430408-16208470	3to3	0.08	0.01	-	-	GCCACATGCCACCCAAACCATGTCACCTCCCATCGAAGGGGTAAGCAACCAAGCAGTAAATCGCGCTGACTGCAATTTATTTAATAAAAAACGCAATGTCGACGACCCAAGCAATTGAAAC	-	-	intergenic	intergenic	-	NA	-	0
A373R1	440	novobreak	TRA	2L	11635382	X	14654037	4	0	somatic_tumour	590	3018.7	2L:11635382 X:14654037	3to3	0.14	0	-	CTGAACAA	GCAAACAGAGGGTCCGAAATTCAGCGAGTTGCTGATCAACCGCCAACAGCAAACAGTCGCAAACGCACTGAACAAAGAGAGAGAGAGAGAGCGGTTTGTTGTTGTTGTGGCAGCGCAGCATCAGCAACATAA	GGGTCCGAAATTCAGCGAGTTGCTGATCAACCGCCAACAGCAAACAGTCGCAAACGCACTGAACAAAGAGAGAGAGAGAGAGCGGTTTGTTGTTGTTGTGG	FoSTeS	intergenic	intergenic	-	NA	mh:0; ins:8; tup:4; tdown:2	0
A373R1	455	novobreak	TRA	2L	11956048	X	15817056	3	0	somatic_tumour	607	3861	2L:11956048 X:15817056	5to3	0.12	0	GAACGA	-	ATAAATGTATCTTTGAGATCTCTGCTGGTTCTAATTGTCCAAGATGACAATGCAGATTGGATTGGTAACGGTAACAGCACGCACACTCCAACAAGAAACAGAAACGAAGAGCAGAGGAACGAGCAGCTGCGTGTTGAGTTTTCGAGGCGGAAAT	CTCCAACAAGAAACAGAAACGAAGAGCAGAGGAACGAGCAGCTGCGTGTTGAGTTTTCGAGGCGGAAATTGAGTTCAAGCGTAGGAAAGTCTGTTTCTAGT	Alt-EJ	CR43314, exon_2	sd, intron	CR43314, sd	NA	mh:6; ins:0; tup:0; tdown:0	0
A373R1	456	novobreak	TRA	2L	12034802	3L	5489988	3	0	somatic_tumour	608	6544.8	2L:12034802 3L:5489988	3to5	0.11	0	-	-	AGGAGCAACCCCACAAAAAAAAAACAGAAAAACTTCACCTACGAAAATATTTCAGAAAGTGGGTGCTCAGTGCGGCCATACTCACGTCAGCGGTGCTGACCCTGCTAACTCCCACTGCAGTGCGACAGGGCGGTCTGTATGCC	AGGAGCAACCCCACAAAAAAAAAAACAGAAAAACTTCACCTACGAAAATATTTCAGAAAGTGGGTGCTCAGTGCGGCCATACTCACGTCAGCGGTGCTGACCC	NHEJ	CG18788, exon_2	intergenic	CG18788	NA	mh:0; ins:0; tup:0; tdown:0	0
A373R1	458	novobreak	TRA	2L	12077864	3L	19491933	3	0	somatic_tumour	610	7414.1	2L:12077864 3L:19491933	3to3	0.16	0	-	-	GGGCAATGGCAGTGACGGCATTCGACTGTCGCCACAAGGCGGAAATGAGCCAACTTGGCTGCCACATGGGGCGCAAAAGACGCCGGCTGACAATATCCGATTGAAATTTTGGTAAATGAAAAATATTCCAATATTTTCTAGATATTGTTTATAAC	-	-	intergenic	intergenic	-	NA	-	0
A373R1	466	novobreak	TRA	2L	12380393	3L	19498719	3	0	somatic_tumour	620	7118.3	2L:12380393 3L:19498719	5to3	0.09	0	-	-	GCTGTAAGTATGTAATTCGCATTTTAGTGCATTTTGATGGCCGGGAATGAAAGCGGGGCATCTGAGCCTCCCAAACATTCAAGGCGGATAGCACATTTGTGATGGTCCAATCG	-	-	bru2, intron	CG9451, exon	bru2, CG9451	NA	bp1_rover_Gypsy=2; bp2_Cr1a_CR1=2	0
A373R1	486	novobreak	TRA	3R	12351025	2L	12910773	9	0	somatic_tumour	3650	559.7	3R:12351025 2L:12910773	2418:486_2418	0.32	0	-	-	TAGTCGGTGATCCTTGCTGAAGGCGGTTGAACTATAGGTCTTAATCAAGACTATATAACTTATGGTTCTCATTGTCAGGTTCTCATCACCAACTTACATATTATTTTTTTTTCGACCGTAGGAAAGTAATCCGTACAGCTTCTCTTTTGCCACATTCATCAAGGGAGCTCCAGAATCTCCCTGAAATGTAAAAT	-	-	CG10041, exon	intergenic	CG10041	NA	bp2_3Cen_mapped_Scaffold_31_D1643_D1653_D1791_3	0
A373R1	496	novobreak	TRA	2L	13256942	3L	10524216	3	0	somatic_tumour	653	2732.7	2L:13256942 3L:10524216	3to5	0.09	0	-	-	GACAGCCATAAACGAGTTGCTGACATCATCGGCGGCTAGCAAACCTGGCCAAGTGGCCACCGTGGCCGGATGGGGAAGTCTTCGGGAGAATGGACCACAGCCTGTC	-	-	CG31728, exon_4	Rbfox1, intron	CG31728, Rbfox1	NA	-	0
A373R1	498	novobreak	TRA	2L	13400090	X	16446231	3	0	somatic_tumour	655	3046.1	2L:13400090 X:16446231	5to5	0.15	0	-	-	CCAAATTGCCCACAAGCAGCTAGTTAAGACTACTCAAGCTTTATGTTTCAGCTCCAGGCCCTTGGTGAGCGATGCCTTGACAGCGTCGATGCCCTCGTAACCGTAGCAGGAGCACTCGATGTCCGCACGGATCTTGAC	-	-	CG7110, intron	eIF-2alpha, exon_1	CG7110, eIF-2alpha	NA	-	0
A373R1	508	novobreak	TRA	3R	23152458	3L	17334887	4	0	somatic_tumour	4129	5817.6	3R:23152458 3L:17334887	2697:508_1971_2697	0.12	0	-	-	ACTCGATACAGCGAAATGAACAGAGTTTAATGAAAATGTTAACCAAGCAACTGGCGAGGACCAGGTCCTCCTTTAAACTGGAACTACACAAATTGCTTGCTTAAAAT	-	-	unk, 3UTR	intergenic	unk	NA	-	0
A373R1	511	novobreak	TRA	2L	13724341	X	14775902	4	0	somatic_tumour	673	1051.6	2L:13724341 X:14775902	5to5	0.25	0	-	GACAG,TGTT	GACAGTTCCAAGTGAAATTAAAAACCGAATTTCCAGTCACACAATGCCCACCCTTTGGAACAAATTGCTTCTACAATCACCGTTCTCTGGCGGGTGATAACCTGTC	AACAGGTTATCACCCGCCAGAGAACGGTGATTGTAGAAGCAATTTGTTCCAAAGGGTGGGCATTGTGTGACTGGAAATTCGGTTTTTAATTTCACTTGGAACTGTC	FoSTeS	intergenic	CG5334, exon	CG5334	NA	mh:0; ins:10; tup:3; tdown:4	0
A373R1	515	novobreak	TANDUP	2L	13879502	2L	14567889	5	0	somatic_tumour	679	688.4	2L:13879502-14567889	3to5	0.1	0.01	-	-	GCAAATGCCCTGCAAAGTGTCGATAATTACCTGTAAAAGTTTGAGCCAAGAGCAACAGTTAACACAGCAGCAGCAACATGTTGGCGGTTAAGAACTTCTTCCTGCCGGAGAGGGCAAAAGCTCCGGAGACTCCACAACGATTCACACGACTGCCAGAGGCGAGCTGTCAACGCCTTTTGGTGCCAGCAAGTTGCAACTGC	-	-	CenG1A, 5UTR	intergenic	CenG1A	NA	-	0
A373R1	518	novobreak	TRA	2L	14071477	X	1911534	3	0	somatic_tumour	687	12159.9	2L:14071477 X:1911534	518:518_1910_2941_3039	0.17	0	-	-	TCTTTAAATTGCTCGGATGCCCAGCTGGAGAAGGCGACTTCATCACCTCCGACCGGGTAATGCTATGGACAGATGAGGGAAAGGGCTACTTGTACAAGCTGCCCGCAAACTGCATTCCCGACAACAAGGAGTTCCACTCGAAGAGTGTGGTCAGGGATGCAC	-	-	nAChRalpha5, intron	Rbcn-3B, exon	nAChRalpha5, mip130, Rbcn-3B	NA	-	0
A373R1	518	novobreak	TRA	3L	14708172	X	1911665	3	0	somatic_tumour	2775	12796.5	3L:14708172 X:1911665	1910:518_1910_2941_3039	0.13	0	-	-	CCCGCAAACTGCATTCCCGACAACAAGGAGTTCCACTCGAAGAGTGTGGTCAGGGATGCACCTCTAACCTTGGTCAAAGTTTTAGCTTGTTTACACAAGAGTGTCAGAATCGGCCAGACAAGTAAACATGAAAGCGAGAGCAAA	-	-	ome, intron	Rbcn-3B, exon	ome, mip130, Rbcn-3B	NA	-	0
A373R1	518	delly	TRA	X	1911425	2L	12860859	4	0	somatic_tumour	BND00001511	10949.4	X:1911425 2L:12860859	2941:518_1910_2941_3039	0.11	0	-	-	AATCCAAGGAGATCCGCTGCCTGAATGCCATCACCATGAATTGCTGCGCCCAGAACACCATTTTTTTTTTTTAAGTGCGTGCGTAGCAAGTGGGGTATTC	-	-	Rbcn-3B, exon	intergenic	mip130, Rbcn-3B	NA	-	0
A373R1	522	novobreak	TRA	2L	14178344	X	1814038	4	0	somatic_tumour	692	12364.3	2L:14178344 X:1814038	523:522_523	0.14	0	ACGAAAC	-	GCATTATAGACAGCTTAACAAATACAATCAATACCTTCACTTTCGTGTTATTCGAACCAGTCTAAAAGAGTTTCGTTTTGCTGTTTGTTTTTTTTTTGGTTTTAGTTAACATATTTA	TAAATATGTTAACTAAAACCAAAAAAAAAAACAAACAGCAAAACGAAACTCTTTTAGACTGGTTCGAATAACACGAAAGTGAAGGTATTGATTGTATTTGTT	Alt-EJ	CG43333, intron	CG42666, intron	CG43333, CG42666	NA	mh:7; ins:0; tup:0; tdown:0	0
A373R1	522	novobreak	TRA	2L	14178344	X	1814038	4	0	somatic_tumour	693	12364.3	2L:14178344 X:1814038	523:522_523	0.14	0	ACGAAAC	-	GCATTATAGACAGCTTAACAAATACAATCAATACCTTCACTTTCGTGTTATTCGAACCAGTCTAAAAGAGTTTCGTTTTGCTGTTTGTTTTTTTTTTTGGTTTTAGTTAACATATTTA	TAAATATGTTAACTAAAACCAAAAAAAAAAACAAACAGCAAAACGAAACTCTTTTAGACTGGTTCGAATAACACGAAAGTGAAGGTATTGATTGTATTTGTT	Alt-EJ	CG43333, intron	CG42666, intron	CG43333, CG42666	NA	mh:7; ins:0; tup:0; tdown:0	0
A373R1	532	novobreak	TRA	2L	14400065	3R	13771599	3	0	somatic_tumour	705	628.5	2L:14400065 3R:13771599	532:532_1890_2374_3121	0.12	0	-	-	GTTTCTGACAATCTCATTAGCTGGGATTCTTTAATACATCAAGACCGTTGAGTTACGAATTGGTTTTGGACCGGGAGAGATCGTCTCGTATACTCGTGTACGGCAAACCGAAATTTCCTTCCTTCAGAC	-	-	elB, intron	CG9297, exon_1	elB, CG9297	NA	-	0
A373R1	532	novobreak	TRA	3R	11087993	X	17037396	3	0	somatic_tumour	3582	5949.4	3R:11087993 X:17037396	2374:532_1890_2374_3121	0.13	0	-	-	TGCTGCTGCTACACGCCCAGTAATTGCCATTGCACTTGTTGTAGATGTAGTCGTTGTAGTCCTTGTCCAACGCCTGTCACGGAAACTTATCCCTCATTGTCCTTGCCCTTCGCCCCGACCCCCCAACCGCCCACTCCATGTCCTTGGCTCG	-	-	intergenic	CG45002, intron	CG45002	NA	-	0
A373R1	532	novobreak	TRA	X	17039927	3R	13773055	3	0	somatic_tumour	5009	3266.9	X:17039927 3R:13773055	3121:532_1890_2374_3121	0.12	0	-	-	CATGTTTGCAAAACAGCAAAGAAAAAGAAAAAATTGAATGATAAATGAGCAACGGCTTGATTTGTTTTCTCACGCTGCTGTTCTGGGCTTTGATTTTGTTTTTTTTCGGTGCCGAGTGCCAAAAACGGGGCCGCAGGGCGTATGATTAATATGCGTGAATTAAGTCAAATCGAATCGAATCAATCAAGACGACAACAACACCAACAAAAACGGAGTGTAGCATGAAAAAG	-	-	CG45002, intron	CG9297, intron	CG45002, CG9297	NA	-	0
A373R1	533	novobreak	TRA	2L	14417213	2R	8193167	9	0	somatic_tumour	706	6224	2L:14417213 2R:8193167	533:533_534_2547	0.23	0	-	-	TATTTATAATTTCGCAATCAGATTCATCCGAAACGTCAAGGCTATTTTCAGTCCAGTCGGCAATACTTGTAGAATGGATTTCATGAGAGTCTCGCAGTTCTCGTCGCCAGTGCCTTGGCTATATCG	-	-	Pburs, exon_1	LRP1, intron	Pburs, LRP1	NA	bp1_roo_BEL=11; bp2_211000022278137_8; bp2_diver2_BEL=2	0
A373R1	536	novobreak	TRA	3R	29825658	X	8015188	4	0	somatic_tumour	4408	21810.5	3R:29825658 X:8015188	2825:536_1238_1239_2825_2826	0.17	0	-	-	GCGTTTGGGTGAACAGCCTCCCTCTGCCTCCGCCCATTTTCGTCTATATATGTACTGGAACACACCTTTCCCCGGATCGGTCATCATCATCATCATAATCATCATCTGTATCGAATGCGACTATCCTAATTAAGCACTATAATTTAT	-	-	neo, 3UTR	Tbh, intron	neo, Tbh	NA	-	0
A373R1	565	novobreak	BND	2L	15560997	2L	19547841	2	1	somatic_tumour	751	3986.8	2L:15560997-19547841	5to5	0.14	0	-	-	GGTTAAATCAGGCATCTTGGGTCAACTTTGGGGCTGCGTAAATTAGCAGCCAGTTTTTCGGCTCTCCAAACTTAAAATATACCGACTAGGAATTTGGAATAATAAAACATTTTGTTCAGC	-	-	kek3, intron	intergenic	kek3	NA	-	0
A373R1	571	novobreak	TRA	3R	18423017	2L	15785953	3	0	somatic_tumour	3920	2637.1	3R:18423017 2L:15785953	2578:571_1274_1275_1581_2578	0.09	0	-	-	CTATAAGAGTTAACTCTCGTAAATTTTCAGATATCAAATGTAATAAAATAACAATCGATGCAGCGACAATTTGCGCACCCACTGCAAGTTCAAGCATCCCATGTACAATCC	-	-	fru, exon	CG18109, exon	fru, CG18109	NA	-	0
A373R1	592	novobreak	TRA	2L	16494892	2R	23582411	3	0	somatic_tumour	783	7087.5	2L:16494892 2R:23582411	5to3	0.09	0	-	-	ATATTAAATATCTTGATTGTTTCGAGAAGCTCTGAGCGGATGTTGTGGCCGACGATTGATAAACTCCAAGTTTTATATCATCGCGAATGGGCGATGGCTAAAGAA	-	-	Tpr2, intron	apt, intron	Tpr2, apt	NA	-	0
A373R1	594	novobreak	DEL	2L	16509529	2L	21146467	5	0	somatic_tumour	787	4636.9	2L:16509529-21146467	5to3	0.13	0	-	-	TATTTATAGAAAACATTAGGCGAATGTGTATTTTGTTAGCGTGAATTAATTTATTCTGTCTGTGTAATGTTTAGGCGTTTTCTTTTTCGATTGGCTTAAGTGTTTCTGTGGAAGGCTCGGGTTTGGGTAACTGCTCTGCAGTTTTCGCTTCCTTCCTCGGTTCGTCCTCAGGCACATTCTCATCGTCGAGTCCATTCCAGGAGGCAGCCACCGAGAGC	-	-	CG5953, 3UTR	del, exon	CG5953, del	NA	-	0
A373R1	598	novobreak	TRA	2L	16567620	3L	25334312	4	0	somatic_tumour	792	8766.7	2L:16567620 3L:25334312	599:598_599	0.18	0	-	-	GTTCTATCTCCTTCTCTGTCACAGCTGCTGCTGTCTCTTACTCTCTGTCTTTCTATCTCCCTCTGTACACCCGGAAGAATATTTGTTTTTAAGCACTAAAGTATCTGAACACGATTTGAAATTATTAAAAAACCACGCCTTAAGTG	-	-	CG42389, intron	CG45782, intron	CG42389, CG45782	NA	bp2_3Cen_mapped_Scaffold_36_D1605_3	0
A373R1	615	novobreak	TRA	2R	13604000	2L	7298204	3	0	somatic_tumour	1488	6305.8	2R:13604000 2L:7298204	1076:615_616_1075_1076	0.09	0	-	-	GTGGTTGGTTGTTCGCTGCATTTCTCATACGCAGTGTGTCCCATCAGCAGTTGTGGCTTCTGCTGCTTTTTGGCATTTTTGTGTACGCATTTCATTTGGTT	-	-	intergenic	intergenic	-	NA	-	0
A373R1	628	novobreak	TRA	2L	17692544	3L	6761859	4	0	somatic_tumour	833	10930.7	2L:17692544 3L:6761859	5to5	0.16	0	T	-	GGCAAATACCCAAGTAAATTCGAGTGCAACAAGGGGCGGGGTCGCTGAACTCCAAGGAGTCACTCTTTTTTACTGGCAATGAAGAAAGGTCAGTGAATAGATGAAAGATTATTGTA	TACAATAATCTTTCATCTATTCACTGACCTTTCTTCATTGCCAGTAAAAAAGAGTGACTCCTTGGAGTTCAGCGACCCCGCCCCTTGTTGCACTCGAATTT	Alt-EJ	CadN, intron	CG32392, intron	CadN, CG32392	NA	mh:1; ins:0; tup:0; tdown:0	0
A373R1	629	novobreak	TRA	2L	17726659	X	21570749	3	0	somatic_tumour	834	3844.1	2L:17726659 X:21570749	3to3	0.13	0	-	-	GACATGTCACACACACCAACACACACAGCCCCCCCTTACAAAGTTCCGATGACTGACAAGCTTTAGCTTTAAGCCAGCCTAATCGATGAAGATTTCCGAGCGGATTTGC	GCAAATCCGCTCGGAAATCTTCATCGATTAGGCTGGCTTAAAGCTAAAGCTTGTCAGTCATCGGAACTTTGTAAGGGGGGGCTGTGTGTGTTGGTGTGTGTGACATGTC	NHEJ	CadN, intron	intergenic	CadN	NA	mh:0; ins:0; tup:0; tdown:0	0
A373R1	641	novobreak	TRA	2L	17918519	3L	22565067	3	0	somatic_tumour	847	4646.5	2L:17918519 3L:22565067	3to3	0.1	0	-	-	GGCACAGATTTACCGACCCCCTTCCACACTATCTGTCCCTTTTATCACTCCTCGCTCCGCCAACTGCCACAATAAATAAACAATGCGAACAAAAGAAAAAGTAAAAAATCAAACTCAGCAATTAGATTATTTCTAAAGAGTAC	-	-	intergenic	intergenic	-	NA	-	0
A373R1	642	novobreak	TRA	2L	17933410	3R	6473122	3	0	somatic_tumour	848	11460.3	2L:17933410 3R:6473122	642:642_853_1843	0.08	0	-	-	AGTTGACAGCGTGGAGCGTGGCAAATATTTAGACCTTAATGAAATGAAAACAAAGTTGGAAAAAAGGTAATGAAACGACGAAGCGAGCAGAAATTCATGCCAAGTCCGCACTTCATGGCAACGCTTTGAG	-	-	intergenic	intergenic	-	NA	-	0
A373R1	646	novobreak	TRA	2L	17981161	3L	4587251	3	0	somatic_tumour	853	13393.9	2L:17981161 3L:4587251	5to3	0.08	0	-	-	CGCTAAGACGCTCTTTAAATTGTTGTCCTCGCTTGGGCACATGCGAATCTCCAAGCCACGGGTGCTTTACGTAGTTTGGCCAAAATAGGCGAGTGAGGGAATCGCAGAGCTGCCAATATTTTATTTTGCGTGCACAAGGGAAACGAGAAAA	CCAAGCCACGGGTGCTTTACGTAGTTTGGCCAAAATAGGCGAGTGAGGGAATCGCAGAGCTGCCAATATTTTATTTTGCGTGCACAAGGGAAACGAGAAAA	NHEJ	btv, exon_5	CG42540, intron	btv, CG42540	NA	mh:0; ins:0; tup:0; tdown:0	0
A373R1	650	novobreak	TRA	2L	18139645	2R	4431052	3	0	somatic_tumour	860	13708.6	2L:18139645 2R:4431052	3to3	0.1	0	-	-	GGTAGCAATTCAGATTGGCCGACATCCGACCAAAGGCGGCTGCCATGCGGTTGGGCAGCCTGCTGAGGTCGACCGGATCTTTACCACAATCCCGCCACGGGA	-	-	Socs36E, exon	Gprk1, intron	Socs36E, Gprk1	NA	-	0
A373R1	656	novobreak	BND	2L	18249668	2L	18349554	3	0	somatic_tumour	866	99.9	2L:18249668-18349554	3to3	0.08	-0.04	GCTCAAG	-	GGATAAAAAGATCAAAAGTCCTTGCACTACGTATAAAAAGCTTCTTTTGGTGATTTCGTTTTGAACCTTGAGCCTAAGCTGTTACCTGCTTTTATTTACTCC	AGAGTAAATAAAAGCAGGTAACAGCTTAGGCTCAAGGTTCAAAACGAAATCACCAAAAGAAGCTTTTTATACGTAGTGCAAGGACTTTTGATCTTTTTATCC	Alt-EJ	CG42750, intron	Fas3, intron	CG42750, Fas3	NA	mh:7; ins:0; tup:0; tdown:0	0
A373R1	672	novobreak	BND	2L	18885742	2L	19598141	4	0	somatic_tumour	884	712.4	2L:18885742-19598141	3to3	0.1	-0.05	GCCA	-	GTTGGCGGGCCCACAAAAAAAAAAAAACAAAAACAGGAACGTAGAAAAGCGCACTCATCATAAAAATAAATAAGCCAACGCGTGCGCGACATTTTCATTGTTAACGCTTTGTTGTTTTAGTT	AAAAAACAAAAACAGGAACGTAGAAAAGCGCACTCATCATAAAAATAAATAAGCCAACGCGTGCGCGACATTTTCATTGTTAACGCTTTGTTGTTTTAGTT	Alt-EJ	intergenic	Lar, intron	Lar	NA	mh:4; ins:0; tup:0; tdown:0	0
A373R1	674	novobreak	TRA	2L	18949106	2R	17122080	4	0	somatic_tumour	886	1827	2L:18949106 2R:17122080	3to3	0.15	0	-	ACCCTAACC	ATACTGGTGTGTCCTCGTTCTTGGCTTTGTTTACTTACAAATTTTTGAAAGATCACCCTAACCCTACAGGAAATCAGCAGGTGTGATATATTGTTTATAACATTTTGGC	ATACTGGTGTGTCCTCGTTCTTGGCTTTGTTTACTTACAAATTTTTGAAAGATCACCCTAACCCTACAGGAAATCAGCAGGTGTGATATATTGTTTATAACATTTTGGC	FoSTeS	CG10428, exon_1	CR45272, exon_1	CG10428, CR45272	NA	mh:0; ins:9; tup:3; tdown:4	0
A373R1	686	novobreak	TRA	2L	19319576	3R	14536681	2	1	somatic_tumour	901	4782.9	2L:19319576 3R:14536681	3to3	0.12	0	-	-	AAGGAACCGAGTGCACATCTGCATATTATTAATGACCGGTAATTACCTAGGCGGAGTCTGAGGTGGGGAATCCCACTTTATGGGATGGAATGGGATGGGTTGGGGTGGTGTGGTTCGTTTTCCTGAGAAATTGCGAACATCACCGCCAGGGGGCGCCTCATGCAATTTCCCGGCTAATGACTGGCCATCCCAGGCAGAAAGTACGTGTTTTCGATGGCAAAATTGAATAACAAACACGCCGCCAGAC	-	-	intergenic	Pde6, intron	Pde6	NA	-	0
A373R1	687	novobreak	TRA	2L	19462745	3L	17190980	3	0	somatic_tumour	904	2271.8	2L:19462745 3L:17190980	687:687_688_1710	0.15	0	-	-	GCATAAAAATGCACCTGTGCACCATGGAATCCTTTGGCCCAAGCAAACACACACATGCCCATGGAGTGGGCCAAAAATTTCCATAGACATAGACGAAAGCGACGGGGGCGGTGGCGAAG	-	-	intergenic	Rbp6, intron	Rbp6	NA	-	0
A373R1	689	novobreak	TRA	2L	19472495	3R	10328915	3	0	somatic_tumour	906	9143.6	2L:19472495 3R:10328915	5to3	0.08	0	-	-	ATTATTGTTTTTTCTTCGCTTCGAGCCGGGTGTTTTCTTTCCGCCGATTCGGCATTTTCATTGTTTTGTTCATTTTCATTCCATTTTTTGTTGGTGCGAGCTCGTGCATTCGGTAGCACAC	-	-	intergenic	Bruce, exon_3	Bruce	NA	-	0
A373R1	691	novobreak	TRA	2L	19515803	2R	15205313	3	0	somatic_tumour	908	4310.5	2L:19515803 2R:15205313	3to5	0.11	0	CGT	-	CCTCTTTACATGTCAGTAATTCTCAGCAGGAGCATGCCATCAACAGCAGCGTCGGAGGAGCACTTCCTCAAGCACTTCTGGCCGAGCAGCGTGGCCTGCTCCTCGTCGCGTGGACACTCGGTGGAGGGTGAGTTGCGAGGATTCTTGTAGACGCGGCCATCGTCGTCAGACTCCAGAGAGTCGTCGTCCTCCTCCCAGTCGTCGTCGTCGTCATCCTGCTGCGGAATCTCCGAGGTCGTCTGG	CCTCTTTACATGTCAGTAATTCTCAGCAGGAGCATGCCATCAACAGCAGCGTCGGAGGAGCACTTCCTCAAGCACTTCTGGCCGAGCAGCGTGGCCTGCTC	Alt-EJ	Hasp, exon_3	Ir51a, exon_1	Hasp, Ir51a	NA	mh:3; ins:0; tup:0; tdown:0	0
A373R1	693	novobreak	TRA	2L	19628390	2R	23232683	3	0	somatic_tumour	911	3604.3	2L:19628390 2R:23232683	5to3	0.11	0	-	-	GTGTGGGACTTAATCCGAACAAATATTGTGTTTCCTTTCGCTTCGAGGGGAATCTGTAGCCAGGCGGCATTTTCAATTTCGCTGAATTGCTCAAAATTAGGAGTCTCACAAAAACACAACTACCTTTCTCCAGGGCACAGACGACC	-	-	CG46244, intron	CG3092, 5UTR	Lar, CG46244, CG3092	NA	-	0
A373R1	698	novobreak	TRA	2L	19792664	3L	12384685	5	0	somatic_tumour	916	7408	2L:19792664 3L:12384685	5to3	0.17	0	T	AGACAG,CTGTCT	AGACAGGGGTCGATCACGTGGCCGACTACAAGCCTCCCAAGGAAAACGAGAAGATGGACGAGGAAACCCTGCTTACATAAATAAGTAGACAGCGAGTGGGGCTGTCT	AGACAGGGGTCGATCACGTGGCCGACTACAAGCCTCCCAAGGAAAACGAGAAGATGGACGAGGAAACCCTGCTTACATAAATAAGTAGACAGCGAGTGGGGCTGTCT	FoSTeS	CG10466, exon	Ncc69, intron	CG10466, Ncc69	NA	mh:1; ins:13; tup:3; tdown:6	0
A373R1	699	novobreak	TRA	2L	19811204	X	10391682	3	0	somatic_tumour	917	9419.5	2L:19811204 X:10391682	5to3	0.12	0	-	-	CATTAGACGAATTAAACTTAATGTTAACTCCCATTTAGCCTACTAGCTGAATCAATAGAATGGAGCAATAAGTTGGTAATTTCATTTCTTGATGAATGCCAGACGTTGCTACTTGTTTAATTATGT	CATTAGACGAATTAAACTTAATGTTAACTCCCATTTAGCCTACTAGCTGAATCAATAGAATGGAGCAATAAGTTGGTAATTTCATTTCTTGATGAATGCCA	NHEJ	sick, intron	flw, intron	sick, flw	NA	mh:0; ins:0; tup:0; tdown:0	0
A373R1	701	novobreak	TRA	2L	16179327	2R	11318535	3	0	somatic_tumour	771	4860.8	2L:16179327 2R:11318535	582:582_701_2850	0.09	0	-	-	AAGTAATGATGCATTAAAATCACTTGTAAGTTCAAACTCATAGTTGAAGGTTACTTGTGGTCTGCGTGTCATTGATTTCTCTAGTGTCCAGGTAAACGATAATCCATATAACTACTCTAACCCAGTAGTTGTGATACTAATTACTTCTGG	-	-	Ca-alpha1D, exon_19	nompA, intron	Ca-alpha1D, nompA	NA	-	0
A373R1	704	novobreak	TRA	3L	3085633	2R	14153587	3	0	somatic_tumour	2184	11068	3L:3085633 2R:14153587	1535:703_704_1535_2107_2291	0.09	0	-	-	TTGCCATTAGTGGCGCTCCACCGAATCCCGCCGCAGCTCCGTTCGTCAGCAGCAAAAATGAGGAGAGCGATGACGATGAGAAGGTGAAGGCGAAACCGGAGAAGCATTCCGAAACGCACAAAAAAACCGATATGAGCGATGTGGATG	-	-	CG11486, exon_6	pea, exon_1	CG11486, pea	NA	bp1_Dmel\F-element_LINE-like=3	0
A373R1	704	novobreak	TRA	3L	22957247	3R	8474285	4	2	somatic_tumour	3097	14483	3L:22957247 3R:8474285	2107:703_704_1535_2107_2291	0.23	0	-	-	ACATCGGTGTTCAGGGCAATTTGGAAGTCCTTCTGAAGGATCGTTGAGTTCGTTGAGAAAATGAGCTGAGTTCAGGCAAAAAAAAACGAAGAACAAGAAGCGGAGCCAACTGGAAATGGAAAACAAAAAGTGAGCAGT	-	-	intergenic	CG45263, intron	CG45263	NA	-	0
A373R1	710	novobreak	COMPLEX_TRA	2L	17252110	2R	24133346	3	0	somatic_tumour	815	6881.2	2L:17252110 2R:24133346	613:612_613_1400_1401_1738_2479_2584	0.12	0	-	-	AACCAGTTTTCCCACGATTTGATGTGATTGTGCCATTGGTAAGCCCACGTTCTCCACACAATTCCCCTTTTCCAATCGCTCGATGATTGTCATCGTAGGTGTGACTAATTGTTGG	-	-	beat-IIIc, intron	tamo, exon_1	beat-IIIc, tamo	NA	-	0
A373R1	710	novobreak	TRA	2L	20424190	2R	24129750	3	0	somatic_tumour	933	3705.6	2L:20424190 2R:24129750	3to3	0.11	0	GCG	-	GGAGGTGGGTGGTGGATGGGCGGGATAGTGAGGATGGGAAGGAGGAGCTCCAGACAGGAAAAGGGCTTGGCTCGCATTAGGGTGACAGCGGGAGTGACGGCAGCGGGATACGTCTGCACTTGGAAGGACATCCTACAGTTCCGCGAGCGTTACGTGG	GGAAAAGGGCTTGGCTCGCATTAGGGTGACAGCGGGAGTGACGGCAGCGGGATACGTCTGCACTTGGAAGGACATCCTACAGTTCCGCGAGCGTTACGTGG	Alt-EJ	CG15130, intron	tamo, exon_4	CG15130, tamo	NA	mh:3; ins:0; tup:0; tdown:0	0
A373R1	710	novobreak	COMPLEX_TRA	2R	24126253	3R	17871707	6	0	somatic_tumour	1968	6254.5	2R:24126253 3R:17871707	1400:612_613_1400_1401_1738_2479_2584	0.22	0	-	-	AGACAGGAACAAGACGTTCCCGAGCGCCAAGCGGATGAGACAGCGAGCTGGTAACAAAGCGACAATATGAATACTATCTAATGTATGATACGAATGAATACTATCCA	-	-	CG43776, exon_1	tinc, 3UTR	CG43775, CG43777, CG43776, tinc	NA	-	0
A373R1	710	novobreak	COMPLEX_TRA	2R	24128278	2L	11977523	3	0	somatic_tumour	1969	12150.8	2R:24128278 2L:11977523	1401:612_613_1400_1401_1738_2479_2584	0.11	0	-	-	GTCTAAGCATTAAATCAACCAGCAGCTGTAAAATTACAGCCGTTCGTTATGGACAGCGAGCCTAGGTCCAAGCTCTGCACCAGCAAGTCCTCGCGGTCACCCAGGTC	-	-	tamo, exon	intergenic	tamo	NA	-	0
A373R1	711	novobreak	TRA	2L	20495067	3L	5238975	5	0	somatic_tumour	935	15256.1	2L:20495067 3L:5238975	3to5	0.22	0	A	-	AACCGAATCAATGTGCAACGGGAAAAGTTTTAGGCCAAAAACTTGGAAACCCTTTTACCCTAACCGAAGGGCATTCGAAACCACCAAATCGGAATATATATTTTGTATAAATAGAAC	AACGGGAAAAGTTTTAGGCCAAAAACTTGGAAACCCTTTTACCCTAACCGAAGGGCATTCGAAACCACCAAATCGGAATATATATTTTGTATAAATAGAAC	Alt-EJ	CG34007, 5UTR	shep, intron	CG34007, shep	NA	bp2_Dmel\1731_Copia=4; mh:1; ins:0; tup:0; tdown:0	0
A373R1	715	novobreak	TRA	2L	20674142	3R	26004104	6	0	somatic_tumour	943	5330	2L:20674142 3R:26004104	716:715_716_2086_2746_2878	0.28	0	-	-	GCCCCCGGCAATGGCCAACATTGCGGCACTTAGTCAATCTTGGAGTGAACTGATCGCCTTTCAACTGGTCCATCGCAAAATGTTTAGCTGGCGCTTTGCTTTTGTTGCCTATAAATAGAAC	-	-	CG31678, intron	intergenic	CG31678	NA	bp2_roo_BEL=3	0
A373R1	719	novobreak	TRA	2L	20828628	2R	11873809	7	0	somatic_tumour	949	8954.8	2L:20828628 2R:11873809	3to3	0.32	0	-	-	GTATTGAAACGAACCACAGGCGCATGAGCCGGCAGTCGACGGATGCGAGAGATGACCAGCTTGATGTCCGCAAGACCTGCGTGCTCAGGATACTGTTCCAGTTGTTCCAGCACACGCTTCTCTATCCGCTCCATGACGGAAGAAGAAAACGTTTTCATTGCATACAAGTATATGTC	CCTGCGTGCTCAGGATACTGTTCCAGTTGTTCCAGCACACGCTTCTCTATCCGCTCCATGACGGAAGAAGAAAACGTTTTCATTGCATACAAGTATATGTC	NHEJ	intergenic	CG13185, exon_8	CG13185	NA	mh:0; ins:0; tup:0; tdown:0	0
A373R1	726	novobreak	TRA	2R	19019261	3R	28186278	3	0	somatic_tumour	1741	9167	2R:19019261 3R:28186278	1247:726_1247_2787	0.09	0	-	-	CAGGAAATATGTTCGGAAGCCGTAGCAGGAAAAACGGAATCCGCAAAACTTTTGCCAGCAAGTTTGAGTTTTTTCTTCCGCTCTGCCGTTCGTGCTTGGCCCTG	-	-	intergenic	CG34354, intron	CG34354	NA	-	0
A373R1	726	novobreak	TRA	3R	28188345	X	15489595	3	0	somatic_tumour	4340	12698.8	3R:28188345 X:15489595	2787:726_1247_2787	0.16	0	-	-	CTTATCAATAATTTATTTATAAGCTTCACCTCAGAACACATGTTGTCAGTATGCCATGTTGGCCTCAACAGCCTCCGTGTCTTGCCGTCGCTTTCCGTTTCGTATTTTGTGTTTTATGGCCCTCGTCCCCATCTCCATCCCCATTCCCATTCCC	-	-	CG34354, intron	Gmap, intron	CG34354, Gmap	NA	-	0
A373R1	741	novobreak	TRA	2L	21740345	3L	10584553	4	0	somatic_tumour	983	11155.8	2L:21740345 3L:10584553	5to3	0.21	0	-	-	CGTTATGTACAAGACAAGGTGTTATTTTCTGTATACGAAATGGATAGTGCACAGCAGTGTATTATAATATTTACTTATATATCAAGAGAGAAAACTAACCGCATGCGTTTTATGTTCTTTT	-	-	step, 3UTR	Rbfox1, intron	step, Rbfox1	NA	-	0
A373R1	747	novobreak	TRA	2L	22041503	X	15476281	3	0	somatic_tumour	997	6565.2	2L:22041503 X:15476281	5to5	0.1	0	TGATGG	-	GTTAGCCATCGTCACATTTTTTTTGCCGGACCAACCTGCTGAATTGATGGTCGGCGTTGGAAGAAGTGGAGCACGCTTGTTCACCTCCGGCTCATTCTGTGTGTAGTAGGGATCGTTGTCCATGTTGTTCATGCCGAACGATATTTCTAGGCTTTTAGGC	CTGTTAGCCATCGTCACATTTTTTTTGCCGGACCAACCTGCTGAATTGATGGTCGGCGTTGGAAGAAGTGGAGCACGCTTGTTCACCTCCGGCTCATTCTGTG	Alt-EJ	CG31601, exon	CG6324, intron	CG31601, CG6324	NA	mh:6; ins:0; tup:0; tdown:0	0
A373R1	761	novobreak	TRA	2L	22997150	X	22671759	3	0	somatic_tumour	1020	325.4	2L:22997150 X:22671759	3to5	0.19	0	TCTAC	-	TCAACTTAATAGCTCAAATCAATAAAATAATGAAAACTCAACAGAAGATCTACTGGAGTGCAGTTCTTTCATGTTTAAAAGATATTGGCTTAGTTCAACTA	TCAACTTAATAGCTCAAATCAATAAAATAATGAAAACTCAACAGAAGATCTACTGGAGTGCAGTTCTTTCATGTTTAAAAGATATTGGCTTAGTTCAACTA	Alt-EJ	intergenic	CR44997, ncRNA	CR44997	NA	mh:5; ins:0; tup:0; tdown:0	0
A373R1	764	novobreak	TRA	2R	335228	2L	3069253	3	0	somatic_tumour	1024	2734	2R:335228 2L:3069253	3to3	0.1	0	-	-	GTCTTAGATCTTGCGATCTTGAAGCGCTTCCCACGCCGAAGGGAACCCCTCATTCGTAAGAGAATCCGAAGGGAAGTACTTTTTTAAACGGGCGCGGACGAGGATCGAAGCCACACAC	GTGTGTGGCTTCGATCCTCGTCCGCGCCCGTTTAAAAAAGTACTTCCCTTCGGATTCTCTTACGAATGAGGGGTTCCCTTCGGCGTGGGAAGCGCTTCAAG	NHEJ	CG45781, intron	toc, 3UTR	CG45781, toc	NA	mh:0; ins:0; tup:0; tdown:0	0
A373R1	789	novobreak	TRA	2R	3524816	X	4602283	5	0	somatic_tumour	1078	1077.5	2R:3524816 X:4602283	5to3	0.22	0	CTGG	-	GGAATGAGAGTCAGAATTTCGTTGTTGATTAACGAATCGAAATTCGCCACTGGTTGCCTTGGCCGATTCTTCACTGGTACATAGAGCCCCCGTTTATATACC	GGAATGAGAGTCAGAATTTCGTTGTTGATTAACGAATCGAAATTCGCCACTGGTTGCCTTGGCCGATTCTTCACTGGTACATAGAGCCCCCGTTTATATACC	Alt-EJ	CR41501, exon_1	CR32773, ncRNA	CR41501, CR32773	NA	mh:4; ins:0; tup:0; tdown:0	0
A373R1	793	novobreak	TRA	3R	14400705	2R	12544913	7	0	somatic_tumour	3734	1855.8	3R:14400705 2R:12544913	2467:793_1656_2467	0.18	0	-	-	TCCATGGATCAATTTGAAAGTTTAACAACTGGCCATTAGCACTGGAGCGAACTATTTCTCATTCTCATTTCCATCGTCGTTCTCATTTCGCTGTGAGCCGGAGCGAATATGGGGGGCACCTGTCCAGGTTTCCTTCCATTTTCCACTGTCTTTGCAGTTATTTAT	-	-	cv-c, intron	fra, intron	cv-c, fra	NA	bp2_Dmel\F-element_LINE-like=7	0
A373R1	817	novobreak	TRA	2R	5808875	X	15879182	3	0	somatic_tumour	1123	10070.3	2R:5808875 X:15879182	817:817_1854	0.18	0	-	-	TCTCCGGGCTTTGTTTATTCTGGTGGTAGTAGATTTCCCACGCGATACGAACGTGCATGGCATTCCAGCGACCCCAGGAACTGGCTGGACGTGGGTGGTGTCGAGAAGAAAGTGAAGGGGAAGGGG	-	-	dpr12, intron	tay, exon_12	dpr12, tay	NA	-	0
A373R1	820	novobreak	TRA	2R	5894879	2L	2397528	5	0	somatic_tumour	1128	3497.4	2R:5894879 2L:2397528	820:820_821_1778	0.16	0	-	-	AATTAGCATATGCCTCCATTTAGGACTCAACTCTTTGTCCGTCGTGCAACAAGAACGGGAGCACAAAAAGTCAACGGCAGCAGCGGTAACAGCATCGGACTAGCAACACCAGCAAGTGCAGAAGAAACACGTACACACGCACACAGTGAATT	-	-	CG43366, intron	VGlut, intron	CG43366, VGlut	NA	-	0
A373R1	822	novobreak	TRA	3L	6324285	4	729789	4	0	somatic_tumour	2361	5594.5	3L:6324285 4:729789	1646:822_1646_1671_2617_2618_2887_2888	0.1	0	-	-	AATCTAGTATACCAGATTTCACTCTACGAGTAACGGGTACAGACAGTCGGTCCGGATTCGGTGGCCGGGCCACTTAATCATCGAAGTCGAACCAAGCAGGACAAATGCCATGCACGACTTCATTATTAGGCAGCCCCATATGCACATCATCATCGCCGCTGAATCGTTGCCATGGACTCGTG	-	-	intergenic	bt, intron	bt	NA	-	0
A373R1	824	novobreak	TRA	2R	5992659	3R	13813479	3	0	somatic_tumour	1133	7820.8	2R:5992659 3R:13813479	5to3	0.13	0	-	-	CTCCAAGCGGAGACATTTAGAAACAAATAATTTGATTTCCAGTGACGCGACAGTGCTGAGTTATTTTGGTTACGTGAACAAATTAATACAACCTGACATTTTGTCAGTAACAGCGACGAGTTAATTGTTTTCAACTCCTCGGTTTTGTCATTCAAGTATTTTTGGTCAATACACGGCATACGAA	-	-	Src42A, intron	tal-2A, 5UTR	Src42A, tal-3A, tal-AA, tal-1A, tal-2A	NA	-	0
A373R1	842	novobreak	COMPLEX_TRA	2R	6618618	3L	4022987	3	0	somatic_tumour	1162	2595.6	2R:6618618 3L:4022987	842:756_757_842_1570_2251	0.08	0	-	-	AACAAGATCACCTTGTACCTGTGTGCGCCAGATTAGCACACTCACCAACGGTGCCCAGGCCATCGAGTTCCAGGGGCAGTGCATGATGCGACGCCGCAATAGCC	-	-	jing, exon_6	CG11594, 3UTR	jing, Mul1, CG11594	NA	-	0
A373R1	842	novobreak	COMPLEX_TRA	3R	7005933	2R	7850976	3	0	somatic_tumour	3384	845	3R:7005933 2R:7850976	2251:756_757_842_1570_2251	0.11	0	-	-	CCTTCACCTTGCTCTCTTCGGTTTCTATTCCATGGCAGATACTTGACGACATCCTTCAGCGGGACCTTGAGTGTCAGCGGATCGAAATGGGAGAGTTTTCGCGCGAGGAGCTTAATGTCAGCTGCAAATGAAAGGGT	-	-	intergenic	Dgk, exon_8	Dgk	NA	bp2_Cr1a_CR1=5	0
A373R1	851	novobreak	TRA	2R	6855417	2L	911647	7	0	somatic_tumour	1177	5943.8	2R:6855417 2L:911647	5to5	0.21	0	-	-	CCTTGCAAACACTTTTTCACGCTTGATTAATTTTGGTTCGGCAGTCGCTAGGCATCCGGAACGGAAGTGGAGCACTCAGCGGCAGCGGAAGAGCCACAACTTGAGCCATTTGTCAGCTGGTGGCACTTGGCTGGAGCCACGGTCTGGTAT	-	-	intergenic	intergenic	-	NA	-	0
A373R1	861	novobreak	TRA	2R	7288520	2L	7256491	3	0	somatic_tumour	1196	32	2R:7288520 2L:7256491	862:861_862	0.08	0	-	-	GAGACAGCTTCCAGCATCACTGAGTCAGCGAATAGCCGACTCGATGACACCTGTCGCATTGATCGCTGGTTTGGCGCCTTGCGAATGGCCTCGTTGTACTTCTGTCTC	-	-	pwn, intron	Wnt4, exon_3	pwn, Wnt4	NA	-	0
A373R1	864	novobreak	TRA	2R	7317301	X	15748502	3	0	somatic_tumour	1198	8431.2	2R:7317301 X:15748502	3to3	0.11	0	-	GGAAGTGAAAGGTT	TGATGATGATGAACGAATCTTGGGCAACCTCTGCGAATCTGGACCTGCAGGTGTCAGTGTGAGTAGCCAACGGTATTGGAATGGCCAAGCGGAAGTGAAAGGTTATCGGCAAAGGCCTGCACTGCCAGGCGGGACT	AATCTGGACCTGCAGGTGTCACTGTGAGTAGCCAACGGTATTGGAATGGCCAAGCGGAAGTGAAAGGTTATCGGCAAAGGCCTGCACTGCCAGGCGGGACT	FoSTeS	intergenic	Tcp-1zeta, exon	Tcp-1zeta	NA	mh:0; ins:14; tup:4; tdown:5	0
A373R1	866	novobreak	TRA	2R	7358331	X	15895290	1	2	somatic_tumour	1200	8537	2R:7358331 X:15895290	866:866_3104	0.16	0	-	-	ACCAAGCTGGATCTGATGGACGAGGGCACCGATGCACGCGACATTCTGGAGAATAAGCTGCTTCCGCTGCGACGTGGCTTCGGTTCCTCCAAAGCTGAATCTCTTGGAAAGAGTTCGAACAATGGAGGTGTCTGTGGGCACCAAATACGCC	-	-	Dscam1, exon_6	shi, exon_4	Dscam1, shi	NA	-	0
A373R1	876	novobreak	BND	2R	7680308	2R	15693666	3	0	somatic_tumour	1219	8013.4	2R:7680308-15693666	3to3	0.06	0	CCA	-	TCGATTTCGATGGAGTTAAACGCTACCTGCAGCTGGGCATCGTGAGCTATGGAATATCTCAACCTTGTAAGTAGTTTTTGTCTTGTTCTTAAGTCTATCTA	TAGATAGACTTAAGAACAAGACAAAAACTACTTACAAGGTTGAGATATTCCATAGCTCACGATGCCCAGCTGCAGGTAGCGTTTAACTCCATCGAAATCGA	Alt-EJ	LRR, exon_16	CG30087, exon	LRR, CR44372, CG30087	NA	mh:3; ins:0; tup:0; tdown:0	0
A373R1	894	novobreak	BND	2R	8342068	2R	23836897	2	1	somatic_tumour	1251	15494.8	2R:8342068-23836897	5to5	0.07	0	-	-	ATCTAGGGGTTACGAGGAGGCCTGGGAACGGGCGGCAGAATCAAAAGTCGCAAGGGGCTACTGCAACAGCAACGCCTACGAAAACTGCCTTGAATCAGAAGACGATTGTCCCTTCAGCGGGAAGTGG	-	-	pdm3, intron	CG5549, exon	pdm3, CG5549	NA	bp2_gypsy6_Gypsy=5	0
A373R1	899	novobreak	TRA	2R	8397888	3L	7531805	3	0	somatic_tumour	1256	866.1	2R:8397888 3L:7531805	3to5	0.09	0	-	T	GTCGAGAACCACATTACTCTAAATTCTTCTCAAAGAACTTTCTTCGCTTTTGCAACTAAATCGATAACAATTTGATTTCCCACACCTGGGCCATCTGGTAGAAGATGAAGAACAGGCCGAAGAACTTGACGGTGTTCACATCCTTACGCGACTTGTTGCCCCGCACCTGGG	ATTACTCTAAATTCTTCTCAAAGAACTTTCTTCGCTTTTGCAACTAAATCGATAACAATTTGATTTCCCACACCTGGGCCATCTGGTAGAAGATGAAGAAC	NHEJ	CG2121, exon_3	lqf, intron	CG2121, lqf	NA	bp2_Juan_Jockey=7; mh:0; ins:1; tup:0; tdown:0	0
A373R1	912	novobreak	BND	2R	8694440	2R	20438390	2	1	somatic_tumour	1270	11744	2R:8694440-20438390	3to3	0.08	0	TCGCC	-	GTGCGGGCCACATTTCATTGAACGAAATGAAAAAATAATTGAAATATTTGCCAATCAGTAGAGCGAATATGGGCAGAGAGCACAGATAAGGCGACTGGGATCTGAACAGCCTGAACGAGCCGTATCCGCACCAGGGCAGCCGTATTAAGG	CCTTAATACGGCTGCCCTGGTGCGGATACGGCTCGTTCAGGCTGTTCAGATCCCAGTCGCCTTATCTGTGCTCTCTGCCCATATTCGCTCTACTGATTGGC	Alt-EJ	CG8586, exon	CG12484, intron	CG8586, CG12484	NA	mh:5; ins:0; tup:0; tdown:0	0
A373R1	915	novobreak	TRA	3L	1264570	3R	26637981	3	0	somatic_tumour	2095	25373.4	3L:1264570 3R:26637981	1473:915_916_917_1473	0.13	0	-	-	CTCTTGGGCTGAGTAATTAATTATTCATAATAGCAGGCTATAGATAAAATCTTAGTAATCCACCTGCTGGGGTTTAAAATCAGATATCTGTGGTATCCCACCATTTATCTTCCCATCACTTCTACGTGATCTCCGACAAACATCGCGTATACGCCATGTGTGACCGTAAGGTAACAAACGAACCACCATTCGCTGAATGAAAAGC	-	-	tfc, intron	CR46233, exon_2	tfc, CR46233	NA	-	0
A373R1	918	novobreak	BND	2R	8853032	2R	13338036	2	1	somatic_tumour	1279	4485	2R:8853032-13338036	3to3	0.1	0	-	-	CAGAATCACCATTCATTCAGCAGCATTCAGCATATGCAAATTTTCTCCGTTCTCTATTCCTCACGCTTTCATCGTTTTCGGTTTCTGACGTATGAATGCTGATGTCAAGCTGCCCTCCTGCTGCCGGCTAATTAGTAAAACTCTCTGCGAA	-	-	sns, 3UTR	CR44206, ncRNA	sns, CR44206	NA	-	0
A373R1	924	novobreak	TRA	2L	2138379	2R	5957839	10	0	somatic_tumour	132	3819.5	2L:2138379 2R:5957839	86:57_58_86_924	0.25	0	-	-	TACCCGACTCAGCCGCTTCTCTGACTTCCAACCTTCAGTTACCTGTGCAGCCCAGTTTAGCCATAAGAAACACCACCACCCACGAAATACGCAATGGCAAAGCCAAAAGTCGGCGAATCGCTTCAGGAGCAATCATTAACGTTCTCAGAGGCGC	-	-	tho2, intron	CG7882, 5UTR	tho2, CR46269, CG7882	NA	bp2_rDNA_2	0
A373R1	931	novobreak	TRA	2R	9254537	3R	15261644	3	0	somatic_tumour	1298	6007.1	2R:9254537 3R:15261644	5to5	0.13	0	-	-	TTACAGTCCCCATTCCCTGGTGACGATGAGGAGGAAGTATTCGATTCAATTGTCAACGCTGCCATAGCCGCTACTATTGCTTGGACTCAGTGAGGTCTGACTGGTGCTTCGCCGGGTGGTGCGTCTATCTACACTGGAGG	-	-	Pkn, exon_8	Su(var)3-9, exon	Pkn, eIF-2gamma, Su(var)3-9	NA	-	0
A373R1	944	novobreak	TRA	2R	9806107	3R	14331603	3	0	somatic_tumour	1320	4525.5	2R:9806107 3R:14331603	3to3	0.16	0	-	-	ATTTTTCCTCAAACTCCAAACGGGCGCAATGATGAAATGACAGGCGCACGTCAAAAGGCAAAAATCGAACCCCCCCCCCTCCTTCTCCTGCGAAGTGGAGTCCTGCGACAAGTGTCGCTATCTCGGAAC	-	-	CG1688, intron	NK7.1, intron	CG1688, NK7.1	NA	-	0
A373R1	947	novobreak	BND	2R	9920812	2R	20076023	3	0	somatic_tumour	1324	10155.2	2R:9920812-20076023	3to3	0.08	0.01	-	-	CAACTAGATCGATGTAAATCAAAATTCCTGCCAATGGCAAATTAATTAGCATAGAAATCATATTAAAAATGAATTCACTTCTCTAATTACATTTTCGAACCGCATAAATATTTGAGCATGAGCAGTAA	-	-	Mef2, intron	intergenic	Mef2	NA	-	0
A373R1	952	novobreak	TRA	2R	9980635	X	18334791	3	0	somatic_tumour	1329	8354.2	2R:9980635 X:18334791	3to3	0.12	0	-	-	GTTTATTTTTATGTTTTTCTTTTTGTTATTCGGCAATTTACAACTAAAAAGTTGCAAGCGGATGTGTGCGTGTGTGTGTGTGTGTGTGGATCGCGGGCTTACGCCTCAGTCTTGTAGGGCTTGAAGAG	-	-	eve, 3UTR	CG6123, intron	eve, CG6123	NA	-	0
A373R1	961	novobreak	TRA	3L	866729	2L	9983336	3	0	somatic_tumour	2072	9116.6	3L:866729 2L:9983336	1459:959_960_961_1459_3131	0.08	0	-	-	TCGCAACAGTGACGAAATTTCTGAGGCCTCCTCGCTTTCTTCGAGCCCCTCTTTTCTTGTGGCCGGGCAAAGAAGTCGTCTGCGTGCATATATTTTCGCGACTTTAAGTGTACAAAGGCCACTTGTCATCGTCTTGGCAGCCCTTTGAACT	-	-	CG12502, exon_2	intergenic	CG12502	NA	-	0
A373R1	967	novobreak	TRA	2R	10243407	X	20347986	3	0	somatic_tumour	1348	10104.6	2R:10243407 X:20347986	3to3	0.11	0	-	-	GAGCCATTGTCATATGCCGTCAAAGCTGTCAGCAGCTGCATAATTTCAATTATCGACTCGAGCTATCGACTCCGAGCTCCACTGGGCCACTCCGGAATTCTCGTGCTGCAGATACAGCGGCTCCACAT	-	-	Hdc, exon_5	intergenic	Hdc	NA	bp1_copia_Copia=2	0
A373R1	973	novobreak	TRA	2R	10428179	2L	10871405	3	0	somatic_tumour	1356	443.2	2R:10428179 2L:10871405	5to3	0.08	0	-	-	CTCCATATTTGTGTGAACCTCAAGAGGGGCCTTAAAAAAACCTGTTTGGGGCGGGCATTTTCCGGGCGGTAATATAAGCACAACTGATGGTTTGAATGGAGAAAATTGCACAGCGCAAATGGCCGATAGTCGTGGGTGGATAAAGTCGTACGAG	-	-	intergenic	intergenic	-	NA	-	0
A373R1	983	novobreak	TRA	2R	10794123	3R	7552948	3	0	somatic_tumour	1367	3241.2	2R:10794123 3R:7552948	3to5	0.1	0	-	-	GTTTATTAATGGGTTAAATTGAAATTTCACGCTTTGCTGGCTCCGCATCTCGTTGTCAGGGCTTGGAATAACCTGGCCATGTTACGTCCTTGAAAGCTTTCTACTGTTTGTCTTTCGTTGCGGTCGCAATTTCAACTGAAATCAACATGCAGGA	-	-	CG33144, intron	intergenic	CG33144	NA	-	0
A373R1	1011	novobreak	TRA	2R	11700529	3L	15203449	3	0	somatic_tumour	1404	3502.9	2R:11700529 3L:15203449	3to5	0.11	0	-	-	ATATTTCATATTTCTTAATTGAGCATTCTTGAGAAGGCTTTCAGTACTTTCCTCTTTAGCTTTTTATAGATTTCTTAGCTACGTTTCCTTATTTATAGAGGACAAGGACAGGTAACATTTTTTGTAAAGACTTTACAACATCAAG	-	-	intergenic	intergenic	-	NA	-	0
A373R1	1013	lumpy	COMPLEX_DEL	X	10639966	X	14498877	6	0	somatic_tumour	12655	3858.9	X:10639966-14498877	3040:1004_1013_2836_3040	0.23	0.03	-	-	-	-	-	X11Lbeta, intron	intergenic	X11Lbeta	NA	-	0
A373R1	1013	novobreak	COMPLEX_DEL	X	10639966	X	14498877	6	0	somatic_tumour	4858	3858.9	X:10639966-14498877	3040:1004_1013_2836_3040	0.23	0.03	-	-	TGCGATTGAGTTTCCACCTCGGCACAGTGGGCAAAGCCAGCAGCTTTCGATTTAAATTTCACGCCCAAACACTTGCCGCATTGACAGTTATTGGGCGAAACAAAGTTGACTTTTTCTTCGCAGGACGATGGCTGATTGGAGA	-	-	X11Lbeta, intron	intergenic	X11Lbeta	NA	-	0
A373R1	1016	novobreak	TRA	2R	11826580	3R	28038328	4	0	somatic_tumour	1411	16211.7	2R:11826580 3R:28038328	3to3	0.22	0	-	-	GCGCTCATCGATGCAAATGCAGCTCGGCTCGGAGCTGTGCATCAAGAATCCTGGAGTGAATGGCGTTCGCATTCGATTTTTGTAAATAATTGCTTTACCATAAAAAATACTTTAATTC	-	-	CG13192, exon	CG34362, intron	CG13192, CG34362	NA	bp1_mdg1_Gypsy/TABOR=3; bp2_HMS-Beagle2_Gypsy=3	0
A373R1	1020	novobreak	TRA	3R	17020960	3L	14366282	3	0	somatic_tumour	3858	2654.7	3R:17020960 3L:14366282	2539:1020_1900_2355_2539	0.14	0	-	-	GCGGGGGAGATCGGTTGGTGGCAAGAGGTGGTGCAACCTAACCGCTCGTAAAATGTTTAAACAAGCGGCGACTTGTAGCCCTCGTAGTTGCTAGCCATTTTTGGGTATACTATGTAGGAGATTATGGACTATAAATCACAAAAACACTGGGCCAATAG	-	-	AdSL, exon	fz, intron	Pxd, AdSL, fz	NA	-	0
A373R1	1026	novobreak	TRA	2R	12184617	3R	18466808	3	0	somatic_tumour	1424	6282.2	2R:12184617 3R:18466808	1026:153_1026_1027_1740_2540_2541_2542	0.09	0	-	-	GAACTTAACTTTGGTGCCCTGCTGGCGGAGAATTTCACTCAGTTTAGACCGGAAGACAGTCCAAACATTTGCCTTTTGAGGTTTATGTCTTGCCATGCCTTCTTCTGCTGTCGTTAATGAA	-	-	CG13175, exon_3	fru, intron	CG33964, CG13175, fru	NA	-	0
A373R1	1031	novobreak	TRA	2R	12256171	3L	5324853	4	0	somatic_tumour	1431	6931.3	2R:12256171 3L:5324853	5to3	0.1	0	-	-	ATGTTTACCCAACACGCACACACACACACACACACACATACGTTTTGAACAATATGAGAGGTCGGCAATCTAATTTTGTTGTTTGTCCTGGCGGACAATTCCTTTATGGTGGCCATTGA	-	-	intergenic	intergenic	-	NA	-	0
A373R1	1039	novobreak	TRA	2R	12473427	2L	903602	3	0	somatic_tumour	1445	11569.8	2R:12473427 2L:903602	1039:45_1039	0.11	0	-	-	TATGGGACTGGCTGCCCAAATGCGGCTTAAGTTAGTGCCTCCTCTTGCAGTCGAAGTCCTTTGGCCGTCCAGGACATCCGCAGTTGGCACTCCCGGATATCAAAGCCCACAGGTGACTCATTTCCCGCTGCATCGAAGAGTATACCTTCCTGTTCAAAGG	-	-	CG8550, exon	intergenic	CG8550	NA	-	0
A373R1	1053	novobreak	TRA	X	16818387	2L	20223158	4	0	somatic_tumour	5004	3404.8	X:16818387 2L:20223158	3117:1052_1053_1054_2103_2104_2288_2564_3117	0.24	0	-	-	ATCCCAACTTCCGTCAAAGCAAAGAAGATTTCTTCTTAGTGTCAATCTAATGACAGGGTTTTCCCGCCCATTATCTTTATTGTGGCCACTGGGCCCAGAAG	-	-	CG4829, intron	intergenic	CG4829	NA	-	0
A373R1	1061	novobreak	BND	2R	13204947	2R	21389437	3	0	somatic_tumour	1469	8184.5	2R:13204947-21389437	3to3	0.08	0.01	-	-	GTGCACTTTGCCCCCCCAAAAGCTTTTCATTCTCGCCGATCCATCCACTTTCGCTCAGTAGTCGCGTGGAGCTCACAGTTGTTGATTGGCTGCAGCACCGCAGCTATGCCCGCACTCTGGAGCAACTGGTGGACTTTGTGGTGGGGCAGGCAGAGCGCGACACCCC	-	-	CG34315, exon_7	Acox57D-d, 5UTR	Orc3, CG34315, Acox57D-d	NA	-	0
A373R1	1079	novobreak	TRA	2R	13835045	3R	11416583	4	0	somatic_tumour	1496	2418.5	2R:13835045 3R:11416583	5to3	0.15	0	-	-	ATCCCATCCAGACTTTGTTCGGTTGATGACTCACATACCTCGTAAGTTTGAAAGTCCACTAGATCCTGGCCATGATTAAAGGCCCATCCACTGTCGATGGTTAGTAGAAGGCAGCAATGCCACGAAAATCGTAATGGAGGCACCGAACGTGGTGTACCAC	-	-	CG6337, exon_1	CG6723, exon_7	CG6337, CG6723	NA	-	0
A373R1	1080	novobreak	BND	2R	13875021	2R	22287377	3	0	somatic_tumour	1497	8412.4	2R:13875021-22287377	5to5	0.08	0.01	-	-	GAGATATGCCATAAATTCGAACCGCTTCACTCCTTCCCACAATTTTAATTTAAAAGGTCTCGTGGAACTCCATGGCCTTCTCCATGGCATCGATGAGGTTCTCCTCGCGCTTGGCATACAGCGCCGTGATGT	-	-	shot, exon_17	intergenic	shot	NA	-	0
A373R1	1094	novobreak	TRA	2R	14601180	X	1991599	3	0	somatic_tumour	1522	12609.6	2R:14601180 X:1991599	1096:1094_1095_1096	0.12	0	-	-	GGTCCGTGAACACGGCGAATTCCAGGTCCGAAGGGAACATGTGCACGTCCATCGCGCGTTTAGACCCCATTTTGCCTTATTTAAGCCACGATTTCTATAAAAACTCGAGAAAAAGATGAGCGCAACAGCCGCACAAGTTGCATTCGCTGCAAGTGTGTGGGTGTACGTGGAGTTGGTGT	-	-	RpI1, 5UTR	Hr4, intron	RpI1, Hr4	NA	-	0
A373R1	1097	novobreak	TRA	2R	14618994	2L	13475800	4	0	somatic_tumour	1525	1143.2	2R:14618994 2L:13475800	5to3	0.2	0	-	-	GGCAATTTAGTGCGGCAACTAATTAAAACACATTTGCCAGCCCGCTCCAGCCAGTTCAACGTCCGTGGGCAGCGGAGGCGATGGCGGTGTCGCCATCGGCGGTGGCCGGCGTTAAAACGACAGTGACCTCGTTGGAGACAGCCACGCCCACGTCTCCGCCGCTGGCCAGCACATCCGCTGCCGCTGCAGCCGCAATGGCGGCCGAGGCGGAGGCAGAG	-	-	Sec61beta, exon_2	CG42784, exon_4	Sec61beta, CG42784	NA	-	0
A373R1	1098	novobreak	TRA	2R	3091235	3L	7252343	3	0	somatic_tumour	1071	4161.1	2R:3091235 3L:7252343	786:786_1098_1099_1684_1685_1686	0.1	0	-	-	ATCTCCTCCAGTGGTCATTTATGCAGACATTGAAGCTGTTCTTGAAAATTACAAAACGTGCTTGAATTCTTCTGCTACTTCGTCAACCACCCAAGTACAAAATCATCTGGCAAGTCGAGCTCATTGTGTGTTTGTTTTGCTTTACTTACCCATTGCAGGCACCT	-	-	dpr21, intron	CG14830, intron	dpr21, CR43470, CG14830	NA	bp1_roo_BEL=9	0
A373R1	1102	novobreak	TRA	2R	14716686	3L	21521629	3	0	somatic_tumour	1530	6804.9	2R:14716686 3L:21521629	3to3	0.11	0	-	-	CAACTACGTTTACCTCACAATGCATTCTGGGCCACCCACAATCATCAGACTTTTGACTCAATTCCTGCTTGGCATTCTGCAAAAATATAAAGTTATTTCCATGCTTGAGATGTACAC	-	-	intergenic	Cdk12, exon	Cdk12	NA	-	0
A373R1	1115	novobreak	TRA	X	4028619	3R	5477306	6	0	somatic_tumour	4695	1448.7	X:4028619 3R:5477306	2966:1115_1116_2966	0.24	0	-	-	CGCAACAAGGATAGCCTGCAGGACGCAAAACCATTGAATGTTTTGGTCTACTCAGACAGCGCCAGTGCGCGGGACATTGACCATTTGGATGTGGATATGAATGTGGATGTGAATGTGGATGTGAGTGTGATTGTGGA	-	-	intergenic	Hcs, exon_4	Hcs	NA	-	0
A373R1	1115	novobreak	TRA	X	4028631	3R	5477306	6	0	somatic_tumour	4696	1448.7	X:4028631 3R:5477306	2966:1115_1116_2966	0.24	0	-	-	CGCAACAAGGATAGCCTGCAGGACGCAAAACCATTGAATGTTTTGGTCTACTCAGACAGCGCCAGTGCGCGGGACATTGACCATTTGGATGTGGATATGAATGTG	-	-	intergenic	Hcs, exon_4	Hcs	NA	-	0
A373R1	1120	novobreak	TRA	2R	15495428	3R	31973366	10	0	somatic_tumour	1564	16477.9	2R:15495428 3R:31973366	3to5	0.28	0	-	-	GACACTCATTGACTTCGGCACCTGTTGTGTTTCCTCTGGGAACTTGCCCGATTTCGGATGCATCAAGATAGAAAAAATCCCAAATACTTGGGACACCCAATGGCAGAAATCCCAATTATTTAGCCAAACATGTGCTAGCTGTAGCAGTGTCGCATCTGTGTGGATTGACTCAAAATTACAAATTGG	-	-	CG12964, intron	heph, intron	CG12964, heph	NA	bp2_17.6_Gypsy-like=9	0
A373R1	1136	novobreak	TRA	2L	12614286	2R	6138632	3	0	somatic_tumour	630	6475.7	2L:12614286 2R:6138632	476:476_1136_3168	0.12	0	-	-	GTAGCAAAGAACTATTGCGATGGAAATTGAAGTTAAGAAGGTTTTCAAGAAATACAGCGAGTAGGGGGTAGGTAGTTAGGCAAATAAAACCGATTATCTGTGGTCCAAAGCACTGAGCTAAAATTGAATAAAAGTTCTTTGGGTGAAGCTGTTTTAA	-	-	Ref2, intron	EcR, intron	nub, Ref2, EcR	NA	bp1_copia_Copia=2; bp2_copia_Copia=2	0
A373R1	1150	novobreak	TRA	2R	16406408	X	8278871	3	0	somatic_tumour	1607	8127.5	2R:16406408 X:8278871	3to3	0.14	0	-	-	TTCCCATTCCAACAAAGCAAACAAAAAATGTGGACAAACTTTGTCGTCCCGCAAAACGAGGGAAAAGCCGAGGAAAATGGGTAAACCAGAAAAAATAAAAGCTTCTTCTATAAAACTCGTGTAGCACTAAAAAATCGTATAAAGGCAACTCCGAGG	-	-	Sema-2b, intron	nAChRalpha3, 3UTR	Sema-2b, nAChRalpha3	NA	-	0
A373R1	1172	novobreak	TRA	2R	16895804	3L	5409780	5	0	somatic_tumour	1635	11486	2R:16895804 3L:5409780	1172:1172_1611_1613	0.13	0	-	-	GGACAGTAAGGAAATAAAATAGACAGAGTGGCGGGCTAAACACAAAATGTTTCCCTTGCATCGTAGATTTCAAAGTAGCTTGTGGCTTTAGTTAGTTTTGC	-	-	intergenic	intergenic	-	NA	-	0
A373R1	1173	novobreak	BND	2R	16910917	2R	17596715	2	1	somatic_tumour	1636	685.8	2R:16910917-17596715	5to5	0.08	0	-	-	GTCAAAAACGTTGCATTTTCATTTTAGCTCCGCTTATCAGCAACATGAAAGCAGTTTCGGTTAATCCATTGTGCCGGCGTGGTGGCAATTGGTTTGCCAGCTTTGGACGTACCCGAAACTCTGGCACCAAGCTGTTTAATATCTCTGGTCATGTTTGCAACCCTTGTAC	-	-	intergenic	ND-51L1, exon	Smurf, ND-51L1	NA	-	0
A373R1	1174	novobreak	TRA	2R	16915185	2L	2497249	3	0	somatic_tumour	1637	14417.9	2R:16915185 2L:2497249	3to3	0.1	0	-	-	CATCATCATCGTCGTCGTCGTCGTCCGCAATGGCCGCCATCGTTGCGTGATAATGAACGCTTGAAAAACCCAACTTACACAATCCACTACACTACACATCCAGGAAAAAAACGAATGCTGACACTTTTTCCGCTCACTCCGCTAATTCGATGGATTGCCCTGCAGTATTA	-	-	intergenic	oaf, 3UTR	oaf	NA	-	0
A373R1	1184	novobreak	TRA	2R	17198000	2L	5449461	9	0	somatic_tumour	1651	11748.5	2R:17198000 2L:5449461	5to3	0.22	0	-	-	CTGATGGTGATGTTGATGTAAATGTTGTCTCCTGGCCGAAATGGTAGTGAAAGTGTTTGGGGCATTTTCGCTTTCCCTCGTCGCGTGGTGCGTTCATAAATATTCCGTTTTTGCTTTGCTGTTGAACGTTCTGCAATGTGTGTGTGTGTGTGTGTGTG	-	-	intergenic	intergenic	-	NA	bp1_Ivk_Jockey=8	0
A373R1	1190	novobreak	TRA	2R	17341008	X	315197	3	0	somatic_tumour	1656	17025.8	2R:17341008 X:315197	5to3	0.16	0	-	-	AGCTTAAATTTATTTGACACATGAAAGAAATATAAAAAATTTTGCAGCCCGATAAAAAGGGCAATGTTTTGCGATCTCCGCTTCTTTATTGTATTATGTGTCTGACAACAAGCTTTGAGCTCTGCAC	-	-	mbl, intron	Or1a, exon_1	mbl, CG3777, Or1a	NA	-	0
A373R1	1191	novobreak	COMPLEX_TRA	2R	17401491	X	12909442	3	0	somatic_tumour	1657	4492	2R:17401491 X:12909442	1191:1191_3065	0.33	0	-	-	GAATAGAGCCAGAGAAACTGGAGTGTTGTTGGCCGGGGGAGTTGGCCATTGGTTGAGTGGATTTTGCGGTTCTCCTTGTTCTCGGCGTATTCCGATTCGGC	-	-	CG10939, intron	Brms1, 5UTR	CG10939, Brms1	NA	-	0
A373R1	1200	novobreak	BND	2R	17661491	2R	25068965	5	0	somatic_tumour	1672	7407.5	2R:17661491-25068965	5to5	0.15	-0.02	-	-	CGCCGAATGCAAACATCCACCGAGCATTTCGAAATATGCATAACTTTTTAGAATTCCATAAGCTGGAAGGGCAAAAAGTCGGTTGGTGAGCCATTTTAAATGCAACCTTTGTGCAATGC	-	-	CCHa1-R, intron	intergenic	CCHa1-R	NA	bp1_HMS-Beagle_Gypsy=4	0
A373R1	1217	novobreak	TRA	2R	18312878	3R	25759290	4	0	somatic_tumour	1703	7446.4	2R:18312878 3R:25759290	1219:1217_1218_1219_1711	0.11	0	-	-	CTATTCAACCAGGGTCACCAGAAATCACCCCACTTAATTTTCCCCTATCGAATGTGCAGACTGCGCTGAATTCGAGACCTGCGATTCCAATAAAAGTCAGCAGGCAGGCAC	-	-	sbb, intron	LpR1, intron	sbb, LpR1	NA	bp2_baggins_LOA=4	0
A373R1	1221	novobreak	TRA	2R	18338896	3L	20760798	3	0	somatic_tumour	1705	2421.9	2R:18338896 3L:20760798	1221:1221_2050	0.13	0	-	-	CTGTTAATCGTTATTTTGGCACTTTTCCGTCGCTTCTGCTGCGCTGCTGCGGAATTGGTTTTTAAGGCTTAAGTTCTTAAGTCCTCAAAATCACATTTAAGCCTTGATTTATGAG	-	-	sbb, intron	intergenic	sbb	NA	-	0
A373R1	1240	Control-Freec	DEL	2R	18795550	2R	18811470	-	-	somatic_tumour	-	15.9	2R:18795550-18811470	Heterozygous deletion	0.29	-0.49	-	-	-	-	-	MFS15, exon_3	CG15096, intron	MFS15, MFS14, CR44468, CG15096	NA	snp_su:36; snp_op:14; snp_ratio:2.57	13.51
A373R1	1245	novobreak	BND	2R	18978791	2R	24902529	3	0	somatic_tumour	1739	5923.7	2R:18978791-24902529	3to3	0.07	-0.01	-	-	TCAGGTCCAGGCACAGCCACAGGCTCAGGTCCAGCAGGCAGCAGCTCAGCCTGCCCAGCTGCTCCTCCCTCAGCTAACGCAGGCGGGCGTTGTTTGCCAGCAGATGGCCTTTAAAATGCAATGCAATGC	-	-	CG18605, exon	NaCP60E, intron	CG18605, NaCP60E	NA	-	0
A373R1	1248	novobreak	TRA	2R	19027450	3L	20547762	2	1	somatic_tumour	1743	1520.3	2R:19027450 3L:20547762	1249:1248_1249_2046_2047	0.11	0	-	-	CCGTTAAATGCCGCACTAAGTTTTCCGTTTGAGTGCCAATGAATGGGTAAGCAAATTTGAATGCAGTTCACAGTCTGGGATCGATAACCATTTCGGCTTATGACAC	-	-	5-HT1B, intron	intergenic	5-HT1B	NA	-	0
A373R1	1251	novobreak	TRA	2R	19101533	2L	1111688	3	0	somatic_tumour	1745	17989.8	2R:19101533 2L:1111688	3to3	0.1	0	-	-	GGTAATAGTTACAACGACATTCGCAATGAGGTGTTTGTGACATTTAAAGCTTTTGGGAGCTGAGCCGGCAGTGCCCATGCTGATCCCCGAATCTCCAGAGCG	-	-	5-HT1A, intron	CG14339, exon_5	5-HT1A, CG14339	NA	bp1_Dmel\X-element_LINE-like=8; bp2_Dmel\R1A1-element_LINE-like=3	0
A373R1	1256	novobreak	COMPLEX_TRA	2R	19343637	3L	4112584	3	0	somatic_tumour	1756	15231	2R:19343637 3L:4112584	1257:1255_1256_1257_1574	0.11	0	-	-	TCCAGAGACTGGTTGAAATTCGAGTAGAGTGCCACAGCTGGCACTCGCACCACCACCGATACCTTCACCGACCTGACCAAGGACTACACCTTGGCGGTGTTCTATGAGTG	-	-	fest, exon_5	Ack, exon	Rgk1, fest, Ack	NA	-	0
A373R1	1256	novobreak	COMPLEX_BND	3L	4112530	3L	11486067	10	3	somatic_tumour	2248	7373.5	3L:4112530-11486067	1574:1255_1256_1257_1574	0.4	0	-	-	CCCACGTACTACAATGAGCAGCCCCAGTTCGACTTTGATCCGGCCAAGATGACAGCTTCACCAGGGCGCCTGCAACCGCCGCCGTACCAGATGCCACCCACTTACTCGAATACAATGGAGTTTGTCCAAAAACGAGACCTTCACCAATTTTTAGTAATCTTCGCTCGCATTTTTTTTTC	-	-	Ack, exon	intergenic	Ack	NA	-	0
A373R1	1261	novobreak	TRA	2R	19448114	3R	22435077	3	0	somatic_tumour	1760	2987	2R:19448114 3R:22435077	1261:1261_1262	0.1	0	-	-	GCACCATGTTGACGGCCAGCTTGCGGAGATCAGCGTTCAGTTGGCCGGGGAATCGGAGGCAGGTGGTTACGCCGGACATGGTCAGGTGGCAGCAGCCTTCGACTGGACCCGAGCAACCGGATCGACTCCCATTCCCAGACCCGAAAAGCATAAAAAACCAATCCC	-	-	betaTub56D, exon	CG13847, intron	betaTub56D, CG13847	NA	-	0
A373R1	1266	novobreak	TRA	2R	19602576	3R	30433815	3	0	somatic_tumour	1767	10831.2	2R:19602576 3R:30433815	5to5	0.12	0	-	-	CCAATTACTTGAAACTTGAGTGGATTATTTTTCTCAACGTCCTTGCCTCGGGTAAGGGTTAATTCAAATTTCAACAACTTTGACGCATACAAAGCGATTTGTGAGAAAATCCGAGGAAAAGTAAAGAAAACAAAGAGCTGAGCAGCATGCC	-	-	sm, intron	CG15534, intron	sm, CG15534	NA	-	0
A373R1	1268	novobreak	TANDUP	2R	19682809	2R	22956430	6	0	somatic_tumour	1770	3273.6	2R:19682809-22956430	3to5	0.12	0	-	-	GGGTAAGGGGGCGTGGCACGAGGTGGTGCTGCACTGTCAAATGGCATGGTCAAGTAGTTTGGCTAAAAACTGCAAACTGGCGGCGGTCACGAGGCGGCGGCGGAGGAGGTTGTACGATCACCGTGGTCGAGGGTTGGGGTGGCACTTGCACCACCTCCACAACGC	-	-	CG34198, exon	intergenic	CG34198	NA	bp2_Idefix_Gypsy=4	0
A373R1	1277	novobreak	TRA	2R	19933462	3R	12788104	3	0	somatic_tumour	1782	7145.4	2R:19933462 3R:12788104	1277:1277_1278	0.12	0	-	-	CCTTTTTTGGAGCGGGAAGCACTAGAAAAAAAAACTCTAACCGCTGACCACGCAAAAGCTGCTGCTCGCATTTTGTGCACAAATTGTTTCAAGGCCTTGGCTCCAATTCAATTGCTTAGTGCAATAC	-	-	intergenic	intergenic	-	NA	-	0
A373R1	1284	novobreak	TRA	X	14405716	3R	7862756	7	0	somatic_tumour	4939	6543	X:14405716 3R:7862756	3086:1284_1285_1409_2276_3086	0.22	0	-	-	CGTACAAACTGGAGGTGTGATAAGATAATCTAAACTAAACTAAACTAGGAACCAATCTGGCAAAAGAAACAAAATTAAGGCAATTGGCGTTAACTTTACCGCTTTGACAGGCGAATATAAGTCGTGAAG	-	-	dpr8, intron	CG17816, intron	dpr8, CG17816	NA	-	0
A373R1	1305	Control-Freec	DUP	2R	20815400	2R	20849230	-	-	somatic_tumour	-	33.8	2R:20815400-20849230	Heterozygous duplication	0.37	0.62	-	-	-	-	-	intergenic	CG17999, exon_3	insc, sktl, CR44667, CG17999	NA	snp_su:120; snp_op:52; snp_ratio:2.31	16.13
A373R1	1312	lumpy	BND	2R	20958142	2R	22909850	3	0	somatic_tumour	5322_1	1951.7	2R:20958142-22909850	5to5	0.09	-0.01	-	-	-	-	-	hbn, intron	nahoda, intron	hbn, nahoda	NA	-	0
A373R1	1317	delly	TRA	2R	21310963	2L	14833497	3	0	somatic_tumour	BND00000533	6477.5	2R:21310963 2L:14833497	5to5	0.11	0	-	-	CTGTTAATGAGTCCTTTAGGAACCAGGATTGCTTTGAGAATTATTCACGCAATGCACGCGGGTCCTCCGCCTCGTAAATTTTTTAGGCA	-	-	Panx, exon	intergenic	Panx	NA	-	0
A373R1	1325	novobreak	TRA	2R	21480889	3L	5922584	3	0	somatic_tumour	1853	15558.3	2R:21480889 3L:5922584	3to3	0.09	0	-	-	CTCCCAGATAAAGAAAACTACCCCCCCGAGCTCGTCCACGAAAATTGTTTTCAAATAGATAAGAAATCGGCGTTAGTGGGAAAGAGAGGGCGCGAGAGGAGACGGAGAGCGAATACGAATGCGTATGGTGTAG	-	-	Sdc, intron	CG32407, 5UTR	Sdc, CG32407	NA	bp2_Dmel\R1A1-element_LINE-like=5	0
A373R1	1326	novobreak	TRA	2R	21551183	3L	3575318	3	0	somatic_tumour	1855	17975.9	2R:21551183 3L:3575318	1327:1326_1327	0.09	0	-	-	GAGCTGATGTGACACTTCAAATGCTGACAAAATACATCGCATTAACGAAGCTTCCTTCGCAGAATCGGTATTCCTGTGAATACTCACGACCTGCGCACAATTGTTGTTCGAAACAAAATGAACGCGCTTCGAACACGAAAACCCGAAAGCAGAAGATGCTGATC	-	-	Egfr, intron	Eip63E, intron	Egfr, Eip63E	NA	bp2_Bari1_Mariner/Tc1=3	0
A373R1	1329	novobreak	TRA	3L	15071695	2R	18353788	3	0	somatic_tumour	2794	3282.1	3L:15071695 2R:18353788	1919:1329_1592_1919_2354	0.11	0	-	-	ATTTATGGCAGAATTTTTTTTTTTTGAGGCATTTGGCACACGCTGTCACCAAATATCAACTGTATCTGACGGTTTGTTGCCAACTTATACCGGCGCACAGT	-	-	Plp, intron	sbb, intron	Plp, sbb	NA	-	0
A373R1	1331	novobreak	TRA	2R	21737255	3R	21535033	3	0	somatic_tumour	1863	202.2	2R:21737255 3R:21535033	5to5	0.15	0	-	-	CGACTGCGAGGCTGGGATTCTGTGGCCTCTGCGTTGTCGAACCTTTTTGTGCCGAGTGGCAGGCACTTTCGCTGATTGCTGCTCCCGAGATCCATTCAACCCCCAATCCAATCGTTTCGCGCCCCCCTCATT	-	-	intergenic	CR44033, ncRNA	CR44033	NA	bp1_HMS-Beagle_Gypsy=2	0
A373R1	1335	novobreak	TRA	2R	21825423	3R	5772570	3	0	somatic_tumour	1871	16052.9	2R:21825423 3R:5772570	3to3	0.12	0	-	-	AGAAAATATAAATATTTCTCATTCTCATTTGTTTACGTCAAGCAATCCCAAATATTTCAATTACCTCTAAAGAACGTAATTTGGGCTGCGCCAGTGAGTTTGAAGTGCAGGTTATCAAGGAGCTGGTGGCCCAGCAACGTTTGCTTCTGTGTTCCGGACAAAAGTGTAACGAATAC	-	-	CG13492, exon_4	CG2082, intron	CG13492, CG2082	NA	-	0
A373R1	1348	novobreak	TRA	2R	22279289	3L	2031385	3	0	somatic_tumour	1892	20247.9	2R:22279289 3L:2031385	3to5	0.09	0	-	-	CACCGGAGGACAGGTAACAGCTGGATGTGCCAGCGAATAACCACACACTAAACGCAACTGCCACCCAAGCGCCACACAAGCCCACACACACACACACACACACAC	-	-	dve, intron	intergenic	dve	NA	bp1_GATE_BEL=4	0
A373R1	1350	novobreak	TRA	2R	22356658	X	9763388	3	0	somatic_tumour	1894	12593.3	2R:22356658 X:9763388	1350:1350_3034	0.1	0	-	-	AAAGGTTAAACAAACTTGGTCTCATGTTGCAGCAACACTTTTCCAACCTGCCGCCTGCAGAGCTGCGGAAAATCAACTACGACGACCTCAACCTTAAGAATTGAGCCAGATGCAGTGAGAGAAGAATCTAAGATTGCATTAGGAGCAACTAAATTTCTACTGGCGGGAATG	-	-	Liprin-gamma, intron	intergenic	Liprin-gamma	NA	-	0
A373R1	1353	novobreak	TRA	2R	22531231	3L	3143309	3	0	somatic_tumour	1899	19387.9	2R:22531231 3L:3143309	5to3	0.1	0	-	-	CTTTAAAACTAACCGCTTACAAAGCCAATTAAAATGGTTTCAGTTATTGTGGCTGGAGCTGGATCACCGGGATCTCTGGGCGGTTTCTGGCAGGGATTTGACTCAGCGGAGCTATTTTCACGAAAATTTAATGCGTTCGTTGCAAACACGGGCCGAGAAC	-	-	px, intron	CG11537, 5UTR	px, CG11537	NA	bp1_Dmel\F-element_LINE-like=6	0
A373R1	1361	novobreak	COMPLEX_BND	2R	22870861	2R	24111678	11	0	somatic_tumour	1913	1240.8	2R:22870861-24111678	1361:1361_1399_2567	0.42	-0.06	-	-	CTGCTGGCTCTCAAGCTGGTGAAGACGCGCTAGGATGTGTTGATGTAAATGTGCCCACTCTTTTCCTTGTAATAATATCCTTAAGGGATCACTCTTTTCGACGTTTTGTTACCTTTTGTTTGCAATAAA	-	-	intergenic	CG4049, exon_2	CG4049	NA	-	0
A373R1	1363	novobreak	TRA	X	17639989	3R	21797560	4	0	somatic_tumour	5018	4157.6	X:17639989 3R:21797560	3126:1363_3126	0.16	0	-	-	GTCTACAATTGTTTACGATTTGCATTTTGCATTTTTCCCTGCTGTCACAGTGAATTTCGAAAATAAAGCTATCCAATCAGCAAGATAATTGCTCTTTGCTAATAAATACAAAAAAAAAAAATCACCCAACTA	-	-	RhoGAPp190, 3UTR	CASK, intron	RhoGAPp190, CASK	NA	-	0
A373R1	1398	novobreak	TRA	2R	24085160	3R	9059241	3	0	somatic_tumour	1966	15025.9	2R:24085160 3R:9059241	3to3	0.11	0	-	-	GTTACGACCTTGAAGCCCATCTATCTGGGCGAGGAGACCGAGACCCCCAGCCTGGAGACCATAACGGTAAGATGGGTATGCGGACGGGCAGCCATTTCATCCT	-	-	CG16786, exon	Kdm2, exon_4	CG16786, Kdm2	NA	-	0
A373R1	1412	novobreak	TRA	2R	24538219	X	15108997	4	0	somatic_tumour	1991	9429.2	2R:24538219 X:15108997	3to5	0.12	0	-	-	TTTAGATAGACGCGCCGCAACATAAATAGCAATTCCAAACAATTTTCAATTGCCAAACGCCCGAGTCGCGGAGCATCTTGGGGCAAGTCCGAGATCTGAGATCCAAGATCCGAATCTCGATCCCAGCTTGTGCCTGGCATTTCCTTACAATGTGTGCCCAACTGCCGACCCGTGTTTCCATTTCTATCATTTGCGTGTGCGCCGCTCATTTAGATCTGAAAGCGGCAATTAGCCCGCTCGACTGCTAAGCTGCAGTTAAATTGACCGACCGGTCAACGGAGGGACTCAGACCGATTGTTAGTTAGAGTCAGAAAGAGAATGC	-	-	ITP, intron	Rab3-GEF, intron	CG4622, ITP, Rab3-GEF	NA	-	0
A373R1	1441	novobreak	TRA	3L	310817	X	8322823	3	0	somatic_tumour	2035	8012	3L:310817 X:8322823	3to5	0.09	0	-	-	ACACACACACATACTGGTGTGGATGGCAGATGGGTGAATGGGGTTTATGGGTAGCCTTTGTCGGAGAACATTGAAACCCTGCCTTTGTCATAGTTTAAATCGGCATGCTGTTATTGACTGGATTCGATAACTTGAAACACTCACAAATATTTAGCACTAGTGTATGTA	-	-	fwd, intron	nAChRalpha3, intron	fwd, nAChRalpha3	NA	-	0
A373R1	1448	novobreak	BND	3L	490197	3L	13551469	3	0	somatic_tumour	2048	13061.3	3L:490197-13551469	3to3	0.07	-0.01	-	-	GTAGTTGGCTTTGTCGTCTGTGTTTATGCAAAAAATTTGTCTACAGTCTACAGCCGTCGAGCCATTCCCCAGCTAAACTTCGCCGAACTCAAAAGTGTACGAAAAACATAGCGAAAAGAGGAAAGGAAAGAGGATTCGCCGACATATGGACGATAATAATAT	-	-	klar, exon_1	CR45825, ncRNA	klar, bru3, CR45825	NA	-	0
A373R1	1450	novobreak	TRA	3L	505947	3R	11847116	3	0	somatic_tumour	2051	11341.2	3L:505947 3R:11847116	3to5	0.09	0	-	-	TGAGAAATGCATGTCAGACTCACACAAAGTCTCCATGGAGCGCGGGCGGTACAAGTGGGTGTTGGGGATGTTGAGGATGTCGGCGAACTCTCCAATTTATTCTCCATTTCGCGCAGCCAACGCCGCAACTCCTTGGGAT	-	-	klar, exon_5	CG6959, intron	klar, CG6959	NA	-	0
A373R1	1460	novobreak	BND	3L	915334	3L	9505222	2	1	somatic_tumour	2075	8589.9	3L:915334-9505222	3to3	0.12	-0.02	-	-	GCACTCTCCGTGCATTTTCCATTTAATTTATTTTTTATTGCTCCGGCCCGCCTTTGTTCTTCGCCTAAAAGGCGATTGACCGGGAGGAGTGTTTGATTTGCGCGGCAT	-	-	Glut1, intron	path, exon_1	Glut1, path	NA	bp1_invader2_Gypsy/INVADER=2	0
A373R1	1462	novobreak	TRA	3L	984766	3R	9243881	3	0	somatic_tumour	2078	8259.1	3L:984766 3R:9243881	3to5	0.12	0	-	-	GCCTCGTAACGTGGAGTGGGCATATCGTTAGGAGCATTTCGTTGCGTTTCGCTCTCCAAAGTTCCACCTTAAATTTGTAGCTCGTATTGCTGTACTTTATTTAGCCAC	-	-	Glut1, intron	Vps15, exon_4	Glut1, Vps15	NA	bp1_copia_Copia=7	0
A373R1	1464	novobreak	TRA	2R	18535166	3R	11836872	3	0	somatic_tumour	1715	6698.3	2R:18535166 3R:11836872	1225:1225_1464	0.11	0	-	-	GATCTATATTTAGACGAACTCAGAGGCTCGTCCACTGATAACCCGCCCGGCTCCCTCCTCCCCATTGCCACGGGGCGAAACTGAATCGCGAGGAGTATTTAAAGCTGGGGCAAATG	-	-	CG10924, 3UTR	CG6959, intron	CG10924, CG6959	NA	-	0
A373R1	1474	novobreak	TRA	3R	5735366	3L	1274081	3	0	somatic_tumour	3322	4461.3	3R:5735366 3L:1274081	2207:379_380_1474_1952_2182_2207	0.12	0	-	-	GATGTGGCTTTTCAAATTGATCTAGCGCTTTGCAAAGCCGGTCGAACTCATCCAGATATGGCTCTTTAGGCAGCCCAATGTACGAGAACGGCGAGGAGGAGAACTGCCTAGAGCTGTGGAACCGCGATGGCAAGGGCCTCAAGTGGAACGACTCGCCGTGCAGCTTCGAGA	-	-	CG2100, exon_1	tfc, exon	CG2100, tfc	NA	bp1_gypsy12_Gypsy=2	0
A373R1	1477	novobreak	TRA	3L	1315347	3R	9093169	3	0	somatic_tumour	2100	7777.8	3L:1315347 3R:9093169	3to5	0.08	0	-	-	GACAGTATCAGCATATGCACAAAGAGATATGGCGTTGAGTGCTGCAACATTTCCACAAATTGTTGCTGGCGCTTGTTCCATCGCGCGGCAGGGTTTATGCCTTCGG	-	-	Sherpa, exon_5	pum, intron	Sherpa, pum	NA	-	0
A373R1	1480	novobreak	TRA	3L	1338603	2R	13081057	8	0	somatic_tumour	2105	11742.5	3L:1338603 2R:13081057	3to3	0.25	0	-	-	GGGACAGGTCCTGTCCAACTGACAGATGGCCTGGCCGGACCGAAACTTCTAGCTGAGATGGGCGATTCCCCGCCACTTCCACTCTTGGCGCTGAAGGAATC	-	-	l(3)02640, exon	intergenic	l(3)02640	NA	-	0
A373R1	1486	novobreak	BND	3L	1502986	3L	19842591	3	0	somatic_tumour	2112	18339.6	3L:1502986-19842591	3to3	0.09	0.01	-	-	ACCGCAACCTGAAGTATCACACGCACAGTCTGGTCAAGCCCAGTAGTTATTACTATGAACCGTTGCCACTGCCACCTGAAGACATTGAGCCTGTTCCCTTACGTGCAGTTTGACATTAGTCACTCGAGAACGTAATCTTTCCAAAATGTATGTTAAGA	-	-	Psa, intron	kto, exon_5	Psa, kto	NA	-	0
A373R1	1487	novobreak	TRA	2R	23489427	3R	15640672	3	0	somatic_tumour	1934	7848.8	2R:23489427 3R:15640672	1373:1373_1487	0.11	0	-	-	TTCGCACTCCCCAAACCCCCGAAAAGCGACCCCACATTCGACTTTTATGGGCAGTTTTCTTTTGAAAAGAAATTAAAATTATATAACCGCATATACCAAATATATAAATATACATTAT	-	-	CG43795, intron	intergenic	CG43795	NA	-	0
A373R1	1492	novobreak	TRA	3L	1725880	3R	21175577	4	0	somatic_tumour	2124	19449.7	3L:1725880 3R:21175577	5to5	0.12	0	-	-	GGTTCTGCCCCATGAGCGGCGGAAATGTTTTCGTTTTGATTTGTTCGCATTCATATTTATCGAGCAGAATAAATGGCAAAAATAATACAGTCCATCCCGCCAGCTCACCAACTCGGGATCCGTCTCCGTTTCCGTGTCCGATGATGTAAGTGAAGGGTTCAAAAACAAAGTCTATATGGG	-	-	drpr, intron	SNF4Agamma, exon_3	drpr, SNF4Agamma	NA	-	0
A373R1	1505	novobreak	BND	3L	2129933	3L	7111671	3	0	somatic_tumour	2141	4981.7	3L:2129933-7111671	3to3	0.07	-0.01	-	-	AGCCTTTGTGTGTCATTGCAACAGATTTGTAGCTGAATAATTTACTCGAACAGCCGTCCAATAATCGGCCATAATGAATAATTCGTTGATGACAATCTTGAAGCGGTATCGCTGCTTCTTGAGATTCTGCAAGGATATTAT	-	-	zormin, intron	form3, exon_3	zormin, form3	NA	bp2_roo_BEL=3	0
A373R1	1506	novobreak	TRA	3L	2151314	3R	30102468	3	0	somatic_tumour	2142	27951.2	3L:2151314 3R:30102468	5to5	0.11	0	-	-	CAAACAAAATGTTTACCAAATAGAAAACGACACAGAATGCACAATATACAATCTCCCATATCTATAGGTTGTGACTGTTATTGTCCACTCAATGCCTTCCGGCATAATATTGGTTGGGTGGGTGTGTTCTCTGGGCGTATGTCACCC	-	-	zormin, intron	sima, intron	zormin, sima	NA	bp2_Dmel\Doc4-element_LINE-like=2	0
A373R1	1508	novobreak	BND	3L	2233996	3L	12006234	2	1	somatic_tumour	2144	9772.2	3L:2233996-12006234	3to3	0.07	0	-	-	CCACCATACTGGACAGGAATGGCACTGAGATCAGACAGAACTTTGAACAGATGGTATGTGGGCACAAGTAGACTAATTAGCTTTTTTTTGTCACCCTCCAAAAACTGATTGCAAATCTCAGCGGCTCGTAGCAGAGCTCTTTCCAAC	-	-	Oseg2, exon	CG6928, intron	Oseg2, CG6928	NA	bp1_hobo_hAT=3	0
A373R1	1513	novobreak	TRA	3L	2342967	X	13887823	3	0	somatic_tumour	2152	11544.9	3L:2342967 X:13887823	3to3	0.13	0	-	-	ATACCATACACGACTACATCCTGACGGACAGTTTGCCGCGGGAGGAGAAGCTCAGCTACAGCTGGGCCTGCTTCATCAAGTTCCATTCGATTTTCGCCCAGGTTCTGCACACCATTTCCATTTGGCTGACGGTGACGCTGGCTGTTTGGCAACTAGCGAAGAGCCAACGCAGCGCAAAAAG	-	-	MsR1, exon_4	mamo, intron	MsR1, mamo	NA	-	0
A373R1	1522	novobreak	TRA	3L	12723299	3R	4776362	4	0	somatic_tumour	2689	7946.9	3L:12723299 3R:4776362	1856:1522_1856	0.11	0	-	-	CAAGAGCGAAATTACCAAGCACTATTCCAAGCCCAATGTGGTTGCCATAAAGGCCATAAAGCCAATGGCTCAAGTTCCGGTTATTTATGCTGGCCAATATGTCACTCCAAATCCTCTTTGACCG	-	-	intergenic	atms, exon_2	atms	NA	-	0
A373R1	1527	novobreak	TRA	2R	16055147	2L	3126157	3	0	somatic_tumour	1590	12929	2R:16055147 2L:3126157	1138:1138_1527	0.07	0	-	-	GTATGTGTCCATAATGCTCAACGCTCACTGCTCCTCAGCTTGCGCAATGCCCCCCAGTCGGCCACCACAACGCCGCATGGAATGAGGATGATGGGACAGGC	-	-	CG8405, intron	toc, exon_2	CG8405, toc	NA	-	0
A373R1	1527	novobreak	TRA	3L	2837594	2R	16051228	3	0	somatic_tumour	2173	13213.6	3L:2837594 2R:16051228	1527:1138_1527	0.15	0	-	-	TGCAAAACTTTTGAATGAAAAAATATCCAATTGCATCGTACCGAGCGAATCCTTTTCTGTGCAATTGAAAATAATAAAAATAAAAAGGGGCACACACGAAA	-	-	Tet, intron	CG8405, intron	Tet, CG8405	NA	-	0
A373R1	1532	novobreak	TRA	3L	3024502	3R	12038287	2	1	somatic_tumour	2181	9013.8	3L:3024502 3R:12038287	3to3	0.1	0	-	-	CCCCCAACTACCCCTTCGCGTAAGTACCAAAAGAGCTCTACAAGGTAGCAGCCACAAGAAACTTCGTTAAGCTCCTCTGCCGGCAAACACGAAAACACTCGCCACTCCAAAACAAATTGAGATAGCTCTCAGCCAG	-	-	aly, 3UTR	intergenic	aly	NA	-	0
A373R1	1548	novobreak	BND	3L	3566902	3L	12369895	2	1	somatic_tumour	2209	8803	3L:3566902-12369895	5to5	0.1	0.01	-	-	CTTTGAGCTCAAACGAAGCAGCAGCCAACTCCATTAGCGGCATGGGGCCCGTTAGCTAGCATTTCGCGGTAATTCGCCATATACCTACCTCAATTTGCAGGATTGCCAGGTGCGCCGCGTACTGATGATGTAGGGC	-	-	Eip63E, intron	Ncc69, intron	Eip63E, Ncc69	NA	bp2_opus_Gypsy=8	0
A373R1	1567	novobreak	COMPLEX_TRA	3L	4001017	3R	9722179	3	0	somatic_tumour	2239	5721.2	3L:4001017 3R:9722179	1567:1567_2204_2225_2337_2600	0.09	0	-	-	GTCTAACTGTGTGCTCAGTGCACTGCGAGAAATAATGGGACATCTTCGCGTCTCAGCAGCCGACACTGCTGCCAGTCGTCCTCCTTGCCCTCTTCCTTGGATGTGGAGGCTGTGTTAGAT	-	-	intergenic	hyd, exon_7	hyd	NA	-	0
A373R1	1567	delly	COMPLEX_DEL	3R	5628549	3R	6360142	7	0	somatic_tumour	DEL00001011	731.6	3R:5628549-6360142	2204:1567_2204_2225_2337_2600	0.2	-0.04	-	-	GAGATCTTGAAACGGCGGGAACGCTGTTACTAACCCTATGACTTGGAGTATTATCGCTGATTTTAGTAAAAGTTTCATTTAGTTCATAAACTGCTTTATTT	-	-	CG31551, exon	Pak, 3UTR	CG31551, Pak	NA	-	0
A373R1	1567	novobreak	COMPLEX_DEL	3R	5628549	3R	6360142	7	0	somatic_tumour	3317	731.6	3R:5628549-6360142	2204:1567_2204_2225_2337_2600	0.2	-0.04	-	-	GAGCAAAAACAGCGCGAGATCTTGAAACGGCGGGAACGCTGTTACTAACCCTATGACTTGGAGTATTATCGCTGATTTTAGTAAAAGTTTCATTTAGTTCATAAACTGCTTTATTT	-	-	CG31551, exon	Pak, 3UTR	CG31551, Pak	NA	-	0
A373R1	1567	novobreak	COMPLEX_TRA	3R	9717018	2L	4966755	5	0	somatic_tumour	3522	4750.3	3R:9717018 2L:4966755	2337:1567_2204_2225_2337_2600	0.17	0	-	-	ATGGAACACGGCTCTGTGCTGCCGGAACTGCGAGAGTTTACTGGACGCTCCGTTTTGTAGGTCTTGAGGCACATCAGGGACTCCGAATCGAACAATTTGGCGGTGGTGTCCTTGGAGGCGGTCACAAACAT	-	-	hyd, exon_13	Trip1, exon	hyd, Trip1	NA	-	0
A373R1	1589	novobreak	TRA	3L	4501770	3R	30846576	5	0	somatic_tumour	2272	26344.8	3L:4501770 3R:30846576	5to5	0.17	0	-	-	ATATTTCATAAAAATAAATTTATAAAATAAATAAATAAATAAACATAGTTGGTTAAACATTAGAGTGGGTTTTGGGATAAATGGGGTTGAGATTAGGAGCCAGGTAGACAAACTACAAGATTAGGCTCCTGGCGAGAACGGCAGAGACTACGAGCTAAGGCATCGGCGTTAATACGTTAGATTTCGGGGATTTGAGCCTTCGCTGACAACTCACCCGCTTCTCTGGTAGTCCATTGTGGACCTGTC	-	-	NT1, 3UTR	intergenic	NT1	NA	-	0
A373R1	1608	novobreak	TRA	3L	5226964	2L	4992332	3	0	somatic_tumour	2306	234.6	3L:5226964 2L:4992332	5to3	0.08	0	-	-	GCACAAGGGCAAAGTAAACAAATGGTTTCCGCTTAATGTAAACAAATCGATGATGGCAAACAATTGATGGAAAAAATCCAGAAGACACCGCGATCATCTTTTTGCTCCACCTACTTACTAATCAAAAC	-	-	shep, intron	CG34126, 3UTR	shep, CG34126	NA	-	0
A373R1	1609	novobreak	BND	3L	5265242	3L	14994585	2	1	somatic_tumour	2307	9729.3	3L:5265242-14994585	3to3	0.08	0.01	-	-	GTCTAAGTGCTCTCTAAATATGCTGTAATGCTGCTTTAAATGCCTATTAAATGAGGAACTAAAATATTTTCCAGGGTGTTTTGTTGCAAGTCTTTGGAGCTAAACG	-	-	shep, intron	Zip71B, exon_2	shep, Zip71B	NA	-	0
A373R1	1619	novobreak	BND	3L	5652412	3L	22008889	3	0	somatic_tumour	2323	16356.5	3L:5652412-22008889	5to5	0.09	0.01	-	-	ACGCACACAATTTGCATGTCCAGGGGGGTTAACATGTGAGCGCAAGCATTGAAGTGGCACTGCCCCTTCCTGCCGCCCCCCACCGAGGTGTTGTTCTCCTCCTCACTCAGAATGAGAATCCTGTGAG	-	-	intergenic	intergenic	-	NA	bp2_roo_BEL=5	0
A373R1	1628	novobreak	TRA	3L	5919793	X	19548572	3	0	somatic_tumour	2337	13628.8	3L:5919793 X:19548572	3to3	0.11	0	-	-	ATACACATATGTATGTGTTTGAGCAACTAAGTGTTCTCTGTGGGCGAATATACGTGGGCAAGTACTTTTCCAAAGTCAAACACGCACACATTGATGGCTGCCTTTTTGCTGAATCCCACGAAGACGTTCCATCATGAGG	-	-	CG10483, exon_2	intergenic	CG10483	NA	bp1_Dmel\297_Gypsy=4	0
A373R1	1629	novobreak	TRA	3L	5938755	3R	4100848	3	0	somatic_tumour	2338	1837.9	3L:5938755 3R:4100848	3to5	0.11	0	-	-	ATGCTCAATAGTCGGACGGACTAGCGAAATGAATTGGGTTTTGGTCATGTAAGGATCCTTTAACAAAGAAGCACTTTTAAACAATGAACAATGGAGGCTTGTGCCACAAAAGAAC	-	-	CG33993, intron	CG42402, intron	CG33993, CG42402	NA	bp2_Dmel\F-element_LINE-like=3	0
A373R1	1672	novobreak	BND	3L	6841542	3L	9313364	2	2	somatic_tumour	2394	2471.8	3L:6841542-9313364	3to3	0.09	-0.01	-	-	TTGCTAATTTTTAATTTATGCAAAACGCATTTTCCTACCTCTTGCCAAATCCTTTATCGCGATTATTGCGTAATTCGAGACACACAAACTAAAACGGAAAATAGACTCACTCGCAAACGCACACACACACATATGTAGGTATATATGCAGCGGGCGCAGTGCTCATT	-	-	intergenic	intergenic	-	NA	bp1_gypsy12_Gypsy=2; bp2_roo_BEL=2	0
A373R1	1679	novobreak	TRA	3L	7032044	2L	15094	11	0	somatic_tumour	2402	7016.9	3L:7032044 2L:15094	1679:11_1679	0.31	0	-	-	TACATAGCCCCTGGACATGGACAGAGCGTTGGTCTTTAAATTGGGTAACTTTACAAACCCAGAAATGTGATACAGAAAGCACATTCTCGTTTCCTTTGTTTGGCCACTGCACAATGGCAGAGCTGTCAATTTACTTAGCCCCAAAAATGCAGGTAATAATGAGAGTCAAGC	-	-	Mp, intron	l(2)gl, exon_3	Mp, l(2)gl	NA	bp1_Dmel\F-element_LINE-like=5; bp2_Dmel\412_Gypsy/TABOR=4	0
A373R1	1693	novobreak	TRA	3L	7549091	3R	8122293	4	0	somatic_tumour	2423	573.2	3L:7549091 3R:8122293	3to3	0.17	0	-	-	TTTTTATGGCCCCCAACTTGTTGCACTTTCGTTGTTTATTCACCAGACATTTAATCAGGTGCGGCCCACTGCACATCATTTCGTTAAATGTTGTTAAAGTGTGACTGAGAAGCTGAGCGCTGTTACTATTATAATTTCCTTTTACTTAGCATTCGCGTTACACTGCTCAGGTG	-	-	intergenic	puc, 3UTR	puc	NA	bp1_gypsy4_Gypsy=2	0
A373R1	1703	novobreak	TRA	3L	7980692	3R	4445690	3	0	somatic_tumour	2439	3535	3L:7980692 3R:4445690	3to5	0.09	0	-	-	AGCACTTAGATGGTATCAACTTAGGCTTAAACGCGATAATTCTATTAATAGAAGCAAATTATCCACCACCACCACCACCAGTAAAAGCCACAGCCTAGCAGGACCACAACCACTGAGCTCCATCGCCAACAAATACCA	-	-	nmo, 5UTR	CG31522, intron	nmo, CG31522	NA	bp2_flea_Gypsy/INVADER=8	0
A373R1	1706	novobreak	BND	3L	8066967	3L	15812621	2	1	somatic_tumour	2442	7745.7	3L:8066967-15812621	3to3	0.07	0.02	-	-	TTGTAGTGATTTTCCTTTTCACTTAGTTGCATTTATCCTCGGAACGAACACTAAAAACTAGGCGCCGTAAAATATTCCGTCTATTCTTCGCTAGCGAATGTATCTTTCCGAGGCAGTGTCAAAATCTAATTGGAATTTTTCCCAATATGAAC	-	-	Ect4, intron	fwe, exon_5	Ect4, fwe	NA	bp2_211000022280447_5	0
A373R1	1726	novobreak	TRA	3L	8638919	3R	29319538	3	0	somatic_tumour	2464	20680.6	3L:8638919 3R:29319538	3to5	0.1	0	-	-	CACTTGTGCGCGCTGTGCTTTTCAACAGTTTTCCCCCACTGCGGTCTGTTGCGGAATAACAAGAATCGAGATCTGGCACGACGAACTATTATGTAATTTAAAGGCATTTGCACCTGAAATTTACGCTTAAAGTGCAATATATTTTGA	-	-	intergenic	Cnx99A, 5UTR	Cnx99A	NA	bp1_Cr1a_CR1=3	0
A373R1	1729	novobreak	TRA	3L	8693576	3R	8439419	3	0	somatic_tumour	2467	254.2	3L:8693576 3R:8439419	3to5	0.1	0	-	-	AACCGGTGGAAAGTTTTGATTTATTTTGACCCTAGCTGCCCCAATTGAATTTACCAGTCTGTGCCATCCGTCGTCGCTTGTCTGGCCGTTTGGCATTAAAA	-	-	intergenic	CG45263, intron	CG45263	NA	-	0
A373R1	1761	novobreak	TRA	3L	9731434	2L	2653329	3	0	somatic_tumour	2524	7078.1	3L:9731434 2L:2653329	5to3	0.1	0	-	-	GATTAAATGGTAGCAATCAGTCTTGAGCTGCACTGGCATCGTCGTCGACCGCTGGGGACGGTGGAGACTGCCTGAAGTTCTCGGATTTCATCCTCCGGAACATGGATC	-	-	CG6749, exon	Prosbeta4R1, exon	CG6749, Prosbeta4R1	NA	-	0
A373R1	1769	novobreak	TRA	3L	9844027	3R	11670459	3	0	somatic_tumour	2534	1826.4	3L:9844027 3R:11670459	5to5	0.07	0	-	-	GACGGAGGTGGCCCAGCCGCTGGTGCGACTCTTTACGCACACGGAGCAGCACCACCATGCTGCCGGAGACGACAACCGCGTCCACACAGTCACCAAGCGAAATGCCACCCACATTTATGGCTCCATATCCCAACGAAC	-	-	RasGAP1, exon_2	CG42327, exon_2	RasGAP1, CG42327	NA	-	0
A373R1	1771	novobreak	TRA	3L	9869262	3R	26400299	3	0	somatic_tumour	2537	16531	3L:9869262 3R:26400299	3to5	0.1	0	-	-	GACAGATGATACGCCCAGTCACTGGCAACAATGTCCTGGCCAAGTTTTTCTGGCCTTCAAGAATGCCATGCTCTACGAGAACCACCGCTGCTCCCTGGATCCTGTC	-	-	CG8108, exon_6	intergenic	CG8108	NA	-	0
A373R1	1785	novobreak	COMPLEX_TRA	2R	20932052	3R	12891609	6	0	somatic_tumour	1834	8040.4	2R:20932052 3R:12891609	1310:1310_1785_1786_1788_2428_2556_2557_2813_2814_3138	0.18	0	-	-	GATATGCATGTTGTGGGCCACCGTCGTCTGTCTGTCGGGCTGAAAATTATGACAGGCCATTGAAAGAATTGAATCGGACGGACGGCTGAATGCTTCGTGTCTGTCGCTGTCTGGAACTGGGACAGCCCTATAATTAGGCTCCCCCTGGCAGGATTCGAGGATTTTTTAATTGAATTAAAG	-	-	Rx, intron	intergenic	Rx	NA	-	0
A373R1	1785	novobreak	COMPLEX_TRA	3L	10282443	3R	29457244	3	0	somatic_tumour	2562	19174.8	3L:10282443 3R:29457244	1786:1310_1785_1786_1788_2428_2556_2557_2813_2814_3138	0.11	0	-	-	GCACGCACGCGGTCTCATTATTGGGTCAACAAACTGGCTCGATGATGGATCGCTGAGCGATAAGCAAATATTCTGCAATTATGCACATTTTATTGGAAATTGTTAGTTGGCAAAGGCGCAGCGAATTCAAATTG	-	-	intergenic	Ptp99A, intron	Ptp99A	NA	-	0
A373R1	1785	novobreak	COMPLEX_TRA	3L	10339599	3R	7823747	3	0	somatic_tumour	2564	2515.9	3L:10339599 3R:7823747	1788:1310_1785_1786_1788_2428_2556_2557_2813_2814_3138	0.1	0	-	-	ACATAGAGCATGATGTCCTGCGGCCGTGTGCAAATGTTTATTTTTTTTTTTTGTTTCTCCTCCTCTGATTTTAATTGAAACATTTTTGACCATATTTTCTTAATGATCTGACATGACA	-	-	CR46006, ncRNA	CG34384, intron	CR46006, CG34384	NA	bp1_Dmel\297_Gypsy=6	0
A373R1	1785	novobreak	COMPLEX_TRA	3L	10339610	3R	7823747	3	0	somatic_tumour	2565	2515.9	3L:10339610 3R:7823747	1788:1310_1785_1786_1788_2428_2556_2557_2813_2814_3138	0.09	0	-	-	ACATAGAGCATGATGTCCTGCGGCCGTGTGCAAATGTTTATTTTTTTTTTTTTGTTTCTCCTCCTCTGATTTTAATTGAAACATTTTTGACCATATTTTCTTAATGATCTGACATGACA	-	-	CR46006, ncRNA	CG34384, intron	CR46006, CG34384	NA	bp1_Dmel\297_Gypsy=6	0
A373R1	1785	novobreak	COMPLEX_TRA	3R	29457244	3L	10282443	3	0	somatic_tumour	4392	19174.8	3R:29457244 3L:10282443	2814:1310_1785_1786_1788_2428_2556_2557_2813_2814_3138	0.11	0	-	-	GCACGCACGCGGTCTCATTATTGGGTCAACAAACTGGCTCGATGATGGGTCGCTGAGCGATAAGCAAATATTCTGCAATTATGCACATTTTATTGGAAATTGTTAGTTGGCAAAGGCGCAGCGAATTCAAATTG	-	-	Ptp99A, intron	intergenic	Ptp99A	NA	-	0
A373R1	1790	novobreak	TRA	3L	10453260	X	16685026	4	0	somatic_tumour	2570	6231.8	3L:10453260 X:16685026	5to5	0.15	0	-	-	ACCCAACATTTTGCAATTGACCATTTTCCGTGGCTTTCTGGGGTTCGGTTTCTTATAAACAAAGTCGATTTGGTTGCAGCTGCTCCAGGATTTCTCTGGGTCACCATATAAGTCCTATATAGTAG	-	-	intergenic	Sep4, 3UTR	Sep-04	NA	-	0
A373R1	1795	novobreak	TRA	3L	10549890	2L	19574969	3	0	somatic_tumour	2580	9025.1	3L:10549890 2L:19574969	3to3	0.11	0	-	-	GGTTGAAACGATGACGATGAAAGGTCACGACGAAGAATTTTTCGCCAATTGCCTGGTGGGTCGCACAGTCTGGGTCGCGAGACGTCTGACTAGGCTAAAATTGATTGCAGGTTTTTTTTTTTTGGTGATAACAACTATTG	-	-	Rbfox1, intron	spi, intron	Rbfox1, spi	NA	-	0
A373R1	1812	novobreak	TRA	3L	11163228	3R	9917754	4	0	somatic_tumour	2611	1245.5	3L:11163228 3R:9917754	5to3	0.15	0	-	-	GTGTTTGCCAACGACAAGCCACGATGGCAATGGAAAAATGTCAATCCATTTCTGTACATGCCAGATATGCAGGTGCAAAATGATGCAATTCGACTGTTGCAAAACGAATGTCACTGATAGTTACTGAAT	-	-	CG32082, 3UTR	Glut4EF, intron	CG32082, Glut4EF	NA	-	0
A373R1	1813	novobreak	TRA	3L	11213687	X	15951538	3	0	somatic_tumour	2613	4737.9	3L:11213687 X:15951538	3to3	0.18	0	-	-	TGCCTGCGGCAGCCAGCCAGGCACAAGTTCTCTTTCTGGATTTCGTGCAGCAGTGCTTGTACTTCGAGGACGATCCGGCCGTCCATGCGATCATCCTCGATGGCAGCGGCGGCGGACTCGGCGGCA	-	-	CG7600, exon	mmd, exon_22	CG7600, mmd	NA	-	0
A373R1	1815	novobreak	COMPLEX_TRA	3L	11403831	X	11299479	3	0	somatic_tumour	2625	104.4	3L:11403831 X:11299479	1823:1815_1822_1823	0.12	0	-	-	TTTGTACTTATTGCTCATCATTCTTTTGCCATAGGAACAGTGATTACCAGGTATCTACCAGTCGTGTTCTTCGATTAGAGGGTTCTTCCTTGTTTGGTTTGGGCGATTGGCTGCTCCTCCGATCTTGGTGTCGTTGGTCG	-	-	intergenic	CG44422, intron	CG44422	NA	-	0
A373R1	1816	novobreak	TRA	3L	11259935	3R	26733727	3	0	somatic_tumour	2617	15473.8	3L:11259935 3R:26733727	3to3	0.09	0	-	-	GAAAAGATTTGGGAAAATCGGAAAAACTCTAGGGAAAATGTGCTCGAGGGCAAAATCCTCAATTGTCATGTTTCTTGACAATTTGTCTAATACGCAATGCGCTCGTAGTTTCTTTACGAC	-	-	intergenic	intergenic	-	NA	-	0
A373R1	1831	novobreak	TRA	3L	11758142	3R	17776760	3	0	somatic_tumour	2638	6018.6	3L:11758142 3R:17776760	3to3	0.1	0	-	-	TTTTGTATATCCCCAAGCTAGAGTTTGTTGAATGTGCAGACAAGCAAATGCTAGTTAGCATCGACACTTGTCGCATGCAAATCAGGGGGAAAACCCATATCAGCCGCTCTCTGAGCGCGAC	-	-	CG6024, intron	CG43102, intron	CG6024, CG43102	NA	bp2_rover_Gypsy=3	0
A373R1	1832	novobreak	TRA	3L	11762048	3R	17762643	3	0	somatic_tumour	2639	6000.6	3L:11762048 3R:17762643	5to5	0.09	0	-	-	GTGCGGGGATAGTCAGCCAAGCGACAAACATGGCCAACAGTTCCAGGAGGAACAATAACAGTAACAACAGCTTAAACTATGACCAAAATGGCCAACACGACGTAACTGTGAAGAAAAATTAGGCGACATACAATTAATGGCCCTGTGCCAGTGGCTTCGTCTTGTATTTAAAGAACTTGGCAAACACATCAAG	-	-	CG6024, intron	TyrR, exon_1	CG6024, TyrR	NA	-	0
A373R1	1834	novobreak	TRA	3L	11917317	2L	15964921	3	0	somatic_tumour	2645	4047.6	3L:11917317 2L:15964921	5to5	0.1	0	-	-	GGTACACAGATTATTTTGCCTGGACTTCTGGACTCCAGATGGGAAAACTTACGTTTTATTTTCCGTATTCTATGCTTTTTTTCTACTACTTTTTTGTACTTTTTTCTTTTGTCC	-	-	CG44837, intron	intergenic	CG44837	NA	-	0
A373R1	1870	novobreak	TRA	3L	13116480	2R	15685883	3	0	somatic_tumour	2706	2569.4	3L:13116480 2R:15685883	3to3	0.16	0	-	-	GTTCCCGTGGAAGGATCTTCAGACTCTGGACCTTTCCGAAAATCCCTTGTCCTGCGACTGCCGTGTGATGTGGCTGCACATTGATCACAAAAAGTTTGTACCTTCGGAAATTTGTGATTTACGAATTGTATTTTTAACAATGATTTTCC	-	-	trn, exon	CG30082, exon_1	trn, Ranbp11, CG30082	NA	-	0
A373R1	1885	novobreak	TRA	3L	13665166	3R	3520032	3	0	somatic_tumour	2729	10145.1	3L:13665166 3R:3520032	1885:1885_2956	0.09	0	-	-	ATTACTAAGCTTCTCTCTTTAGAGCTTGTGATGCGTACTCGGCCTTAAAACTCTTTATTTTGTTTGGTGTAAACTATTTCAAAGGATTTCAAATTAGTTTAAAGTTCAAAGAAAAATTTGACAAACGTTTGCACAGTGCACAAATTGAATTATCAAACACTTCACAAATTACGAATC	-	-	bru3, intron	Parp, intron	bru3, Parp	NA	-	0
A373R1	1913	novobreak	TRA	3R	15663172	4	397823	3	0	somatic_tumour	3788	15265.3	3R:15663172 4:397823	2503:1913_2503	0.11	0	-	-	TGGCATAGTCTAACTTAGCAGTACTAAGTTATCTTAATAAAAGTAGCGGTCTCGAGCCCGATTCCCCGCCCCTGAAAAGAGTTCCTGTTAATGATTGTATGAGATTGA	-	-	intergenic	intergenic	-	NA	bp1_GATE_BEL=2	0
A373R1	1916	novobreak	TRA	3L	14918762	2R	21756112	3	0	somatic_tumour	2786	6837.3	3L:14918762 2R:21756112	3to3	0.1	0	-	-	AGGGCTATAAATATTTGCAATGTAAAATGCTGACTCGACCTAAACGAATGAGATGGGCTGAATGCGTAAGAAGGAGTCGGAAAAGGACGAAGGACGAAGGATTAGTACTTAATTTGATTAGGCCATTCAAGTTGGCAG	-	-	DCX-EMAP, intron	intergenic	DCX-EMAP	NA	bp1_Stalker4_Gypsy=7	0
A373R1	1926	novobreak	TRA	3L	15328350	2L	21172823	4	0	somatic_tumour	2807	5844.5	3L:15328350 2L:21172823	3to5	0.27	0	-	-	GAAGCAATCGAATTATGGTATTGTTATTCAATTCTTTTCAAATTGTTTATATTATATTTTGACTATATCGAGTGTGCAGCTTTAAAAGTATATTTTTCTATTTTATATTTAGCCATAACTATTTTGCTCAGTGCACTCGACTGACAATTGTTAGGGATAAACGAAAGGGGG	-	-	intergenic	Acon, 3UTR	Acon	NA	-	0
A373R1	1928	novobreak	TRA	3L	15461278	2L	17877675	4	0	somatic_tumour	2812	2416.4	3L:15461278 2L:17877675	1929:637_638_1928_1929_2456_2478_2893	0.12	0	-	-	GTCTGGAAATTTGTTGCGCAGGCTATAAAGTCAGTTAAGCCCGGCCCGAAAGGTATTTGTATTCATTCATGATGATTGCAGAAGGAATGAAATGGCGGAAAAGCTGGAAAAAGTGTGGAACGGGACAAGCCGGCAGAGC	-	-	intergenic	intergenic	-	NA	-	0
A373R1	1931	novobreak	BND	3L	15536381	3L	18522851	3	0	somatic_tumour	2815	2986.5	3L:15536381-18522851	3to3	0.07	0.02	-	-	AAATTGATTTTGTTATGAAGATTTCAGTCACACTTCCTTGCTTAAAGCCATATTTAATGTAATTTAAACTGACATTTCGTAGCTGGAAACATTTACAATGCTCTAAGAACTCTTTTAGTTGTTTTTTTTTATTGCGGTTCGGGGATGGTGTG	-	-	CrebA, 5UTR	intergenic	CrebA	NA	-	0
A373R1	1938	novobreak	TRA	3L	15957251	2R	10368274	9	0	somatic_tumour	2823	5589	3L:15957251 2R:10368274	3to3	0.27	0	-	-	CCTTATGGCTGCACGGCTGTTCTCAAGCTAGACGCCTACAATTCCCATTTGGACGAATGCATTCACAATCCGAAGCGACCATTTCCCTCGAACTCGCTTTCCATTATCTTAAATAGGTTTATTC	-	-	elgi, exon_3	CG42732, intron	elgi, CG42732	NA	-	0
A373R1	1946	novobreak	TRA	3L	16378404	3R	17829423	3	0	somatic_tumour	2834	1451	3L:16378404 3R:17829423	1946:1946_2566_2567_3044	0.11	0	-	-	AACCAGTTCTACATTTCTAGTTTTGTTTTCTGCGCTTTATATTTAGCTACTCGAATTCTCTGAAAAATTTTGGCACTGGTGCTGCACTGACTCACCTTCAAAATGCACATATTATTGCATTAAAGG	-	-	roq, intron	tinc, intron	roq, tinc	NA	-	0
A373R1	1950	novobreak	TRA	3L	16515633	3R	23429985	7	0	somatic_tumour	2842	6914.4	3L:16515633 3R:23429985	3to5	0.29	0	-	-	CTAGTGAAGCTGTGTGCCAAAGCAGCTGCTGCTGTATGTGTGTGTGTGTGTGCATGTGTATCGTTTGTGTGGCTGCGTGTGCTTTGCATCTGTGTGCGTGGCACTGTGCAC	-	-	CG43373, intron	CG4374, intron	CG43373, CG4374	NA	-	0
A373R1	1955	novobreak	TRA	3L	16669222	X	1733289	3	0	somatic_tumour	2849	14935.9	3L:16669222 X:1733289	3to5	0.18	0	-	-	AACTACTTCTTGGCTTTCTTAAATGCCCAGCTCCATAAAGTAGGTGGCCCACGACGGGCTGGTTTCAAGGTTCCAGTTGTTCCTAATTGTCTGTTTGCAAGTCGTCTGGGAGCTGAGAAAGAGTCACGCTTCGAGATAGAGACATTTGGGCATGGCCCTGC	-	-	intergenic	intergenic	-	NA	-	0
A373R1	1956	novobreak	TRA	3L	16733509	2R	16469695	3	0	somatic_tumour	2852	263.8	3L:16733509 2R:16469695	3to3	0.08	0	-	-	GCTCCCATGGTGATGCCACTTTCCTGTTTATCCTCCGTGAATGCAATCCCAGTGACTTAGCTGCATCCAAAGGTCGGCTGTGCGGGCTCCACGTTATAGACAAGTTCTCAG	-	-	intergenic	intergenic	-	NA	-	0
A373R1	1969	novobreak	TRA	3L	17223570	3R	13134835	3	0	somatic_tumour	2876	4088.7	3L:17223570 3R:13134835	3to3	0.1	0	-	-	CGTTAGACTATGCCAAACAATTTGTCATTAATCAATGTTTGGAATTTTCCTGTTTCTCCGCTCGGCTTCGATTTAGGCCTTTGCCTTTTGCAAACTTTTGTTTCTTCTTTGTGCTTTCCTGGAATTTGTCTCCTCGTACAATGC	-	-	Rbp6, intron	CR45109, ncRNA	Rbp6, timeout, 2mit, CR45109	NA	-	0
A373R1	1972	novobreak	TRA	3L	17413610	2L	4003209	3	0	somatic_tumour	2882	13410.4	3L:17413610 2L:4003209	5to3	0.08	0	-	-	CCGTATGGCTAATTTGGAGATCATCCAGCGGGTAGACCAAATGAAATCAAGTAACTCTTAACCCCAGTTCCTTGATCGAAGTGACAATTCAAAGAGCGAATGAAATGCGAAATGCAGCACGAACCACTCAATTAAGT	-	-	blot, intron	intergenic	blot	NA	-	0
A373R1	1976	novobreak	TRA	3L	17672493	3R	11143854	3	0	somatic_tumour	2888	6528.6	3L:17672493 3R:11143854	5to3	0.09	0	-	-	GTGCACCTATTGAGGCTCATTATCTTTTGTTGTTTGCCGGGAATAAACCTCCTTTAGTCCTGGCAACCCCGCTCATCCTCCCTTGGCATTCATGTATGTCTGTATATGGAGCATGGTCGAGGTGGGGGTTATGCGATTTGGATTCGGATTTGTCTGTGGGCGTGTCTTTGGCGAAAAGCTATGGAGAAGCTCCATAGCTTTTCGCCAAAGACACGCCCACAG	-	-	CG34251, intron	intergenic	CG34251	NA	bp2_rover_Gypsy=3	0
A373R1	2005	novobreak	TRA	3L	18755343	X	2543470	3	0	somatic_tumour	2931	16211.9	3L:18755343 X:2543470	2006:2005_2006	0.1	0	-	-	GGGGGCGGTGGTCTGAACGGACCAAGTTCCGTGGGCAACTTCCGATGTGATAAAAAGTGTGAGCGCTGCAGCAAAACAAATCGAATGGAAACGACATGCTCGACAAAATCAAGCAGAGTACCAGAA	-	-	ftz-f1, exon_5	trol, intron	ftz-f1, trol	NA	-	0
A373R1	2015	novobreak	TRA	3L	19175287	3R	6537214	3	0	somatic_tumour	2949	12638.1	3L:19175287 3R:6537214	5to3	0.13	0	-	-	TCATTAAGTCAAAGTGGGGAAAACCTTAGCCGACATGATGTGTCCTTTTTTGCCGGCAGCAAGCTCCTCGGGCTGGATCTCCATAAAACCAAAGTGTTAGTT	-	-	fz2, intron	dpr11, intron	fz2, dpr11	NA	-	0
A373R1	2016	novobreak	TRA	2L	18935742	X	5594873	3	0	somatic_tumour	885	13340.9	2L:18935742 X:5594873	673:673_2016_2518	0.15	0	-	-	CTCCAGACTCTCGGCCGCTGCAGCGGCGGCAGCAGCGGCTGCCATGAAAATGAGCGCAAATTAAAGGAAAACAATCAGATGGAAAAGAAAGTGGAAAGGGTTTCTAA	-	-	ssp3, intron	Vsx1, exon_1	ssp3, Vsx1	NA	-	0
A373R1	2019	novobreak	TRA	3L	19461262	3R	26184705	3	0	somatic_tumour	2963	6723.4	3L:19461262 3R:26184705	2020:2019_2020	0.12	0	-	-	CTCCATTGGCATCGGCAGCGCCATCTCAGTCGTCTTGGATGCACGTGGAAATCCTTTTCTTTTCCTTCGAATCTCTCTGTGTCTAGGATCGCAATCGCACC	-	-	intergenic	CG31323, 3UTR	CG31323	NA	-	0
A373R1	2043	novobreak	TRA	3L	20235301	2L	13213687	3	0	somatic_tumour	2995	7021.6	3L:20235301 2L:13213687	3to3	0.07	0	-	-	TCGTTAGACGTGACACAAAAACATCATGTCCGAATTTTCGAATCTTTGATTCATCCTCACGCAACAGTTCTATGTAGATGCGCTGCTTTTGCAGCAGATGCAGGTCAACCAGCAACATCACCAGCAGCAACAGGTGCAGCAA	-	-	CG17233, exon_6	kek4, exon_2	CG17233, kek4	NA	-	0
A373R1	2043	novobreak	TRA	3L	20235301	2L	13213687	3	0	somatic_tumour	2996	7021.6	3L:20235301 2L:13213687	3to3	0.07	0	-	-	TCGTTAGACGTGACACAAAAACATCATGTCCGAATTTTCGAATCTTTGATTCATCCTCACGCAACAGTTCTATGTAGATGCGCTGCTTTTGCAGCAGATGCAGGTCAACCAGCAACATCACCAGCAGCAGCAACAGGTGCAGCAAATGGCGGGTGGCGAATCAACCTACAA	-	-	CG17233, exon_6	kek4, exon_2	CG17233, kek4	NA	-	0
A373R1	2044	novobreak	TRA	3L	20515625	Y	1113653	3	0	somatic_tumour	3002	19402	3L:20515625 Y:1113653	5to5	0.16	0	-	-	CACAAATGGTCATTCATTGAATTATTATTTACATCACCTTAAACGAGTTATTGGTGAAAACAGCTTTACATATGAAGAATTTGCATCGCTGATATGTCAAATC	-	-	CG5059, intron	intergenic	CG5059	NA	bp1_rooA_BEL=4; bp2_rooA_BEL=7	0
A373R1	2056	novobreak	TRA	3L	21187911	3R	16508180	3	0	somatic_tumour	3025	4679.7	3L:21187911 3R:16508180	3to3	0.1	0	-	-	ATGTTGATGATGATGATTTTGTCCAGTGCAAGAAGTTCGTTTGCATTGGAAATATTTAGAGAAAAGCTGTGGGTTCACTTCGCACCTGGTGGGTCATCCGCATACGCAGTTGACTTATTGATAAGTTTGCGAAAGACTTCATAGCTTTGACTCACTGTGCGGTGAGTGAGCGAGTTTGTTAACC	-	-	CG42337, intron	CG42342, intron	CG42337, CG42342	NA	-	0
A373R1	2079	novobreak	TRA	3L	21886023	3R	31405444	3	0	somatic_tumour	3055	9519.4	3L:21886023 3R:31405444	3to5	0.12	0	-	-	GAAAACCGCAAGAGCGTCGAGCCCTTGTTTTGCGAGCCTTTTCGAAAAAAGCAAACAGTTGCCCAATTTGCCGGAGTCGCATTGCCTAGATAGTTTTTACCCTGTC	-	-	CR43878, ncRNA	Gprk2, exon_1	mub, CR43878, PNPase, Gprk2	NA	-	0
A373R1	2082	novobreak	TRA	3L	21989678	X	7894615	3	0	somatic_tumour	3060	14095.1	3L:21989678 X:7894615	5to3	0.12	0	-	-	CATAATGACGAATGCGCACATCACTGACTACATCCTGCGAATGTGTCCCTACAGGATTCTGGTCAGTCCGATGGGCGTTTCCAAGCTGATGGATCTGCTGACGGACAGCCGCGAAGTGATTCGCAAC	-	-	intergenic	p115, exon	p115	NA	-	0
A373R1	2084	novobreak	TRA	3L	22077625	2R	19333276	3	0	somatic_tumour	3065	2744.3	3L:22077625 2R:19333276	3to5	0.12	0	-	-	CACAAATGTTCCCGAACGTCGGCAAACGGGAATTGCGGAGCGTTTAACTCTTCACGTATGCCGTCAGCCATCTGCAGACACACTCGCTCCCGGTCATCCGGATATTTACAAAGTAATTACTTGCGATAAAATGAATTTCACAAGATGAGAAAA	-	-	intergenic	CG34045, intron	Rgk1, CG34045	NA	-	0
A373R1	2132	novobreak	TRA	3L	26724963	3R	28984135	3	0	somatic_tumour	3159	2259.2	3L:26724963 3R:28984135	3to5	0.13	0	-	-	ACGGAAAAGCGCCGCTTTCCCTAATGACAAATTTTTTCGTACATATAAATTATGCATTAGCCAACGGCAAGCTCGGCGCGGAAAGAGATCACCTGCTATTCCGGATTTTGCCGGTGACGCTGTACGGGAGGAATA	-	-	intergenic	intergenic	-	NA	bp1_ninja-Dsim-like_BEL/PAO=3	0
A373R1	2136	novobreak	TRA	3R	8774378	2L	15436924	3	0	somatic_tumour	3471	6662.5	3R:8774378 2L:15436924	2300:2136_2300_2301	0.11	0	-	-	CATCGGAATGAAGCCACCTGCTTTCAATTCCCCGAAAGAGCAGTTGACATAAACCTTTCGCCGGCAGCTCCTCCGCCAAAGGCGCTGACAAGTGGTTGGGTTGTGC	-	-	Pif1B, 3UTR	intergenic	Pif1A, Pif1B	NA	-	0
A373R1	2144	novobreak	TRA	3R	5321214	Tomelloso	42030	4	0	somatic_tumour	3304	5279.2	3R:5321214 Tomelloso:42030	2192:2144_2192_2764_2908	0.32	0	-	-	GACTTAAAATCAATAAAAGTTAAAACCAGATGCGGCTATGCGTAGATACAAAATGGGACAATGCTCGAGATGCATTCGTCAATTTTACCAAAATCCAATCCC	-	-	mtd, intron	intergenic	mtd	NA	-	0
A373R1	2144	novobreak	TRA	3R	27023522	Tomelloso	37708	3	0	somatic_tumour	4290	26985.8	3R:27023522 Tomelloso:37708	2764:2144_2192_2764_2908	0.17	0	-	-	CTGATTCTTCGATTGTTGGATGTTAACGAGTATGGAAATTTGTATGTGTTGCCAGTAAATTCCAATCGAGACACCGTACACATTTAAGGTTGGCTCTCAGATGATACCATTGAATTTTATTGGCGAACCAGGCAAAATCTATGAAATTACTTATAAAAATGAGGTTTTACGCCAACGTTGGCGTAAAACCTCATTTTTATAAGTAATTTCATAGATTTTGCCTGGTTCGCCAATAAAATTCAATGGTATCATCTGAGAGCCAACCTTAAATGTGTACGGTGTCTGTCTC	-	-	RYa-R, intron	intergenic	RYa-R	NA	-	0
A373R1	2147	novobreak	BND	3R	2495844	3R	4817494	3	0	somatic_tumour	3211	2321.7	3R:2495844-4817494	3to3	0.07	-0.01	-	-	GTCCTTGACAGTAGGTGACTATAATGACAAACACATAACTAGGGGGTCCAGACTTACCACTCCAAAGGGACGTCGACTTTATGAAGCAATAAGAAACATCCACCTTGATCTGGGAGGCCTGCGCAGCTTCCTCGGAAGCCGCCTCCAATCGCCGCCTGGCGTCATTCGCATTGTATTGGAT	-	-	Myo81F, intron	CG1126, exon	Myo81F, CG1126	NA	bp1_Porto1_Jockey=5; bp2_Porto1_Jockey=2	0
A373R1	2148	novobreak	TRA	3R	2877391	X	3167258	3	0	somatic_tumour	3217	289.9	3R:2877391 X:3167258	5to3	0.14	0	-	-	GGTATAACCAGCTCACCGATAAGGCGCAGTCCAAGCCAAACGCAGAGCATCGAAAAAATGGTGGATATTAATAAGGTTGAGGCTAGGGCGTCAATGGGCGGTGTCCTGAGGCTTTACGCGGCTGACGCTAGAACATTTCGGCCTGCCACTACGATGGTCACGATTGCGAACGGA	-	-	Pzl, intron	N, exon_6	Pzl, N	NA	bp1_Dmel\X-element_LINE-like=3; bp2_Dmel\X-element_LINE-like=2	0
A373R1	2154	novobreak	BND	3R	3324730	3R	18155284	3	0	somatic_tumour	3227	14830.6	3R:3324730-18155284	5to5	0.09	0.01	-	-	TTGCTGCACCGCACCCGTAACCAAAAACAAAAAACTCGTCTTTTAAGTAGGCATTCTTGGAAGCGGTGCAAATAAATAATTTGCAGTAGCCGGGCGGCGACCACTCGACGACCCACTGTTGGCCTACCTACCAACCAACCAACCGACTTGGCCAACTGAAACCCCAACTTCGCTCCATCGAAAGCGACGGCCAGACAAATATTT	-	-	spok, intron	intergenic	spok	NA	-	0
A373R1	2158	novobreak	TRA	3R	3743466	X	1929859	3	0	somatic_tumour	3233	1813.6	3R:3743466 X:1929859	3to3	0.14	0	-	-	GGGTGAATCTCGGGCCGCTGCTGTACCATTTTAGCGACGTCAGCGGGCAAAACAGCATCGAGCCACTAATAACCAACCTATGTGACCGGTACCTAATTATTT	-	-	Tim17b, intron	CG11596, exon	Tim17b, CG11596	NA	bp2_Dmel\297_Gypsy=5	0
A373R1	2166	novobreak	TRA	3R	4492825	3L	23785097	3	0	somatic_tumour	3255	19292.3	3R:4492825 3L:23785097	3to5	0.12	0	-	-	AGCGGCTTCGGAGCTTTAGTCTATCAACCGGCAGTATGTTATGGTATTGACTGATCACAACATTTTCAAATTGATATCATTCACATACTCACACCGCACTG	-	-	CG34357, 3UTR	CG43968, exon	CG34357, CG43968	NA	-	0
A373R1	2171	novobreak	TRA	3R	4527497	3L	19704476	4	0	somatic_tumour	3260	15177	3R:4527497 3L:19704476	3to5	0.15	0	-	-	ATGTCGTTCGTGCAAGAAGAACGAAGTGAGCGTAAACTTATGGCACTCACTGTTTGGGCATGTTATTGCTCGCCGATGCTTGGGTTATCCCCATTCAACTCAAGCGCCGTCTTTTGTTGTCGTATTTTATATTTTCCAATGTTGCTCTTGCTG	-	-	CG34357, intron	serp, intron	CG34357, serp	NA	-	0
A373R1	2178	lumpy	COMPLEX_BND	3R	4698474	3R	28674525	5	0	somatic_tumour	11654	23976.1	3R:4698474-28674525	2179:2178_2179	0.17	0	-	-	-	-	-	CG43427, intron	intergenic	CG43427	NA	-	0
A373R1	2178	novobreak	COMPLEX_BND	3R	4698474	3R	28674525	5	0	somatic_tumour	3272	23976.1	3R:4698474-28674525	2179:2178_2179	0.17	0	-	-	AAGCTAGTCGAAAATGTGATTTTCAAACGGCTAATTTTAAGCTCATTTTCAAAGATTTGTTGATTAATGTGCTATAAGTGCTACTAGAATTATTTATCTAACCTAATCTACAAATTTACCCGGGCTCTCTTAGTA	-	-	CG43427, intron	intergenic	CG43427	NA	-	0
A373R1	2187	novobreak	TRA	3R	5132850	2L	8869424	3	0	somatic_tumour	3291	3736.6	3R:5132850 2L:8869424	3to3	0.1	0	-	-	CTTCAATGTCAACTGGTAGCTGGCTATCGAAGGCTTTCGCATAATTAAATGCAACGAAATGTGGCACCCATTTTTCCTCGCACTGGACTTTTTTGTTTTCCATACTACGATACTATTTTCTAC	-	-	intergenic	intergenic	-	NA	-	0
A373R1	2197	novobreak	TRA	3R	5528084	2R	21689196	3	0	somatic_tumour	3312	16161.1	3R:5528084 2R:21689196	2199:2197_2198_2199_3049	0.08	0	-	-	CCATATACAAAAAGGCATTCTCCCTGAATCTTTCCCACTACCAAATCTCCGACGTTCCGGGCATCATCGAGAAGTGCGAGACGCTGATGAAGCTGTCCGCCTAAGAAGTTCAGGGGTAAGATGGGATATCTTATAC	-	-	Itp-r83A, exon_3	CG10307, exon_1	Itp-r83A, CG10307	NA	-	0
A373R1	2232	novobreak	TRA	2L	929585	Tomelloso	110406	4	0	somatic_tumour	77	819.2	2L:929585 Tomelloso:110406	46:46_2232_2445	0.18	0	-	-	CACAACAACTGACCACTAATTAACCTAATTCCTAACCCCACATTCCGAATAGGTGGGGCTCCCAGTCGATCCAATTCGATTGCATCCAATTCAATGCTCACCGTTCAAATTATTCAATCAAAAGGGCAGCGTTGGAATC	-	-	CG4341, intron	intergenic	CG4341	NA	bp1_Tomelloso_2	0
A373R1	2258	novobreak	TRA	3R	7303920	2L	6657755	3	0	somatic_tumour	3395	646.2	3R:7303920 2L:6657755	5to5	0.1	0	-	-	CCGTATAAAAGAAACCCAATCTGCCGGAGCTCACCGTTTTCCCCCGATCTGCCTCAAGACAATGAGTCCGCGTTAATTGAAATGGTAAAAATCGTTATTTTATGAGGGAAACCTCTCCTCAC	-	-	rn, intron	CG31636, 5UTR	rn, CG31636	NA	-	0
A373R1	2274	novobreak	TRA	3R	7814495	X	1078413	3	0	somatic_tumour	3424	6736.1	3R:7814495 X:1078413	5to5	0.1	0	-	-	GGGAATCAGAACGGGCTATCCTCACAGCTCCCGAGGCCAACGTACACAGAGTTATGGATGTGTGTGGTCCTGACCCAAAGGGATTCCGAGCAGGACATAAAAATAGACACGAAGTACTGAAACAATAACTCGAGGCGGCGAGCTAGTGTAGAATTTTTTACATATAGAGTTACGAGGGGAGGAATCAGGAAGTGGCGGATAATTAAGGACAAAAACGCAATTTCAATTATCGTTAGTG	-	-	CG34384, 5UTR	CG3655, intron	CG34384, CR44779, CG3655	NA	bp1_Dmel\F-element_LINE-like=3	0
A373R1	2281	novobreak	TRA	3R	8036115	3L	15094480	3	0	somatic_tumour	3436	7058.4	3R:8036115 3L:15094480	3to5	0.09	0	-	-	AAAGATTTCGGAAAATTGGCAGGAAAACAACATTTTTATTAGCAGCTCAGGTGAGAGAGTGCCGAGAGGGGGAGAGAGAAGCACACCTTTCTGTTTTAGCAACAGCTTGTGCCGGAGCTCTGGCCATTATTACTTCAGTGTCCGTCAAGTGCTGCGAGAAGATC	-	-	unc-45, exon	sstn, exon_1	unc-45, Plp, sstn	NA	-	0
A373R1	2284	novobreak	TRA	3R	8131210	X	2306420	3	0	somatic_tumour	3441	5824.8	3R:8131210 X:2306420	5to3	0.13	0	-	-	GTTTGGCTCTTATTTTGCTTTATTTTCTTGCAGACTGTCAGTAGCCGAGTCGGGAGATGGTAAGTTTCCGCGGAGGTGGCAAGGGTAAGAAGGCCAAAACGCGACGACAACTTGGCTGACAAAGGATGTGGCCAGGACTGCTCTGATTCGAATGGGTTTCATC	-	-	intergenic	Raf, intron	Raf	NA	bp2_Tomelloso_2	0
A373R1	2285	lumpy	BND	3R	8146531	3R	23340339	3	0	somatic_tumour	10945_1	15193.8	3R:8146531-23340339	3to3	0.09	0	-	-	-	-	-	intergenic	pnt, exon_2	pnt	NA	-	0
A373R1	2296	novobreak	TRA	3R	8583155	3L	12516644	3	0	somatic_tumour	3463	3933.5	3R:8583155 3L:12516644	2297:433_2296_2297	0.09	0	-	-	ATATAATTGTCCAACTGTGTACTTGGCCTTTTAATTAAGTTGCCACAACGGCAAATAGCTGGCACTCGGACATCAAGGACATTCGCGTTGTCAACAACCACACGCTGCCGCACCACAATGACCCGGCGATCATGCAGGCGCAGCTCCAGAACGGACC	-	-	5-HT2B, intron	tral, exon_2	5-HT2B, tral	NA	-	0
A373R1	2307	novobreak	TRA	3R	8860391	2R	11071276	3	0	somatic_tumour	3478	2210.9	3R:8860391 2R:11071276	5to3	0.11	0	-	-	ATTTACGAGCCACTGCAGCCAAAGGGGAAGTCCCTGGTCAAATTGAAAATCGTGCAGCTTCATCGCATCCCACTAATGACAAATAATAATTGCTGGCAATTTCTTTAATTCCACT	-	-	pyd, intron	luna, intron	pyd, luna	NA	-	0
A373R1	2308	delly	TRA	3R	8879051	2L	23025980	3	0	somatic_tumour	BND00001060	14146.9	3R:8879051 2L:23025980	5to5	0.14	0	-	-	GCCCCAACGAAACGCATTCAAATTAGCATTTGGGAAGACAAATAAAAAAAAAAAGGGAATGCCACCAGGAGAGAGCAGCATTATTGAATCAGAGAG	-	-	pyd, intron	intergenic	pyd	NA	-	0
A373R1	2321	novobreak	BND	3R	9314343	3R	24292891	2	2	somatic_tumour	3497	14978.5	3R:9314343-24292891	3to3	0.07	0	-	-	ATTTTAATGTGCTTTGCGTGGATTTATGAAGAGCCCTCCAACTATTTTTGCGCCTTATTCACTTCCACTTAAAATCCCGGCACGGATCAACCGGAAACATGGCTCTCTACATGAA	-	-	CG8861, intron	CG6364, exon_5	CG8861, CG6364	NA	bp1_Burdock_Gypsy=3	0
A373R1	2333	lumpy	BND	3R	9503210	3R	9630428	3	0	somatic_tumour	9288_1	127.2	3R:9503210-9630428	5to5	0.09	-0.02	-	-	-	-	-	intergenic	Calr, intron	Calr	NA	-	0
A373R1	2333	novobreak	BND	3R	9503210	3R	9630428	3	0	somatic_tumour	3512	127.2	3R:9503210-9630428	5to5	0.09	-0.02	-	-	GTCCTCACCCCCGGTACCTTCTACAACGATGCTGAGGCCGACAAAGGTAGCGTATATGTGTCGATGTAGGGGTAATTAAGCCAAAGAACCGCCTTGCGGGTTAGACCGAATAAAATGCGTTTACTGCGAGTATGTGGCACTGGCGTACATGAGTTCAATTAGCCGACACGTTGATGGGGCACTACATTAATT	-	-	intergenic	Calr, intron	Calr	NA	-	0
A373R1	2334	novobreak	TRA	3R	9544827	2R	15985547	3	0	somatic_tumour	3515	6440.7	3R:9544827 2R:15985547	3to3	0.1	0	-	-	ACCTACGCAAAGTTAAGCAAAATACATCAATCAATAGTCATCAATATACTTAGCTATCAATCAAGAAACTCAACTAAAATGCCCGACCTATCCGTCAAAGTGGGCACCCGGACACGCCTCCTAACCGAAATACGCAGCTCA	-	-	mura, intron	Strn-Mlck, exon_3	mura, Strn-Mlck	NA	-	0
A373R1	2344	novobreak	COMPLEX_TRA	3R	10078173	2L	12871782	9	0	somatic_tumour	3536	2793.6	3R:10078173 2L:12871782	2344:2344_2345_2706	0.3	0	-	-	TCAGTCGCCTTCAAAGTAAATCACTTGAGAGCGGCTCTGGAAAGGCCCACGCCCACTCTGACGCCCACAAATTACAAAACCCTCTCATTGACGTCAGATAGCTGTCTC	-	-	intergenic	intergenic	-	NA	bp1_Dmel\F-element_LINE-like=7	0
A373R1	2350	novobreak	TRA	3R	10366352	2L	8552903	3	0	somatic_tumour	3547	1813.4	3R:10366352 2L:8552903	2350:2268_2350	0.13	0	-	-	GGTTCCTAGCCAAAGGGGATGGATGGGAATGAATGGATGGGGACATCCATGTCCGACGGTAACTGTTGGTGCTAAAATCACTTAAATCATCATTAATAATATTAATATTATTAAAGCCACAGGAATTACTTCCATAACGTT	-	-	Rfx, intron	Sema-1a, intron	Rfx, Sema-1a	NA	bp2_17.6_Gypsy-like=6	0
A373R1	2352	novobreak	TRA	3R	10391617	2R	10222646	3	0	somatic_tumour	3549	169	3R:10391617 2R:10222646	3to3	0.11	0	-	-	GCTCCACATGTCAAACATACGTTGCGTATACATAATTATTAGTGGGAAATGCGAAGCTTTGGTGACGTTTCAAGCTTCTATCTTGTATCTCCTGTTGATTTTTTTGACGTGTTGTCTTGCTGAACATCTGTGAG	-	-	cwo, intron	CG12912, intron	cwo, Hr3, CG12912	NA	-	0
A373R1	2377	novobreak	TRA	3R	18495869	3L	4009987	3	0	somatic_tumour	3927	14485.9	3R:18495869 3L:4009987	2582:1569_2377_2582	0.11	0	-	-	GGTAGAGATTCAGATCCAGGTCCAGATCCTGGCACGACACACAGACAGTTGGTCAGGGCAAGAGAAGTAAAAATAAGATGAAATAAAATGAAAATAATGCCGGACGATAAGGATGGGGATTGGCG	-	-	fru, intron	intergenic	fru	NA	-	0
A373R1	2381	novobreak	TRA	3R	11371083	3L	21265650	4	0	somatic_tumour	3599	9894.6	3R:11371083 3L:21265650	3to5	0.23	0	-	-	GGTTACACCGGGTGGTATCCTTAATTCAGCGCAGCCCATCAACCCTCCCGGCTGCCGTTTTATGCTCCATGTGTACCTTTCGCTTATTGAACTAGAATATCAGGCTGGCGAGCAAGCGATATGCACTTGACACTCAAGTGGACGCTTCACACA	-	-	pros, intron	Eip78C, 3UTR	pros, Eip78C	NA	-	0
A373R1	2405	novobreak	TRA	3R	11978865	2L	18647011	3	0	somatic_tumour	3634	6668.1	3R:11978865 2L:18647011	3to5	0.09	0	-	-	CAGATTCCGTATGTACTCATTCCAAGTGACAAACTTGGCAAACTTGGGCAATTTCCGCTCCACGGAAAAGTGCGGGAATCGCAGAGATCGCGCACTTGGGGCTGT	-	-	CG18547, intron	MESR3, intron	CG18547, MESR3	NA	-	0
A373R1	2411	novobreak	TRA	X	14825192	2L	9684163	3	0	somatic_tumour	4947	5141	X:14825192 2L:9684163	3092:374_2411_3092	0.13	0	-	-	CTCTCTCTCTCTCTCCCTTGGTTATTGCTTTTCTTTGCTCTCTCTCTTCGCGTGCCCTTTTTGATTATCTAATCCTTGGGGCAGGTGACATTTTGCTGGCCAACAAAATATACACTTACTCGCAAGGTACCCACACCAACTACTCAAAACTCAAA	-	-	rut, intron	Pka-C1, 3UTR	rut, Pka-C1	NA	bp2_Cr1a_CR1=2	0
A373R1	2425	novobreak	TRA	2R	20326536	2L	15133112	3	0	somatic_tumour	1807	5193.4	2R:20326536 2L:15133112	1295:1295_2425	0.1	0	-	-	GTCTGGAACAATGTCGTGTGAAAAGACCGGCACCCGACCCTCTGTGATGTTGATGAGGGTGTCATCCCGGTCCATGGAGACCAGAAGGGGCAGGACCGTTCGATTTCTTAGCGGCGGACACTGCTCCTTTGCCAACCACATTATCGCAGCGCAACGTGCCACCCCATTGGCGTTGCATAAATT	-	-	MED8, exon	intergenic	MED8	NA	-	0
A373R1	2440	novobreak	TRA	3R	13456855	Tomelloso	83396	9	0	somatic_tumour	3693	13373.5	3R:13456855 Tomelloso:83396	2440:98_2440_2441_2442_2628	0.57	0	-	-	GTTGAAACATCTCCAATTAAAGTTTCGATGTGTGGGGCCGGCAGTTTGGACAGGCGCGTTTGTGGTCATCGCCCACGGCATTCGGCTCGCTTGAATATTGGTGGCATTGCGTCAGTTTCGATACCATCTTCGCTAACAACCCTGGAG	-	-	CR17025, ncRNA	intergenic	CG14372, CR17025	NA	bp1_Tomelloso_4	0
A373R1	2448	novobreak	TRA	3R	13603320	3L	14322590	3	0	somatic_tumour	3702	719.3	3R:13603320 3L:14322590	2448:1899_2448	0.1	0	-	-	CTTTAATTGATTTAGTTTGGCAGTGTGTGGTTTTTTTTTTGTTTTTAGTGGGCGACATTTATTCGAAACAATAGAGCTTGCCACGGTTTCACTTTTTTCGCTTCGCGCATCATTTGTGAGGCTTCTGTTTCTTTTACCCTGACTCGGAGATTATT	-	-	intergenic	CR45025, exon_2	fz, CR45025	NA	bp1_rover_Gypsy=3	0
A373R1	2462	novobreak	TRA	3R	14097309	X	12236550	3	0	somatic_tumour	3721	1860.8	3R:14097309 X:12236550	5to3	0.14	0	-	-	TTATACCACAACGTCATAGCAGGCAGAAAAAGAGTTTTGATAAGACACAAAAGGCACACTCACCCTGCCCGTTTTGCTGTAACAAAAGCACACGAAGATGAAGTTGGAGCTGGAGCAGGAACAGTAGGATTCCGGACTCAGGATCCTGGGATCCTGGATCCACGACTTTGGCAGTGGGTTGAAT	-	-	CG9920, 3UTR	Ten-a, intron	CG9920, Ten-a	NA	-	0
A373R1	2469	novobreak	TANDUP	3R	14487592	3R	26073116	5	0	somatic_tumour	3737	11585.5	3R:14487592-26073116	3to5	0.13	0	-	-	GCGGCGGGCTGTGCCTTTGTTTGTCTAGTCAGCGGATCTGAAAACGACGCAATCAATGGATCCGCGACATGCAACGCGGCTGGTCCTCTTCTTTTCTAGCTGGTTTTCCTACTGCTGCTTCTTCTTTTTCCCCTTCTATGCCTTGTTAGGTGCAATGGATGAT	-	-	intergenic	intergenic	-	NA	bp1_roo_BEL=3; bp2_mdg1_Gypsy/TABOR=4	0
A373R1	2470	novobreak	TRA	3R	14517981	X	1052238	3	0	somatic_tumour	3738	13465.7	3R:14517981 X:1052238	2470:2470_2471	0.14	0	-	-	AAGTCGATTAGCCCGGAGTGGGATCTGCCCCAGCTGGTCTTGGGTCCGAAGCAGTGCGTCTGCATAAACATGCGAAGCACTGCGCGACAGGTGTCATCGTCGACCAGCTCAAAGTCTGGAATACAATGAAATATTTAGAATAGAATAC	-	-	Pde6, exon_10	CG14629, exon	Pde6, CR44779, CG14629	NA	-	0
A373R1	2499	novobreak	BND	3R	15632832	3R	22865891	5	0	somatic_tumour	3783	7233.1	3R:15632832-22865891	3to3	0.17	0	-	-	ACATTTATGGTCAGAACCCACACCCCACATATTTTTTGTATGGCCCGCCGATCGTGGCAATAAAATTGCATTTAATTACACGAGTGCAGTTACATGAACACCTCTCCAATCATTTAATTATTTAAATTTAATGCAGCGCCTTTTTTG	-	-	intergenic	intergenic	-	NA	bp2_blood_Gypsy/TABOR=26	0
A373R1	2510	novobreak	TRA	2L	8093153	X	17811386	7	0	somatic_tumour	433	9718.2	2L:8093153 X:17811386	318:318_2510	0.23	0	-	-	GTAATTTCCCTTTCAATGTCATCGTCGCCTGGCGTTGGCTTCAGTTTAGTTTGGTCTCATATTGGATTGGGTTGCGTCTGGCTGGGCTTGGGTTGAGTTTGAGTTTGGAACTTGAGTTCTATGGGATAATTGTGCGCCCTATCAATGGCTGGC	-	-	Bsg, intron	OdsH, intron	Bsg, OdsH	NA	-	0
A373R1	2510	novobreak	TRA	3R	15965831	2L	8095215	4	0	somatic_tumour	3805	7870.6	3R:15965831 2L:8095215	2510:318_2510	0.14	0	-	-	GACCTTGGAAATGTGAAACAATTTTCTGTTCTTTCATTTGTGTCCGGATTTTGATTAGAGTGCCGTTGTGTTATTTACCATCAACGAGGCAAACGATTCGGTGGCCAAGAACTGCTGCTGGAACGTGTCACTAACCCGTCTGCTGCGCAGCTTTAAGATGAACG	-	-	Rbf2, exon	Bsg, intron	Rbf2, Bsg	NA	-	0
A373R1	2513	novobreak	TRA	3R	16107173	4	1079805	2	1	somatic_tumour	3810	15027.4	3R:16107173 4:1079805	2513:2366_2513	0.12	0	-	-	TTTTTCGCGCTTTTCATTTGCCAAGCAATTTTTCTATTTTCACCTCCAGCTCTTGGGGAAAAAAAAAAAATTGTCGGCGGCATTTTTTGGGTCGTTAGAGT	-	-	intergenic	Actbeta, intron	Actbeta	NA	bp1_roo_BEL=8; bp2_INE-1_Helitron=3	0
A373R1	2514	novobreak	BND	3R	16137027	3R	17537987	2	1	somatic_tumour	3812	1401	3R:16137027-17537987	3to3	0.08	0	-	-	ACAGTCCCAACTCAGATTCCCCATCGTAAGTGGTAAGGCAGTCGTCGTAGCATCGAGCGACCGCCCAGCCGTATTCAACTTCCTGCAGGGCATTGTACACATGTC	-	-	Sb, intron	l(3)07882, exon_2	Sb, l(3)07882	NA	-	0
A373R1	2535	novobreak	TRA	3R	16837724	2R	16346437	3	0	somatic_tumour	3853	491.3	3R:16837724 2R:16346437	3to3	0.12	0	-	-	CTTGGAGTCACTAGACCATGTGAATCCCTTCACTTTGCCCTCCTGCTTGAAGCTGTGCAGCAGCTCATTTGTTTTGGCCGAAGTGGTTGATCCGGTTTACGGAATCCCCACCCAATCCCCTTGAAACCACTATCCG	-	-	iab-8, ncRNA	wcd, exon	iab-8, wcd	NA	-	0
A373R1	2544	novobreak	TRA	3R	17224933	X	16333798	4	1	somatic_tumour	3869	891.1	3R:17224933 X:16333798	3to3	0.17	0	-	-	TTTCCGCATTCGCATTGATACGATACCATACTGTGTGCTGTGTACTGTGTACTGTATAGCATATATACCATACCACCTACAAAATGTAGACAGATAAATAT	-	-	intergenic	Dsp1, exon_1	Dsp1	NA	-	0
A373R1	2548	novobreak	TRA	3R	17314237	3L	15862703	3	0	somatic_tumour	3875	1451.5	3R:17314237 3L:15862703	3to3	0.1	0	-	-	AGCCAAAAATTGCCTAGTTTAAGTTAAGAAGTCATGCAATGCACAAGGACTCAAAGGAGTTGGGCGTTTACCAAATACGAGTGCAGGAAATAGACTTGAACTGTATATATAAATGTAATCCATCCCTTGTTCAACTCAAAG	-	-	intergenic	pHCl, intron	pHCl	NA	bp1_rDNA_3	0
A373R1	2570	lumpy	BND	3R	17965477	3R	19184464	2	1	somatic_tumour	10423_1	1219	3R:17965477-19184464	3to3	0.08	0	-	-	-	-	-	cpo, intron	CG31475, intron	cpo, CG31475	NA	bp2_Juan_Jockey=4	0
A373R1	2575	novobreak	TRA	2L	754880	2R	9245145	2	1	somatic_tumour	68	8490.3	2L:754880 2R:9245145	39:39_2575	0.1	0	-	-	CCATAAACCTTTGAGCCATAAACATTTCCACAGCCCACAAATTATGAGGTCCACAAATTCACTTAGAGCATTTGCATTTGGCCTTTGAAGTTTCACCCATTTCCATGTGCTGTCCCATAAATCCTGGGTCCCCAGGATGGATG	-	-	GABA-B-R3, intron	hig, intron	GABA-B-R3, hig	NA	-	0
A373R1	2601	novobreak	TRA	3R	19248035	3L	21214277	3	0	somatic_tumour	3964	1966.2	3R:19248035 3L:21214277	3to3	0.1	0	-	-	ACTTTGGAGCGGGGGCCACCTCGGGACCTTCCACAGACAGGCCCTCGGGGTCGGCAAGCGGAATATCTTGCAGACTGGACATCTTCGTCCTCGTCCTGGACTATTTGTAGGATTTGCGTAGCCCTA	-	-	CG5217, 5UTR	CG10508, exon_2	CG5217, CG10508	NA	-	0
A373R1	2607	novobreak	BND	3R	19415605	3R	24504160	3	0	somatic_tumour	3972	5088.6	3R:19415605-24504160	5to5	0.1	-0.01	-	-	GTCCGCACACTTGACGTGTATTTCCGTTTCCGTTATGCGAAAACTTTTTTTCAAATTTTTCTCTTATCTTTTCAGTGTAGAAAAATGTAAAAAGTCGACTAAAAACATATATCT	-	-	CG31221, intron	intergenic	CG31221	NA	-	0
A373R1	2642	novobreak	BND	3R	20723488	3R	27111159	2	1	somatic_tumour	4028	6387.7	3R:20723488-27111159	3to3	0.08	-0.01	-	-	TGATTGGGTCCGGCCATAATTTGAGCCATACGTGCGCCGCTATTCAACGGGAAATTCATTTAGCGCACAAATAACGCAATTCTATTAAATAAATTGATTTCGAATTACTTTATTATCGCCAGAAGGAAC	-	-	intergenic	gb, intron	gb	NA	bp2_Dmel\F-element_LINE-like=2	0
A373R1	2649	novobreak	TRA	3R	21011147	X	16658279	3	0	somatic_tumour	4039	4352.9	3R:21011147 X:16658279	3to3	0.16	0	-	-	GTAAAAACCCCGCTTTAATCTCTGTTCTTTATCTATTTCCCGTCACCACTTCGTTTGTATGCCACCACAAACTATGTCTGTCTAGTTATACCCTTCAGGGATTTGTCCACAATTAGTTGGCTCGAGTGGGCCAATGCC	-	-	Calx, intron	r, exon_3	Calx, r	NA	bp1_Quasimodo_Gypsy=3	0
A373R1	2651	novobreak	BND	3R	21111973	3R	29996361	2	1	somatic_tumour	4045	8884.4	3R:21111973-29996361	3to3	0.07	-0.01	-	-	GTCCTGTTGCAAAGCCAGAGTGTGCACTCTAAAAGAGCAAAATGACAAACTGCACGGGGATGTGGCCAACATCAGGAAGACTAATTGAAACTAATTGGAGAATAACAAAAAGTGCACTCGAAGAGCCCAAAGTTCATGTGATGGTAT	-	-	Rab11, intron	Sas-6, exon_2	Rab11, Sas-6	NA	-	0
A373R1	2660	novobreak	TRA	3R	21522369	2R	20880549	3	0	somatic_tumour	4059	641.8	3R:21522369 2R:20880549	2660:1309_2660	0.14	0	-	-	CTTAAGGGCAGTCCTCATTAGTCGGCGGTCAATATTTGCAAGCTCGATGAAAAATTCATTTTTAAGTTTCTGAATGAAAAGTTAAGTTAACTGAAGTTACTCATAGTGTATTTTATAAATACTTTAGG	-	-	CG7956, intron	Cib2, intron	CG7956, Cib2	NA	-	0
A373R1	2677	novobreak	BND	3R	22380685	3R	23743829	2	1	somatic_tumour	4097	1363.1	3R:22380685-23743829	3to3	0.1	-0.01	-	-	GTCCAGGAGTTCCGGATTTGCCAGCAGCGTAGCAAGTACTATCACCAGCGTAAATTGGTAGTGATGGAGCCCTTGGCTGAGAACCACGAGTTGGAGCCGCCTTCCACTCCAGAGCATATGCCCGTGGTGGCCATTGCTGATCAAAGCGGGCTACCCAGAAATCCCAAAAGGGGAGAATGCGATGCGTCATTATTTGCCTTGGTACCTCACTTC	-	-	CG34149, exon	Hmgcr, intron	CG34149, Hmgcr	NA	-	0
A373R1	2688	novobreak	BND	3R	22729440	3R	31190245	3	0	somatic_tumour	4114	8460.8	3R:22729440-31190245	3to3	0.08	-0.02	-	-	AACTAATTAATGCACTTTTCAGTGTCTGCCTCTCTGTGTGTGCGATTGCGGAATTTGTAAGGCCAAGCTCTTTTAAATGCTGTCAAATGCCAGTCTGAGGCCATTAACCAATCTGTAGACGCCAGAGCCATAATCATG	-	-	CG45049, exon_3	mesh, intron	CG45049, mesh	NA	-	0
A373R1	2692	novobreak	TRA	3R	22858550	3L	19921160	3	0	somatic_tumour	4121	2937.4	3R:22858550 3L:19921160	5to5	0.09	0	-	-	GTACGAGATATAAATGCCTTCTCTTTACCTTGAGTCCACCGGATACAGATACACTACGTGCACGTGCTGGTGACCGAGGTGCGTCGCACGGGGCCGCAGGTGCGGGCAAACGAGGAGCCAGATGGACCGGCCAAGTCGTAGGGCGATCCGGC	-	-	intergenic	Su(z)12, exon_4	Su(z)12	NA	-	0
A373R1	2693	novobreak	BND	3R	22880093	3R	31167338	3	0	somatic_tumour	4122	8287.2	3R:22880093-31167338	3to3	0.09	-0.02	-	-	CGCTTACGCACACATATGCATTTAAATTAAATTATTTAGTTGGCCCGGCTCCACTTACCCAGCAGCTTGACTTAATTTGCAACAAATCGTATTTGAATTTATGCAGACAAAGCTATTTTT	-	-	intergenic	stops, exon_3	Gycbeta100B, stops	NA	-	0
A373R1	2701	novobreak	BND	3R	23290823	3R	26814498	3	0	somatic_tumour	4136	3523.7	3R:23290823-26814498	5to5	0.08	0.01	-	-	ATACAAGCCACTGTGAAATAAATATTCCCCGAAAACTTTTGACATGCAGCCATGAATAAAATGTTGCGCTCTAATATCACTTTTGGGGGACACATGCTTTATGGCCTCTATCAACGTTCGATCCTTGC	-	-	pnt, 3UTR	Tl, intron	pnt, Tl	NA	bp1_jockey_Jockey=54	0
A373R1	2708	novobreak	TRA	2R	16573386	X	654211	3	0	somatic_tumour	1615	15919.2	2R:16573386 X:654211	1157:1157_2708	0.19	0	-	-	CAATAGCACCACGGATGATGCCCAGCCGCAGGATTTCCGGGTGCTCAACTATGTGGTGCATCCGGCTTACGGCGAGGATGATGACACGGGCAGTCGCAAGAACGACATTGCCGGGTTGATTGGGTTTGGTGGAATTGGTATATCTAAGA	-	-	CG4927, exon	Hmt4-20, intron	CG4927, Hmt4-20	NA	-	0
A373R1	2718	novobreak	TRA	3R	24068453	X	8554485	4	0	somatic_tumour	4169	15514	3R:24068453 X:8554485	5to3	0.13	0	-	-	ATCCAGATCGCAACTAACGCGAAACCTAGCATGTATATTTCCCATGTGCATGTGGGCAAAGGTTCAGCAACAGGAAGTTGAGCTCATGGTAAATGTAGAGATGTAAATGTAAAATAGAACCCGACACAGGCAGTGCAGTTGTTGTTGTTGTTCT	-	-	4EHP, intron	Nrg, 3UTR	4EHP, Nrg	NA	-	0
A373R1	2723	novobreak	TRA	3R	24424110	2R	16067336	4	0	somatic_tumour	4184	8356.8	3R:24424110 2R:16067336	3to5	0.12	0	-	-	AACGGGAAGAAAAATTGAGAAAATATGTTGCAAATGTAAACAAAGTGTGGGAAAAGTGAAAGAAAGGAACTTTGATTTTGTTTGGTTGGGATTGAGGGAAGAGACCGGCTTATTGCGGAACGAGCTTGATTTCAGCACTTGGAAG	-	-	nAChRalpha1, intron	intergenic	nAChRalpha1	NA	bp2_Dmel\F-element_LINE-like=2	0
A373R1	2724	novobreak	BND	3R	24464861	3R	29934585	3	0	somatic_tumour	4186	5469.7	3R:24464861-29934585	3to3	0.09	-0.01	-	-	GTAATGTCGAGCCCCTATTTATTCATCTCAAACAGTCATATTAAACAAAGGTATTTAAGTAGGCCTTCGTCGCCTCTCTCTCGCTCTCTCGCTCTCTCTCTCTCCCTCTGTTACCAACACACAT	-	-	intergenic	eIF2B-alpha, 3UTR	CG42558, CG42557, eIF2B-alpha	NA	-	0
A373R1	2731	novobreak	TRA	3R	25178095	X	9023520	11	0	somatic_tumour	4210	16154.6	3R:25178095 X:9023520	2731:697_2731_3027	0.41	0	-	-	GAGAGAGAGAGCAAGCAAGCGAAAACGTATTACCAAACGAGCAAGACAGCGAATTTTAGTGACATCTGCAGTTCACCCGGAATGTTACGCCTCCATTTCCGAACTAATATTGTCAGGGGAC	-	-	lobo, intron	CR43836, ncRNA	lobo, rdgA, CR43836	NA	-	0
A373R1	2733	novobreak	COMPLEX_BND	3R	25224799	3R	27858723	7	0	somatic_tumour	4214	2633.9	3R:25224799-27858723	2733:2733_2780	0.19	-0.01	-	-	GTGAAATTTTTCGCAGCCAAGATTGTTATATACTTCAACGAGGAGTTTGTGCGTTAATAGGAAAATCGTGTGGCCGCATAGCTCTCCCGCTGGCGCTCCCGGTCCCGCTCCCTCTCTCGTTCCCGCTCCAGCAAGGCGGCGGAACTACCGAGGGCCATGCTACTAC	-	-	Cad96Cb, exon_5	CG34353, intron	Cad96Cb, CG34353	NA	-	0
A373R1	2733	lumpy	COMPLEX_TANDUP	3R	27858723	3R	29378659	7	0	somatic_tumour	11752_1	1519.9	3R:27858723-29378659	2780:2733_2780	0.27	-0.01	-	-	-	-	-	CG34353, intron	Ptp99A, intron	CG34353, Ptp99A	NA	-	0
A373R1	2737	novobreak	TRA	3R	25451883	2L	3915983	3	0	somatic_tumour	4220	21535.9	3R:25451883 2L:3915983	3to5	0.12	0	-	-	ATTTGATTTCTCAAATCCCTTAAGCCGTCTTGTAACCAATTAAAAACAAGGCACCATCTTCGCCAGTTTCCAGCCAAAGGCATCGGAGGAGTTTACAGTAC	-	-	Fur1, intron	fred, intron	Fur1, fred	NA	-	0
A373R1	2759	novobreak	TRA	3R	26601204	3L	16506756	3	0	somatic_tumour	4273	10094.4	3R:26601204 3L:16506756	2759:1949_2759	0.12	0	-	-	AGGCTTTCTTGGCCTTGCTTCCATTAGTAGTTAGTGTGCTCCAATCCCTCAGTCGCATTTCCTCAGAGGAATCATTTCAAATCACTGACAGTGTGTCAAAGCG	-	-	scrib, intron	CG43373, intron	scrib, CG43373	NA	-	0
A373R1	2784	novobreak	TRA	3R	27886177	4	681646	7	0	somatic_tumour	4328	27204.5	3R:27886177 4:681646	2781:2781_2784	0.19	0	-	-	CCCCAGGTAAGCTGCACAGCAGCACCATAGCCACCATTGCCACCAGCTGCAGAGCGATATTAATGTGAATGGCTGCCAAGCCGTGGCTCTAGAGGTGGCTCGAGGCGAACAGCTCTTTTCTACGCATACAGTGATAGCAGACAACTGTAT	-	-	CG34353, intron	CG11360, intron	CG34353, CG11360	NA	bp1_INE-1_Helitron=2; bp2_211000022278682_2; bp2_Dmel\F-element_LINE-like=3	0
A373R1	2793	novobreak	TRA	3R	28505348	2L	19858175	5	0	somatic_tumour	4349	8647.2	3R:28505348 2L:19858175	3to3	0.15	0	-	-	TTATGAGTCACTCCCATTTTTTGCGTTAATTGTTTTTTACACGACCAAAAAAAAAAAAAAAAAGCACCTGCATTTGAGCCCCACGCGGGTCGACATTGAGC	-	-	Dhc98D, intron	sick, intron	Dhc98D, sick	NA	-	0
A373R1	2799	novobreak	TRA	3L	22345448	X	1084302	3	0	somatic_tumour	3079	21261.1	3L:22345448 X:1084302	2092:2092_2799	0.12	0	-	-	GTCACGTTTCATGTGTCGACGGATACAGATCCAGGCGAGCGATTAAATCAATTATACGGAAATTATGAAAACTCAATTTGCAGGAAAATTCAAGTGATCTAGGGCATCACGCCAACAGCTCAGCCCCAT	-	-	CR45963, ncRNA	CG3655, intron	Ten-m, CR45963, CR44779, CG3655	NA	bp2_211000022280427_3	0
A373R1	2804	novobreak	COMPLEX_TRA	3R	29093901	X	9570740	3	0	somatic_tumour	4376	19523.2	3R:29093901 X:9570740	2804:2804_2990	0.17	0	-	-	TATAGTTATTGAGCTTTTATAGTCTGAGACCTTTTATTTTATTAAGTCTGCAGAAACACTTTGCCACTACCTTTCAGTTCAAAGTTTTTTCCAGCTGCCTTCCTCCACTCCGCTTTTC	-	-	CG11873, intron	Cubn, intron	CG11873, Cubn	NA	-	0
A373R1	2805	novobreak	TRA	3R	29124945	2L	19976776	3	0	somatic_tumour	4377	9148.2	3R:29124945 2L:19976776	5to5	0.14	0	-	-	AGGTTTAGAAGGTAGTAAGATTTCAATTAAGAAGATACTTCCCCAAAGACCAGCCCATCCAAAGCCATTCTTAAAGTTCATTTATCCAGTAGAAAACTTTGCT	-	-	CG11880, intron	CG43861, intron	CG11880, CG43861	NA	-	0
A373R1	2807	novobreak	TRA	3R	29167919	2R	15445156	3	0	somatic_tumour	4379	13722.8	3R:29167919 2R:15445156	3to5	0.11	0	-	-	CGCATGCGAATTAGAAGGGAACTTGATTTATTGGCAAACAGAATGATATTTCATCCTTGAATAGGATATCTACCTCCTGGACGATCCACTATCCGCCGTGGACTCTCATGTGAGCAAGATGCTCC	-	-	CG11898, exon_3	CG43729, intron	CG11898, CG43729	NA	-	0
A373R1	2811	novobreak	TRA	3R	29356650	X	14475084	3	0	somatic_tumour	4386	14881.6	3R:29356650 X:14475084	5to3	0.14	0	-	-	AATGTATCCTGTTTTCGGAAACCGGAAAAACTTTTCCAGGCACTGCATGATCCTGGCTGATCACCGGCTGGTCCGTTTCCGTTGCCGGGCAGGGACACAGGCAGTGGTGGTGGTCCGTAGTTCGGTGGCGGGGCATCGAAGATCTGCTTG	-	-	CR45547, exon_1	CG9411, exon_2	CR45547, CG9411	NA	-	0
A373R1	2816	novobreak	TRA	3R	29496606	3L	19987997	3	0	somatic_tumour	4394	9508.6	3R:29496606 3L:19987997	5to5	0.18	0	-	-	ATTCGGAACCACTTGCTTATATAAAAAAAAAAATATAGCTACACACGGGGCAAACTACAAAATCAAACCAACATTCAAGATCAATGAACTTTACACTTTCTTTGATGAATAGCATATCTA	-	-	CG2010, 5UTR	schuy, exon	CG2010, schuy	NA	-	0
A373R1	2818	novobreak	TRA	X	10029282	2R	17794206	4	0	somatic_tumour	4848	7764.9	X:10029282 2R:17794206	3037:1205_2818_3037	0.16	0	-	-	AAAAAAAAACATAAAACAAAACGAAAACTAAAACCTTCGGCGCGTTAATGCAATTAGCAAACTTGATTGTTCATCTCATAATCACATCGTATATAGTATAC	-	-	Cht6, intron	Dhit, exon_1	Cht6, Dhit	NA	bp1_roo_BEL=2; bp2_Dmel\R1A1-element_LINE-like=3	0
A373R1	2829	novobreak	TRA	3R	29896992	2L	17290172	3	0	somatic_tumour	4414	12606.8	3R:29896992 2L:17290172	3to3	0.09	0	-	-	CCAGTTTAAATCCACTTAAAAGCCTTGAGTTAAGGATCAACAATTAAATGTCTTGCAAATGGAAAGCTTCGCTGAAGGTGGGAAAATAATGGGCGCTTTCCTTAATGGTAAATGCATTTAATCCGATCCTCAGCTCCTCGTCGTCCTTCTCGTCCAGATTGAAGAAGCC	-	-	CG31038, exon_2	intergenic	CG31038	NA	bp1_mdg1_Gypsy/TABOR=8	0
A373R1	2837	novobreak	TRA	3R	30958706	X	15633295	3	0	somatic_tumour	4443	15325.4	3R:30958706 X:15633295	3to3	0.13	0	-	-	AAAAACTAGGGGCGACAATGAACAATGAAATAGAATATCGAGATATGGAAATATATGTTCTATATGTTCGTTTCGTTTATATGTATATGCGGGCATATATCAAGGAAATAAAAGTGGTTCCTTGACAACTTTGCCGCCTCCTTCGGCTTTTC	-	-	intergenic	sog, exon_1	sog	NA	-	0
A373R1	2853	novobreak	TRA	2L	8796945	3L	8681254	2	1	somatic_tumour	466	115.7	2L:8796945 3L:8681254	346:346_2853	0.12	0	-	-	GTTTGGGATTATTGTTTTAAAAAATTATCATTGCATCTCATGCCTGATGCTTTTATTTTAATGGTACATATGTTGTGCGCAACTGTGGCGAATTCGTTTTGTATTGTGGGCTGATGGC	-	-	intergenic	intergenic	-	NA	bp2_HeT-A_Jockey=3	0
A373R1	2857	novobreak	TRA	3R	31723068	2R	19386269	3	0	somatic_tumour	4481	12336.8	3R:31723068 2R:19386269	5to3	0.12	0	-	-	GTTAATTTGTGAGCCCTGTCACCGATTATACTTCCAACCTCCGCTCTCGCACACACACATGCATCTACCGCCCCACGAGGATGCCTCCAAAGGAGGATTCATTGCCGAAAGGGCACAGGCCAATCTTTATGAT	-	-	ttk, intron	CG10081, exon_2	ttk, CG10081	NA	-	0
A373R1	2865	delly	TRA	4	153406	2R	13870504	3	0	somatic_tumour	BND00001438	13717.1	4:153406 2R:13870504	5to3	0.2	0	-	-	GCGCCATTATAAAAATAGAAGGTTCACAAAAGAAGTTTTAGTTAAAAATACTTACGCGCTTGCGCCAATCGTCCCAGCTGAAGTTGCGGGCACGCTCCACA	-	-	CG32006, 3UTR	shot, intron	CG32006, shot	NA	-	0
A373R1	2872	Control-Freec	DUP	4	238800	4	246760	-	-	somatic_tumour	-	8	4:238800-246760	Heterozygous duplication	0.42	0.56	-	-	-	-	-	CG1674, intron	intergenic	CG1674	NA	snp_su:0; snp_op:1	0
A373R1	2875	novobreak	TRA	4	361203	2R	7716386	3	0	somatic_tumour	4511	7355.2	4:361203 2R:7716386	3to5	0.11	0	-	-	CGAGGTGGACATATTTGATCAGGTGGCTAATCCTCCGGACTCCTCGCTCCGTCGCTTCCAGAATGTGGTCAATAAATTAACATATTTAAGAAAAATTAAAT	-	-	Hcf, intron	CG1946, exon_5	Hcf, CG1946	NA	-	0
A373R1	2890	novobreak	TRA	4	767082	3R	29444279	3	0	somatic_tumour	4536	28677.2	4:767082 3R:29444279	3to5	0.11	0	-	-	CTTTATAATCGAGCATCAAACACAAAAAGCAGCGAGAGCATAAAAAGAAAATCAGAGCGCTTCTTCGAGCTAAAGACCCAATTGACCCACCATCGCCACCGGGCAGTCCTCAAATC	-	-	bt, exon_33	Ptp99A, intron	bt, Ptp99A	NA	bp1_17.6_Gypsy-like=8	0
A373R1	2911	novobreak	TRA	Tomelloso	89374	X	5502632	3	0	somatic_tumour	4581	5413.3	Tomelloso:89374 X:5502632	-	0.33	0	-	-	ACAGCACTTAATTCGTTGCTATTTTTCTTTACTGCTTCACATTTTCTTGGTCGCCGACCAGTGAAAAACCATGAGGAACGTCTTATTGTAATTGGGTGAACCTGT	-	-	intergenic	CG4151, 3UTR	CG4151	NA	-	0
A373R1	2932	novobreak	TRA	X	1507824	2L	2326470	3	0	somatic_tumour	4628	818.6	X:1507824 2L:2326470	3to3	0.14	0	-	-	GAACGGAGCGCGCTCTGCGGACTGAATTCGATGAGCCACCGAATGGCACTGTCAGGCAGCCATGGGATGGCTCCCGGTGCACATGTCTGTTATGGTCTTGGCACGGCATAAGCAC	-	-	inc, intron	eys, intron	inc, CG9967, eys	NA	-	0
A373R1	2937	novobreak	TRA	3L	6688918	X	2201760	1	2	somatic_tumour	2385	4487.2	3L:6688918 X:2201760	1665:512_1664_1665_1689_1690_2937	0.13	0	-	-	CTATAAACATGTAGCAGAGGGTCCAAAACAACATCTTCCCCCTCCGGTCGAACACCTTCATCCACGATAACTGAGTCCATAGTCCTGTGTAAATATTTTGCCAGCACTTGGTCTGGCAATATACGAGTCCTTGTGTGGAAAGACGGAGAAAACGGCACAGGAT	-	-	intergenic	CR43637, exon_1	Mct1, CR43637	NA	-	0
A373R1	2945	novobreak	COMPLEX_TRA	X	2361568	2L	1040805	3	0	somatic_tumour	4655	1320.8	X:2361568 2L:1040805	2945:2945_2946_3045	0.15	0	-	-	GAGTTTTTATATTTTATTTTCGTCAGCAGCTTTCAGGTTCAAAGCAATTAAGTAATAACACAAATCAAAGTTAACAAAGGCTAAACGTAAAAATAAAGGCCTCTTCGGCGAAAAAGGACCTCTCCGTCC	-	-	CG2841, intron	IA-2, intron	CG2841, IA-2	NA	-	0
A373R1	2945	novobreak	COMPLEX_TRA	X	10913342	3R	31508451	3	0	somatic_tumour	4864	20595.1	X:10913342 3R:31508451	3045:2945_2946_3045	0.1	0	-	-	CTTCGATGTGTCGTTGGCTCTTTATAAGGAGCCGAACAGAGGCCTTGGCCATTCAGTTGTCCGCTGGGCAAATGTTTATGTCAAACGAGAAGCTGCTCCCCGAGCCAAGCTGGGCAGGATGTCAAC	-	-	CG43901, intron	intergenic	CG43901	NA	-	0
A373R1	2953	Control-Freec	DEL	X	2992960	X	3136240	-	-	somatic_tumour	-	143.3	X:2992960-3136240	2953:2953_2954	0.95	-3.36	-	-	-	-	-	kirre, intron	N, intron	kirre, CG4116, N	NA	snp_su:0; snp_op:0	0
A373R1	2953	novobreak	DEL	X	2993986	X	3135245	4	5	somatic_tumour	4673	141.3	X:2993986-3135245	2954:2953_2954	1	-3.4	-	-	CATATAGACAGATTCCAAGTGTCCCCCAGTCTCCGAAAACCAAAACCAAATCCAAATCCAAATCCAAAGCCAAAGCCAAAAACCAAAACTTCCCAAATACATTTCAATTTGTGCGGCTATGGCGATAAGTCCAAGTTTATCCTGTGGCAAACTGGAAGCGCAAGAGGAAGAGAGCAAGAGTGCGGCGTCGGTTTGAATTTGAATTTGTGGCTCGATCCTCGCGAAGAGA	-	-	kirre, intron	N, 5UTR	kirre, CG4116, N	NA	snp_su:0; snp_op:0	0
A373R1	2953	CNV-Seq	DEL	X	2994440	X	3135403	-	-	somatic_tumour	-	140	X:2994440-3135403	2954:2953_2954	0.96	-3.4	-	-	-	-	-	kirre, intron	N, 5UTR	kirre, CG4116, N	NA	snp_su:0; snp_op:0	0
A373R1	2968	lumpy	BND	X	4041826	X	6740758	4	0	somatic_tumour	12421_1	2698.9	X:4041826-6740758	3to3	0.15	0.01	-	-	-	-	-	intergenic	intergenic	-	NA	-	0
A373R1	2974	novobreak	TRA	X	4858505	2L	99087	3	0	somatic_tumour	4709	4759.4	X:4858505 2L:99087	3to3	0.13	0	-	-	ACAGGTGCTAAAAGTATGTGCACAGGACTCGCATATATAGAAAGCTTCGGCATTAGTTTTTAGTTTTGAAGCATTTGGTGCACTCTATGCGGACTTAAATCCATA	-	-	CG42594, intron	Zir, exon_6	CG42594, Zir	NA	-	0
A373R1	2998	novobreak	BND	X	6488371	X	6723574	3	0	somatic_tumour	4756	235.2	X:6488371-6723574	3to3	0.12	-0.03	-	-	TCTTGCGACCAAAGCTATCGGCGATGCTGCCCCAGAAGTAAGCGCCCACCATCATGCCGATGAAGATGATCGAGTTCAGCCAGCCCTTGCTTCAGTTTTCCCGCTTTGCCCCACTTTCATTGAACTCTGCGTACACGGAGAGAAATCAATTGCAAACTCATTACTA	-	-	CG42340, intron	CG3168, exon_3	CG42340, CG3168	NA	-	0
A373R1	3006	novobreak	TRA	2R	20675427	3R	25614365	3	0	somatic_tumour	1822	4938.9	2R:20675427 3R:25614365	1303:1303_3006	0.11	0	-	-	ATGTTTCTACCTTGAAAATGCATCAAAAAATATTTCATATCAGTTTCGATTCTATCCTTGCAATGGACAACAATGGTTCTGCAGCCGGATTCGGAATGGTGTCTGATGGC	-	-	intergenic	CG5079, 3UTR	Npl4, CG5079	NA	-	0
A373R1	3031	novobreak	COMPLEX_BND	3L	773471	3L	17169554	3	0	somatic_tumour	2065	16396.1	3L:773471-17169554	1455:1455_3031	0.1	0	-	-	CAGCAATTGTTGCATGTAATTAACCAACTTTGACATGTCTAGTTATGCGTTGCTTCGGTAGGCGTAACTTCAATCCAATGTTCAAGTGGGTCACACAAAATTGCAGAACAAAAGCAGGAGGAGGCCGAGTGCCACAAAGTTGAGGACAGAGATTGTTGCAATTTCAGGGGTGACGATA	-	-	intergenic	Rbp6, intron	Rbp6	NA	-	0
A373R1	3047	novobreak	TRA	3L	2792826	2R	6691710	3	0	somatic_tumour	2170	3898.9	3L:2792826 2R:6691710	1525:1525_3047	0.1	0	-	-	TCCTTGGGTTGTATACCCAATCCCAGGCAGGTTCCGTCCTTTAAGTGCTCGGCGGTGGGTGGACGAGTGCCGCCTCAAAATGATGCACTACCGCAAGGCCGAGAA	-	-	Tet, exon_6	CG9422, 5UTR	Tet, CG9422	NA	-	0
A373R1	3071	novobreak	TRA	X	13204168	3L	10945030	3	0	somatic_tumour	4908	2259.1	X:13204168 3L:10945030	3to5	0.11	0	-	-	CAGGTCAACAGCAGCAGCAGCAGCAAGAGCAACAGCAGCAATCCGAACGTGTTGCTGATACGTGCGGAAAAAAGGATGGAAAGTTTTTGTAAGTATTATGTTATCTTCAAAATAAGTTGTACAAATTAT	-	-	sno, intron	intergenic	sno	NA	-	0
A373R1	3074	novobreak	COMPLEX_TRA	X	13367330	2R	16621538	3	0	somatic_tumour	4914	3254.2	X:13367330 2R:16621538	3075:1160_3074_3075	0.16	0	-	-	AGACAGGTAAAGGACAATAACTTTGCAAGCATTTACCATATGATTCCATGTTAAACTTGGGCTTCTCCTGACGCAGTGATTCGAAGAGCTAAGGAATATATCTGTCT	-	-	Syt12, 3UTR	CG5065, exon_4	Syt12, CG5065	NA	bp1_opus_Gypsy=7	0
A373R1	3096	novobreak	TRA	3R	7717269	3L	2366535	4	0	somatic_tumour	3418	5350.7	3R:7717269 3L:2366535	2271:751_2271_3096_3097	0.13	0	-	-	TGTTTGTTCTGCGGTGCAGAGTTCAATGGGTCGTGAAATTTCGGCGCCATAAAATTGCATTGCATTTTGATGCCATGTCAGCCGGGAGAATGTTTGCGA	-	-	intergenic	intergenic	-	NA	-	0
A373R1	3130	novobreak	BND	X	18123863	X	18124056	7	0	somatic_tumour	5028	0.2	X:18123863-18124056	3to3	0.46	0	-	-	CCCCAGACATAATCTGCAAAGGACACTGTTTGCGACATCAGAGATGGCGATGTGATGCTGGTTCTGCCGCTGAGTCGCGATGATAAAAAAAATGAAGGAAAAAGGAAAATACCGAGGAGCACGAAGGCTTGGGGCCCAGTGACGTCACGGCTGGCATTCATTCACAGGATGTGAGGCATGCATCCAATGGCGGCCGCGCTGCTGTGCTGCAAATTGAGATTTTCAATTTTGCGTTTTTACGTGGAACG	-	-	intergenic	intergenic	-	NA	bp1_Dmel\F-element_LINE-like=5; bp2_Dmel\F-element_LINE-like=5	0
A373R1	3135	novobreak	TRA	2L	3430606	2R	13302064	5	0	somatic_tumour	207	9871.5	2L:3430606 2R:13302064	143:143_1065_1304_3135	0.18	0	-	-	GCATAAGGAAAGTGGGAACAATTGCAATGCGAAAATTTAATTAAGTTGCAGCCGGAGCAAGCAGGAACTTTTCTGCCCCCCACCTGGATCCTTCGCGGGAACCCGAGGGGCTCCACCGGCTGGCTGGCTGGGTGAGAGTGATTCTCGGAGCCGGCGCTGCTAAATGAGCCATGATCGCTGGAAGAA	-	-	intergenic	intergenic	-	NA	-	0
A373R1	3135	novobreak	TRA	2R	13307015	3L	8948818	3	1	somatic_tumour	1474	4358.2	2R:13307015 3L:8948818	1065:143_1065_1304_3135	0.13	0	-	-	ATCCGCATCCCTCTTCGGCGTAAGTAAAAAGTGCAGCAATAGTGAAATGCTGTCCAAGAAATAGGAAAACGCCTATCTAAGTTACCATAAGCGTTATGGCCATGGCCAAAACAGTGTCGATGATGCCCGAAAAGTTGGCGCAATGGAGCGCGAAACTAATAAGGATAACGCGCGGG	-	-	intergenic	orb2, intron	CG43783, orb2	NA	-	0
A373R1	3142	novobreak	TRA	3L	1240576	2L	16116646	3	0	somatic_tumour	2092	14876.1	3L:1240576 2L:16116646	1470:576_578_1470_3142	0.11	0	-	-	AGACAGTCTTTTAACTTTTTAATGAACTCCAAGTTAACTTTAAATTCAGTTTAAAGGTCTAAATTGAGAAATCAAAGGGATCAAGGCCCTAGACTCCATGCCCAGATCTGCTCACCAAAGGCAACGCCAGAAGGACAGAGAACGGGAACGATCTCC	-	-	CG9194, exon_5	intergenic	CG9194	NA	bp1_Circe_Circe=3	0
A373R1	3144	novobreak	TRA	X	19590257	3R	4898617	3	0	somatic_tumour	5063	14691.6	X:19590257 3R:4898617	3144:1561_3144	0.16	0	-	-	CACACGTTCAGCGCTGATAATCAATTCTTATCTATAGTCTCCTTCCATCAGCTAATATTGATTGCTATTGATGAGATCCCGCCTTTGATGATATGGGTACTGT	-	-	intergenic	intergenic	-	NA	-	0
A373R1	3150	novobreak	TRA	X	20285348	2L	6186256	3	0	somatic_tumour	5079	14099.1	X:20285348 2L:6186256	5to5	0.14	0	-	-	GCGCCTTGGGATCAAATTAGTCGAGTTTTTGAAAAAAAAGCTTACATATACGTGTGGCAATCAATGCAACTGAGCGGGGCACGTCATCAGTGATGGTAGCGAAACAAGGATCATTGCGGCTGGTGCATACCCCTCAGCCGTATGTATGT	-	-	intergenic	CG34380, intron	CG34380	NA	-	0
A373R1	3157	novobreak	TRA	X	21233073	2R	3184553	3	0	somatic_tumour	5094	18048.5	X:21233073 2R:3184553	3to3	0.14	0	-	-	GACCACCTTTGGCCCGAACTTTTCCGGCAGAAAAGCAGAAAAACAGTTTTCGCTCTCCACTCTGCCTGTTTCAATAGAAAGTGATGCCATTCGGACTGCACTCCGC	-	-	CG32521, intron	dpr21, intron	CG32521, dpr21	NA	bp2_gypsy8_Gypsy=4	0
A373R1	3166	novobreak	TRA	Y	472705	3L	17470613	3	0	somatic_tumour	5121	16997.9	Y:472705 3L:17470613	3to3	0.13	0	-	-	CACTCACTTCTTCTCCGTGCTATCCTTCGAACCACACTCGGCGACAGCGACCATACGCTGCCGCTAGCGAAATGATTCGATTTCGTTGGCTTGTAAAATTATATGCT	-	-	kl-3, intron	CG7589, 5UTR	kl-3, CG7589	NA	bp1_Stalker4_Gypsy=2; bp2_Stalker4_Gypsy=6	0
A373R3	3	novobreak	TRA	2L	647432	X	6244020	3	0	somatic_tumour	4	5596.6	2L:647432 X:6244020	5to5	0.07	0	-	-	TTATTGACAATCAATGATGACAACAATTGCTTGTTCCTGCGTTGCTTTGTAATGGAAGTAACCGTGTTCCAAACGCTATTCTCATCGGTCGGCTCTTCGGATGTGGAACCAGTACCACCACTTGCTCCG	TCCGAAGAGCCGACCGATGAGAATAGCGTTTGGAACACGGTTACTTCCATTACAAAGCAACGCAGGAACAAGCAATTGTTGTCATCATTGATTGTCAATAA	NHEJ	ds, intron	Rbcn-3A, exon_5	ds, Rbcn-3A	NA	mh:0; ins:0; tup:0; tdown:0	0
A373R3	9	novobreak	BND	2L	2380873	2L	12288901	3	2	somatic_tumour	10	9908	2L:2380873-12288901	3to3	0.06	0	TTTACGAA	-	CATAAATTGTCCGGAATAGTGTGAAGCCATTCAAAAATTCGTATTAAAATAACGGTCTAAATGGTTTACGAAACCGATTGCAGTTGAATTATTTATCATGTCAGATGATGATGAG	CATAAATTGTCCGGAATAGTGTGAAGCCATTCAAAAATTCGTATTAAAATAACGGTCTAAATGGTTTACGAAACCGATTGCAGTTGAATTATTTATCATGTCAGATGATGATGAG	Alt-EJ	intergenic	bru1, intron	bru1	NA	mh:8; ins:0; tup:0; tdown:0	0
A373R3	12	novobreak	TRA	2L	2565270	2R	13513152	3	0	somatic_tumour	13	10947.9	2L:2565270 2R:13513152	5to3	0.06	0	T	-	GGCCAATGGAACACCTATAAGGACACAAGTGAAAGTTCACCAACAACTTCAGTTACATATTTGTATTTTGCATTTGCATTGTTTCAAATTTATTGATGGGCGAGTATATTAAACTCAACGCAA	GGCCAATGGAACACCTATAAGGACACAAGTGAAAGTTCACCAACAACTTCAGTTACATATTTGTATTTTGCATTTGCATTGTTTCAAATTTATTGATGGGC	Alt-EJ	Cyp309a2, intron	Vmat, 3UTR	Cyp309a2, Vmat	NA	mh:1; ins:0; tup:0; tdown:0	0
A373R3	13	novobreak	BND	2L	2615845	2L	6605512	3	0	somatic_tumour	14	3989.7	2L:2615845-6605512	5to5	0.04	-0.04	GCC	-	ATGGAAGAGACAGGAAAAAAAAAATAGGAAAAAACTCATCAGGCTTAAACTACTTAAACTTTAGTCCGTAGTAAAGATTTTTGGTGTCAAAGTTTCAGTGCAACAAGTTTGGGAAAATATAAAAGATAAATATATGTATC	GCACTGAAACTTTGACACCAAAAATCTTTACTACGGACTAAAGTTTAAGTAGTTTAAGCCTGATGAGTTTTTTCCTATTTTTTTTTTCCTGTCTCTTCCAT	Alt-EJ	intergenic	intergenic	-	NA	bp2_Dmel\1360_P=2; mh:3; ins:0; tup:0; tdown:0	0
A373R3	15	novobreak	TRA	2L	3829232	X	18495746	3	0	somatic_tumour	17	14666.5	2L:3829232 X:18495746	5to5	0.08	0	GGGATTTC	-	GGTATACCCAACCAATTCTATTCTAAAGTGATATGTAGTTTAAGAAATCCCCCAGGCTTGGATCCTCCCAAATATCAATTGAATATCTATTGTATGAGATTCGCCGATCGAAATGGGAATGGGTTCACTA	AATCTCATACAATAGATATTCAATTGATATTTGGGAGGATCCAAGCCTGGGGGATTTCTTAAACTACATATCACTTTAGAATAGAATTGGTTGGGTATACC	Alt-EJ	intergenic	GalNAc-T2, 3UTR	GalNAc-T2	NA	mh:8; ins:0; tup:0; tdown:0	0
A373R3	22	novobreak	TRA	2L	5445521	3R	12213592	3	0	somatic_tumour	24	6768.1	2L:5445521 3R:12213592	3to3	0.06	0	CAAATTA	-	CTTCATTGCTGCGTAGCTGTCACAATTTGTAGGAAATTAATTCCAAGTGGCCAAAATAAATAAACAGTCACAAATTACATTGGATAACTTTAAAACGAAAAACTTACCA	CTTCATTGCTGCGTAGCTGTCACAATTTGTAGGAAATTAATTCCAAGTGGCCAAAATAAATAAACAGTCACAAATTACATTGGATAACTTTAAAACGAAAAACTTACCA	Alt-EJ	intergenic	intergenic	-	NA	mh:7; ins:0; tup:0; tdown:0	0
A373R3	24	novobreak	TRA	2L	6096637	2R	19944064	3	0	somatic_tumour	26	13847.4	2L:6096637 2R:19944064	3to5	0.05	0	C	-	GTCGGTTTACCATTTGCATTTGATTTGTTGTCACCCATTGTTATTGCCTCTGTTATTTTATGCAAATTCGCTCGTTGGAATATTTTACCATGTTTGCCACCTCATTGAAAGCGAATAAAACATCGAAATTTCATTACTGAATGCATTTTTATATAT	GTCGGTTTACCATTTGCATTTGATTTGTTGTCACCCATTGTTATTGCCTCTGTTATTTTATGCAAATTCGCTCGTTGGAATATTTTACCATGTTTGCCACC	Alt-EJ	intergenic	intergenic	-	NA	mh:1; ins:0; tup:0; tdown:0	0
A373R3	33	novobreak	TRA	2L	8797450	2R	11568588	3	0	somatic_tumour	33	2771.1	2L:8797450 2R:11568588	3to5	0.05	0	-	-	TGTCCAAAAGGGGACCTGGTGGGGGGGGGGATCGGATCCTAGAAAATGCACTGAGAAACAAGGATTTTATTTTAGGATTCATGTTGGCCATGCGCGAGCCTCGACCT	AAAGGGGACCTGGTGGGGGGGGGGATCGGATCCTAGAAAATGCACTGAGAAACAAGGATTTTATTTTAGGATTCATGTTGGCCATGCGCGAGCCTCGACCT	NHEJ	intergenic	intergenic	-	NA	mh:0; ins:0; tup:0; tdown:0	0
A373R3	39	novobreak	TRA	2L	9843172	2R	8311676	3	0	somatic_tumour	39	1531.5	2L:9843172 2R:8311676	5to5	0.05	0	-	-	GTTTTCAAATGTTAAACATCTTCCAAAAGCAAACCATAGAAAATGTTGATTAAAGTTTTGCTTTTTCAGTTTCCTGGCTAAATTGCACAAAAACTGGAGGGTAATCGGAGGGGAGAGCACGTGTGTATGGAGTGTGTGTTCTTAACATAACACATAAACACAAGTA	CCCTCCAGTTTTTGTGCAATTTAGCCAGGAAACTGAAAAAGCAAAACTTTAATCAACATTTTCTATGGTTTGCTTTTGGAAGATGTTTAACATTTGAAAAC	NHEJ	nAChRalpha6, intron	CR44450, exon_1	nAChRalpha6, CR44450	NA	mh:0; ins:0; tup:0; tdown:0	0
A373R3	60	novobreak	TRA	2L	16418430	2R	13530335	4	0	somatic_tumour	58	2888.1	2L:16418430 2R:13530335	3to3	0.08	0	-	-	AAATGAAGCCGATGGCAATTGGGCGACAGGGGAAATGAAAGGCCAACCTGGGAGCTGCTGACTGGCAGCAATCGAAAGCTATGCAAATTAAAAAAATTGCAATAAATTCTCCTGGTTTACATGCATTATTCTGGTATGGAATAAAAACATACACGCGATATG	-	NHEJ	CG5888, intron	Vmat, intron	CG5888, Vmat	NA	bp1_rDNA_2; mh:0; ins:0; tup:0; tdown:0	0
A373R3	80	novobreak	TRA	2R	5850303	3R	5246121	3	0	somatic_tumour	85	604.2	2R:5850303 3R:5246121	3to5	0.04	0	-	-	AACTTTATGGCATTTTAAACAACATCGCAAGCCATACCAAATGGAGGCCTGCCATGCATACAAAAGCAGGAATAAATAATGTGAGTGTGTGTGTGTACAAACATTTTCGCTTTCTATCTTTTCACCACCAAAACCA	AACTTTATGGCATTTTAAACAACATCGCAAGCCATACCAAATGGAGGCCTGCCATGCATACAAAAGCAGGAATAAATAATGTGAGTGTGTGTGTGTACAAA	NHEJ	dpr12, intron	CG12163, intron	dpr12, CG12163	NA	mh:0; ins:0; tup:0; tdown:0	0
A373R3	81	novobreak	TRA	2R	6532200	2L	21283344	3	0	somatic_tumour	86	14751.1	2R:6532200 2L:21283344	3to3	0.04	0	T	-	CAATCCGGTCAGGGTGTCATAGCTAAGTTGGTGGTTATGGCTAGACTGAAGGTCAACCCGGAGCTCCGCCTGCAATCGATATTTACCTGCGACTACTTGGCCGTTAAGGGTTTCGGGTACCAGTGAATCAGTTC	GTTATGGCTAGACTGAAGGTCAACCCGGAGCTCCGCCTGCAATCGATATTTACCTGCGACTACTTGGCCGTTAAGGGTTTCGGGTACCAGTGAATCAGTTC	Alt-EJ	jing, intron	Cyp6t2Psi, exon_1	jing, Cyp6t2Psi	NA	bp1_copia_Copia=17; mh:1; ins:0; tup:0; tdown:0	0
A373R3	91	novobreak	TRA	2R	9334321	3L	12325601	4	0	somatic_tumour	99	2991.3	2R:9334321 3L:12325601	3to5	0.07	0	CCAAAAC	-	TGCCTAGGTCCTGCGGAACCTACCCAAACTCCGAGTGGCGAGCCTTGCCAAAACCAGACGATAACTTTGACCGGAGACCGGAGCCGAAACCTTTTGCCTGTTTGCATTAAAAGCTTTTTAATTTGTATTC	TGCCTAGGTCCTGCGGAACCTACCCAAACTCCGAGTGGCGAGCCTTGCCAAAACCAGACGATAACTTTGACCGGAGACCGGAGCCGAAACCTTTTGCCTGT	Alt-EJ	CG13954, intron	intergenic	CG13739, CG13954	NA	bp1_Dmel\1360_P=4; mh:7; ins:0; tup:0; tdown:0	0
A373R3	92	novobreak	BND	2R	9418566	2R	10140104	2	1	somatic_tumour	100	721.5	2R:9418566-10140104	3to3	0.03	0.02	GCACT	-	CTGTTCATCTTCATCAAGTGCCAGCTGGACATTCTGGCCGTCCGACTGGACAAGATCGGTCGGTTAATCACTACTTCTGGTGGCACTCAGGCCACTCGGACATCACGAAAAGATTGATGTGGCCGTAAAAGATCGAAAGACAAACAAGACATC	AGATCGGTCGGTTAATCACTACTTCTGGTGGCACTCAGGCCACTCGGACATCACGAAAAGATTGATGTGGCCGTAAAAGATCGAAAGACAAACAAGACATC	Alt-EJ	intergenic	Or46a, exon_1	CR43467, Or46a	NA	mh:5; ins:0; tup:0; tdown:0	0
A373R3	95	novobreak	TRA	2R	10667716	3L	9876984	14	0	somatic_tumour	104	790.7	2R:10667716 3L:9876984	5to5	0.21	0	CAA	-	CTCCTGACTGCGGCTGACGGACGGAGTCAAGTCGGTGGCCAAAATACATTCAATCAATTTTCGGTGTTCAGTGTGCGCAAGCAGTTTAAGCTTCAATTAAAAAT	CTCCTGACTGCGGCTGACGGACGGAGTCAAGTCGGTGGCCAAAATACATTCAATCAATTTTCGGTGTTCAGTGTGCGCAAGCAGTTTAAGCTTCAATTAAAAAT	Alt-EJ	intergenic	intergenic	-	NA	mh:3; ins:0; tup:0; tdown:0	0
A373R3	100	novobreak	TRA	2R	12455384	3L	8284008	1	2	somatic_tumour	113	4171.4	2R:12455384 3L:8284008	3to3	0.05	0	G	-	TCGTTACATCCGATAGCCAGCTTAATTCCCGGGGCTTTGTATCTATCAGCTATCAGCTTCGGCTTGTGCAATCTTTAATTGCCACGGCATTGAGCAGATCGATCGCGTGTGCAAGGAGCAACTGCATTACGCACGCGAGGGCGT	TATCAGCTATCAGCTTCGGCTTGTGCAATCTTTAATTGCCACGGCATTGAGCAGATCGATCGCGTGTGCAAGGAGCAACTGCATTACGCACGCGAGGGCGT	Alt-EJ	Lac, intron	cert, intron	Lac, cert	NA	mh:1; ins:0; tup:0; tdown:0	0
A373R3	101	novobreak	TRA	2R	12682096	3R	14789306	3	0	somatic_tumour	114	2107.2	2R:12682096 3R:14789306	3to3	0.04	0	-	-	GTTCCGAGAGCAGGTGGAGCGATTAAATCGCGAGGATATCAAACAGCTGCGCAAGGAGCGCGACCGTCTGCTTGACAAGTTTGGAGAACTCGGTGAGCCTGGAGAAATCGCAGGGCCTCAATAATTCGGACAGTTC	GAACTGTCCGAATTATTGAGGCCCTGCGATTTCTCCAGGCTCACCGAGTTCTCCAAACTTGTCAAGCAGACGGTCGCGCTCCTTGCGCAGCTGTTTGATAT	NHEJ	CG8771, exon_6	jvl, exon_4	CG8771, jvl	NA	mh:0; ins:0; tup:0; tdown:0	0
A373R3	113	Control-Freec	DUP	2R	17263776	2R	17279648	-	-	somatic_tumour	-	15.9	2R:17263776-17279648	Heterozygous duplication	0.34	0.56	-	-	-	-	-	mbl, intron	mbl, intron	mbl	NA	snp_su:37; snp_op:28; snp_ratio:1.32	11.72
A373R3	121	novobreak	TRA	2R	21549103	3R	13697225	3	0	somatic_tumour	139	7851.9	2R:21549103 3R:13697225	5to3	0.05	0	G	-	GGCGGTGTCTGTTTGCACAGTACTTTGAGGCAAATGTTTGTATTTGGCGGGCAAACAGAAAAGTAAAAATTAAATGGATCTGGAATGGAAGATAATTATTATAATTGGGATTTCATTTCA	GTACTTTGAGGCAAATGTTTGTATTTGGCGGGCAAACAGAAAAGTAAAAATTAAATGGATCTGGAATGGAAGATAATTATTATAATTGGGATTTCATTTCA	Alt-EJ	Egfr, intron	f-cup, exon_8	Egfr, f-cup	NA	mh:1; ins:0; tup:0; tdown:0	0
A373R3	128	novobreak	TRA	2R	23141212	3R	21364381	3	0	somatic_tumour	147	1776.8	2R:23141212 3R:21364381	5to5	0.04	0	CCCTT	-	CATAGATAGCGACCAAACTGGAAACTGGAAATGGCGTCAAGGGAGGTAGATGTGTTTTGACAGACATTAGTTGAGGTTATTTTGGGAGATCCAGGTGAGACCACTAACTAGTGCACAAT	GTCTCACCTGGATCTCCCAAAATAACCTCAACTAATGTCTGTCAAAACACATCTACCTCCCTTGACGCCATTTCCAGTTTCCAGTTTGGTCGCTATCTATG	Alt-EJ	intergenic	pre-mod(mdg4)-AB, 5UTR	mod(mdg4), pre-mod(mdg4)-C, pre-mod(mdg4)-E, pre-mod(mdg4)-AB	NA	mh:5; ins:0; tup:0; tdown:0	0
A373R3	130	novobreak	TRA	2R	23480790	3R	6773848	3	0	somatic_tumour	150	16706.9	2R:23480790 3R:6773848	3to3	0.05	0	GTAG	-	TTTCTCCGGCCGACGGGCAAGGAAAGCCGGAGAAAGGACGTGGCTATGGCCACAACTCCGGCGTGAAAATGCGGACGAGTAGTTTTCGGGGGGCCGAAAGGAAAATGGCTTCATCGGAAGGCGACTGTAAAAATTCGCCATGA	GCTATGGCCACAACTCCGGCGTGAAAATGCGGACGAGTAGTTTTCGGGGGGCCGAAAGGAAAATGGCTTCAACGGAAGGCGACTGTAAAAATTCGCCATGA	Alt-EJ	CG43795, intron	CR42721, ncRNA	CG43795, CR42721	NA	mh:4; ins:0; tup:0; tdown:0	0
A373R3	139	novobreak	BND	3L	1355758	3L	17182517	3	0	somatic_tumour	159	15826.8	3L:1355758-17182517	5to5	0.03	0.01	-	-	CACTCGCTTTCCTCTTCAAAATTTATGTTTGCTGGCTATGAAAATGAAATGACTGTGGTAAACATTTTAATTAAATCCACGTTGCCAGAGGAACTAGTTAAATGGATCTGTCGAGAGGGTAGGTAAATCATTTTGCTAATTCGTTTTGCATTCAATGCCAATT	-	NHEJ	Ptp61F, intron	Rbp6, intron	Ptp61F, Rbp6	NA	mh:0; ins:0; tup:0; tdown:0	0
A373R3	143	novobreak	TRA	3L	3277631	3R	18109064	4	0	somatic_tumour	165	14831.4	3L:3277631 3R:18109064	3to5	0.07	0	-	-	GCATAGTTGCCTTCCAAGCAGTTGACCCGGGTTCGATTCCCGTTCGACTTGAGTAACGAGACGAGTCGAGATGTGTCCACTCGAGCCGAGCTGAGTCCGTGG	-	NHEJ	intergenic	tRNA:Gly-TCC-1-4, tRNA	sr, tRNA:Gly-TCC-1-4	NA	mh:0; ins:0; tup:0; tdown:0	0
A373R3	145	novobreak	BND	3L	3943272	3L	8345790	3	0	somatic_tumour	167	4402.5	3L:3943272-8345790	3to3	0.03	0	TGCG	-	GGTCACAACTCTATCGTCTTGGTCCTCCCTGTCGGAGGGTACAGTGTGCTCCATCCGGAACACCAGCTCCTCCTTGTCAAAGTCGCAAAAACTAGACCAGACCAAGGTGAAACGAATGAGCCAGCGACGACACGCAC	GTGCGTGTCGTCGCTGGCTCATTCGTTTCGCCTTGGTCTGGTCTAGTTTTTGCGACTTTGACAAGGAGGAGCTGGTGTTCCGGATGGAGCACACTGTACCC	Alt-EJ	CG14982, exon_1	CG7182, exon	CG14982, CG7182	NA	mh:4; ins:0; tup:0; tdown:0	0
A373R3	147	novobreak	BND	3L	4542472	3L	6515347	3	1	somatic_tumour	170	1972.9	3L:4542472-6515347	3to3	0.04	0	-	-	CAATTAAAGTCGGACAACACCATCGTTAAATGAATTAAAAGTGAATAAAAGCGCTGTCAACGCCTTTTTGGCCCTGCCTCATGTAAAAGCAATAAATAATGGCCCAGTTTATAC	-	-	CG11357, exon_1	sfl, intron	CG11357, sfl	NA	-	0
A373R3	148	novobreak	TRA	3L	4762617	2L	13601230	3	0	somatic_tumour	171	8838.6	3L:4762617 2L:13601230	3to3	0.06	0	C	-	CTCATCGATCCTTTGCCTTTGCCTAAACTGACGTAAATTTATAATGACAAATTGCATTTGGCGAAGTGCAACCGATGTATTTCATTGTGTTGGTAAATTATAATTAAGC	GCTTAATTATAATTTACCAACACAATGAAATACATCGGTTGCACTTCGCCAAATGCAATTTGTCATTATAAATTTACGTCAGTTTAGGCAAAGGCAAAGGATCGATGAG	Alt-EJ	RhoGEF64C, intron	kuz, intron	RhoGEF64C, kuz	NA	bp2_Stalker4_Gypsy=2; mh:1; ins:0; tup:0; tdown:0	0
A373R3	152	novobreak	TRA	3L	7116471	2R	4966685	20	0	somatic_tumour	177	2149.8	3L:7116471 2R:4966685	5to5	0.27	0	A	-	CCTTTAAAAAATTCTAATTCCGAATGAAAGTCAACAGAACTCGTATTTGCCTTCGTTATTTCAGGGGGATTGTTAGAACCGTGTCAAGAATAGACATTTTCGATTACTGAAGTATTTTTATGGAGTGTCCAAAGAGTCGAAAACACAATTGGAA	CCTTTAAAAAATTCTAATTCCGAATGAAAGTCAACAGAACTCGTATTTGCCTTCGTTATTTCAGGGGGATTGTTAGAACCGTGTCAAGAATAGACATTTTC	Alt-EJ	form3, intron	Ir41a, intron	form3, Ir41a	NA	bp1_gypsy9_Gypsy=3; bp2_gypsy9_Gypsy=12; mh:1; ins:0; tup:0; tdown:0	0
A373R3	158	novobreak	BND	3L	9039625	3L	12080473	3	0	somatic_tumour	184	3040.8	3L:9039625-12080473	5to5	0.03	0.02	CTGCTGC	-	GAACGGCGCCAGAGAATCGTAAAATATTTTTATACAAATATCGCAGCAGATAAACGAATGTATTGGGGTGTCATAAAAGCGGTTTGTTGGGGAACTCGGTTAAATCGAGATCATTG	CAATGATCTCGATTTAACCGAGTTCCCCAACAAACCGCTTTTATGACACCCCAATACATTCGTTTATCTGCTGCGATATTTGTATAAAAATATTTTACGATTCTCTGGCGCCGTTC	Alt-EJ	intergenic	Sema-5c, intron	Sema-5c	NA	mh:7; ins:0; tup:0; tdown:0	0
A373R3	163	novobreak	TRA	3L	12130274	3R	10211411	3	0	somatic_tumour	190	1918.9	3L:12130274 3R:10211411	3to5	0.06	0	GTGCCA	-	GCCTACTAACCGGATTTTCTCTCCCTCAATAAGCAATTGCGGTTAAGATAATGTTAAGGTGCCAACCGAATCCGGCTATGCCAGCAACCTGCGCACCTACTACGGCGTACCCCAATGGCACCGGGAGAA	GCCTACTAACCGGATTTTCTCTCCCTCAATAAGCAATTGCGGTTAAGATAATGTTAAGGTGCCAACCGAATCCGGCTATGCCAGCAACCTGCGCACCTACT	Alt-EJ	Lsp2, exon	Timp, intron	CR11538, Lsp2, Syn, Timp	NA	mh:6; ins:0; tup:0; tdown:0	0
A373R3	168	novobreak	TRA	3L	16590696	3R	31425288	3	0	somatic_tumour	200	14834.6	3L:16590696 3R:31425288	5to3	0.05	0	C	-	CTTGTGCTCCTTCTTTCTGCTGTCCCTCTCCCTGTTAGCAATCAGTGAGCGCCAAAATCAATTTATCTAAGAGCTAATCAAAGCCGGTCGGTCTGCCAATCCTTTCGACCGGCAATTAAAGCG	CTTGTGCTCCTTCTTTCTGCTGTCCCTCTCCCTGTTAGCAATCAGTGAGCGCCAAAATCAATTTATCTAAGAGCTAATCAAAGCCGGTCGGTCTGCCAATC	Alt-EJ	tra, exon_2	Gprk2, intron	tra, Gprk2	NA	mh:1; ins:0; tup:0; tdown:0	0
A373R3	170	novobreak	BND	3L	16701356	3L	21227591	7	0	somatic_tumour	203	4526.2	3L:16701356-21227591	3to3	0.08	0.02	-	-	GCCTAATGCTCCTCTTCTACGCAATCAAATGTCTGTTTGCTCTTCTCTATTTAAATTGGGCATTACCAACGCTCCGGTGATATATGTTTCCTCCTGCTTAACTTGGAGCTGCTGCTGCTCCGAAGACGAGTGCTTCACACAGGTTTCGACCAGCAGTTT	-	-	CR45897, ncRNA	Eip78C, exon_2	Lasp, CG43954, CR45897, Eip78C	NA	-	0
A373R3	178	novobreak	TRA	3L	22127698	X	3678445	3	0	somatic_tumour	216	18449.3	3L:22127698 X:3678445	5to3	0.06	0	TTACCCC	-	CTTAAGGCAGGCGGGAGATGGCAGGAGTATTCTAATCCAATCGAAGCATTTATCAGCGTAACCGATCGACAAAAGTCGAGAGTTATGCATCAAAGTCACGAGGCGATGAGCTAACTGAGATAGTCTCGTCCCCAGAGCAATTACCCCTTCATTTTTATTTGCTAGCATCCAAGTCAATGTTACTTGACATTTATC	GTCACGAGGCGATGAGCTAACTGAGATAGTCTCGTCCCCAGAGCAATTACCCCTTCTTTGTTATTTGCTAGCATCCAAGTCAATGTTACTTGACATTTATC	Alt-EJ	intergenic	Mnt, intron	Mnt	NA	mh:7; ins:0; tup:0; tdown:0	0
A373R3	196	novobreak	BND	3R	9861512	3R	30513691	3	0	somatic_tumour	240	20652.2	3R:9861512-30513691	3to3	0.03	0.01	T	-	GCCAGAATCCATTGTTCGGCAATCGTCCATCGCGATTGATTCATCAAATGTCGACCCATTGCAAGGCAATCGATAGGTGACAAATTTCCATTACTTGTTCGGTTCAATTGGAGA	TCTCCAATTGAACCGAACAAGTAATGGAAATTTGTCACCTATCGATTGCCTTGCAATGGGTCGACATTTGATGAATCAATCGCGATGGACGATTGCCGAAC	Alt-EJ	Teh1, intron	CG31524, exon_4	Teh1, CG31524	NA	mh:1; ins:0; tup:0; tdown:0	0
A373R3	198	novobreak	TRA	3R	11181613	2R	24432165	3	0	somatic_tumour	244	13250.6	3R:11181613 2R:24432165	5to5	0.05	0	AG	-	GGAGATCCCCCCTCCAAGAGGAGTGCCCGCAGCCTGGACCTGGCCTCCACTTCCACTTGTTGTTTCGGCCACATCGCGGGTAAATACGTTTAAGTGTCGGTGCTCTTCTTCCCAAAAG	ACCGACACTTAAACGTATTTACCCGCGATGTGGCCGAAACAACAAGTGGAAGTGGAGGCCAGGTCCAGGCTGCGGGCACTCCTCTTGGAGGGGGGATCTCC	Alt-EJ	intergenic	Pgam5-2, exon	Pgam5-2	NA	mh:2; ins:0; tup:0; tdown:0	0
A373R3	200	delly	DEL	3R	11562988	3R	11563037	14	4	somatic_tumour	DEL00000024	0.1	3R:11562988-11563037	5to3	0.35	0	A	-	CAACAAAGTGGACAGAGCTTTTGGGGCGGACTGGAAAAGCTCCGCTGAAGAACAACAAGAAGACATTTTTTCTTTAGCGATTACACAATGAGTTCACACACACACAATGCGCGTAGCCTACGCA	GGGGCGGACTGGAAAAGCTCCGCTGAAGAACAACAAGAAGACATTTTTTCTTTAGCGATTACACAATGAGTTCACACACACACAATGCGCGTAGCCTACGCACACCCACGCG	Alt-EJ	sea, intron	sea, intron	fabp, sea	NA	mh:1; ins:0; tup:0; tdown:0	0
A373R3	209	novobreak	BND	3R	16378760	3R	20573305	2	1	somatic_tumour	262	4194.5	3R:16378760-20573305	3to3	0.03	0.03	TTGGC	-	GTGTACCACTTAATAAATGGTTCCACTTCGCTGCCCGTCATGGAGAATCTTACTACAGTCGGACCTGTTTTTGCCAACATGGGGCGCATTTTCAATTTGCGCGCATTTTGATTTATACGCCCCAAAAACCCCGGGCGAATAAGAG	ATCAAAATGCGCGCAAATTGAAAATGCGCCCCATGTTGGCAAAAACAGGTCCGACTGTAGTAAGATTCTCCATGACGGGCAGCGAAGTGGAACCATTTATT	Alt-EJ	ss, intron	intergenic	ss	NA	mh:5; ins:0; tup:0; tdown:0	0
A373R3	225	novobreak	BND	3R	24200976	3R	26609536	2	1	somatic_tumour	287	2408.6	3R:24200976-26609536	3to3	0.03	0.01	-	-	ATATTAAAGCGGGTGCTTTAAAATCGAATTTAAGCGATGCATTTCCAGTTGCAACAGCTGTTGCAGACAGATAAAGGAGTCGGAGTCCGAACCGCTGGCCATCGGAGAGATTAGGTTCCACATTCCCACTGCCACTGTATCGCTGTATCGCCGAGCGGTGCACCC	-	NHEJ	twin, exon_1	intergenic	twin	NA	mh:0; ins:0; tup:0; tdown:0	0
A373R3	229	novobreak	TRA	3R	25330986	X	12452678	3	0	somatic_tumour	290	12878.3	3R:25330986 X:12452678	3to5	0.05	0	TCAATTTGTAGG	-	ATTAAGGTATTGAATATATTACCAACATGTTGTAGTCTTAATTTTATAGATTTAGCTATCATCTACTTTTAATGCTTACCTCTCAATTTGTAGGCGCAGCACGATCGTCAAATAGTTTTCCCCTT	ACATGTTGTAGTCTTAATTTTATAGATTTAGCTATCATCTACTTTTAATGCTTACCTCTCAATTTGTAGGCGCAGCACGATCGTCAAATAGTTTTCCCCTT	Alt-EJ	CHKov2, exon_1	Pkcdelta, exon_14	CHKov2, Pkcdelta	NA	mh:12; ins:0; tup:0; tdown:0	0
A373R3	238	novobreak	TRA	4	418098	2L	13037524	3	0	somatic_tumour	300	12619.4	4:418098 2L:13037524	5to5	0.04	0	AGACA	-	CCATACATGAGACGGGTCTCAATGGCAGGCTTAAATGTCAAGTGTCCGTGTCTTATTTTCAATTAATACATTTCCAAAAACGTTTTAGCCAAGTCCAATCTAATGCCCATAATC	GATTATGGGCATTAGATTGGACTTGGCTAAAACGTTTTTGGAAATGTATTAATTGAAAATAAGACACGGACACTTGACATTTAAGCCTGCCATTGAGACCCGTCTCATGTATGG	Alt-EJ	intergenic	CG9932, intron	CG9932	NA	mh:5; ins:0; tup:0; tdown:0	0
A373R3	244	novobreak	DEL	X	3135326	X	3139096	15	8	somatic_tumour	339	3.8	X:3135326-3139096	5to3	0.74	-1.2	A	GA	GTATCTACCTCGAGTCGCGCGTGTGTGAGAGTGAGACGAAAGCCGAGTGCAAGAAGCGCAAGAGGAAGAGAGCAAGAGTGCGGCGTCGGTTTGAATTTGAATTTGTGGCTCGATCCTCGCGAAGAGATATGAAATCGGCTAATTTCTCAAGTGTTAAATCTGCTGTTACTCCTTGCCTTTCGCTTGGCCAAAATAAAAAAAAAAACAAAACCTGTAAG	GAGCAAGAGTGCGGCGTCGGTTTGAATTTGAATTTGTGGCTCGATCCTCGCGAAGAGATATGAAATCGGCTAATTTCTCAAGTGTTAAATCTGCTGTTACTCCTTGCCT	Alt-EJ	N, 5UTR	N, intron	N	NA	mh:1; ins:2; tup:0; tdown:0; snp_su:0; snp_op:0	0
A373R3	244	lumpy	DEL	X	3135326	X	3139096	15	8	somatic_tumour	10666	3.8	X:3135326-3139096	5to3	0.74	-1.2	A	GA	-	GAGCAAGAGTGCGGCGTCGGTTTGAATTTGAATTTGTGGCTCGATCCTCGCGAAGAGATATGAAATCGGCTAATTTCTCAAGTGTTAAATCTGCTGTTACTCCTTGCCT	Alt-EJ	N, 5UTR	N, intron	N	NA	mh:1; ins:2; tup:0; tdown:0; snp_su:0; snp_op:0	0
A373R3	246	novobreak	BND	X	4697763	X	5073382	2	1	somatic_tumour	341	375.6	X:4697763-5073382	3to3	0.09	0.03	GATGGAAA	-	GTTTTTGGGGTCACATTTTTGGTTACCCCAGTGACAGAACCTACTCACACCCCCGCCCCCCATTTGGGCTGATGGAAAATGGATGTATAACTGTGAAGCCAAGAAAAGTCCAATTAAGAACACATTCACAC	GTGACAGAACCTACTCACACCCCCGCCCCCCATTTGGGCTGATGGAAAATGGATGTATAACTGTGAAGCCAAGAAAAGTCCAATTAAGAACACATTCACAC	Alt-EJ	ctp, intron	CG32767, 3UTR	ctp, CG32767	NA	mh:8; ins:0; tup:0; tdown:0	0
A373R3	259	novobreak	TRA	2R	23186121	3L	14239313	3	0	somatic_tumour	149	8946.8	2R:23186121 3L:14239313	129:129_259	0.04	0	CTTGGCCAT	-	GACTTAGTTTCGCTCCATCTGGCCGCCTGCTGCGTGTCTGGCCTTCTTTGCTCTGTTTTTGGCCAGGTCCGCAGTGCCACGCATGCGTCTTGGCCATAAGCCAGAAAAAAGGGGTTAAAAGCATCATCGAATTGATTTAAAATCTGATTTTTATAAACGTCTCAGT	GGTCCGCAGTGCCACGCATGCGTCTTGGCCATAAGCCAGAAAAAAGGGGTTAAAAGCATCATCGAATTGATTTAAAATCTGATTTTTATAAACGTCTCAGT	Alt-EJ	CG34371, intron	CR45399, exon_1	CG34371, CR45399	NA	mh:9; ins:0; tup:0; tdown:0	0
A373R5	4	novobreak	BND	2L	5103277	2L	16264626	2	1	somatic_tumour	3	11161.3	2L:5103277-16264626	5to5	0.03	0.02	C	-	GTACTGGTGGTGCGACAGTGGCGTCTGTCGATTGCTGATGGTTTTTATAGAGTTCAAGGAATCATCAATTAAACATGCTTAAACAATTTCGGCATCTCGTTCAA	TTGAACGAGATGCCGAAATTGTTTAAGCATGTTTAATTGATGATTCCTTGAACTCTATAAAAACCATCAGCAATCGACAGACGCCACTGTCGCACCACCAGTAC	Alt-EJ	Msp300, exon_2	crp, 3UTR	Msp300, crp	NA	mh:1; ins:0; tup:0; tdown:0	0
A373R5	16	novobreak	TRA	3L	2558343	Tomelloso	81606	3	0	somatic_tumour	11	2476.7	3L:2558343 Tomelloso:81606	-	0.07	0	-	-	AACGTCGCTCATATTGATATTTATCATTGCGATTGTTTACGTTTTGAATACTGTAAACAAAACTACCAGTCTGCAGCCACTTTATGAGGAATTGTTAAAGCAGAGCGTTTATCGCCAGCAGCGGAAGCGGTGGTCTCGGTTTGGGGGGCGGTACCGTTGTGGGC	AACCGAGACCACCGCTTCCGCTGCTGGCGATAAACGCTCTGCTTTAACAATTCCTCATAAAGTGGCTGCAGACTGGTAGTTTTGTTTACAGTATTCAAAAC	NHEJ	msn, exon_13	intergenic	msn	NA	bp1_Tomelloso_2; mh:0; ins:0; tup:0; tdown:0	0
A373R5	17	novobreak	TRA	3L	3312018	Tomelloso	102060	4	0	somatic_tumour	12	3210	3L:3312018 Tomelloso:102060	-	0.13	0	-	-	CGGCAAGCGACTCTTCAAAACTTCATCAGTGTTGCCAATCAAAATCTGACAACCGTGTCGACCAATTGAACGATAGGCATGCGTTGTTATATTTTCCTTCTGCTTCTCGTAGGCAAAGTCGTTTTGCTCATCCTCGCCCTCGTCCATGTTGGCCAACTCAGTGAGGCGGC	-	NHEJ	ZnT63C, exon_5	intergenic	ZnT63C	NA	bp1_Tomelloso_2; mh:0; ins:0; tup:0; tdown:0	0
A373R5	24	novobreak	BND	3R	11288316	3R	21490211	3	0	somatic_tumour	19	10201.9	3R:11288316-21490211	5to5	0.03	0.04	ATAGA	-	CATAACGCGGGGATGGACAGCGCTGTTCTAACTCCTTTCTATCATATCTCCTGACAAATTGATATTGTCTAAGCCATTTTCGATATGCATATTTATGTTCTCGATAGGTTTCTTTGTTTGACTCACGAC	AGAACATAAATATGCATATCGAAAATGGCTTAGACAATATCAATTTGTCAGGAGATATGATAGAAAGGAGTTAGAACAGCGCTGTCCATCCCCGCGTTATG	Alt-EJ	CR31386, ncRNA	intergenic	CR31386	NA	mh:5; ins:0; tup:0; tdown:0	0
A373R5	25	novobreak	TRA	3R	14990196	2R	18680738	3	0	somatic_tumour	22	3690.5	3R:14990196 2R:18680738	5to3	0.04	0	AAGGACATTGA	-	AATTTCGGCACAAGAGGCAGCAGGAAGTCACTCAGCCAGTTGCCTTGCGTCCTTGCAAACAAAAAGAGCAACAAAGGACATTGATGGCTCAGACAAGGACGTGGTCCT	GCACAAGAGGCAGCAGGAAGTCACTCAGCCAGTTGCCTTGCGTCCTTGCAAACAAAAAGAGCAACAAAGGACATTGATGGCTCAGACAAGGACGTGGTCCT	Alt-EJ	intergenic	CG44435, exon_1	CG44434, CG44435	NA	mh:11; ins:0; tup:0; tdown:0	0
A373R5	28	novobreak	TRA	3R	21395894	2L	15133724	3	0	somatic_tumour	24	6262.2	3R:21395894 2L:15133724	5to3	0.04	0	-	-	ATTAGCAGCAATTTTCAATTTCCTTTCTGATGAAGCACATGGCAAGAGAGCAAATTACATGGCGCACAAAGTGCAGAGGCGGCTTTGGAAATTGGAGGGCGTGGCTGTCCGTCCGGAAAGGACAGCCGACAGCAGCATTGATGGATACGATGCGCACGTG	ATTAGCAGCAATTTTCAATTTCCTTTCTGATGAAGCACATGGCAAGAGAGCAAATTACATGGCGCACAAAGTGCAGAGGCGGCTTTGGAAATTGGAGGGCG	NHEJ	intergenic	intergenic	-	NA	mh:0; ins:0; tup:0; tdown:0	0
A373R5	41	lumpy	DEL	X	3117762	X	3177111	2	2	somatic_tumour	13962	59.3	X:3117762-3177111	41:41_42_43	0.26	-0.82	-	-	-	-	-	kirre, intron	dnc, intron	kirre, N, CG18508, Fcp3C, CG3939, dnc	NA	snp_su:0; snp_op:0	0
A373R5	41	Control-Freec	DEL	X	3117915	X	3274245	-	-	somatic_tumour	-	156.3	X:3117915-3274245	42:41_42_43	0.63	-0.68	-	-	-	-	-	kirre, intron	dnc, intron	kirre, N, CG18508, Fcp3C, CG3939, CG14265, ng2, ng3, ng1, ng4, Pig1, Sgs4, dnc	NA	snp_su:0; snp_op:0	0
A373R5	41	novobreak	DEL	X	3189060	X	3273846	13	14	somatic_tumour	61	84.8	X:3189060-3273846	43:41_42_43	0.63	-0.62	-	-	GATGGAATCGCACTGAGCGTTTATTTTTCGAATTCATTATCATATGATGTTTTGATGTTTAAATATTGCTCGATTTATATGGATAGTTTATGTTGCTTCAGCGATATTTCAAGGAAATGTGCACTTTTTTTTGCCTTTTGAGATATGAACAAATCACGTAGGCTTAAACTTCTATTTGTTGACGTGATCTTTTTGATTTGCTTTAGTTATAATTAAGATTTGTCCGCTTCGTGATTTGCCATTTCCTTTGCTTAGTTTTCTCTCACGTTTCACGACGTTTTCGCTTTCCATTTTCATTTCCATGAAATTTCTAGCATTCCTTTGCGGCTTTTTGTGGTGTTCACTGTACCTGTCCTAACGGAACAATTTGCCACAATAGCTG	-	-	dnc, intron	dnc, intron	dnc, CG14265, ng2, ng3, ng1, ng4, Pig1, Sgs4	NA	snp_su:0; snp_op:0	0
A373R5	41	lumpy	DEL	X	3189060	X	3273846	13	14	somatic_tumour	13965	84.8	X:3189060-3273846	43:41_42_43	0.63	-0.62	-	-	-	-	-	dnc, intron	dnc, intron	dnc, CG14265, ng2, ng3, ng1, ng4, Pig1, Sgs4	NA	snp_su:0; snp_op:0	0
A373R5	41	novobreak	DEL	X	3189060	X	3273846	13	14	somatic_tumour	62	84.8	X:3189060-3273846	43:41_42_43	0.63	-0.62	-	-	TAATTAAGATTTGTCCGCTTCGTGATTTGCCATTTCCTTTGCTTAGTTTTCTCTCACGTTTCACGACGTTTTCGCTTTCCATTTTCATTTCCATGAAATTTCTAGCATTCCTTTGCGGCTTTTTGTGGTGTTCACTGTACCTGTCCTAACGGAACAATTTGCCACAATAGCTGCGACCCGTGCTCACTC	-	-	dnc, intron	dnc, intron	dnc, CG14265, ng2, ng3, ng1, ng4, Pig1, Sgs4	NA	snp_su:0; snp_op:0	0
A373R7	4	lumpy	BND	2L	205135	2L	205916	1	3	somatic_tumour	45_1	0.8	2L:205135-205916	3to3	0.22	0.24	GCATCCAGC	-	-	GGTTGGCTAAGGCCTCTGCTGCTTCCAGTTCGTCCTTATGATGAAGCATCCAGCATCCCGAGCTACAAAGAGATTATTTACTCCCGACATTAAGAGGATGC	Alt-EJ	CG11617, exon	CG11617, exon_3	CG11617	NA	mh:9; ins:0; tup:0; tdown:0	0
A373R7	5	lumpy	BND	2L	520438	2L	1504681	3	0	somatic_tumour	151_1	984.2	2L:520438-1504681	5to5	0.16	0.02	-	-	-	CAAAAACATACAGGAAATGGAGTCACGTGTCCTTTACGTTTAAATTACTCCGCAGGGAATTAATTTCGCTACAATGAAGTCATCGCTTATCTGCCAGACTTCATAAA	NHEJ	ush, intron	intergenic	ush	NA	mh:0; ins:0; tup:0; tdown:0	0
A373R7	5	novobreak	BND	2L	520438	2L	1504681	3	0	somatic_tumour	6	984.2	2L:520438-1504681	5to5	0.16	0.02	-	-	TTTATGAAGTCTGGCAGATAAGCGATGACTTCATTGTAGCGAAATTAATTCCCTGCGGAGTAATTTAAACGTAAAGGACACGTGACTCCATTTCCTGTATGTTTTTGGCATCTTTACGACTTTTTGTCTGTTGGTTGTCACATTTTTCTCGGTTTTTGTTGCTCCTGCGTGTTGACTCGGTTTCGTGCGCTGAGTTCTCTTT	CAAAAACATACAGGAAATGGAGTCACGTGTCCTTTACGTTTAAATTACTCCGCAGGGAATTAATTTCGCTACAATGAAGTCATCGCTTATCTGCCAGACTTCATAAA	NHEJ	ush, intron	intergenic	ush	NA	mh:0; ins:0; tup:0; tdown:0	0
A373R7	24	novobreak	TRA	2L	3093585	3L	11664665	3	0	somatic_tumour	25	8571.1	2L:3093585 3L:11664665	3to5	0.29	0	ACCAAAT	-	GCAGAATGACACTAATAGGCGGTGTTTATCTTTATGGGATTCGTCTATACGACTTGCTTAACTAATTTGGTGGTAAATAGCTAAAATATATATATATATATATATTTTAGCTATTTACCACCAAATTAGTTAAGCAAGTCGTATAGACGAATCCCATAAAGATAATCACCGCCTATTAGTGGCATTCTGCCCCACCTCAATGCAAAGCATTCCCACCAAGTATATAAATATTTTATTTGCTTATAAACGAACCCACACAGCCAAGTGC	ATATATATATATATATATATTTTAGCTATTTACCACCAAATTAGTTAAGCAAGTCGTATAGACGAATCCCATAAAGATAATCACCGCCTATTAGTGGCATTCTGC	Alt-EJ	toc, intron	CG32085, intron	toc, CG32085	NA	mh:7; ins:0; tup:0; tdown:0	0
A373R7	27	novobreak	TRA	2L	4138262	3L	7069104	3	0	somatic_tumour	28	2930.8	2L:4138262 3L:7069104	5to3	0.29	0	GCA	-	GAGTGTCGTCGAGTTTGGCCCATTCCATTAACTTTTACCACTTGGCGGGCACTTCTTTGGCCGCATTCATGTCGCGACAGTTTTTGTAAAATGAACGCAAGGGCTTCTTGCGACCTGTGGACCGACCCCCTGATAGCATAACTCCAGAATAACCTTTATGATATATCTTCGCCTATCATCCAC	TTTGTAAAATGAACGCAAGGGCTTCTTGCGACCTGTGGACCGACCCCCTGATAGCATAACTCCAGAATAACCTTTATGATATATCTTCGCCTATCATCCAC	Alt-EJ	intergenic	CG32391, exon_1	CG8641, CG14823, CG32391	NA	mh:3; ins:0; tup:0; tdown:0	0
A373R7	33	novobreak	TRA	2L	4855422	Tomelloso	46531	4	0	somatic_tumour	33	4808.9	2L:4855422 Tomelloso:46531	33:33_387	0.34	0	-	-	TCGATGTGGAGCCGGAAGGTGGGGCCATCGCTTCCCTATAAAGTATATAACCCATCGTCTTGGGCGATATTAACAATTCAACATTAGGATTGGACCTGGCAAATCGGCCGTTGC	-	-	smog, intron	intergenic	smog	NA	-	0
A373R7	40	novobreak	TRA	2L	6084142	2R	14186700	3	0	somatic_tumour	40	8102.6	2L:6084142 2R:14186700	3to5	0.19	0	CG	-	CAATTTGAGCGAATCTCAGAGCGTGCCAAAGCTGCCAATGAGCGGAACAGCTGATGCTCCCGCATCGGTGACGACCTTTTGAGTCATCATGACAATAGGCTAATATAAATCGTTCTAGGT	AGCGTGCCAAAGCTGCCAATGAGCGGAACAGCTGATGCTCCCGCATCGGTGACGACCTTTTGAGTCATCATGACAATAGGCTAATATAAATCGTTCTAGGT	Alt-EJ	Kr-h1, intron	CG30069, exon_1	Kr-h1, CG30069	NA	mh:2; ins:0; tup:0; tdown:0	0
A373R7	44	Control-Freec	COMPLEX_DUP	2L	7188642	2L	7233813	-	-	somatic_tumour	-	45.2	2L:7188642-7233813	44:44_45	0.34	0.44	-	-	-	-	-	CG4496, intron	Ndae1, intron	CG4496, CG4497, CG4502, CG13784, ico, CR44989, CG43799, CG43800, Ndae1	NA	snp_su:52; snp_op:46; snp_ratio:1.13	10.93
A373R7	44	novobreak	COMPLEX_TRA	2L	7193295	3R	16377837	3	0	somatic_tumour	43	9184.5	2L:7193295 3R:16377837	45:44_45	0.27	0	GTCCATGG	-	CCGTGGGGGAGGTGCTCGGAGGCACTACCAGCTGGTCCGCCTCGGAGAAGTAGGTGGACGCCAGTCCCGTGTCCAGGTAGCTGACCTTAAAGTCCATGGGCACTGTCGATGGGTTCTCCTGCTGCTTCTCCTCGGCGCTCGCTTTC	GAAGTAGGTGGACGCCAGTCCCGTGTCCAGGTAGCTGACCTTAAAGTCCATGGGCACTGTCGATGGGTTCTCCTGCTGCTTCTCCTCGGCGCTCGCTTTCG	Alt-EJ	CG4497, exon_2	ss, exon_7	CG4497, ss	NA	mh:8; ins:0; tup:0; tdown:0	0
A373R7	46	lumpy	BND	2L	7244006	2L	7244123	5	1	somatic_tumour	681_1	0.1	2L:7244006-7244123	3to3	0.38	0	-	-	-	-	-	Ndae1, intron	Ndae1, intron	Ndae1	NA	-	0
A373R7	47	novobreak	TRA	2L	7327272	3L	6323990	3	0	somatic_tumour	44	1003.3	2L:7327272 3L:6323990	3to5	0.44	0	-	-	ATTAAATATAGGTGCAGTTGGCCTAGGCGGTATATGATATTATGAATCGCCCGCTCAGACAGTTGGGACAGTTTTTTTCTCTTTGCTCCATCTCTTTCCCCATCTAGATGCAGTCCAGTTGAGTGGATTTCGGTTTGGTTTCCTGCCTTTTTTTTGGCCTCGGAC	-	-	intergenic	intergenic	-	NA	-	0
A373R7	61	Control-Freec	COMPLEX_DEL	2L	10079586	2L	10111851	-	-	somatic_tumour	-	32.3	2L:10079586-10111851	61:61_62	0.31	-0.68	-	-	-	-	-	CG44153, intron	CG34109, intron	CG44153, CG13133, CG34109	NA	snp_su:6; snp_op:2; snp_ratio:2.99	22.95
A373R7	61	novobreak	COMPLEX_TRA	2L	10081313	X	2078459	3	0	somatic_tumour	59	8002.9	2L:10081313 X:2078459	62:61_62	0.36	0	-	-	TCCTTACCTCATGCAGCATATCGATGAGGAAGCTGGCCTCGCCCGGCAGGAAACTATGCCTTCTCTGGAGTGTTTGTCTCGCTTGTCTATCAATCACTAGCGCTTGCGATC	-	-	CG44153, exon_10	CG16903, 3UTR	CG44153, CG16903	NA	-	0
A373R7	67	novobreak	TRA	3R	25853350	2L	11197465	3	0	somatic_tumour	437	14655.9	3R:25853350 2L:11197465	362:67_362_363	0.34	0	-	-	GTCGTACATGTTTGATAATTGAAATTGGCTGTCACAAAAAAAAAAAGAACCAAATGAAGCTGCTAACGACGAATGAATCGAAGACTTCCATTGAGGAAAAGAAGAAGGCCGAGGAGC	-	-	CG5886, exon	Ca-beta, intron	CG5886, Ca-beta	NA	-	0
A373R7	79	novobreak	TRA	2L	14068330	3L	21540255	3	0	somatic_tumour	81	7471.9	2L:14068330 3L:21540255	3to3	0.21	0	-	GTAGATG	GCTGCCTGATGCTCACCGCAGCAACTTGCTGGCTGTTGTAAGTACATGTGTATATAAGTGCTCGCTGCTTTTTAAAATGCTTATCAATGGCTCATCTACACACACACACACACACACACGAACATACACACACACACAGAGAAAAACAAA	TGCATTTGTTTCACTGTGTGTGTGCGTATGTTTGCGTGTGTGTGTGTGTGTGTGTGTAGATGAGCCATTGATAAGCATTTTAAAAAGCAGCGAGCACTTATATAC	FoSTeS	nAChRalpha5, intron	VhaM9.7-b, intron	nAChRalpha5, VhaM9.7-b	NA	mh:0; ins:7; tup:3; tdown:3	0
A373R7	80	novobreak	TRA	2L	14395906	3L	10969893	4	0	somatic_tumour	83	3426	2L:14395906 3L:10969893	5to5	0.22	0	TTAGA	-	ATGCGACACTGCACACACACACACAATGGCCCAGGAAAAATGCATGAGAGTGCTTTAGACACTTTGAACTAAACACACTCAGCTGTCATGATTTGATTTGATTTATTATCGCCTGTGTACATATTTTTAAAATGCTAATTTTATTTTAAAGGTGTGTTAAGTTGGCCACAGGGCCAGTAGTTGATC	ATGCGACACTGCACACACACACACAATGGCCCAGGAAAAATGCATGAGAGTGCTTTAGACACTTTGAACTAAACACACTCAGCTGTCATGATTTGATTTGA	Alt-EJ	elB, intron	intergenic	elB	NA	mh:5; ins:0; tup:0; tdown:0	0
A373R7	83	novobreak	COMPLEX_TRA	2L	15398132	3L	10605554	3	0	somatic_tumour	88	4792.6	2L:15398132 3L:10605554	83:83_215	0.4	0	-	-	GTTGGTTTGAGGGCTGCAGTTGGAGTTGGCAAACTCCCCCAACTTATGCACGGGTCGCTCGGGTTGCTCTTTCGCTTTTTTCCGGCTGGCGATCGCCTCGGTTGCCAACACTTGACGGATTTAATTATTTCGACTCTCCAGGCCCCTCACCAGCATCCTCTCCAGCGCAAAGT	-	-	intergenic	intergenic	-	NA	-	0
A373R7	83	lumpy	COMPLEX_BND	3L	1955201	3L	10605713	5	0	somatic_tumour	5201_1	8650.5	3L:1955201-10605713	215:83_215	0.38	-0.03	-	-	-	-	-	mv, exon_10	intergenic	mv	NA	-	0
A373R7	83	novobreak	COMPLEX_BND	3L	1955201	3L	10605713	5	0	somatic_tumour	255	8650.5	3L:1955201-10605713	215:83_215	0.38	-0.03	-	-	CCACCAACTGAATGATGGCCTGGCGTACGGCGCAGCTGCGCTGGTTGGCCAGAACCAAAAGCAGTTCCAGTTTCACGTAGTGGCGAGTGCCCGATCCGGGATGCTGGGTGCCCCCCCCCCCAGTAACTGTAACTG	-	-	mv, exon_10	intergenic	mv	NA	-	0
A373R7	87	novobreak	TRA	2L	16914967	X	8404036	3	0	somatic_tumour	93	8510.9	2L:16914967 X:8404036	5to5	0.36	0	-	-	GTTAAAATTAATCTTGTTTTAGGATTATTGGCACAAGCTGTAGGCCTGGTTGTGCCCTCACTAGTGACTCGTTTGCCACGTCATGGTAATGTGTTGGGTGGCACTGTCGAACTTCGGGGACAGAACATCTCCCTGGCC	-	-	tweek, exon_20	CG10555, 3UTR	tweek, CG10555	NA	-	0
A373R7	99	Control-Freec	DUP	2L	20533446	2L	20591523	-	-	somatic_tumour	-	58.1	2L:20533446-20591523	Heterozygous duplication	0.27	0.31	-	-	-	-	-	intergenic	CR44909, ncRNA	CR45707, CR45347, mir-4973, CR44909	TRUE	low FC; snp_su:14; snp_op:6; snp_ratio:2.33	14.5
A373R7	109	novobreak	TRA	2R	1603549	3L	1432885	3	0	somatic_tumour	125	170.7	2R:1603549 3L:1432885	3to3	0.48	0	-	-	ATGGGTTGACAGTTGGCAAGAGGAGTTAACGAAATAAAAAAGCGAGCAGAAACCCCTTCGCTGCCGAAATGTAAACTCCCGAAATAGTAACGAAAATCACAAGCGTAATTTTTCCCGAGTACCGGATTATAAAAGTTAACTTAT	-	-	intergenic	Ptp61F, intron	Ptp61F	NA	-	0
A373R7	117	lumpy	BND	2R	5880389	2R	23467229	3	0	somatic_tumour	4064_1	17586.8	2R:5880389-23467229	5to5	0.14	-0.02	-	-	-	-	-	CG44438, exon_1	CG43795, exon_3	CG44438, CG43795	NA	-	0
A373R7	117	novobreak	BND	2R	5880389	2R	23467229	3	0	somatic_tumour	134	17586.8	2R:5880389-23467229	5to5	0.14	-0.02	-	-	GTATGGACTGTGGGCTTATCAGGCCGTAGGTTCACTCAACCCGATTTGGCAAGCTTTCAATGCCGAGAAGGTGATAGCCCGCAACGAGCAGTATCTCAAGTGTAAGTATATCGGGCATGTCCCCTCTGATTTATTTGCCTGATTTATGGG	-	-	CG44438, exon_1	CG43795, exon_3	CG44438, CG43795	NA	-	0
A373R7	118	novobreak	TRA	2R	5914303	2L	16449217	3	0	somatic_tumour	135	10534.9	2R:5914303 2L:16449217	3to5	0.21	0	-	-	GTGTTTTTTCCAGGTCTGGGCAAGCTGCTCAATCCCGATCTGGAGCAAAGCGGTCCGATGAAAGGCGACGCCTTTGGAGGTCCGCAAGGATACTTTAAGGTCGCAGTCCGTTTAAGAAGTCTTCTCTATTTCCAAATCTCTGCCAATGCTTGAC	-	-	CG43366, intron	Idgf2, 5UTR	CG43366, Idgf2	NA	-	0
A373R7	124	novobreak	TRA	2R	6845242	3L	628140	3	0	somatic_tumour	143	6217.1	2R:6845242 3L:628140	5to3	0.31	0	-	-	GGCATGAAATATTCAATAACCTAAACCGACAAAGATTTACTGCTCAGCCGTTTATTTCGTGCGACCCAAAAAATGTTAGATGCCGACCGCCCTCCGCAGGCC	-	-	intergenic	intergenic	-	NA	-	0
A373R7	141	novobreak	TRA	2R	11000740	3L	11885435	3	0	somatic_tumour	166	884.7	2R:11000740 3L:11885435	3to5	0.44	0	-	-	GATTGATATTGAAATGAGGTTTAATCATCATCTGAAAGGAATGTTGTTGCAATGTTGAATTGACCCCAATCAAGCCGGTTGCTGTTTGCAGATAGCCATTGTTTCTGTTGGTGTTTTGGCTCGTTTTACACATTCCCCCCCCCTCGGCCCTTGCC	-	-	luna, intron	CG44837, intron	luna, CG44837	NA	-	0
A373R7	146	Control-Freec	DUP	2R	12338136	2R	12402666	-	-	somatic_tumour	-	64.5	2R:12338136-12402666	Heterozygous duplication	0.24	0.23	-	-	-	-	-	Den1, intron	Cpr49Ae, intron	Den1, Cpr49Ae	TRUE	low FC; snp_su:79; snp_op:32; snp_ratio:2.47	16.88
A373R7	148	novobreak	TRA	2R	12543310	3L	8329993	3	0	somatic_tumour	172	4213.3	2R:12543310 3L:8329993	5to3	0.29	0	-	-	ATTAAACGCTTCGATGGATTTTATGGAGCATAAACAGGAAATTTGAAGAAGAATGTCCAATTTGCCATGGCCAAAAGGCCACCCGGGCCACTGGTCAATAGCAGTCCAAGCGATGGAAATTGGCAA	-	-	fra, intron	CG34462, exon	fra, CG34462	NA	-	0
A373R7	149	novobreak	TRA	2R	13165174	2L	8745467	3	0	somatic_tumour	174	4419.7	2R:13165174 2L:8745467	149:149_150	0.4	0	-	-	GGACGACGCCGCTGATGTCGATGATGGCGGTTGGCGTGGTACTTGGCCAGCTGCTCATCTTGCAGTTCAAAGTCGGCGGAGGGCGCCGCATCGGATTAAAG	-	-	GLaz, intron	intergenic	GLaz	NA	bp1_GATE_BEL=6	0
A373R7	163	lumpy	BND	2R	15439905	2R	21349225	2	1	somatic_tumour	3855_1	5909.3	2R:15439905-21349225	3to3	0.17	-0.01	-	-	-	-	-	CG43729, intron	CG17974, exon	CG43729, CG17974	NA	-	0
A373R7	163	novobreak	BND	2R	15439905	2R	21349225	2	1	somatic_tumour	194	5909.3	2R:15439905-21349225	3to3	0.17	-0.01	-	-	CTTTTGCTTACTGCTCATCCCGCTTTGCTTATTGGCAGAGAGGTCCTTGGTCCTTGTGCCTTATCCCTTGTGACTATCCATCCGTGTATATCTACAACTTTATCTGCAACTATGCTTCACTC	-	-	CG43729, intron	CG17974, exon	CG43729, CG17974	NA	-	0
A373R7	165	novobreak	TRA	2R	15995449	4	1227056	3	0	somatic_tumour	197	14768.4	2R:15995449 4:1227056	3to3	0.36	0	-	-	ACGGCGAAGCCATGGATGTTTTAAAGCCTCGGAAGGTGTTAATCGCTTGTCTGCATCCCATTCAAGGCAACCAAGCCTCTGGTGGCCTGGTGCATTGGTAC	-	-	ATPCL, exon_7	Dyrk3, exon_5	ATPCL, Dyrk3	NA	-	0
A373R7	172	Control-Freec	COMPLEX_DUP	2R	17048826	2R	17068185	-	-	somatic_tumour	-	19.4	2R:17048826-17068185	172:172_173	0.4	0.51	-	-	-	-	-	intergenic	CG30460, exon_6	CG9646, fat-spondin, tef, CG8950, CG6967, CG30460	NA	snp_su:10; snp_op:3; snp_ratio:3.33	20.76
A373R7	174	novobreak	TRA	2R	17084978	3L	95682	3	0	somatic_tumour	206	16989.3	2R:17084978 3L:95682	5to5	0.34	0	-	-	GTTATAGAATGAATGAAATATCGCCCAAAGGCAACCTGTTGAGTTTGTGCTTTGCTCTTTCTCATTGACGCGCGCTGATGTCAGTGATGGCAATCATCTGAGCTTGGTGAGTCCGCTTAGAAGTCGTCAACACGTCACTCCAGTCTACGGTCTACGGTCTACAGTCTCTCTGGGGATCGTGCGAAGGT	-	-	CG30460, intron	intergenic	CG30460	NA	-	0
A373R7	178	Control-Freec	DUP	2R	18939555	2R	18971820	-	-	somatic_tumour	-	32.3	2R:18939555-18971820	Heterozygous duplication	0.36	0.47	-	-	-	-	-	sano, intron	CG15107, intron	sano, prod, CG15107	NA	snp_su:19; snp_op:12; snp_ratio:1.58	12.31
A373R7	182	novobreak	TRA	2R	19811510	Tomelloso	58598	3	0	somatic_tumour	217	19752.9	2R:19811510 Tomelloso:58598	-	0.87	0	-	-	GTGCAGCGGCGCAATGAAATGAAAAATGGTGAGAAGGAGATGTCGGTGGTCTGGCAATTGCCACTGGTCGATCGTGTCCAACAGCGTTCCTCTGGGGTCGTGACGATTGGAC	-	-	intergenic	intergenic	-	NA	bp1_Tomelloso_2	0
A373R7	185	novobreak	BND	2R	20309206	2R	20309560	3	0	somatic_tumour	220	0.4	2R:20309206-20309560	3to3	0.44	0	-	-	GTATTCAAAGTATTCAAATAGGTTCGGAACTCTAAGTTGCAGCTGCGTTGTCAATGTCTTTTATCGCCTGTTCCTCCATCTTCGTTTCCGTTTCCGTAGCAGCGACATCCTTAGGTTCTTCTAATTTCAAACTATATATATACTTATGCGCAACTATATAAT	-	-	CG13868, 3UTR	CG13868, 3UTR	CG13868	NA	-	0
A373R7	192	novobreak	DEL	2R	21382619	2R	21384283	5	0	somatic_tumour	227	1.7	2R:21382619-21384283	5to3	0.28	0.44	ACTGCAAT	-	GATGATTGGCCAGCAAATGCTTTAAGGTTTGTTTTTCAGCTCTACACGAGTTCATTTGAATATATGTTCATTGCAGTTCGCGGGGGCAGGCTCCAAAATTGTTGTTGTTTTTTAACATTGGCATTTTGGGATTGGGGCAGTGTGACCGCACTCGGAG	CAATTTTGGAGCCTGCCCCCGCGAACTGCAATGAACATATATTCAAATGAACTCGTGTAGAGCTGAAAAACAAACCTTAAAGCATTTGCTGGCCAATCATC	Alt-EJ	intergenic	CG10795, 5UTR	CG10795	NA	mh:8; ins:0; tup:0; tdown:0; snp_su:3; snp_op:0; snp_ratio:301.0	15.33
A373R7	193	Control-Freec	DUP	2R	21578832	2R	21604644	-	-	somatic_tumour	-	25.8	2R:21578832-21604644	Heterozygous duplication	0.37	0.56	-	-	-	-	-	intergenic	CR45150, ncRNA	CG30222, CG33225, CR45150	NA	snp_su:0; snp_op:0	0
A373R7	203	novobreak	TRA	2R	24741903	3R	26935443	3	0	somatic_tumour	239	2193.5	2R:24741903 3R:26935443	5to3	0.17	0	-	-	CTCTCTCTCTCTCTCTCTTTATTTTTGGGCTGGGGTGGCGCATTGTGTTTGCGGGTGTGTTTGCCACCCACTGGGCAAGCTTTTGAAACATTTGGCGCCGGCAATCGGCAAATCGCCTCTGTGTAAT	-	-	intergenic	sda, intron	sda	NA	bp2_rooA_BEL=4	0
A373R7	208	novobreak	TRA	3L	703559	2R	19372878	3	0	somatic_tumour	247	18669.3	3L:703559 2R:19372878	3to3	0.16	0	-	-	TATATATATAGCTACATATATCTGCACTCTAGATGAACGGGTATTCGTAGAGTCGCTCTTCAGCAGGTTATTGACTCAAGCCCTTGCAGCGTGTCGCGCGT	-	-	intergenic	CG9416, intron	CG9416	NA	-	0
A373R7	211	Control-Freec	DUP	3L	1097010	3L	1187352	-	-	somatic_tumour	-	90.3	3L:1097010-1187352	Heterozygous duplication	0.3	0.41	-	-	-	-	-	bab1, intron	intergenic	bab1, bab2	NA	snp_su:46; snp_op:32; snp_ratio:1.44	13.91
A373R7	216	novobreak	TRA	3L	2160153	3R	9595325	3	0	somatic_tumour	256	7435.2	3L:2160153 3R:9595325	5to3	0.36	0	-	-	AAAAAAACAAAAGACTCAAGCAACGAACTCGACTCACCCAAGTCGATGGCGGTCTCTATGTCGTTTTGCACACCGGCATGCATCTGCCATTGAGGTTATTGCTGGCCACTTGGATACTTGGCCACTTGGCTACTGCTAATTGTGTATTGCCTTCTGGGCGG	-	-	CG15822, exon_5	CG8312, intron	CG15822, CG8312	NA	-	0
A373R7	224	lumpy	BND	3L	5908521	3L	6517403	4	0	somatic_tumour	4787_1	608.9	3L:5908521-6517403	3to3	0.29	-0.11	-	-	-	-	-	CG13288, intron	sfl, intron	CG13288, sfl	NA	bp1_mdg1_Gypsy/TABOR=7	0
A373R7	224	novobreak	BND	3L	5908521	3L	6517403	4	0	somatic_tumour	272	608.9	3L:5908521-6517403	3to3	0.29	-0.11	-	-	AATTGGGGCAGCAATTCGTTTTCTTTTAATGGACGCCCACGTGGCTGGACTCCAGGGCACACGCTTTCTATTTACACGGAAAAAAGCCCCAGAAGTGTCCCCTTCGCC	-	-	CG13288, intron	sfl, intron	CG13288, sfl	NA	bp1_mdg1_Gypsy/TABOR=7	0
A373R7	226	Control-Freec	DEL	3L	5956119	3L	6040008	-	-	somatic_tumour	-	83.9	3L:5956119-6040008	Heterozygous deletion	0.29	-0.48	-	-	-	-	-	intergenic	Jon65Aiv, exon	CG10479, CR45439, CR45440, PVRAP, alphaKap4, CG10477, yip7, CR43952, CG6462, Jon65Aiv	NA	snp_su:4; snp_op:5; snp_ratio:0.8	8.61
A373R7	233	Control-Freec	DUP	3L	8214669	3L	8266293	-	-	somatic_tumour	-	51.6	3L:8214669-8266293	Heterozygous duplication	0.31	0.39	-	-	-	-	-	intergenic	Dscam4, intron	CG8012, CG13674, CG13678, eIF4E-3, CR43953, CG7213, Dscam4	TRUE	low FC; snp_su:35; snp_op:15; snp_ratio:2.33	14.42
A373R7	234	novobreak	TRA	3L	8618621	2L	20649480	3	0	somatic_tumour	280	12030.9	3L:8618621 2L:20649480	3to3	0.26	0	-	-	TCCCCAGGTAGTTCCGTTATTAATCAATCCCATTTCAGGTCAATATCCGAGGCCTTATTCCTCTGTGCGAAAACGTCGTTGGCTGCAACTCCTTCCGACCAGGTAGATAAGAAAATAGAAAAAGTATCTATAGTTCTCATGACCGATG	-	-	S-Lap1, exon_2	CG18810, exon	S-Lap1, CG18810	NA	-	0
A373R7	243	Control-Freec	COMPLEX_DUP	3L	12634974	3L	12718863	-	-	somatic_tumour	-	83.9	3L:12634974-12718863	243:243_244	0.23	0.26	-	-	-	-	-	CR32111, ncRNA	intergenic	CR32111	TRUE	low FC; snp_su:52; snp_op:24; snp_ratio:2.17	16.81
A373R7	251	Control-Freec	DUP	3L	14293395	3L	14338566	-	-	somatic_tumour	-	45.2	3L:14293395-14338566	Heterozygous duplication	0.37	0.51	-	-	-	-	-	fz, intron	fz, intron	fz, CR45025, CG13482	NA	snp_su:0; snp_op:0	0
A373R7	255	novobreak	TRA	3L	15282449	X	1902350	3	0	somatic_tumour	308	13380.1	3L:15282449 X:1902350	3to3	0.24	0	-	-	TTCAGATCGGCGGCTCGCTCTCCACTTTTGAGCGGCAACCAGCCGTACACCTGCGACTCCAGGAGCGGAACAGCTTTTCCGAGCGGGAAATTCAGGAACGAAGATCGGGAATATGCCAAACTTTAGGCCTTCTGTTGTGTCGGCCACACA	-	-	intergenic	CG32801, exon	CR43864, CG32801	NA	bp1_rDNA_2	0
A373R7	258	novobreak	TRA	3L	16239911	3R	19633734	3	0	somatic_tumour	313	3393.8	3L:16239911 3R:19633734	3to5	0.24	0	-	-	GAGTTGTGCTCGTTTACAGATTGGCACTCACTTGGGCTGCATAAATATAAGTTTGAGCCACTTAATAAATCATTTTCAATTAACAGATTGCTTAAAAGTAATTATTTAAATGTTAGTATTGTCAAGTGAACTCACTACAGAAATTGAATAGCTACATATAGT	-	-	intergenic	subdued, 3UTR	subdued	NA	-	0
A373R7	265	novobreak	TRA	3L	17624216	2L	19996001	3	0	somatic_tumour	320	2371.8	3L:17624216 2L:19996001	5to5	0.27	0	-	-	GACCACGGCCATGGTCGTCGGCTGATTTGCATAAGAGAGCTGGCGGGCTCAGCTGCAATTCCGGATGCGATTATATGTTATTTAACTGCTCTCCCTTCGCGTTCGTTGGCATCTGACTTTAGAATTTCG	-	-	CG7510, intron	CG43861, intron	CG7510, CG43861	NA	-	0
A373R7	269	Control-Freec	DEL	3L	18100665	3L	18184554	-	-	somatic_tumour	-	83.9	3L:18100665-18184554	Heterozygous deletion	0.22	-0.34	-	-	-	-	-	CG13698, intron	hid, intron	CG13698, mRpS26, CG5147, mus304, CG32195, CG7341, CG42853, Cyp312a1, CR44669, geko, CG7330, CG13699, hid	TRUE	low FC; snp_su:19; snp_op:4; snp_ratio:4.74	16.59
A373R7	271	novobreak	TRA	3L	19022981	X	1700354	3	0	somatic_tumour	327	17322.6	3L:19022981 X:1700354	5to5	0.29	0	-	-	AAATAAAAACTTTCCGAAATGGGAAAACTTTTTTCTCCAACGAGGACACACAGAGTCCAAATTGTTTTCCATTATTTTTCTGACTCAGCACTAGTGGCAGCTGAAAGGAGCGGCTCTTCATCAGCTTTTGATTGCTGTC	-	-	nkd, intron	intergenic	nkd	NA	-	0
A373R7	272	lumpy	BND	3L	19172922	3L	23321377	3	0	somatic_tumour	6334_1	4148.5	3L:19172922-23321377	3to3	0.21	-0.03	-	-	-	-	-	fz2, intron	alpha-Cat, intron	fz2, alpha-Cat	NA	bp1_gypsy4_Gypsy=2; bp2_gypsy4_Gypsy=4	0
A373R7	273	Control-Freec	DUP	3L	20301138	3L	20320497	-	-	somatic_tumour	-	19.4	3L:20301138-20320497	Heterozygous duplication	0.38	0.49	-	-	-	-	-	SCCRO4, intron	intergenic	Pex23, CR43872, SCCRO4, CG32225, polo, alphaSnap, CR43875, Spn77Ba	NA	snp_su:13; snp_op:10; snp_ratio:1.3	13.48
A373R7	277	lumpy	BND	3L	21197206	3L	21197822	2	1	somatic_tumour	6207_1	0.6	3L:21197206-21197822	3to3	0.17	-0.02	-	-	-	-	-	CG34261, exon_2	CG33054, exon_2	CG34261, CG33054	NA	bp1_opus_Gypsy=13	0
A373R7	291	novobreak	TRA	3R	4816329	2L	1314494	10	0	somatic_tumour	349	3501.8	3R:4816329 2L:1314494	5to3	0.77	0	-	-	TTGCCTAGCAACCGTTTAACCAGTGGATTTGCACCCCAACAAAGACGTTAGTTGTCTCGGTCTCATTAAATGCTCACCCTGCCTTACAGCCCCATTCCAATTGCTCCTTCGACCTTTGGGTTTCCCTCTCATCTGGCGATTTTCCAAAT	-	-	CG1126, 5UTR	intergenic	CG1126	NA	-	0
A373R7	292	novobreak	TRA	3R	5064625	X	17655961	4	0	somatic_tumour	351	12591.3	3R:5064625 X:17655961	3to3	0.42	0	-	-	GTCTTCTATTGTATTATTTCTGTAGAACGTGTGGGAATACCGCTGCCTTAGAAAAGATACAGAAAACCATAAGCGGCGTTACATTGTACCGTGGATTGCTCCACCTTCGATGGCCAACGATTCGCGGCCCACGCCCTCCAATCAATCCCAGCTGTGACGTGCCCCATGTGATCGCCAATTGCGACGAGGATGGCAGCGATGGCAAGCACCGGTT	-	-	intergenic	IntS2, exon_1	IntS2	NA	-	0
A373R7	294	lumpy	BND	3R	5086759	3R	5087180	3	0	somatic_tumour	6535_1	0.4	3R:5086759-5087180	3to3	0.16	0	-	-	-	-	-	corto, 5UTR	intergenic	corto	NA	-	0
A373R7	306	lumpy	BND	3R	8438933	3R	11766133	3	0	somatic_tumour	7060_1	3327.2	3R:8438933-11766133	3to3	0.23	-0.01	-	-	-	-	-	CG45263, intron	l(3)neo38, 3UTR	CG45263, l(3)neo38	NA	-	0
A373R7	306	novobreak	BND	3R	8438933	3R	11766133	3	0	somatic_tumour	364	3327.2	3R:8438933-11766133	3to3	0.23	-0.01	-	-	CTTGTGTTTCGCTTACGCTCCTTCGATCATTTTTGTGTTTGCTTTTGTTTTTGTGTTTATAATTTATTTAAATGCACTAAAAGTTGCACGGACCGTTTGCCAGCAGCCTGTGAAGTCGATCGTCGTCGGTTCGGCTGTGTTGCGATCTAGATAATGGGCATTCAGGCAAATAGGCAAATCCGTATGAAAGCAGCGACC	-	-	CG45263, intron	l(3)neo38, 3UTR	CG45263, l(3)neo38	NA	-	0
A373R7	321	novobreak	TRA	3R	11790676	3L	12408736	3	0	somatic_tumour	382	618.1	3R:11790676 3L:12408736	5to3	0.29	0	-	-	GCCTTGTACTTTGTGCAGTTCTTCATGGAGTGCTCCGTGCACTTCTCGTGATAGGAGTTTCCGCAGTCCATGCACCGGTAGCCAACCGGTCCCCAGTGCTTTTCGCGCCTGCCCCTCGCTCTTTTCCCCCACCAACTCCGTTGGGGCAGCGCGCGTGCGGCCTCTG	-	-	Sbf, exon_7	CG32103, intron	Sbf, CG32103	NA	-	0
A373R7	332	novobreak	TRA	3R	15016376	3L	2990399	4	0	somatic_tumour	395	12026	3R:15016376 3L:2990399	5to5	0.48	0	-	-	GTCATAAATATCATAGCCTTAAAAATCCTCTACCTGAAAAATAAAGTCCCGGGAAAGCGGCACCACTGGCAGTTGGAATTTGGCTGGGGCAACGACTCCCCGAGGAGCGAAATGTGCGCCAC	-	-	intergenic	intergenic	-	NA	-	0
A373R7	337	novobreak	TRA	3R	16086670	X	11712848	3	0	somatic_tumour	404	4373.8	3R:16086670 X:11712848	5to3	0.24	0	-	-	GTATGTGGAGTCAATTCACACGGATCTAACGCTGCTCGGCAATCCGAGTACTAAGCTCAGTCATGCCTCCTTCTTTGCCAACTGGGGCCTCGGGCAGCCGTTTGTGCTGAGTGAACCGGTGCCAGTGGAGGCGCCGGATCCAGGCGGC	-	-	sxe2, exon	Amun, exon_3	Mhcl, sxe2, Amun	NA	-	0
A373R7	344	Control-Freec	DUP	3R	18707247	3R	18739512	-	-	somatic_tumour	-	32.3	3R:18707247-18739512	Heterozygous duplication	0.36	0.45	-	-	-	-	-	ChAT, intron	Mekk1, exon_1	VAChT, ChAT, CR46265, CG34283, CG7714, CG7715, CG14302, Mekk1	NA	snp_su:0; snp_op:0	0
A373R7	346	lumpy	BND	3R	20957204	3R	20958231	3	0	somatic_tumour	7885_1	1	3R:20957204-20958231	3to3	0.34	0.16	-	-	-	-	-	Atpalpha, intron	Atpalpha, intron	Atpalpha	NA	-	0
A373R7	351	delly	TRA	4	372985	2R	5741633	3	0	somatic_tumour	BND00002940	5368.7	4:372985 2R:5741633	381:351_381	0.26	0	-	-	ATTACATATTTTTAATAGACTCATCTTCTACTCTAGAAATAACGGTTGTAATAATGGCTAACACCCACCCCAAACTCCGTCAAGGTTATTATACGGTCAC	-	-	Hcf, 3UTR	intergenic	Hcf	NA	-	0
A373R7	356	novobreak	COMPLEX_BND	3R	24453333	3R	25506393	3	0	somatic_tumour	428	1053.1	3R:24453333-25506393	356:143_356	0.22	-0.05	-	-	TAGTAGGGCTCCTCCCACAACTTGATATCACGCTCCCGCAGACGAGCTCGCAGCCACACCCAGTTGACAAATTGCCAGGGGAAAATTAAATATTTTTTTTTGCAGTTGT	-	-	nAChRalpha1, intron	CG5111, exon	nAChRalpha1, CG5111	NA	-	0
A373R7	357	novobreak	TRA	3R	24540725	2R	12131662	3	0	somatic_tumour	431	12409.1	3R:24540725 2R:12131662	5to3	0.23	0	-	-	GTACATATCGTTCCACATGTGCTCGACGGTCTGATCCAAGATGCTGACTGTACTCGAAAAATTTGTGCTCAGCTCTTGGATGTTGGCCAAAATGTGTAGATGCATTTGTATCTGTATCTGTATCCGTA	-	-	CG5789, exon_5	intergenic	CG5789	NA	-	0
A373R7	361	novobreak	TRA	3R	25312774	2L	18521808	4	0	somatic_tumour	435	6791	3R:25312774 2L:18521808	3to3	0.42	0	-	-	TTTTTGCTTTTGGCACTTGCCTGCCTGATAGCAACTGGCATCTTCCGTCATTTCAAGGCGCTACAACTGGTTGTCATCTTACATAAGTCGAACAATCATTTCGTATACGACCTGTTAGCCATGCTAACAGTG	-	-	CG31087, intron	CG10211, intron	CG31087, CG10211	NA	-	0
A373R7	365	novobreak	TRA	3R	26021865	3L	4250181	4	0	somatic_tumour	440	21771.7	3R:26021865 3L:4250181	5to3	0.39	0	-	-	GGCCGGGAGAGCCTGATCCCCGTTTGCCGGGAGAGCGTGGCTGTCATATAAAAGTAGGGCTGGGAACTAGTTTGCCACTCATTTCGTAAAAGTGCCGCCACTCGAACGCACCGCGATCCCACCGAACTATACGAGACGGATGCACTCACATTCTCCTCCTGATC	-	-	E(spl)m3-HLH, 5UTR	ago, exon_2	E(spl)m3-HLH, ago	NA	-	0
A373R7	371	lumpy	BND	3R	27607253	3R	29064119	3	0	somatic_tumour	8581_1	1456.9	3R:27607253-29064119	3to3	0.13	-0.02	-	-	-	-	-	dsd, 5UTR	CG11873, 5UTR	dsd, CG11873	NA	-	0
A373R7	371	novobreak	BND	3R	27607253	3R	29064119	3	0	somatic_tumour	446	1456.9	3R:27607253-29064119	3to3	0.13	-0.02	-	-	GGGCAACCCAAGGCCCCGCACTTGAACGCACACACACACACACGCACACACTAGCACGCACACACTCACTCGCCAGCAGCCAGCACACACACACAAACACA	-	-	dsd, 5UTR	CG11873, 5UTR	dsd, CG11873	NA	-	0
A373R7	372	novobreak	TRA	3R	28812189	2L	19468659	3	0	somatic_tumour	447	9343.5	3R:28812189 2L:19468659	5to5	0.44	0	-	-	AAAACAAAAAACCCGAATTTCATCAAAAATACTTGCGCAACTCTTCGACCGGACCTAGTGACCGTTGATTAAAAATTCAGTCCTTACTAGCCCATTTCGGTAGCTGACACTGACAGTTAGCTGGAGCAGCCCATTAAAGCATTTGGAAAAAAGTGAACATCACGAGGC	-	-	CG1646, exon_1	intergenic	CG1646	NA	-	0
A373R7	385	novobreak	TRA	A.pasteurianus_NC_013212.1	9356	2L	2619352	4	0	somatic_tumour	514	2610	A.pasteurianus_NC_013212.1:9356 2L:2619352	-	0.48	0	-	-	ATTACTTTTTATGATACTATACACGTAATACTTTATTATTAAGCGTCGCCAAAATGGAGAATTTTTAAAAGATATAGCTGAGGATTTTGGAATTAGTGTTGGGACAGTCTCACGGATTACAACTGGAGCAGACAGT	-	-	intergenic	intergenic	-	NA	bp2_A.pasteurianus_NC_013212.1_3	0
A373R7	388	novobreak	TRA	X	774155	3L	11379862	3	0	somatic_tumour	533	10605.7	X:774155 3L:11379862	3to3	0.34	0	-	-	GAACTTACCTACCGGCAAATGTGACCTCAAGCTTAGTTCATAGAGCTTCCTACGTTTCTCCCATCGCCTTGCTAGTTTCGAATTCGAGGGTATTACAAAGTT	-	-	fz3, intron	intergenic	fz3	NA	-	0
A373R7	403	novobreak	TRA	X	10040491	2L	5612239	3	0	somatic_tumour	565	4428.3	X:10040491 2L:5612239	5to3	0.27	0	-	-	CACTGCACTGAATGTAGCTAGTCAACGTAGTAACAGCACCGTAGCCAATTATATTAATCGATTCAAGTCAAACAGTTACACAAACAGGACGGGATGCGAAGTCGGTGGCCCACACCGGCGAAATGAGAGGACAAAGCTTTCCACTTCAATG	-	-	Cht6, exon_12	DIP-eta, intron	Cht6, DIP-eta	NA	-	0
A373R7	408	novobreak	TRA	X	11278544	2R	6761634	3	0	somatic_tumour	570	4516.9	X:11278544 2R:6761634	3to5	0.15	0	-	-	GAAGAACCACAGAGTTCCACACCCACAATTTATTGGACCTAAGGGAAATCTGCTGGGAAATTTGCTGAATAATTTACAGACTTATTAACTAGAATACAAACCTGTCT	-	-	CG44422, intron	Epac, 3UTR	CG44422, Epac	NA	-	0
A373R7	421	novobreak	TRA	X	17630206	3L	22584723	4	0	somatic_tumour	586	4954.5	X:17630206 3L:22584723	3to3	0.73	0	-	-	TTCGGCCACCCAGCGACTTCAGATGCGAAGAGGCGAATTTGCCTCGTTTAGCGAGGGAATAATGACACAAATCGCATAATTCGACGAGGCAGAAAGGATTCATCTTTGGGTGTACTCTCGGAGCCTTGCATCCGTCGTCCACATTCAACAACTTTGATGATCAATCA	-	-	corolla, exon	CG14459, intron	corolla, CG14459	NA	-	0
A373R7	422	novobreak	TRA	X	18410837	3R	10180122	3	0	somatic_tumour	587	8230.7	X:18410837 3R:10180122	3to5	0.4	0	-	-	GATTTATATTTACTTTCAAAAGGCATACAGAGGCAGCATCCCGTTCGCCCTTTGGCTTGCCAAAAAGAGAAAAATATGAAATTTTGTGCAGTCATTGAAGCAATTAATTTCACATCCGATCATCCGCCGCCCGCTGCAAATTTGGCATTTATTTAATTACCCTTTTCGAATAAATTGTTA	-	-	intergenic	CG12814, intron	CG12814	NA	-	0
A373R7	425	novobreak	TRA	X	19786978	3L	8257481	3	0	somatic_tumour	591	11529.5	X:19786978 3L:8257481	5to5	0.44	0	-	-	GTTGCACGCAGAGGAACCAAAAACCCGACCCGAGCGATAGAAGGACTAGGACATCCACAACCCACAACATCCCACATCCCATCCAAAACAGGGCAGAACTTCTGCTGACAGTGATGAATGA	-	-	CR44885, exon_3	Dscam4, intron	CR44885, Dscam4	NA	-	0
A373R7	426	lumpy	TANDUP	X	19860618	X	19862863	4	0	somatic_tumour	9515	2.2	X:19860618-19862863	3to5	0.73	-1.56	-	-	-	-	-	CG15618, exon	CG15618, exon_5	CG15618	NA	snp_su:0; snp_op:0	0
A373R7	426	novobreak	TANDUP	X	19860618	X	19862863	4	0	somatic_tumour	592	2.2	X:19860618-19862863	3to5	0.73	-1.56	-	-	CCACTGCAATGCCCTGAAGGTAAGCGGCTCGTGGATTGTGCCACCGTGCGTTGGCGTGGGCCCACCTCCTCCCGCTGCTCACGACTAAGGGTCTCGAAATATCGGCGAATGTCGCGTGAAAACTCAAAGTGCTCGATA	-	-	CG15618, exon	CG15618, exon_5	CG15618	NA	snp_su:0; snp_op:0	0
A373R9	10	CNV-Seq	TANDUP	2R	1328600	2R	1333994	-	-	somatic_tumour	-	5.4	2R:1328600-1333994	10:10_11	0.38	0.63	-		-		-	intergenic	intergenic	-	NA	snp_su:0; snp_op:0	0
A373R9	13	Control-Freec	DUP	2R	2953206	2R	2969730	-	-	somatic_tumour	-	16.5	2R:2953206-2969730	Heterozygous duplication	0.33	0.52	-		-		-	Scp1, intron	intergenic	Scp1	NA	snp_su:0; snp_op:1	0
A373R9	14	Control-Freec	DUP	2R	6086340	2R	6092766	-	-	somatic_tumour	-	6.4	2R:6086340-6092766	Heterozygous duplication	0.39	0.65	-		-		-	intergenic	EcR, exon	EcR	NA	snp_su:0; snp_op:1	0
A373R9	15	Control-Freec	DUP	2R	6159780	2R	6173550	-	-	somatic_tumour	-	13.8	2R:6159780-6173550	Heterozygous duplication	0.38	0.56	-		-		-	EcR, intron	intergenic	EcR, tRNA:Arg-ACG-1-2, tRNA:Asn-GTT-1-4, tRNA:Asn-GTT-1-5, tRNA:Asn-GTT-1-6, tRNA:Lys-CTT-1-2, tRNA:Lys-CTT-1-3, tRNA:Lys-CTT-1-4, tRNA:Ile-AAT-1-1, tRNA:Arg-ACG-1-3, tRNA:Lys-CTT-1-5, tRNA:Arg-ACG-1-4	NA	snp_su:0; snp_op:0	0
A373R9	23	Control-Freec	DUP	3L	22784760	3L	22793940	-	-	somatic_tumour	-	9.2	3L:22784760-22793940	Heterozygous duplication	0.37	0.44	-		-		-	SPoCk, 3UTR	jim, 3UTR	SPoCk, CG14448, jim	NA	snp_su:0; snp_op:0	0
A373R9	26	Control-Freec	DUP	3R	4296240	3R	4307256	-	-	somatic_tumour	-	11	3R:4296240-4307256	Heterozygous duplication	0.32	0.41	-		-		-	cpx, 3UTR	intergenic	cpx	NA	snp_su:0; snp_op:0	0
A373R9	29	Control-Freec	DUP	3R	15169950	3R	15184638	-	-	somatic_tumour	-	14.7	3R:15169950-15184638	Heterozygous duplication	0.34	0.42	-		-		-	Gyc88E, intron	Gyc88E, intron	Gyc88E, Mf	NA	snp_su:0; snp_op:0	0
A373R9	31	Control-Freec	DUP	3R	18413244	3R	18420588	-	-	somatic_tumour	-	7.3	3R:18413244-18420588	Heterozygous duplication	0.34	0.46	-		-		-	intergenic	fru, 3UTR	fru	NA	snp_su:9; snp_op:7; snp_ratio:1.29	10.33
A373R9	33	Control-Freec	DUP	3R	21584934	3R	21622572	-	-	somatic_tumour	-	37.6	3R:21584934-21622572	Heterozygous duplication	0.27	0.31	-		-		-	InR, intron	E2f1, intron	InR, CR43653, CR44034, mir-998, mir-11, E2f1	TRUE	low FC; snp_su:49; snp_op:19; snp_ratio:2.58	18.11
A373R9	34	Control-Freec	DUP	3R	22007214	3R	22012722	-	-	somatic_tumour	-	5.5	3R:22007214-22012722	Heterozygous duplication	0.4	0.55	-		-		-	Eip93F, 3UTR	Eip93F, 3UTR	Eip93F	NA	snp_su:2; snp_op:2	11.72
A373R9	51	Control-Freec	DUP	4	687582	4	690336	-	-	somatic_tumour	-	2.8	4:687582-690336	Heterozygous duplication	0.48	0.56	-		-		-	CG11360, 3UTR	CG11360, 3UTR	CG11360	NA	snp_su:0; snp_op:0	0
A373R9	55	Control-Freec	DUP	4	878526	4	882198	-	-	somatic_tumour	-	3.7	4:878526-882198	Heterozygous duplication	0.47	0.47	-		-		-	unc-13, intron	CR44029, ncRNA	unc-13, CR44029	NA	snp_su:0; snp_op:0	0
A512R17	5	lumpy	BND	2L	2860962	2L	2861103	4	0	somatic_tumour	157_1	0.1	2L:2860962-2861103	3to3	0.3	0	GTGAGCT	-	-	GAAATTAATTGAGTTATGCGCGCCGAACTAGTGTGGCAAACTTTTTGGCTCAGGCGACCGCTTTCCAGTTAATTTGAAGGTCGTGAGCTAGTGAAGATTGCACAACTGCGACACGAGCCAAAGAATATTTGAATTTTAAATGCTCTTTTCG	Alt-EJ	CG2991, intron	CG2991, intron	CG2991	NA	mh:7; ins:0; tup:0; tdown:0	0
A512R17	6	lumpy	BND	2L	3040831	2L	3041097	3	0	somatic_tumour	172_1	0.3	2L:3040831-3041097	5to5	0.23	0	GCC	-	-	GGTGATGTACTGGCGAAAGTCGTACTTCGATTCCGCCGCCTTCTGACCACCTTGTCCAGCGCAGTCCAGCACAATGTCATAGGGTGCGTATTTGCACAGCTCCTCCATGGCCAGCGTGTTGTATGCCGGATTGACGGCTTGGTCGGGACTGTAC	Alt-EJ	CG17221, exon_3	CG17221, exon_3	CG17221	NA	mh:3; ins:0; tup:0; tdown:0	0
A512R17	10	novobreak	BND	2L	4462260	2L	4462471	3	0	somatic_tumour	9	0.2	2L:4462260-4462471	3to3	0.36	0	-	-	ATCTAACTTGTGCTCCTGTGTCACTATTTCCAGTTGGTGCACTATGTACATGAAGTACTCGCTGGCTGGCTGGCCGTGGAGCTTCTCAGGCAGATTCTGGCCAATGTACCTTCGATCCTCGTCACTCACATGCTGCGGGCAGCTACATGGTCACCTACCTTGATGGCAAGGCCGAACGCCTCAAGCGCAGTTGCCTGTGGACACTGGCCAACGTTCTGGGCACATGCGACAAGGCC	-	NHEJ	CG15443, exon	CG15443, exon	CG15443	NA	mh:0; ins:0; tup:0; tdown:0	0
A512R17	17	lumpy	BND	2L	7263746	2L	7264071	4	0	somatic_tumour	405_1	0.3	2L:7263746-7264071	3to3	0.2	0	AATGCAGAC	-	-	CATAGGTGAGATGGAATTCTAGATGAAAAATCCTCAAAGGGTGCGGTTCCACTCCAGTTGTGTGCGCCAAGCCTTTGTTTCTGCCACTGAATGCAGACAAATTGCTGGAATGCCGTTCAAGCATAAACGAGAAAATACCAGCCATAAACGC	Alt-EJ	Wnt4, intron	Wnt4, intron	Wnt4	NA	mh:9; ins:0; tup:0; tdown:0	0
A512R17	32	Control-Freec	DEL	2L	14750150	2L	14836500	-	-	somatic_tumour	-	86.3	2L:14750150-14836500	Heterozygous deletion	0.24	-0.47	-	-	-	-	-	intergenic	intergenic	CG4691, CR44858, CSN1a, CG4701, CG4650, CR15280, CG18636, CG18420, CG33308, CG33309	NA	snp_su:9; snp_op:2; snp_ratio:4.48	18.58
A512R17	38	lumpy	BND	2L	16090871	2L	16091001	3	0	somatic_tumour	920	0.1	2L:16090871-16091001	5to5	0.36	0	-	-	-	-	-	intergenic	intergenic	-	NA	-	0
A512R17	63	novobreak	BND	2R	9081204	2R	9081323	3	0	somatic_tumour	35	0.1	2R:9081204-9081323	3to3	0.24	0	-	-	GTTTCTGGGCTATGCCACCGATGGAGCCGAGTTCGTGTTCGGCGACTTCCTGGTGAACAATAATGTGTTCGCCTTCGCCATCCTGCCGGTTATCTTCTTCTTCAGCTTCTTCATCTCCATCCTGTACTACATGGGTACAATGCAGTGGGTGGTGATCAAACTGGGCTGGATCCTGCAGCAGATCCTGGGCACCATGATGCTGTGGATTTCGCTCTTGGTCAGCTTGTTGATATACGGCCGAATGAGCAGCGGGCTCTCGGACATGCCAAGGAAGATGTTGGCTGCGGCCGTCACGCTTTCGCAAACAGT	-	-	CG8083, exon_5	CG8083, exon_5	CG8083	NA	-	0
A512R17	82	novobreak	BND	2R	19397420	2R	19397694	3	0	somatic_tumour	50	0.3	2R:19397420-19397694	5to5	0.36	0	-	-	AAAACTTTAAGGCACAACTTAAACGCATTTACATTTCAAATTAACTGACATAAAATTAAAACCCCGATGATTAATGCCAGATAAATCGAATGTTTCTGCTTTCCTCAGAGTAATCGCATGTTTTAATGCGGGCGTGGTGTATTTTTGGATTTTCGTTTTCTTCATAATTTATTGGTTTTTATAAATATATATATGTATATG	-	-	hts, 3UTR	hts, 3UTR	hts	NA	-	0
A512R17	87	lumpy	BND	2R	20897804	2R	20898407	4	0	somatic_tumour	2429_1	0.6	2R:20897804-20898407	3to3	0.48	0	-	-	-	-	-	CR43160, ncRNA	CR43160, exon_3	otp, CR43160	NA	-	0
A512R17	88	Control-Freec	DUP	2R	20928100	2R	20967350	-	-	somatic_tumour	-	39.2	2R:20928100-20967350	Heterozygous duplication	0.32	0.44	-	-	-	-	-	Rx, intron	intergenic	Rx, Act57B, snoRNA:660, CG33704, hbn	NA	snp_su:16; snp_op:7; snp_ratio:2.28	14.93
A512R17	100	novobreak	TRA	3L	532148	3R	15826739	3	0	somatic_tumour	60	15294.6	3L:532148 3R:15826739	3to5	0.23	0	-	-	CCCATGATTAATGCAAGTTGAATAAGCGTTTTTCGTGCTTCCTTTGGCAACGGGGAAGTTCTAAGCCGACAAATTGAAAACCATTATGCAGTTCCATTTGTTCAGATTGCATGTTATGCTTGTCAATCGATATAACTATAGAACACTTTGCCAACGCTAGCATTATCCCAATATGCACCTGATCCGCCTATTTGCGTGTTCGGCTCCAAAAGTTCCCCGCCCGAATTCGGGCTACAAATTTGATGACGAAGCAGTATTTTGACAAACAATTAACTCAGCCCTAATTTATGATCGCATCTGATTATTGCAATTGATCCCTGGGCTGAGATTCGCAGATCGCATTAC	-	-	klar, intron	CG4576, intron	klar, rec, CG4576	NA	-	0
A512R17	104	lumpy	BND	3L	3888244	3L	3888407	3	0	somatic_tumour	2909_1	0.2	3L:3888244-3888407	3to3	0.31	0	-	-	-	-	-	intergenic	intergenic	-	NA	-	0
A512R17	110	novobreak	TRA	3L	6396400	3R	10467400	3	0	somatic_tumour	65	4071	3L:6396400 3R:10467400	3to3	0.19	0	-	-	CCCAAAAACGTAGAATCCTCTTCGACCGGCTAAGTCCCCGCCAGGTTGGGCTCCTACTTTGGCCTCCACTCCATCTTAAAGTCCAACTCCAGATCCGTTCCCATGTCCGCGGAGCAGAGTGTCCACCGTCCAATGTCCACAGTCCAGTGTCCAGTTCAATGGCCATGGAC	-	-	intergenic	intergenic	-	NA	-	0
A512R17	111	lumpy	BND	3L	6577863	3L	11592806	3	0	somatic_tumour	3394_1	5014.9	3L:6577863-11592806	3to3	0.31	0	-	-	-	-	-	jv, intron	intergenic	CG18769, jv	NA	-	0
A512R17	112	Control-Freec	DUP	3L	6609700	3L	6680350	-	-	somatic_tumour	-	70.7	3L:6609700-6680350	Heterozygous duplication	0.25	0.27	-	-	-	-	-	CG8398, exon_1	intergenic	CG8398	TRUE	low FC; snp_su:26; snp_op:9; snp_ratio:2.89	19.16
A512R17	114	novobreak	BND	3L	6740464	3L	6740720	3	0	somatic_tumour	68	0.3	3L:6740464-6740720	3to3	0.31	0	-	-	CCATAAGATAATGCATATATCGAATAGAAATAGATCAAAAAGCATGCTTACAGATTGTTTTTGAAAACGAAATCCAACCAATTCTTCCATATACAAAATTAAATGATGGGCAAAACTGAAATTAAGTGCTCATCCTTGTTCCGTCTATGCTGATCCTGGATTTATCGACGATGTTGATGATGGCGATTTGGCTTTTCAACTGCAGCAACAGCAGCAGCAACAACAGCAGCAATCGCAGCAGCGCACACGCAGACGGTTAGCACGCCAATGTTCCTAGGAAGGCTGGCGGACGCGACGGCCACATCCATTCTACTCACAGAGCGCGAATCA	-	NHEJ	dikar, 3UTR	dikar, exon_5	dikar	NA	mh:0; ins:0; tup:0; tdown:0	0
A512R17	121	novobreak	BND	3L	10730925	3L	10731250	3	0	somatic_tumour	72	0.3	3L:10730925-10731250	3to3	0.21	0	-	-	GCAAAAAAGTTTTCGAAAACCTCTTTCTTCCTTCTCCAACTAAAAAAAAAAAAGAAACTAAACTAAATGAAATTTTCAGTGCCGGAAAAAAAAAGGAAAGGATCTGCTGAAGAGGAGGACAAACTTTTATGGAGCCCAAAAGTAATAGGCAAAGACGTTTGGAGT	-	-	intergenic	intergenic	-	NA	-	0
A512R17	123	lumpy	BND	3L	11397415	3L	11397826	2	1	somatic_tumour	3381_1	0.4	3L:11397415-11397826	3to3	0.29	0	-	-	-	-	-	intergenic	CG44362, exon	CG44362	NA	-	0
A512R17	123	novobreak	BND	3L	11397415	3L	11397826	2	1	somatic_tumour	73	0.4	3L:11397415-11397826	3to3	0.29	0	-	-	CAATTACACGCAGGAGCCACAGAACATGCCCGTGGGCGGATGGATGGTCACGGAGTTTGTGGGGGGTGTGCCACTCCGTCCGGCACTCTGGCATTCTGGCACTCTGGCATTCCGGCTTACTGGCATTCTGGCATTTTGGCCCGGTAGTTGAATCTACACATGGAGAAAAACAAGTACATATATGAATATACAATTTAACACATTTTTTACTGT	-	-	intergenic	CG44362, exon	CG44362	NA	-	0
A512R17	125	lumpy	BND	3L	13007223	3L	13007494	3	0	somatic_tumour	3486_1	0.3	3L:13007223-13007494	3to3	0.29	0	-	-	-	-	-	CG11263, exon	CG11263, exon	CG11263	NA	-	0
A512R17	127	lumpy	BND	3L	13514819	3L	13515007	3	0	somatic_tumour	3509_1	0.2	3L:13514819-13515007	3to3	0.24	0	-	-	-	-	-	Liprin-beta, intron	Liprin-beta, exon	Liprin-beta	NA	-	0
A512R17	127	novobreak	BND	3L	13514819	3L	13515007	3	0	somatic_tumour	76	0.2	3L:13514819-13515007	3to3	0.24	0	-	-	GTTGTTCGGTGAGAATGAAAAACATTGGACAACCTGGGGAGCGCAGGAGGTGTGCAATTGGTTGGCATACATGGGTCTAGGCTGCTATGAGGACAATTGCCGGTAAGTTTTGTCATCAAACTCCTTCCCAGTTAGGTCGTCGATGGCCAACAAGATTTTTTTCCGATGAAGTGGCATCTTTAGGTTTAGCTCTCGTTCGATGTCGACAGG	-	-	Liprin-beta, intron	Liprin-beta, exon	Liprin-beta	NA	-	0
A512R17	131	lumpy	BND	3L	16059644	3L	16059794	4	0	somatic_tumour	3705_1	0.1	3L:16059644-16059794	3to3	0.41	0	-	-	-	-	-	Mbs, intron	Mbs, intron	Mbs	NA	-	0
A512R17	139	lumpy	BND	3L	20502027	3L	20502614	1	4	somatic_tumour	3975	0.6	3L:20502027-20502614	3to3	0.45	0	-	-	-	-	-	CG32425, intron	CG32425, intron	CG32425	NA	bp1_INE-1_Helitron=6; bp2_INE-1_Helitron=6	0
A512R17	157	lumpy	COMPLEX_BND	3R	10648178	3R	10648881	2	1	somatic_tumour	4522_1	0.7	3R:10648178-10648881	3to3	0.19	0.2	-	-	-	-	-	intergenic	intergenic	-	NA	-	0
A512R17	159	novobreak	BND	3R	11480462	3R	11480630	3	1	somatic_tumour	99	0.2	3R:11480462-11480630	5to5	0.41	0	CGCGCGG	-	TCCTTGCCGCTTGTTGTTTTTCTTTTTTTCGCCAGCAAAATCCTTTTGGATGCAGCTACCATAACTCATCGCACCGAAAAACACTCGAGTCCCGGGGTCAGAGCGATAAAAACGTGTGAAAAGGCATTTGGCAAAGGCCGTAATCTCATACCCATTCCCATTCCCCAGCCGCATCCGCATCCTCATCCTCATCCGCAGCCTCTCTCTCATCTCGGGACTGACATCCTGTGTCGTCCCGGTCCATCTCACTTCACCTTTTGGCAAATGATAG	TCGCTTTTGGTTTTTGATTTGTTGCAATTTCCTTTGGACAGCCTTTTTGTTTTGCTTCTCTTTTATTTTGACTTGGTTTACGCGCGCGGAGTGAACGGCCATCGATTGCTTCGCGACAAAAGTGTTTAGTTCAACAATCGCTTATCGATAA	Alt-EJ	intergenic	intergenic	-	NA	mh:7; ins:0; tup:0; tdown:0	0
A512R17	165	lumpy	BND	3R	15764276	3R	15764643	2	1	somatic_tumour	4809	0.4	3R:15764276-15764643	3to3	0.25	0	-	-	-	-	-	intergenic	intergenic	-	NA	-	0
A512R17	165	novobreak	BND	3R	15764276	3R	15764643	2	1	somatic_tumour	104	0.4	3R:15764276-15764643	3to3	0.25	0	-	-	GGTCCATCTATGGAAACGTGCGTTGTCTGCTACCTGACGGTTGACTTTCTTTCTCTAATGAAATGCGGTTACAAATGCAATTTTACATTTTTCACAAAAAAGCATTTTATCTGTCGACACCAGGCCCGGCCCGAACAGGAACACGCTCGAAACACAAACACAATAGAGGAAATTCCACCCACTGGCAAAGGGAC	-	-	intergenic	intergenic	-	NA	-	0
A512R17	169	novobreak	BND	3R	17501281	3R	17501416	2	1	somatic_tumour	107	0.1	3R:17501281-17501416	3to3	0.2	0	-	-	GCAACGTTTAACCTCAGCCAGGACATGAGAGCTTCACTGAAAAAAATCAAAGCGCATATAGGCACAGTATTTAATACAAAACTTCACCGTAACTGGCCATCAATATTTGTTGATTTTGGTATATGAAAAAGAAATATACATTAATTAGCGATTGAATCTATAGACTGCATTGATTTTTCTCAGTGTTCTTGGGATCAGGGGGTGATTTTCGCTCGACTGCCTCGGCAACACA	-	-	Dscam3, intron	Dscam3, intron	Dscam3	NA	-	0
A512R17	173	novobreak	BND	3R	18465048	3R	18465601	3	0	somatic_tumour	109	0.6	3R:18465048-18465601	3to3	0.25	0	-	-	GTTTTCCCCTGCTTTACAACTCGATCGTGTTTGCCTGTTGTGGGCCAAATAAATTTTTATAAATAATAAGCTTGGGCCAACGGACGTGGATGTTGCTGCAGTTGCAGTTGCAGTTACCGTTGCAACTGGCAGTTGCATATTTACCCAGGAATGTCAACAATTTCCTTTTAATAATTTGCCAGTTTGACAAGTTTTTTTACCCTCTTTTTTTCTGTGTTTCTGTTGTTCCCCCTCTGATTGAT	-	-	fru, intron	fru, intron	fru	NA	bp1_Dmel\Doc3-element_LINE-like=2	0
A512R17	175	novobreak	BND	3R	19180309	3R	19180780	3	0	somatic_tumour	111	0.5	3R:19180309-19180780	5to5	0.29	0	-	-	CGTTACAATCAGTGTTGGTAGGCATTATCGATAAGCGATTGTTGAACTAAACACTTTTGTCGCGAAGCAATCGATGGCCGTTCACTCCGCGCGCGTAAACCAAGTCAAAATAAAAGAGAAGCAAAACAAAAAGGCTGTCCAAAGGAAATTGCAACAAATCAAAAACCAAAAGCGAAAGCAAAAGTGAGTGCAATAGTTTTTTGTGATTTAATTC	-	-	CG5555, 5UTR	CG31475, exon_1	CG5555, CG31475	NA	-	0
A512R17	176	delly	DEL	3R	19335160	3R	19342014	3	1	somatic_tumour	DEL00000131	6.8	3R:19335160-19342014	5to3	0.3	-0.12	-	-	CGGCATATCTGGGTCAGCGATTAAGCGATTTTAAATGCCAATTATCGGCAGCGATTTTGCGTGGAAAGAATTCGACTTCCTGGACAAGTCGTAAAATATTTTTAAGCAACGCCAGGGATAATTTGTTTTCGGCCCACCTACTGTTCTGAGG	-	-	intergenic	intergenic	-	NA	-	0
A512R17	176	lumpy	DEL	3R	19335160	3R	19342014	3	1	somatic_tumour	5039	6.9	3R:19335160-19342014	5to3	0.3	-0.12	-	-	-	-	-	intergenic	intergenic	-	NA	-	0
A512R17	176	novobreak	DEL	3R	19335160	3R	19342014	3	1	somatic_tumour	112	6.9	3R:19335160-19342014	5to3	0.3	-0.12	-	-	CGTTGCGGCATATCTGGGTCAGCGATTAAGCGATTTTAAATGCCAATTATCGGCAGCGATTTTGCGTGGAAAGAATTCGACTTCCTGGACAAGTCGTAAAATATTTTTAAGCAACGCCAGGGATAATTTGTTTTCGGCCCACCTACTGTTCTGAGG	-	-	intergenic	intergenic	-	NA	-	0
A512R17	177	lumpy	BND	3R	19718241	3R	19718619	2	1	somatic_tumour	5057_1	0.4	3R:19718241-19718619	3to3	0.31	0	-	-	-	-	-	intergenic	intergenic	-	NA	-	0
A512R17	180	lumpy	BND	3R	23305763	3R	23306234	1	2	somatic_tumour	5277_1	0.5	3R:23305763-23306234	3to3	0.25	0	-	-	-	-	-	pnt, intron	pnt, intron	pnt	NA	-	0
A512R17	189	Control-Freec	DUP	3R	27718350	3R	27757600	-	-	somatic_tumour	-	39.2	3R:27718350-27757600	Heterozygous duplication	0.31	0.42	-	-	-	-	-	intergenic	intergenic	Ets98B	NA	snp_su:2; snp_op:2	11.39
A512R17	195	novobreak	TRA	3R	31012632	2R	22971230	3	0	somatic_tumour	126	8041.4	3R:31012632 2R:22971230	195:94_195	0.22	0	-	-	TGGTTGGGCAGTGAAAATCGCAAATCTGCCAACGGCAGGCCGCAGATGATCCACTTGATTGGAGGCAGTCAAGGCAGCGATGAGCTGCGGGCTTAAATTCGCAATTATGTCGTTTTAATAAACAGGGACCAACGAGCCAACTTTGGCAGCAAATAAAACCTCAAATGGAGCGTCGAGTTAGCTAAAACCCAAACGCAGCTGCAGCTGCATTTACAGCACCAGCACCACAACCGATGGATTTGAAATAAAAATGAAATTTTTGTGGCCATTTACAA	-	-	5-HT7, intron	intergenic	5-HT7	NA	-	0
A512R17	200	novobreak	BND	4	1100210	4	1100555	3	0	somatic_tumour	128	0.3	4:1100210-1100555	5to5	0.27	0	-	-	CTATAATATAAACGTACCCGTTACTCAGATAGTGGTAGTGCGGCCTTGAAATTTCCACACTTCTGGCATATCGATCGATATGTTATCAAGAAAAATAAAACAATACAAAAAATTCTACATACTCTACAAGCCCAATCTCACCTTCCTGGTTATCCTAATCAAGTATGTATATATTTTTTATTTAAATGGTCGGAAACGCATCCTGATACATCATTTTCAACAT	-	-	sv, intron	sv, intron	sv	NA	-	0
A512R17	204	lumpy	BND	X	14125860	X	14126091	3	0	somatic_tumour	6161_1	0.2	X:14125860-14126091	3to3	0.36	0	-	-	-	-	-	intergenic	intergenic	-	NA	-	0
A512R19	5	CNV-Seq	DEL	X	2796789	X	3312289	-	-	somatic_tumour	-	515	X:2796789-3312289	Homozygous deletion	0.75	-1.04	-		-		-	kirre, intron	dnc, intron	kirre, CG12498, CG14416, CG14417, CG14418, CG14419, CG3526, CG3588, CG14424, CG32793, CG3592, CG3598, CG14420, CG14421, CG14422, CG14423, CG17959, CG3603, rst, CG4116, N, CG18508, Fcp3C, CG3939, CG14265, ng2, ng3, ng1, ng4, Pig1, Sgs4, dnc	NA	snp_su:0; snp_op:0	0
A512R21	5	Control-Freec	DUP	3L	10725616	3L	10732768	-	-	somatic_tumour	-	7.2	3L:10725616-10732768	Heterozygous duplication	0.38	0.42	-	-	-	-	-	intergenic	intergenic	-	NA	snp_su:10; snp_op:3; snp_ratio:3.33	13.81
A512R21	6	novobreak	DEL	3L	11261338	3L	11263598	11	0	somatic_tumour	7	2.3	3L:11261338-11263598	5to3	0.31	-0.58	T	-	ATTTGTTTGTACACTTTCCATTTGTACCTGGCTTGGCAACAAAGCGACAATCACAAAAAGCAGAAGAAGCACTAGCAGCAAACAGCAACAACAAACAACAACAACAACAACACTAATGAACGGCGAAGGTTTCGTTAGTGTAATACTGTGATATTTAGATGGCATCTACCCGGGAATTCAGATAGCATTTGCACAGCAACTGCAGTGCTGCATTGATGCAGTGCAGCACAT	ACAAAAAGCAGAAGAAGCACTAGCAGCAAACAGCAACAACAAACAACAACAACAACAACACTAATGAACGGCGAAGGTTTCGTTAGTGTAATACTGTGATATTTAGATGGCATCTACCCGGGAATTCAGATAGCATTTGCACAGCAACTGCAGTGCTGCATTGATGCAGTGCAGCACAT	Alt-EJ	intergenic	intergenic	-	NA	mh:1; ins:0; tup:0; tdown:0; snp_su:1; snp_op:2	8.17
A512R21	6	delly	DEL	3L	11261338	3L	11263598	11	0	somatic_tumour	DEL00000028	2.3	3L:11261338-11263598	5to3	0.31	-0.58	T	-	ACAAAGCGACAATCACAAAAAGCAGAAGAAGCACTAGCAGCAAACAGCAACAACAAACAACAACAACAACAACACTAATGAACGGCGAAGGTTTCGTTAGTGTAATACTGTGATATTTAGATGGCATCTACCCGGGAATTCAGATAGCATTTGCACAGCAACTGCAGTGCTGCATTGATGCAGTGCAGCAC	ACAAAAAGCAGAAGAAGCACTAGCAGCAAACAGCAACAACAAACAACAACAACAACAACACTAATGAACGGCGAAGGTTTCGTTAGTGTAATACTGTGATATTTAGATGGCATCTACCCGGGAATTCAGATAGCATTTGCACAGCAACTGCAGTGCTGCATTGATGCAGTGCAGCACAT	Alt-EJ	intergenic	intergenic	-	NA	mh:1; ins:0; tup:0; tdown:0; snp_su:1; snp_op:2	8.17
A512R21	6	lumpy	DEL	3L	11261338	3L	11263598	11	0	somatic_tumour	2077	2.3	3L:11261338-11263598	5to3	0.31	-0.58	T	-	-	ACAAAAAGCAGAAGAAGCACTAGCAGCAAACAGCAACAACAAACAACAACAACAACAACACTAATGAACGGCGAAGGTTTCGTTAGTGTAATACTGTGATATTTAGATGGCATCTACCCGGGAATTCAGATAGCATTTGCACAGCAACTGCAGTGCTGCATTGATGCAGTGCAGCACAT	Alt-EJ	intergenic	intergenic	-	NA	mh:1; ins:0; tup:0; tdown:0; snp_su:1; snp_op:2	8.17
A512R21	8	Control-Freec	DUP	3R	4162464	3R	4169616	-	-	somatic_tumour	-	7.2	3R:4162464-4169616	Heterozygous duplication	0.4	0.49	-	-	-	-	-	intergenic	intergenic	-	NA	snp_su:0; snp_op:0	0
A512R21	14	Control-Freec	DUP	4	228864	4	236016	-	-	somatic_tumour	-	7.2	4:228864-236016	Heterozygous duplication	0.39	0.42	-	-	-	-	-	CR46065, exon_2	CG1674, intron	yellow-h, CR46065, CG1674	NA	snp_su:1; snp_op:1	16.07
A512R21	15	Control-Freec	DUP	4	407664	4	419584	-	-	somatic_tumour	-	11.9	4:407664-419584	Heterozygous duplication	0.36	0.25	-	-	-	-	-	intergenic	intergenic	-	TRUE	low FC; snp_su:5; snp_op:1; snp_ratio:4.96	22.79
A512R21	16	CNV-Seq	DEL	X	3060852	X	3177592	-	-	somatic_tumour	-	116	X:3060852-3177592	16:16_17	0.85	-1.07	-	-	-	-	-	kirre, intron	dnc, intron	kirre, CG4116, N, CG18508, Fcp3C, CG3939, dnc	NA	snp_su:0; snp_op:0	0
A512R21	16	Control-Freec	DEL	X	3061056	X	3201712	-	-	somatic_tumour	-	140.7	X:3061056-3201712	17:16_17	0.84	-1.03	-	-	-	-	-	kirre, intron	dnc, intron	kirre, CG4116, N, CG18508, Fcp3C, CG3939, dnc	NA	snp_su:0; snp_op:0	0
A512R23	35	CNV-Seq	COMPLEX_DEL	X	3057571	X	3277390	-	-	somatic_tumour		219.8	X:3057571-3277390	37:35_37	0.26	-0.12	-	-		-	-	kirre, intron	dnc, intron	kirre, N, dnc	TRUE	low FC; snp_su:1; snp_op:1	6.41
A512R23	35	delly	COMPLEX_BND	X	3057571	X	3277389	9	5	somatic_tumour	INV00000015	219.8	X:3057571-3277389	35:35_37	0.24	-0.12	-	-	GGTTGTTTTCTTCCTTTTGCTCCGTGAGTGTGTCATAATTTACAACAGTTGCTGGCCAAGTTGCGATTAGATTACACTTTCCATTTCCTGCAAATTGTATCAAAAATGCAGGTACACATGTCAACATCATTAGCCATATATCAACTTCACTTTCAATGCCTGCCCAATGAATTTCCTTAGCAGGCGGC	-	-	kirre, intron	dnc, intron	kirre, dnc	NA	-	0
A512R23	35	lumpy	COMPLEX_BND	X	3057571	X	3277389	9	5	somatic_tumour	4204_1	219.8	X:3057571-3277389	35:35_37	0.24	-0.12	-	-	-	-	-	kirre, intron	dnc, intron	kirre, dnc	NA	-	0
A512R23	35	novobreak	COMPLEX_BND	X	3057571	X	3277389	9	5	somatic_tumour	166	219.8	X:3057571-3277389	35:35_37	0.24	-0.12	-	-	TTTTCTTCCTTTTGCTCCGTGAGTGTGTCATAATTTACAACAGTTGCTGGCCAAGTTGCGATTAGATTACACTTTCCATTTCCTGCAAATTGTATCAAAAATGCAGGTACACATGTCAACATCATTAGCCATATATCAACTTCACTTTCAATGCCTGCCCAATGAATTTCCTTAGCAGGCGGCGTGATAAAAAAAAATAAAAGGCAGGCCGATGA	-	-	kirre, intron	dnc, intron	kirre, dnc	NA	-	0
A573R25	13	CNV-Seq	DEL	X	3145469	X	3148044	-	-	somatic_tumour	-	2.6	X:3145469-3148044	13:13_14	0.85	-1.59	-	-	-	-	-	N, intron	N, exon_2	N	NA	snp_su:0; snp_op:0	0
A573R25	13	Control-Freec	DEL	X	3145925	X	3148700	-	-	somatic_tumour	-	2.8	X:3145925-3148700	14:13_14	0.84	-1.6	-	-	-	-	-	N, intron	N, intron	N	NA	snp_su:0; snp_op:0	0
A573R25	6	lumpy	COMPLEX_BND	3R	32066206	3R	32068392	38	24	somatic_tumour	5858_1	2.2	3R:32066206-32068392	10:6_7_8_9_10	0.61	0.29	-	-	-	-	-	Map205, intron	Map205, 5UTR	Map205	NA	snp_su:2; snp_op:0	14.02
A573R25	6	novobreak	COMPLEX_BND	3R	32066206	3R	32068392	38	24	somatic_tumour	7	2.2	3R:32066206-32068392	10:6_7_8_9_10	0.61	0.29	-	-	CTAAATACTACTCATTTGTAATCGAATAAATTATTGATTTTAAAAAAAGTAAGCCCCAAAAGAAAGAGAGTTATAAGGAGAGTTTGGGAATGAATGAAGTCCACAGGCGCTGTAGCGTATCATGCACATTAGTGCATGCAAGCAATCGGCAAGCAATTCAAAAGTAAGAGCAACCGGAGCGAACAAAAAAGGGAATAACTTACTAAAATCTCTGAAAGAAAAATAAAAAGACTAACGGG	-	-	Map205, intron	Map205, 5UTR	Map205	NA	snp_su:2; snp_op:0	14.02
A573R25	15	delly	DEL	X	4574313	X	4576608	8	5	somatic_tumour	DEL00000007	2.3	X:4574313-4576608	5to3	0.61	-1.6	-	-	ATCAAGCGGCAAGCCCAACATAGTTTTTTTTTTCTCACTGTTGTCTGTAGTCTAAAAATCTTGCAACACTTTCGTTCATTCTTGTCTCCAAAGAGTGATCTCTACTTCAGAGTGGCTTTTTCTATTATCGAAGTTTATAGGGGCTATTACAT	-	-	CR32773, ncRNA	CR32773, ncRNA	CR32773	NA	snp_su:0; snp_op:0	0
A573R25	15	lumpy	DEL	X	4574313	X	4576608	8	5	somatic_tumour	5980	2.3	X:4574313-4576608	5to3	0.61	-1.6	-	-	-	-	-	CR32773, ncRNA	CR32773, ncRNA	CR32773	NA	snp_su:0; snp_op:0	0
A573R25	15	novobreak	DEL	X	4574313	X	4576608	8	5	somatic_tumour	20	2.3	X:4574313-4576608	5to3	0.61	-1.6	-	-	ATTTTATACATTATCAAGCGGCAAGCCCAACATAGTTTTTTTTTTCTCACTGTTGTCTGTAGTCTAAAAATCTTGCAACACTTTCGTTCATTCTTGTCTCCAAAGAGTGATCTCTACTTCAGAGTGGCTTTTTCTATTATCGAAGTTTATAGGGGCTATTACATTTAAGAAAAATGTATAAAAAATAAAAAGATCATCATACTACATATGCGCTATCTCCC	-	-	CR32773, ncRNA	CR32773, ncRNA	CR32773	NA	snp_su:0; snp_op:0	0
A573R25	6	Control-Freec	COMPLEX_DUP	3R	32061425	3R	32069750	-	-	somatic_tumour	-	8.3	3R:32061425-32069750	9:6_7_8_9_10	0.43	0.57	-	-	-	-	-	Map205, intron	intergenic	Map205	NA	snp_su:13; snp_op:0; snp_ratio:1301.0	35.93
A573R25	2	novobreak	DEL	2L	5890205	2L	5890721	12	16	somatic_tumour	2	0.5	2L:5890205-5890721	5to3	0.42	0	-	-	GATGCCGAGCAACTCGGCGAGAAGGACTGTCATGAATCAAATCTTATCACAAATTTAATCGCATGGGTTCGCAGCTAAGCAAACATTTTGCGTTTTGGATGTCTACTCTGAATGGGAATCAATGTTTCGGTTGTTTTTCGTTTCCGTTTCCTGTCCTGCGTCGCAACGAATGCGATTTAATTTCCATTGTCCCATTGCCAATCAATACAAAAGTCATTTCGAAAGTATCCAGCCAGTACACTGCAGTGTGAGAGTTGGCTAAGTAGTAGACACTTAGCCGTGAAGTGTTCAGATAGCAGCCGTGGCCAGGTGTTCACTTGAACACGGCGCTCT	ACTGTCATGAATCAAATCTTATCACAAATTTAATCGCATGGGTTCGCAGCTAAGCAAACATTTTGCGTTTTGGATGTCTACTCTGAATGGGAATCAATGTTTCGGTTGTTTTTCGT	NHEJ	intergenic	intergenic	-	NA	mh:0; ins:0; tup:0; tdown:0	0
A573R25	5	novobreak	DEL	3R	14006281	3R	14008254	16	9	somatic_tumour	5	2	3R:14006281-14008254	5to3	0.41	-0.47	-	-	TCGCAGCATTGTGCATTGTATTGTTTTGCTTTTTTTGTTGTTTTCGATACTGCTTTTTTTTGTTTATTTTGTGTACATAAAAGAGAGAAGATCCCTGGATGACATGCACTCGGTGTTACAAGCACACATAAACCCAAAACAACCAACACTTTATCGTCAAACTCATTCGACTTGTTGTCCAATTGTGCAATAAACTAACAACGACAAATAATTGTGGAAAATGCAAATTTTTTAGGCAAAAGAGCAACAGAAAAAAATGTTGAATGCAAAGAAGTCTGGAAAACGAACGCAATATATTG	-	-	rdx, intron	rdx, intron	rdx	TRUE	contamination at bp1=3; snp_su:5; snp_op:2; snp_ratio:2.49	24.42
A573R25	5	lumpy	DEL	3R	14006281	3R	14008254	16	9	somatic_tumour	4730	2	3R:14006281-14008254	5to3	0.41	-0.47	-	-	-	-	-	rdx, intron	rdx, intron	rdx	TRUE	contamination at bp1=3; snp_su:5; snp_op:2; snp_ratio:2.49	24.42
A573R25	5	novobreak	DEL	3R	14006281	3R	14008254	16	9	somatic_tumour	6	2	3R:14006281-14008254	5to3	0.41	-0.47	-	-	CAACATAAATGTCATCGGATGATAAACATACCTGGAACGACAAGAGTTAAAGGTTTACAACCGATTAATAAAGGGTCACAAGGGGGAAAGGGGAGGGGAAAAACGCGACATGTAAGGGAATATTAAACAACATAAATAACATATTGTACAATGAGACTCAACAGTTTTGCAGCCTTTGCTTGATAAAGATCGCAGCATTGTGCATTGTATTGTTTTGCTTTTTTTGTTGTTTTCGATACTGCTTTTTTTTGTTTATTTTGTGTACATAAAAGAGAGAAGATCCCTGGATGACATGCACTCGGTGTTACAAGCACACATAAACCCAAAACAACCAACACTTTATCGTCAAACTCATTCGACTTGTTGTCCAATTGTGCAATAAACTAAC	-	-	rdx, intron	rdx, intron	rdx	TRUE	contamination at bp1=3; snp_su:5; snp_op:2; snp_ratio:2.49	24.42
A573R25	6	lumpy	COMPLEX_BND	3R	32060908	3R	32061191	12	7	somatic_tumour	5856_1	0.3	3R:32060908-32061191	8:6_7_8_9_10	0.18	0	-	-	-	-	-	Map205, intron	Map205, intron	Map205	NA	-	0
A573R27	9	Control-Freec	DUP	3R	9292540	3R	9296160	-	-	somatic_tumour	-	3.6	3R:9292540-9296160	Heterozygous duplication	0.29	0.48	-	-	-	-	-	intergenic	CG8861, intron	CG8861	NA	snp_su:2; snp_op:2	7.86
A573R27	10	Control-Freec	DUP	3R	11250055	3R	11253675	-	-	somatic_tumour	-	3.6	3R:11250055-11253675	Heterozygous duplication	0.32	0.54	-	-	-	-	-	CR43283, exon_3	CR43283, exon_2	CR43283	NA	snp_su:2; snp_op:2	11.64
A573R27	22	novobreak	COMPLEX_TRA	Tomelloso	29478	X	3098320	12	0	somatic_tumour	26	3068.8	Tomelloso:29478 X:3098320	18:18_19_22_23_24_25	1	0	TA	-	TTGTAGGTGTAAAAGCTGATTGTTGGGCGGCCTCATCAATAATTGCATTCACACTTGCCTTGTTTTTAAAAACATAATGTGAGTTAATGTTTTAGACACCAAATGACATAAAACTATATATGTATTAAAGCACTGCT	AGGTGTAAAAGCTGATTGTTGGGCGGCCTCATCAATAATTGCATTCACACTTGCCTTGTTTTTAAAAACATAATGTGAGTTAATGTTTTAGACACCAAATGACATAAAACTATATATG	Alt-EJ	intergenic	kirre, intron	kirre	NA	bp2_Tomelloso_9; mh:2; ins:0; tup:0; tdown:0	0
A573R27	22	novobreak	COMPLEX_TRA	Tomelloso	44579	X	3135040	28	0	somatic_tumour	27	3090.5	Tomelloso:44579 X:3135040	19:18_19_22_23_24_25	1	0	-	-	GGTATAATCAAACGACATGCTTCGCCCGGTATAATTGTCTCATCGGCCGAATCGGCATACGACAAAATGACACAGCAAGCAAATGCAATGAAATGAAAAGGATGGCCCCAGCGGGAAAGCCGTTCAGCAAGAGCAAGGAGTGCCTGTCGCAGGGATAGCAACGAGAGAGCGACACAGAGAGCGAGAGAGAGAGAGGGAG	CGCTGGGGCCATCCTTTTCATTTCATTGCATTTGCTTGCTGTGTCATTTTGTCGTATGCCGATTCGGCCGATGAGACAATTATACCGGGCGAAGCATGTCGTTTGATTATACC	NHEJ	intergenic	N, 5UTR	N	NA	bp2_Tomelloso_17; mh:0; ins:0; tup:0; tdown:0	0
A573R27	22	CNV-Seq	COMPLEX_DUP	X	3098318	X	3125700	-	-	somatic_tumour	-	27	X:3098318-3125700	22:18_19_22_23_24_25	0.92	0.86	-	-	-	-	-	kirre, intron	kirre, intron	kirre	NA	snp_su:0; snp_op:0	0
A573R27	22	Control-Freec	COMPLEX_DUP	X	3098720	X	3125870	-	-	somatic_tumour	-	27.1	X:3098720-3125870	22:18_19_22_23_24_25	0.92	0.85	-	-	-	-	-	kirre, intron	kirre, intron	kirre	NA	snp_su:0; snp_op:0	0
A573R27	22	lumpy	COMPLEX_BND	X	3125694	X	3126976	9	3	somatic_tumour	6988_1	1.3	X:3125694-3126976	23:18_19_22_23_24_25	0.48	-0.13	-	CCGTGTG,TGTC	-	TTCAACCGTCTCTATGACACTGCACTTGTGTGGGTGTAGGTGTGTCTGTGCCGTGTGTCCGGCAGTGTGTGGCAGGACCCCATGGGTCCTTCGGCCAAAGTCGTACATGTC	FoSTeS	kirre, intron	kirre, intron	kirre	NA	mh:0; ins:12; tup:5; tdown:5	0
A573R27	22	novobreak	COMPLEX_BND	X	3125694	X	3126976	9	3	somatic_tumour	31	1.3	X:3125694-3126976	23:18_19_22_23_24_25	0.48	-0.13	-	CCGTGTG,TGTC	TTTTTTTTCAACCGTCTCTATGACACTGCACTTGTGTGGGTGTAGGTGTGTCTGTGCCGTGTGTCCGGCAGTGTGTGGCAGGACCCCATGGGTCCTTCGGCCAAAGT	TTCAACCGTCTCTATGACACTGCACTTGTGTGGGTGTAGGTGTGTCTGTGCCGTGTGTCCGGCAGTGTGTGGCAGGACCCCATGGGTCCTTCGGCCAAAGTCGTACATGTC	FoSTeS	kirre, intron	kirre, intron	kirre	NA	mh:0; ins:12; tup:5; tdown:5	0
A573R27	22	novobreak	COMPLEX_BND	X	3125694	X	3126976	9	3	somatic_tumour	32	1.3	X:3125694-3126976	23:18_19_22_23_24_25	0.48	-0.13	-	CCGTGTG,TGTC	GTGTGGGGTCTAGAGACTATCGGGGAAGTGGTTTTTACTATCCAACGAGAATCTACCGCAACTAAAAACAAAAGTTATGTGTGCACGAAAAATCATGTCCAGTCATTTCCTGTACAACTTTGGCCGAAGGACCCATGGGGTCCTGCCACACACTGCCGGACACACGGCACAGACACACCTACACCCACACAAGTGCAGTGTCATAGAGACGGTTGAAAAAAAAAAAGAAGGAAAAGGAAAAGGAA	TTCAACCGTCTCTATGACACTGCACTTGTGTGGGTGTAGGTGTGTCTGTGCCGTGTGTCCGGCAGTGTGTGGCAGGACCCCATGGGTCCTTCGGCCAAAGTCGTACATGTC	FoSTeS	kirre, intron	kirre, intron	kirre	NA	mh:0; ins:12; tup:5; tdown:5	0
A573R27	22	delly	COMPLEX_BND	X	3125694	X	3126976	9	3	somatic_tumour	INV00000006	1.3	X:3125694-3126976	23:18_19_22_23_24_25	0.48	-0.13	-	CCGTGTG,TGTC	TCCTGGTTTTCCTTTTCCTTTTCCTTCTTTTTTTTTTTCAACCGTCTCTATGACACTGCACTTGTGTGGGTGTAGGTGTGTCTGTGCCGTGTGTCCGGCAGTGTGTGGCAGGACCCCATGGGTCCTTCGGCCAAAGTTGTACAG	TTCAACCGTCTCTATGACACTGCACTTGTGTGGGTGTAGGTGTGTCTGTGCCGTGTGTCCGGCAGTGTGTGGCAGGACCCCATGGGTCCTTCGGCCAAAGTCGTACATGTC	FoSTeS	kirre, intron	kirre, intron	kirre	NA	mh:0; ins:12; tup:5; tdown:5	0
A573R27	22	Control-Freec	COMPLEX_DEL	X	3125870	X	3134920	-	-	somatic_tumour	-	9.1	X:3125870-3134920	24:18_19_22_23_24_25	0.77	-1.3	-	-	-	-	-	kirre, intron	N, 5UTR	kirre, N	NA	snp_su:0; snp_op:0	0
A573R27	22	CNV-Seq	COMPLEX_DEL	X	3126976	X	3135039	-	-	somatic_tumour	-	8	X:3126976-3135039	25:18_19_22_23_24_25	0.81	-1.46	-	-	-	-	-	kirre, intron	N, 5UTR	kirre, N	NA	snp_su:0; snp_op:0	0
A573R27	28	CNV-Seq	COMPLEX_DEL	X	17286052	X	17294628	-	-	somatic_tumour	-	7	X:17286052-17294628	28:27_28_30_31_32	0.73	-1.16	-	-	-	-	-	Fim, 3UTR	Fim, intron	CG5445, Fim	NA	snp_su:0; snp_op:0	0
A573R27	28	delly	COMPLEX_BND	X	17286052	X	17311472	5	4	somatic_tumour	INV00000015	25.4	X:17286052-17311472	27:27_28_30_31_32	0.27	0.08	C	-	ATATAAAATTAGTTTCTCTGTTTTTCTCGACTTCTTTTGTTTCTGAATATTCCCCATTCTTTTTGAAGGTGTCGTAATTGCACTCAGCTCACTTGATTCCCGATAAAAGCGGAACACAGGGAATTCGGATTTCGAATGCAAACAA	ATATAAAATTAGTTTCTCTGTTTTTCTCGACTTCTTTTGTTTCTGAATATTCCCCATTCTTTTTGAAGGTGTCGTAATTGCACTCAGCTCACTTGATTCCCGATAAAAGCGGAACA	Alt-EJ	Fim, 3UTR	intergenic	CG5445, Fim	NA	mh:1; ins:0; tup:0; tdown:0	0
A573R27	28	Control-Freec	COMPLEX_DEL	X	17286405	X	17294550	-	-	somatic_tumour	-	8.1	X:17286405-17294550	30:27_28_30_31_32	0.74	-1.15	-	-	-	-	-	Fim, 3UTR	Fim, intron	CG5445, Fim	NA	snp_su:0; snp_op:0	0
A573R27	28	lumpy	COMPLEX_BND	X	17293197	X	17294628	10	0	somatic_tumour	7312_1	1.4	X:17293197-17294628	31:27_28_30_31_32	0.41	-0.07	CT	-	-	GTGCACGCTCGTAAAGTATCTATTGGTGGTCTTTTTTACGGCCGTGCAACGGTAAACAACTCGATAATTACTCCAAATTGCAATAATTTAACAAATATTTACCTCATAAGATG	Alt-EJ	Fim, intron	Fim, intron	CG5445, Fim	NA	mh:2; ins:0; tup:0; tdown:0	0
A573R27	28	novobreak	COMPLEX_BND	X	17293197	X	17294628	10	0	somatic_tumour	38	1.4	X:17293197-17294628	31:27_28_30_31_32	0.41	-0.07	CT	-	CTTTAATTGTATCTCAAAAATGCACGTATACGAAAAATCATCAGTTTAATCTTTTTGTGCTGAAATAAATATAATATAGAATATGTTTCCACTTTTGTGGGGTGCACGCTCGTAAAGTATCTATTGGTGGTCTTTTTTACGGCCGTGCAACGGTAAACAACTCGATAATTACTCCAAATTGCAATAATTTAACAAATATTTACCTCATAAGATGAGTTTATTGTACTTCAATTCACAAAATATATTGCACTTAATTAGCACCTGTAGTACGCCTACCATTTCATTGATTGGAACGCGTTCATTTACACATTTAAATTTGTTAAAAGCCACTTTCAAGTATCTTATTT	GTGCACGCTCGTAAAGTATCTATTGGTGGTCTTTTTTACGGCCGTGCAACGGTAAACAACTCGATAATTACTCCAAATTGCAATAATTTAACAAATATTTACCTCATAAGATG	Alt-EJ	Fim, intron	Fim, intron	CG5445, Fim	NA	mh:2; ins:0; tup:0; tdown:0	0
A573R27	28	delly	COMPLEX_BND	X	17293197	X	17294628	10	0	somatic_tumour	INV00000016	1.4	X:17293197-17294628	31:27_28_30_31_32	0.41	-0.07	CT	-	TATTTTGTGAATTGAAGTACAATAAACTCATCTTATGAGGTAAATATTTGTTAAATTATTGCAATTTGGAGTAATTATCGAGTTGTTTACCGTTGCACGGCCGTAAAAAAGACCACCAATAGATACTTTACGAGCGTGCA	GTGCACGCTCGTAAAGTATCTATTGGTGGTCTTTTTTACGGCCGTGCAACGGTAAACAACTCGATAATTACTCCAAATTGCAATAATTTAACAAATATTTACCTCATAAGATG	Alt-EJ	Fim, intron	Fim, intron	CG5445, Fim	NA	mh:2; ins:0; tup:0; tdown:0	0
A573R27	28	CNV-Seq	COMPLEX_DUP	X	17294628	X	17311472	-	-	somatic_tumour	-	7	X:17294628-17311472	32:27_28_30_31_32	0.84	0.7	-	-	-	-	-	Fim, intron	intergenic	CG5445, Fim	NA	snp_su:0; snp_op:0	0
A573R27	29	lumpy	BND	X	17286052	X	17311472	5	4	somatic_tumour	7313_1	25.4	X:17286052-17311472	3to3	0.27	0.08	-	-	-	-	-	Fim, 3UTR	intergenic	CG5445, Fim	NA	-	0
A573R27	29	novobreak	BND	X	17286052	X	17311472	5	4	somatic_tumour	37	25.4	X:17286052-17311472	3to3	0.27	0.08	-	-	GCTTTTTAATTTGTTTGCATTCGAAATCCGAATTCCCTGTGTTCCGCTTTTATCGGGAATCAAGTGAGCTGAGTGCAATTACGACACCTTCAAAAAGAATGGGGAATATTCAGAAACAAAAGAAGTCGAGAAAAACAGAGAAACTAATTTTATATTTACTATAAATTTTTTTG	-	-	Fim, 3UTR	intergenic	CG5445, Fim	NA	-	0
A573R29	5	novobreak	TRA	2L	21808001	Tomelloso	7008	3	0	somatic_tumour	12	21801	2L:21808001 Tomelloso:7008	5:5_11	0.09	0	G	-	AACTACAATCATAAATTTGCATTCCGATTAAAAAAGTTATAAGCATTTAAAACAGTGAATATGCTGTGTTACCCATGCCACCCTACGTCGATTCTCAGCAGACAAATCACTAAACTTGCCCACTTTATACGTATACTTTCGAATATCACCAG	AACTACAATCATAAATTTGCATTCCGATTAAAAAAGTTATAAGCATTTAAAACAGTGAATATGCTGTGTTACCCATGCCACCCTACGTCGATTCTCAGCAGACAAATCACTAAAC	Alt-EJ	intergenic	intergenic	-	NA	bp1_Tomelloso_2; mh:1; ins:0; tup:0; tdown:0	0
A573R29	6	novobreak	BND	2R	5306714	2R	7159623	9	0	somatic_tumour	13	1852.9	2R:5306714-7159623	3to3	0.13	0	TATGTGAT	GT	GCGTTTAATTAAGCAAAAAACCCTTTATTTTTAGCTTTAAAGTCAAAAATTCAACTTATTTTACAGTGTGTAAACAGTTTCTTGACAAACTGTATGTGATTATCTGCGCACATTCGTAGTATAAAGTTTTAATTAAGTAATCTTTTGAATCAGTCTTTGTTTTTGCGTTACTCCTTTTCATTCAGATACA	ACACAGTGTGTAAACAGTTTCTTGACAAACTGTATGTGATCAGAAAATTATTATACTCCTGAAATACATAACGTTAAAGCACTTTCATGGTAATTCCTAGTCTGTGGA	Alt-EJ	intergenic	pk, intron	pk	NA	bp2_roo_BEL=6; mh:8; ins:2; tup:0; tdown:0	0
A573R29	7	novobreak	TRA	3L	120417	3R	29280935	6	2	somatic_tumour	17	29160.5	3L:120417 3R:29280935	3to3	0.08	0	-	G	CTCAAAAGAGTGAAGTGGAGCAATGGAATGATAAACTCATAGCTTGTATAGCTGGCAGTGTATGCTGAGATAACAAGCCCCCGCCTTGGTTTAGAAATGAAAACAATACAACTACCATGGAAATCAAAACAACACAACTTCTGTGGCGCTTTGACCTA	CCATGGTAGTTGTATTGTTTTCATTTCTAAACCAAGGCGGGGGCTTGTTATCTCAGCATACACTGCCAGCTATACAAGCTATGAGTTTATCATTCCATTGC	NHEJ	intergenic	intergenic	-	NA	mh:0; ins:1; tup:0; tdown:0	0
A573R29	10	delly	DEL	3R	24856498	3R	24856996	24	7	somatic_tumour	DEL00000009	0.5	3R:24856498-24856996	5to3	0.26	0	TC	-	ATGATATTCACTTGGCTAAAACACTTATTTTGCTTTACTTCTATAAACTGGTCGGTCATGGCCATCGGCTGCAGACCGGCCTCCTTGTTGCTTTTGTAACTGGCATTCTTGTGAACGATGTGCACCT	TACATGATATTCACTTGGCTAAAACACTTATTTTGCTTTACTTCTATAAACTGGTCGGTCATGGCCATCGGCTGCAGACCGGCCTCCTTGTTGCTTTTGTAACTGGCATTCTTGTGAA	Alt-EJ	CG10899, exon	CG10899, exon_2	CG10899	NA	mh:2; ins:0; tup:0; tdown:0	0
A573R29	10	novobreak	DEL	3R	24856498	3R	24856996	24	7	somatic_tumour	29	0.5	3R:24856498-24856996	5to3	0.26	0	TC	-	ATACACTATGTGACTTGGACAATACATATTACATGATATTCACTTGGCTAAAACACTTATTTTGCTTTACTTCTATAAACTGGTCGGTCATGGCCATCGGCTGCAGACCGGCCTCCTTGTTGCTTTTGTAACTGGCATTCTTGTGAACGATGTGCACCTCCCCATCGTAATAGTTGCCATCCAAGCAGTGCT	TACATGATATTCACTTGGCTAAAACACTTATTTTGCTTTACTTCTATAAACTGGTCGGTCATGGCCATCGGCTGCAGACCGGCCTCCTTGTTGCTTTTGTAACTGGCATTCTTGTGAA	Alt-EJ	CG10899, exon	CG10899, exon_2	CG10899	NA	mh:2; ins:0; tup:0; tdown:0	0
A573R29	12	novobreak	TRA	Tomelloso	20114	2R	24646497	3	0	somatic_tumour	58	24626.4	Tomelloso:20114 2R:24646497	-	0.1	0	AC	-	CAGTTGGCCCTCTCAGCTTTCGGATTTCTTTGTTGGCCAAGGAAGACGCGCCATGAATGCCAGACGTCAGTCGTATTAGGCCGACATCATATTTGAAATCAGCACGATTGCTTTCCTTGTTGGCTACGCGAGCACCATCCATAAATACAATAACTTCGCATGCCCGATAGCCGCGCAAAAGTTCAATATTGTCAATCAATTTTTTCATATAATCAAACCTGT	CAGTTGGCCCTCTCAGCTTTCGGATTTCTTTGTTGGCCAAGGAAGACGCGCCATGAATGCCAGACGTCAGTCGTATTAGGCCGACATCATATTTGAAATCA	Alt-EJ	intergenic	intergenic	-	NA	mh:2; ins:0; tup:0; tdown:0	0
A573R29	15	CNV-Seq	DEL	X	3160180	X	3207188	-	-	somatic_tumour	-	46	X:3160180-3207188	Homozygous deletion	0.87	-1.57	-	-	-	-	-	N, intron	dnc, intron	N, CG18508, Fcp3C, CG3939, dnc	NA	snp_su:0; snp_op:1	0
A573R29	15	Control-Freec	DEL	X	3160388	X	3207446	-	-	somatic_tumour	-	47.1	X:3160388-3207446	Homozygous deletion	0.87	-1.56	-	-	-	-	-	N, intron	dnc, intron	N, CG18508, Fcp3C, CG3939, dnc	NA	snp_su:0; snp_op:1	0
A573R29	16	lumpy	BND	X	3550817	X	3551238	2	1	somatic_tumour	6752_1	0.4	X:3550817-3551238	3to3	0.06	0	TTTTTTT	-	-	GATACAGTACCACAATTAAAATAAGTCATCTTTTTTTGTCCTTCGGTGATTTCACTCGTGTGTTACATAGCAAAACTAAACGAAACGAAAGTTTTATTGTCCGTT	Alt-EJ	DIP-alpha, intron	DIP-alpha, intron	DIP-alpha	NA	mh:7; ins:0; tup:0; tdown:0	0
A573R31	5	Control-Freec	DUP	3R	9834685	3R	9837100	-	-	somatic_tumour	-	2.4	3R:9834685-9837100	Heterozygous duplication	0.36	0.47	-	-	-	-	-	Teh1, intron	Teh1, intron	Teh1	NA	snp_su:2; snp_op:2	12.51
A573R31	9	lumpy	TANDUP	3R	31043462	3R	31073816	18	3	somatic_tumour	5880	30.4	3R:31043462-31073816	10:9_10	0.16	0.39	T	-	-	GCCAAGGACAGTGATGAGCTCCAAGCTGAAATATTACACTGTATTGCATTTGAAAAGCAGGGTTTCGAGGAAGGTAAGTTTGGGGATCCACAGAGCGATTCTGTCCGTACTAGACTGTGTGTCAATGT	Alt-EJ	CanA1, exon_9	Sox100B, intron	CanA1, CG33920, Alp4, mir-4948, l(3)03670, dco, Sox100B	NA	mh:1; ins:0; tup:0; tdown:0; snp_su:35; snp_op:42; snp_ratio:0.83	9.15
A573R31	9	delly	TANDUP	3R	31043462	3R	31073816	18	3	somatic_tumour	DUP00000005	30.4	3R:31043462-31073816	10:9_10	0.16	0.39	T	-	GCCAAGGACAGTGATGAGCTCCAAGCTGAAATATTACACTGTATTGCATTTGAAAAGCAGGGTTTCGAGGAAGGTAAGTTTGGGGATCCACAGAGCGATTCTGTCCGTACTAGACTGTGTGTCAATGTC	GCCAAGGACAGTGATGAGCTCCAAGCTGAAATATTACACTGTATTGCATTTGAAAAGCAGGGTTTCGAGGAAGGTAAGTTTGGGGATCCACAGAGCGATTCTGTCCGTACTAGACTGTGTGTCAATGT	Alt-EJ	CanA1, exon_9	Sox100B, intron	CanA1, CG33920, Alp4, mir-4948, l(3)03670, dco, Sox100B	NA	mh:1; ins:0; tup:0; tdown:0; snp_su:35; snp_op:42; snp_ratio:0.83	9.15
A573R31	9	novobreak	TANDUP	3R	31043462	3R	31073816	18	3	somatic_tumour	13	30.4	3R:31043462-31073816	10:9_10	0.16	0.39	T	-	AGATAAATATATTAGGTTCACCTGATGGACACTTGCCAAGGACAGTGATGAGCTCCAAGCTGAAATATTACACTGTATTGCATTTGAAAAGCAGGGTTTCGAGGAAGGTAAGTTTGGGGATCCACAGAGCGATTCTGTCCGTACTAGACTGTGTGTCAATGTCGCAGTGCTTTGGATGTTGTGGGGCCAATACGGATACACGTGAATTACAAACTAATCTTCTATTAAAAATATTTTCCGAAACCAAATATCGAAATACGACAACTGCAATCT	GCCAAGGACAGTGATGAGCTCCAAGCTGAAATATTACACTGTATTGCATTTGAAAAGCAGGGTTTCGAGGAAGGTAAGTTTGGGGATCCACAGAGCGATTCTGTCCGTACTAGACTGTGTGTCAATGT	Alt-EJ	CanA1, exon_9	Sox100B, intron	CanA1, CG33920, Alp4, mir-4948, l(3)03670, dco, Sox100B	NA	mh:1; ins:0; tup:0; tdown:0; snp_su:35; snp_op:42; snp_ratio:0.83	9.15
A573R31	11	novobreak	TRA	3R	31063194	X	3136742	11	9	somatic_tumour	14	27926.5	3R:31063194 X:3136742	11:11_14	0.6	0	-	-	TTTGGTTTCGTTTAGCAGTCGGCTTGAAGATTTTTGTATTTCCTTTTTTGCTCGTCGGCGGCTTAGATCAAATAATGCGATTTCATGGCAAGTTCACCAGGGGACTGGAAAAACTCGCCTTTTGCCGACGGTAAAAACGGTCTTTCTTGTTTCGAAAAGGTGGGTTTCCAAATCTGAGAGAGCATGCGCAGTCGG	-	-	intergenic	N, intron	N	NA	bp1_Dmel\I-element_LINE-like=6	0
A573R31	11	delly	TRA	X	3136742	3R	31063202	13	0	somatic_tumour	BND00000007	27926.5	X:3136742 3R:31063202	14:11_14	0.44	0	-	-	CTCTCAGATTTGGAAACCCACCTTTTCGAAACAAGAAAGACCGTTTTTACCGTCGGCAAAAGGCGAGTTTTTCCAGTCCCCTGGTGAACTTGCCATGAAATCGCATTATTTGATCTAAGCCGCCGACGAGCAAAAAAGGAAATACAAAAATC	-	-	N, intron	intergenic	N	NA	bp2_Dmel\I-element_LINE-like=6	0
A573R31	12	CNV-Seq	COMPLEX_DUP	X	1129707	X	1131480	-	-	somatic_tumour	-	1.7	X:1129707-1131480	12:12_13	0.99	0.72	-	-	-	-	-	CG3655, intron	CG3655, intron	CG3655	NA	snp_su:0; snp_op:0	0
A573R31	12	lumpy	COMPLEX_BND	X	1130471	X	1131480	18	3	somatic_tumour	5996_1	1	X:1130471-1131480	13:12_13	0.18	0.42	-	-	-	-	-	CG3655, intron	CG3655, intron	CG3655	NA	snp_su:0; snp_op:0	0
A573R31	15	Control-Freec	DEL	X	12467035	X	12545925	-	-	somatic_tumour	-	78.9	X:12467035-12545925	15:15_16_17	0.92	-1.76	-	-	-	-	-	CG42258, intron	CG43921, intron	CG42258, Cpr11A, Lsp1alpha, Mks1, CG2556, snoRNA:Me18S-G894, CG43921	NA	snp_su:0; snp_op:0	0
A573R31	15	CNV-Seq	DEL	X	12467160	X	12577262	-	-	somatic_tumour	-	110	X:12467160-12577262	16:15_16_17	0.92	-1.75	-	-	-	-	-	CG42258, intron	CG11138, intron	CG42258, Cpr11A, Lsp1alpha, Mks1, CG2556, snoRNA:Me18S-G894, CG43921, Cpr11B, CG11138	NA	snp_su:0; snp_op:0	0
A573R31	15	Control-Freec	DEL	X	12546730	X	12577320	-	-	somatic_tumour	-	30.6	X:12546730-12577320	17:15_16_17	0.93	-1.76	-	-	-	-	-	CG43921, 5UTR	CG11138, intron	CG43921, Cpr11B, CG11138	NA	snp_su:0; snp_op:0	0
A573R31	18	lumpy	DEL	X	13954981	X	13983925	10	1	somatic_tumour	6260	28.9	X:13954981-13983925	5to3	0.45	0.01	-	-	-	-	-	mamo, intron	mamo, intron	mamo	NA	bp1_Dmel\I-element_LINE-like=4	0
A573R31	18	novobreak	DEL	X	13954981	X	13983925	10	1	somatic_tumour	30	28.9	X:13954981-13983925	5to3	0.45	0.01	-	-	GAAGTGTGCATTTTTCTCAGAACCTCTTTAAATTTAAGAGCGCGATAATTTCTACTTCAATTTTAGATCAATCGAGCTTTTTGTGTAATACCATTTACCCTATTGATTTGCTGTTCTTATTGTTATATCATTTTATATCATTGTTTCATGATGGATTACATGAAGTGCAGACTTCTCTTAAAAAAAAAACCCACTTTAATTTAAGAACAATACACTTATATAAGCTTAATAAATTATATTTGTTTCAAATCGTAGCTATATAAAAG	-	-	mamo, intron	mamo, intron	mamo	NA	bp1_Dmel\I-element_LINE-like=4	0
A573R33	27	delly	DEL	X	3671510	X	3673441	16	11	somatic_tumour	DEL00000005	1.9	X:3671510-3673441	5to3	0.75	-0.98	-	-	GATTGGTAAACCTTTTGGAATATCGGAAAAATCAAGTGTGACCTGAATTCTTGCATACCGGTGTATATCATGTGATCCCGAATTGTTTGAAATGTTTGGGCTTAAAAGATCGAATAAAAACATCTGCAAATGGATCTAGAAG	-	-	intergenic	Mnt, intron	Mnt	NA	snp_su:0; snp_op:0	0
A573R33	27	lumpy	DEL	X	3671510	X	3673441	16	11	somatic_tumour	8202	1.9	X:3671510-3673441	5to3	0.75	-0.98	-	-	-	-	-	intergenic	Mnt, intron	Mnt	NA	snp_su:0; snp_op:0	0
A573R33	27	novobreak	DEL	X	3671510	X	3673441	16	11	somatic_tumour	143	1.9	X:3671510-3673441	5to3	0.75	-0.98	-	-	CATCTAGGGAGTTCGCCAGATTTTCCGGCTCCTCCTCCGTTTCTATTTCGGAAATCCCGCCATCCGGCGACTTCGACATCCTGGCGCAGTTTAAGCACAAAGCCTTGCCGAGTCGATTGGTCAGCACGGATGCACTTGCTCTGCGGCGATTTGCCGTAGATTGGTAAACCTTTTGGAATATCGGAAAAATCAAGTGTGACCTGAATTCTTGCATACCGGTGTATATCATGTGATCCCGAATTGTTTGAAATGTTTGGGCTTAAAAGATCGAATAAAAACATCTGCAAATGGATCTAGAAGTTATTTATTTTGTTAAACGCCTTAATCTATAAGTATATTTA	-	-	intergenic	Mnt, intron	Mnt	NA	snp_su:0; snp_op:0	0
A573R33	25	Control-Freec	DEL	3R	32014848	3R	32079331	-	-	somatic_tumour	-	64.5	3R:32014848-32079331	Heterozygous deletion	0.31	-0.64	-	-	-	-	-	heph, exon_1	intergenic	heph, CR45557, CG2053, krz, mod, Map205	NA	snp_su:62; snp_op:7; snp_ratio:8.85	23.41
A573R33	6	Control-Freec	COMPLEX_DEL	2L	13540608	2L	13572096	-	-	somatic_tumour	-	31.5	2L:13540608-13572096	7:6_7_8	0.27	-0.51	-	-	-	-	-	B4, intron	kuz, intron	B4, CG16852, CG9263, CG16853, kuz	NA	snp_su:132; snp_op:18; snp_ratio:7.33	22.5
A573R33	6	novobreak	COMPLEX_BND	2L	13540579	2L	13587180	7	3	somatic_tumour	8	46.6	2L:13540579-13587180	6:6_7_8	0.1	-0.17	-	AATTGCATGCATGGGTAAGGTTGC	GTCATAATTGTCATATTAGACAGGAAAATCCATAGACGACAGTCGACCCTGAAGTGTCGATGGACAGCAGCTTCTGGTTTTGCCCGGCCAGACAGGAAAGGAAATTGCAATTGCATGCATGGGTAAGGTTGCATGTTTTTTCTTTGTTAATTTACACATACGTGTGATATATTGCTTGTGGGTTTAACAGAAAGGCGTTGACTGTGTAAGTACTGACTGAAG	GCAGCTTCTGGTTTTGCCCGGCCAGACAGGAAAGGAAATTGCAATTGCATGCATGGGTAAGGTTGCATGTTTTTTCTTTGTTAATTTACACATACGTGTGATATAT	FoSTeS	B4, intron	kuz, intron	B4, kuz	NA	mh:0; ins:24; tup:6; tdown:4	0
A573R33	4	novobreak	BND	2L	9190416	2L	13552614	7	0	somatic_tumour	6	4362.2	2L:9190416-13552614	5to5	0.09	0.01	-	-	AACAAAAGGGGACTTACAAAATTTTAAAACTATATACTTCGGTATGAAACACACAGTAGGAATGAAACATTTAGCTTATACATCTACATATATAATATTACATAATTAAATTATGTAATCCATGTAAGTGTGTGTGTGTGTGTATGCGTAGTTTACATACATATACATATGCATATGCATGTACTTCGTATGGCAACAGAAAATGTTGTTGAT	-	NHEJ	tai, intron	kuz, intron	tai, kuz	NA	bp1_roo_BEL=16; bp2_rover_Gypsy=3; mh:0; ins:0; tup:0; tdown:0	0
A573R33	12	novobreak	BND	2R	16371025	2R	17742832	6	0	somatic_tumour	16	1371.8	2R:16371025-17742832	5to5	0.07	0.01	GT	-	GGTTAAATATGCCCACTTAATTGAGTTTAATTGTGTGTGCGCTAAGCAGGCGGAAATATTTTACTACACAAACTAACCACATTTATATGCAGAACATACAAAGCTTCGCCATGTGTCTGGAGGAAATTGCCAAGGAGG	TTGTATGTTCTGCATATAAATGTGGTTAGTTTGTGTAGTAAAATATTTCCGCCTGCTTAGCGCACACACAATTAAACTCAATTAAGTGGGCATATTTAAAC	Alt-EJ	intergenic	Vps54L, intron	Vps54L	NA	mh:2; ins:0; tup:0; tdown:0	0
A573R33	2	novobreak	BND	2L	3314020	2L	14210317	2	1	somatic_tumour	2	10896.3	2L:3314020-14210317	3to3	0.02	0	GGATG	-	CTGCTGCTGACCATTGACCACCACCTCGACATCATCGATTCCAAGTCGCTGCTTAATCATAGTGGAGCAGCACCAAAATCCAGTCCATCCCATCCGGACAACGACTGTTGTTCACCGCGCTTACAAGGACATTGTACGAAGTGCCTAAAAG	CTTTTAGGCACTTCGTACAATGTCCTTGTAAGCGCGGTGAACAACAGTCGTTGTCCGGATGGGATGGACTGGATTTTGGTGCTGCTCCACTATGATTAAGC	Alt-EJ	CG3277, exon_4	Dyrk2, intron	CG3277, Dyrk2	NA	mh:5; ins:0; tup:0; tdown:0	0
A785-A788R11	1	lumpy	DEL	2L	3878663	2L	3881247	3	7	somatic_tumour	552	2.6	2L:3878663-3881247	5to3	0.15	-0.44	-	-	-	-	-	capu, intron	capu, intron	capu	TRUE	contamination at bp2=5; snp_su:10; snp_op:3; snp_ratio:3.33	17.81
A785-A788R11	1	novobreak	DEL	2L	3878663	2L	3881247	3	7	somatic_tumour	1	2.6	2L:3878663-3881247	5to3	0.15	-0.44	-	-	TTCTAGCATTTTAAATATTCGGTTTGAATGATTTTTCTTACAGTGTCACAGCGACAGTCATTATCAATAGTTTTTCCTGAAACGCTAATGACATTTGCATAACTGCTTGCCAAGCGAATGCAACAAACGTACACCAAAAAAAAAAAAACAATTTAATTGCTTCTTTTTAAAGCATTTTTTTTT	-	-	capu, intron	capu, intron	capu	TRUE	contamination at bp2=5; snp_su:10; snp_op:3; snp_ratio:3.33	17.81
A785-A788R11	5	Control-Freec	DEL	3L	0	3L	567690	-	-	somatic_tumour	-	567.7	3L:0-567690	Heterozygous deletion	0.27	-0.36	-	-	-	-	-	intergenic	Hipk, intron	mthl8, CG43149, Lsp1gamma, CR44510, CR44511, CR43150, CR43988, CG13405, CG12483, CR45401, CR45402, CR45400, Pdk1, CR45805, CG6845, Dic61B, p130CAS, CR43151, CG7049, CR45806, Vdup1, CG13875, CG34140, Mkp, Mtch, rno, mri, Gk1, NitFhit, CG13876, CG7028, thoc7, CG16940, Kaz1-ORFA, Kaz1-ORFB, pyx, CG13877, CG33229, CR42862, CG42846, CG34454, CG34453, E(bx), mthl14, DIP2, wac, Tudor-SN, snoRNA:Tudor-SN-a, snoRNA:Psi18S-996, mRpL17, CG34263, miple1, miple2, CG32845, ttm2, RhoGEF3, fwd, CG34264, CG32344, Atac3, Ptpmeg, mthl9, mthl10, mth, CG1231, Cdc5, Roc1b, CG1233, CG13884, trh, CR45378, CR43969, CG13891, klar, snmRNA:438, CG34267, CG34268, CR46002, CR45118, CR45117, CG34269, CG17180, Cypl, CR46249, CR45808, Hipk	TRUE	low FC; snp_su:873; snp_op:378; snp_ratio:2.31	14.51
A785-A788R11	11	Control-Freec	COMPLEX_DUP	X	2988642	X	3086982	-	-	somatic_tumour	-	98.3	X:2988642-3086982	12:11_12_13_14	0.92	0.77	-	-	-	-	-	kirre, intron	kirre, intron	kirre, CG4116	NA	snp_su:0; snp_op:0	0
A785-A788R11	11	lumpy	COMPLEX_DEL	X	3086782	X	3175562	23	9	somatic_tumour	10625	88.8	X:3086782-3175562	13:11_12_13_14	0.67	-1.56	-	ACAACTATAACTAACCA	-	TTTTGTGCTACGGTCGCAGGGTTTTTACCAGCCCCTAAACATTGTGATTAACAACTATAACTAACCAATCAAGCTGTACGAGAACCAGCGCAGCCCCATCTAC	FoSTeS	kirre, intron	CG3939, exon_1	kirre, N, CG18508, Fcp3C, CG3939	NA	bp1_Dmel\I-element_LINE-like=7; mh:0; ins:17; tup:4; tdown:5; snp_su:0; snp_op:0	0
A785-A788R11	11	novobreak	COMPLEX_DEL	X	3086782	X	3175562	23	9	somatic_tumour	6	88.8	X:3086782-3175562	13:11_12_13_14	0.67	-1.56	-	ACAACTATAACTAACCA	CCCAGGCGGCGTGACAAATTGCTGGGACGCAGATTTCAGATTGGTTTTTGTGCTACGGTCGCAGGGTTTTTACCAGCCCCTAAACATTGTGATTAACAACTATAACTAACCAATCAAGCTGTACGAGAACCAGCGCAGCCCCATCTACATCTACTTCTACGGCGAGAAAGACAAGGACGGACGCAGCTGGTGTCCGGACTGCGTGGCGGGT	TTTTGTGCTACGGTCGCAGGGTTTTTACCAGCCCCTAAACATTGTGATTAACAACTATAACTAACCAATCAAGCTGTACGAGAACCAGCGCAGCCCCATCTAC	FoSTeS	kirre, intron	CG3939, exon_1	kirre, N, CG18508, Fcp3C, CG3939	NA	bp1_Dmel\I-element_LINE-like=7; mh:0; ins:17; tup:4; tdown:5; snp_su:0; snp_op:0	0
A785-A788R11	11	Control-Freec	COMPLEX_DEL	X	3113802	X	3175488	-	-	somatic_tumour	-	61.7	X:3113802-3175488	14:11_12_13_14	0.93	-2.25	-	-	-	-	-	kirre, intron	CG3939, 5UTR	kirre, N, CG18508, Fcp3C, CG3939	NA	snp_su:0; snp_op:0	0
A785-A788R1	2	delly	DEL	2L	243952	2L	244928	8	4	somatic_tumour	DEL00000018	1	2L:243952-244928	5to3	0.26	-0.43	-	-	CTTATTGGACAATCATTTAACCAGTCGTCGTCCCCTCTACACCCTAAGAAATCCATAGGTAACTAGTTTTGATAAAGCTCCCCCACGTTATGAGCCATGAAAATCGCCCCCAAAAGAGTTTACTCAAGTCACACATTT	GTCGTCGTCCCCTCTACACCCTAAGAAATCCATAGGTAACTAGTTTTGATAAAGCTCCCCCACGTTATGAGCCATGAAAATCGCCCCCAAAAGAGTTTACTCAAGTCACACATTT	NHEJ	kis, intron	kis, intron	kis	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:2; snp_op:2	17.11
A785-A788R1	3	Control-Freec	DUP	2L	9086000	2L	9090720	-	-	somatic_tumour	-	4.7	2L:9086000-9090720	Heterozygous duplication	0.33	0.47	-	-	-	-	-	Toll-4, intron	intergenic	Toll-4	NA	snp_su:1; snp_op:1	8.97
A785-A788R1	10	lumpy	DEL	2R	24999094	2R	25000297	22	10	somatic_tumour	7294	1.2	2R:24999094-25000297	5to3	0.39	-0.38	-	-	-	GTATATTTGCAGCTTATCACGTTCACAGCAGAAAAATAATCTCAACTTCGTCTGCAGCTTCAGCACCATGACCCAAATTTAAACGGGCAAAAAACGAGCCCAGAAAGTAAAACCCAGAATAG	NHEJ	zip, intron	zip, intron	zip	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:2; snp_op:1	14.96
A785-A788R1	21	novobreak	BND	3R	14911511	3R	24435410	19	0	somatic_tumour	22	9523.9	3R:14911511-24435410	5to5	0.22	0.02	AG	-	CCGCCCCTTTGTGTTGGACTCTCCAACATAAATTTGCCCGGGTTGCCATTCAAATGCTTAAAGTGCGCCTATCATTTGGGATTTAATTGAAAATTGCTGTTGACCATAGAACATGGA	TCCATGTTCTATGGTCAACAGCAATTTTCAATTAAATCCCAAATGATAGGCGCACTTTAAGCATTTGAATGGCAACCCGGGCAAATTTATGTTGGAGAGTC	Alt-EJ	CR46199, exon_2	nAChRalpha1, intron	CR46199, nAChRalpha1	NA	mh:2; ins:0; tup:0; tdown:0	0
A785-A788R1	25	lumpy	DEL	3R	19828917	3R	19829842	15	10	somatic_tumour	13500	0.9	3R:19828917-19829842	5to3	0.31	-0.24	-	-	-	CTGTTGCTGTTGCGGATCTTCATCTTCGTCTTCCCCGCTGATAATGCATAGAAACAAATCCAATTGGCGACAACACCAGAGGCAACACAAAATTCTGTCCCATCAACATGTTAATTG	NHEJ	bnl, 5UTR	bnl, intron	bnl	NA	mh:0; ins:0; tup:0; tdown:0	0
A785-A788R1	28	lumpy	DEL	4	493427	4	494456	10	6	somatic_tumour	15657	1	4:493427-494456	5to3	0.31	-0.2	-	-	-	GAATTGTTTTGTACGTTTTGATCTCAAATTATACAGAAAAATTATTTATTGGAAGCGTTATTCCAATGTTTTCTTGCAGTAATTGTACACGTTACTCGTAGAGTAAAATGGTAAAC	NHEJ	intergenic	intergenic	-	NA	bp1_INE-1_Helitron=8; mh:0; ins:0; tup:0; tdown:0	0
A785-A788R1	28	delly	DEL	4	493427	4	494456	10	6	somatic_tumour	DEL00000026	1	4:493427-494456	5to3	0.31	-0.2	-	-	TTGTTACAGAATTGTTTTGTACGTTTTGATCTCAAATTATACAGAAAAATTATTTATTGGAAGCGTTATTCCAATGTTTTCTTGCAGTAATTGTACACGTTACTCGTAGAGTAAAATGGTAAA	GAATTGTTTTGTACGTTTTGATCTCAAATTATACAGAAAAATTATTTATTGGAAGCGTTATTCCAATGTTTTCTTGCAGTAATTGTACACGTTACTCGTAGAGTAAAATGGTAAAC	NHEJ	intergenic	intergenic	-	NA	bp1_INE-1_Helitron=8; mh:0; ins:0; tup:0; tdown:0	0
A785-A788R1	31	Control-Freec	DEL	X	3158624	X	3266240	-	-	somatic_tumour	-	107.6	X:3158624-3266240	Homozygous deletion	0.84	-1.51	-	-	-	-	-	N, intron	dnc, intron	N, CG18508, Fcp3C, CG3939, CG14265, ng2, ng3, ng1, ng4, Pig1, Sgs4, dnc	NA	snp_su:0; snp_op:0	0
A785-A788R1	31	CNV-Seq	DEL	X	3159055	X	3266215	-	-	somatic_tumour	-	107	X:3159055-3266215	Homozygous deletion	0.84	-1.51	-	-	-	-	-	N, intron	dnc, intron	N, CG18508, Fcp3C, CG3939, CG14265, ng2, ng3, ng1, ng4, Pig1, Sgs4, dnc	NA	snp_su:0; snp_op:0	0
A785-A788R1	33	Control-Freec	DEL	Y	1103536	Y	1127136	-	-	somatic_tumour	-	23.6	Y:1103536-1127136	Homozygous deletion	0.93	-2.1	-	-	-	-	-	intergenic	intergenic	CR40629	NA	snp_su:0; snp_op:0	0
A785-A788R3	4	lumpy	DEL	3L	17655991	3L	17656585	11	5	somatic_tumour	4018	0.6	3L:17655991-17656585	5to3	0.34	-0.47	-	-	-	GCTGTGGACACAGTTTGAGAGTAACTGAAAAGCCAGTTACTGCAATGCGACGCCGTGGGAGTTTTCGATTCTGGGCTTGGAAGATCTAAACTGTGAAAAGCTTAAAATATTGTAC	NHEJ	intergenic	intergenic	-	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:1; snp_op:0	18.81
A785-A788R3	4	novobreak	DEL	3L	17655991	3L	17656585	11	5	somatic_tumour	2	0.6	3L:17655991-17656585	5to3	0.34	-0.47	-	-	ACTGCAAGGTGGCGTGAGCTTTTCTACGCGCCACCGCGGAAAAGCTGTGGACACAGTTTGAGAGTAACTGAAAAGCCAGTTACTGCAATGCGACGCCGTGGGAGTTTTCGATTCTGGGCTTGGAAGATCTAAACTGTGAAAAGCTTAAAATATTGTACAATGTGGATTATTTTATAGCTGACCTCCATAAAAA	GCTGTGGACACAGTTTGAGAGTAACTGAAAAGCCAGTTACTGCAATGCGACGCCGTGGGAGTTTTCGATTCTGGGCTTGGAAGATCTAAACTGTGAAAAGCTTAAAATATTGTAC	NHEJ	intergenic	intergenic	-	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:1; snp_op:0	18.81
A785-A788R3	6	delly	TANDUP	4	472400	4	559427	8	0	somatic_tumour	DUP00000014	87	4:472400-559427	7:6_7	0.09	0.29	AG	-	ACATATTTACATGTATATTTGTAACTCTTTAGATAGATCTTGGCGTCACAGCATGATTAAACAAAAACAACTAACGAGTTGTAAAATTTTTTACTCCTTCGGTTTTGACGACATGACCGTGTCCA	TTGTAACTCTTTAGATAGATCTTGGCGTCACAGCATGATTAAACAAAAACAACTAACGAGTTGTAAAATTTTTTACTCCTTCGGTTTTGACGACATGACCGTGTCCAGTTTTTT	Alt-EJ	Asator, exon	Pur-alpha, intron	Asator, zfh2, Thd1, CR43958, Pur-alpha	NA	mh:2; ins:0; tup:0; tdown:0; snp_su:0; snp_op:1	0
A785-A788R3	6	novobreak	TANDUP	4	472400	4	559427	8	0	somatic_tumour	3	87	4:472400-559427	7:6_7	0.09	0.29	AG	-	ATATACATACATATTTACATGTATATTTGTAACTCTTTAGATAGATCTTGGCGTCACAGCATGATTAAACAAAAACAACTAACGAGTTGTAAAATTTTTTACTCCTTCGGTTTTGACGACATGACCGTGTCCAGTTTTTTCCGCGCTCATTACAGTGCCGTTATCATCAGAATTTTCAAGCATTGCATTAGGAATGCCACGGGTTCTTAAAAAATTTATATTCAATTAGAGTGCAATATACACATTCATTATAAGGACATACCTGCTAGAAGTTCGAGATCGAGGTCTTTGGAATTTAAGTGGCAATTGTGTTGGGTCCGTGACATACTTTCCTTCAGTTGATTCTCTACGCCGACGTAAGCCTAAATCAATATAAATCAAATAAACGTGGTGATAATTCACGTTTTGGCCCATAAATGTAATGCAAGAGCATAAAAAAAG	TTGTAACTCTTTAGATAGATCTTGGCGTCACAGCATGATTAAACAAAAACAACTAACGAGTTGTAAAATTTTTTACTCCTTCGGTTTTGACGACATGACCGTGTCCAGTTTTTT	Alt-EJ	Asator, exon	Pur-alpha, intron	Asator, zfh2, Thd1, CR43958, Pur-alpha	NA	mh:2; ins:0; tup:0; tdown:0; snp_su:0; snp_op:1	0
A785-A788R3	8	Control-Freec	DEL	X	2796520	X	3212294	-	-	somatic_tumour	-	415.8	X:2796520-3212294	8:8_9	0.86	-1.58	-	-	-	-	-	kirre, intron	dnc, intron	kirre, CG12498, CG14416, CG14417, CG14418, CG14419, CG3526, CG3588, CG14424, CG32793, CG3592, CG3598, CG14420, CG14421, CG14422, CG14423, CG17959, CG3603, rst, CG4116, N, CG18508, Fcp3C, CG3939, dnc	NA	snp_su:1; snp_op:0	27.27
A785-A788R3	8	delly	DEL	X	2797173	X	3212395	11	8	somatic_tumour	DEL00000015	415.2	X:2797173-3212395	9:8_9	0.55	-1.58	-	CTGTAGTG	ACTTCGGACACTCCGGTCGTTGTCGTCATCGTTAGCACCTCATCTCAGGCCCCGGAATCATGAACTGCCGCCATCAGCTGCTGTAGTGAGTTTCGCCTCTGGATTTTTTCTTCAAGTTGGTTGTGTTTGGCTTTTGACATGGCCAGATGGTTCCATCGAGC	TCGTCATCGTTAGCACCTCATCTCAGGCCCCGGAATCATGAACTGCCGCCATCAGCTGCTGTAGTGAGTTTCGCCTCTGGATTTTTTCTTCAAGTTGGTTGTGTTTGGCTTTTGAC	FoSTeS	kirre, intron	dnc, intron	kirre, CG12498, CG14416, CG14417, CG14418, CG14419, CG3526, CG3588, CG14424, CG32793, CG3592, CG3598, CG14420, CG14421, CG14422, CG14423, CG17959, CG3603, rst, CG4116, N, CG18508, Fcp3C, CG3939, dnc	NA	mh:0; ins:8; tup:3; tdown:3; snp_su:1; snp_op:0	27.27
A785-A788R3	8	lumpy	DEL	X	2797173	X	3212395	11	8	somatic_tumour	5969	415.2	X:2797173-3212395	9:8_9	0.55	-1.58	-	CTGTAGTG	-	TCGTCATCGTTAGCACCTCATCTCAGGCCCCGGAATCATGAACTGCCGCCATCAGCTGCTGTAGTGAGTTTCGCCTCTGGATTTTTTCTTCAAGTTGGTTGTGTTTGGCTTTTGAC	FoSTeS	kirre, intron	dnc, intron	kirre, CG12498, CG14416, CG14417, CG14418, CG14419, CG3526, CG3588, CG14424, CG32793, CG3592, CG3598, CG14420, CG14421, CG14422, CG14423, CG17959, CG3603, rst, CG4116, N, CG18508, Fcp3C, CG3939, dnc	NA	mh:0; ins:8; tup:3; tdown:3; snp_su:1; snp_op:0	27.27
A785-A788R3	8	novobreak	DEL	X	2797173	X	3212395	11	8	somatic_tumour	8	415.2	X:2797173-3212395	9:8_9	0.55	-1.58	-	CTGTAGTG	CCTATCCGCACCCGTACTTCGGACACTCCGGTCGTTGTCGTCATCGTTAGCACCTCATCTCAGGCCCCGGAATCATGAACTGCCGCCATCAGCTGCTGTAGTGAGTTTCGCCTCTGGATTTTTTCTTCAAGTTGGTTGTGTTTGGCTTTTGACATGGCCAGATGGTTCCATCGAGCTGTGGGCCAAGGTCAATGTAAATT	TCGTCATCGTTAGCACCTCATCTCAGGCCCCGGAATCATGAACTGCCGCCATCAGCTGCTGTAGTGAGTTTCGCCTCTGGATTTTTTCTTCAAGTTGGTTGTGTTTGGCTTTTGAC	FoSTeS	kirre, intron	dnc, intron	kirre, CG12498, CG14416, CG14417, CG14418, CG14419, CG3526, CG3588, CG14424, CG32793, CG3592, CG3598, CG14420, CG14421, CG14422, CG14423, CG17959, CG3603, rst, CG4116, N, CG18508, Fcp3C, CG3939, dnc	NA	mh:0; ins:8; tup:3; tdown:3; snp_su:1; snp_op:0	27.27
A785-A788R5	3	delly	DEL	2L	20938086	2L	20938103	9	1	somatic_tumour	DEL00000002	0	2L:20938086-20938103	5to3	0.15	0	-	-	GGCAAAACGTGCGCCCTAAACTATGCAACACTTTGTGGGACGTAATAATCTTTTGGCCAACTTCATTGCCATGGCATGTCGAGCTACTCATGTGTAATTGAAATTTAGTTGGCAAAACTAATTGGAATTGCTGCATTATGCAAACGCCGATAAAGCCCCAAACAGAAATGCCTCACAGTGGG	-	NHEJ	intergenic	intergenic	-	NA	mh:0; ins:0; tup:0; tdown:0	0
A785-A788R5	6	delly	DEL	3L	283730	3L	284290	20	16	somatic_tumour	DEL00000005	0.6	3L:283730-284290	5to3	0.32	-0.42	CA	-	GTGTTGCGCTATGTCCATTTCCCTTTCTTCTCTACAAAAATTCGGCAATCATGCAGCCTACCATTCGATAATTATGAGTCTGATCATTATGAGCACGGGCTTGCAAATATGGTA	AGCGCGTCCTGTGTTGCGCTATGTCCATTTCCCTTTCTTCTCTACAAAAATTCGGCAATCATGCAGCCTACCATTCGATAATTATGAGTCTGATCATTATGAGCACGGGCTTGCAAATATGGTA	Alt-EJ	RhoGEF3, intron	RhoGEF3, intron	RhoGEF3	NA	mh:2; ins:0; tup:0; tdown:0; snp_su:0; snp_op:0	0
A785-A788R5	6	novobreak	DEL	3L	283730	3L	284290	20	16	somatic_tumour	6	0.6	3L:283730-284290	5to3	0.32	-0.42	CA	-	GGGCATATTAATATAATTAATTACCAAACCTTACGTTCACGTGATGGATGACAGTGTATATGTACATATGACAGAACTCGGCGCGTTTACATCTGCGTGTAAATATCCTGCGGCATGGTGAATAGACATAAATCAACCTCAGAGCACAAATTCAGGAAAACAACGAGCGGCTAATGCAAGTGTAATCGTGGATATGTGCTTTTTTCCGCCAACTTTTTCCAACCATATCCCTTGATTATAAACTGAACGATATATGTATAAGTTTTTTTCAATAGCGCGTCCTGTGTTGCGCTATGTCCATTTCCCTTTCTTCTCTACAAAAATTCGGCAATCATGCAGCCTACCATTCGATAATTATGAGTCTGATCATTATGAGCACGGGCTTGCAAATATGGTATAGAAAACGAGAAACTCGTTTCCTATGGCCGCAACTTCATTTGGTCATTGGCTTTTAGTCAATGCCGCTGGAGCTCGACCAACGTTACCACATCGTGCACCATCGAAGAAGCAGCTTCTGGGCTAGTAAAATGGAAAAGTGCAAGTTGCCTAACAGGTATGCGAGATAATGCAATCGATTTACTAGTACCCGTCCACGTCCACGTCCTCCTCCACTTCCTTGGCCCGCCCTCGTCCTCTGCTCTTCTGCTCTGCTTTGCTGAAGACAAGTGCGGCTTAACATGATTGAAAACCAGTTTTATGA	AGCGCGTCCTGTGTTGCGCTATGTCCATTTCCCTTTCTTCTCTACAAAAATTCGGCAATCATGCAGCCTACCATTCGATAATTATGAGTCTGATCATTATGAGCACGGGCTTGCAAATATGGTA	Alt-EJ	RhoGEF3, intron	RhoGEF3, intron	RhoGEF3	NA	mh:2; ins:0; tup:0; tdown:0; snp_su:0; snp_op:0	0
A785-A788R5	8	Control-Freec	DUP	3R	4162935	3R	4171545	-	-	somatic_tumour	-	8.6	3R:4162935-4171545	8:8_9	0.4	0.49	-	-	-	-	-	intergenic	intergenic	-	NA	snp_su:0; snp_op:0	0
A785-A788R5	8	Control-Freec	DUP	3R	4171545	3R	4181016	-	-	somatic_tumour	-	9.5	3R:4171545-4181016	9:8_9	0.47	0.75	-	-	-	-	-	intergenic	CG12581, intron	CG12581	NA	snp_su:0; snp_op:0	0
A785-A788R5	12	novobreak	TRA	3R	25930184	3L	14290873	7	0	somatic_tumour	11	11639.3	3R:25930184 3L:14290873	3to5	0.09	0	-	CAAATTG	CCATTATCTGCAATGAGCCAGACGCACAATTGGTATTTTTATTTTTTGGCTAGCAATTACTAAAAACCAAAATTCCAAATTGTCCAAAGGCGGCTATAAAAAGTAACAGATAGATAGGTCAAAGGACTGTTGTTGCAATGGAAATGCGTTCGGTATATAAA	ACGCACAATTGGTATTTTTATTTTTTGGCTAGCAATTACTAAAAACCAAAATTCCAAATTGTCCAAAGGCGGCTATAAAAAGTAACAGATAGAT	FoSTeS	CCAP-R, intron	fz, intron	CCAP-R, fz	NA	mh:0; ins:7; tup:4; tdown:5	0
A785-A788R5	15	Control-Freec	DUP	4	800730	4	803313	-	-	somatic_tumour	-	2.6	4:800730-803313	Heterozygous duplication	0.38	0.42	-	-	-	-	-	Sox102F, 3UTR	Sox102F, 5UTR	Sox102F	NA	snp_su:0; snp_op:0	0
A785-A788R5	16	Control-Freec	DUP	Y	557928	Y	561372	-	-	somatic_tumour	-	3.4	Y:557928-561372	Homozygous triplication	0.93	1.38	-	-	-	-	-	kl-3, intron	kl-3, intron	kl-3	NA	snp_su:0; snp_op:0	0
A785-A788R5	17	Control-Freec	DEL	Y	1114995	Y	1127049	-	-	somatic_tumour	-	12.1	Y:1114995-1127049	Homozygous deletion	0.8	-0.75	-	-	-	-	-	intergenic	intergenic	CR40629	NA	snp_su:0; snp_op:0	0
A785-A788R7	3	Control-Freec	DUP	2L	11559201	2L	11579550	-	-	somatic_tumour	-	20.3	2L:11559201-11579550	Heterozygous duplication	0.25	0.33	-	-	-	-	-	intergenic	intergenic	CR44495	TRUE	low FC; snp_su:35; snp_op:14; snp_ratio:2.5	12.26
A785-A788R7	18	lumpy	TANDUP	X	5149225	X	5149329	9	0	somatic_tumour	6250	0.1	X:5149225-5149329	3to5	0.37	0	-	-	-	-	NHEJ	rg, intron	rg, intron	CG15465, rg	NA	mh:0; ins:0; tup:0; tdown:0	0
A785-A788R9	12	novobreak	TRA	3L	24906840	3R	26861450	3	0	somatic_tumour	8	1954.6	3L:24906840 3R:26861450	3to5	0.05	0	GACAAACGC	-	ATATTAATCAAAGTTCTACCCACCGTTCTTTTGGATTTGTGGCTTTACTATCAAATAGACAAACGCATAACTTGCCGGCTTGGAGTCAGCCGTCGTGGGTACCGCCCTACCGGTGGATTTCGCGGCAGGTACATGGTCCCGTTTTGGGGACCTGCAC	ATATTAATCAAAGTTCTACCCACCGTTCTTTTGGATTTGTGGCTTTACTATCAAATAGACAAACGCATAACTTGCCGGCTTGGAGTCAGCCGTCGTGGGTA	Alt-EJ	intergenic	Lerp, exon_6	Lerp	NA	bp2_Rt1a_R1=2; mh:9; ins:0; tup:0; tdown:0	0
A785-A788R9	24	Control-Freec	DEL	X	3001596	X	3162198	-	-	somatic_tumour	-	160.6	X:3001596-3162198	24:24_25	0.94	-2.88	-	-	-	-	-	kirre, intron	N, intron	kirre, CG4116, N	NA	snp_su:0; snp_op:1	0
A785-A788R9	24	lumpy	DEL	X	3002207	X	3162172	20	7	somatic_tumour	18022	160	X:3002207-3162172	25:24_25	1	-2.89	-	-	-	-	NHEJ	kirre, intron	N, intron	kirre, CG4116, N	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:0; snp_op:1	0
B241R35	1	lumpy	DEL	2L	4113213	2L	4118212	6	4	somatic_tumour	366	5	2L:4113213-4118212	5to3	0.31	-0.55	-	-	-	TAAGCTAGACCTTAAGTATTAGCGTGTAATATCTTTTCCCTAACATGGCTATTTTTTCTCATATTTGTTACTTAACATAATCAAGAAAACAATGCATGCATGGTA	NHEJ	ed, intron	intergenic	ed	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:11; snp_op:5; snp_ratio:2.2	18.11
B241R35	3	Control-Freec	DEL	3R	4137600	3R	4173600	-	-	somatic_tumour	-	36	3R:4137600-4173600	Heterozygous deletion	0.31	-0.54	-	-	-	-	-	Gfat1, exon	intergenic	Gfat1, CR41601, CG40198	NA	snp_su:0; snp_op:0	0
B241R35	4	lumpy	DEL	3R	8812327	3R	8815424	3	5	somatic_tumour	2930	3.1	3R:8812327-8815424	5to3	0.26	-0.49	-	-	-	-	-	CG9837, intron	CG9821, 3UTR	CG9837, CG9821	NA	snp_su:1; snp_op:0	21.25
B241R35	4	novobreak	DEL	3R	8812327	3R	8815424	3	5	somatic_tumour	1	3.1	3R:8812327-8815424	5to3	0.26	-0.49	-	-	TACTCTGCGTGCTTTTCGTCACTACGTAAACACCGTCCTCAGTTATACATACATACATATGTTCATGTATATGTATTTCTCGGGGGTGGCCTGAAAAATCTAAGCTGTTCTCCGCTTAAACTGACGTCCAGTAAGTAACAAACGTTTTGCTTAC	-	-	CG9837, intron	CG9821, 3UTR	CG9837, CG9821	NA	snp_su:1; snp_op:0	21.25
B241R35	5	Control-Freec	DEL	X	3120000	X	3194400	-	-	somatic_tumour	-	74.4	X:3120000-3194400	5:5_6	0.77	-0.98	-	-	-	-	-	kirre, intron	dnc, intron	kirre, N, CG18508, Fcp3C, CG3939, dnc	NA	snp_su:0; snp_op:0	0
B241R35	5	CNV-Seq	DEL	X	3120718	X	3194680	-	-	somatic_tumour	-	73	X:3120718-3194680	6:5_6	0.77	-0.99	-	-	-	-	-	kirre, intron	dnc, intron	kirre, N, CG18508, Fcp3C, CG3939, dnc	NA	snp_su:0; snp_op:0	0
B241R37	2	Control-Freec	DUP	2R	14139624	2R	14146728	-	-	somatic_tumour	-	7.1	2R:14139624-14146728	Heterozygous duplication	0.4	0.59	-	-	-	-	-	Prosap, intron	intergenic	Prosap, mir-989	NA	snp_su:0; snp_op:0	0
B241R37	4	Control-Freec	DUP	2R	21765768	2R	21770208	-	-	somatic_tumour	-	4.4	2R:21765768-21770208	Heterozygous duplication	0.4	0.64	-	-	-	-	-	CG30395, exon_2	intergenic	CG30395	NA	snp_su:0; snp_op:0	0
B241R37	7	delly	DEL	3L	14059217	3L	14059363	15	0	somatic_tumour	DEL00000001	0.1	3L:14059217-14059363	5to3	0.21	0	-	AAATCT	GCTTCCATTATTTGTCGGCAAAACGAAAAAGATAGTGAATACCATCTGCATATTACTCACCTCAAATCTTCGAAGCTTACTCATTTGGCATGAGCGTAGACAGATTGAAATTGAATGGGGGTTGCCAGGCTTACAG	GCTTCCATTATTTGTCGGCAAAACGAAAAAGATAGTGAATACCATCTGCATATTACTCACCTCAAATCTTCGAAGCTTACTCATTTGGCATGAGCGTAGACAGATTGAAAT	FoSTeS	Frl, intron	Frl, intron	Frl	NA	mh:0; ins:6; tup:4; tdown:4	0
B241R37	7	lumpy	DEL	3L	14059217	3L	14059363	15	0	somatic_tumour	2776	0.1	3L:14059217-14059363	5to3	0.21	0	-	AAATCT	-	GCTTCCATTATTTGTCGGCAAAACGAAAAAGATAGTGAATACCATCTGCATATTACTCACCTCAAATCTTCGAAGCTTACTCATTTGGCATGAGCGTAGACAGATTGAAAT	FoSTeS	Frl, intron	Frl, intron	Frl	NA	mh:0; ins:6; tup:4; tdown:4	0
B241R37	7	novobreak	DEL	3L	14059217	3L	14059363	15	0	somatic_tumour	3	0.1	3L:14059217-14059363	5to3	0.21	0	-	AAATCT	CTTTATTGATTGTGTTCATGATTCGCATGAAAATCAATTTATGTAGCCCATGTGGCTTTTCCAATAAAATTCCAATAAAATGTACTTTTGCTTCCATTATTTGTCGGCAAAACGAAAAAGATAGTGAATACCATCTGCATATTACTCACCTCAAATCTTCGAAGCTTACTCATTTGGCATGAGCGTAGACAGATTGAAATTGAATGGGGGTTGCCAGGCTTACAGTCCGTAGCGCGTCCCATTATGCACATGCACACACATGTACATATAGATAGAGGGGACACAAAAATAAAACAAATTTAAAATGCGTATCCGGTATGCCGGTCAAGTAATTCATTATGTACACCGATATTTACATTTACATACATATGTATGTACATATGTACAT	GCTTCCATTATTTGTCGGCAAAACGAAAAAGATAGTGAATACCATCTGCATATTACTCACCTCAAATCTTCGAAGCTTACTCATTTGGCATGAGCGTAGACAGATTGAAAT	FoSTeS	Frl, intron	Frl, intron	Frl	NA	mh:0; ins:6; tup:4; tdown:4	0
B241R37	10	Control-Freec	DUP	3R	6894432	3R	6897984	-	-	somatic_tumour	-	3.6	3R:6894432-6897984	Heterozygous duplication	0.39	0.69	-	-	-	-	-	intergenic	Antp, 3UTR	CR44932, Antp	NA	snp_su:1; snp_op:2	9.85
B241R37	11	Control-Freec	DUP	3R	10581408	3R	10584072	-	-	somatic_tumour	-	2.7	3R:10581408-10584072	Heterozygous duplication	0.41	0.79	-	-	-	-	-	hth, 3UTR	hth, 3UTR	hth	NA	snp_su:1; snp_op:0	10.1
B241R37	12	lumpy	DEL	3R	18794445	3R	20261187	23	4	somatic_tumour	3767	1466.7	3R:18794445-20261187	5to3	0.22	0.05	-	ACGTAAGT	-	ATTAATTTATCAAAATCCGAAAACTACAGGCCATAAAAAGCACACATCAAATCGGCCGTTTACGTAAGTATATATGGTTATGTATGGTCATATAATATATC	FoSTeS	CG7720, intron	cic, intron	CG7720, cic	NA	bp2_rover_Gypsy=2; mh:0; ins:8; tup:3; tdown:3	0
B241R37	12	novobreak	DEL	3R	18794445	3R	20261187	23	4	somatic_tumour	7	1466.7	3R:18794445-20261187	5to3	0.22	0.05	-	ACGTAAGT	CATAATCAAATATGAATATATGTATTTGTTGTAAAATATCCCCCTGGTCGAAATCTGTTTTCAATTAGTCAGAGTGAGGCGTTTTCGAGAGAACCTGTTCGTTCCACTGGCAGCTGACTACGAGTATTTAGCGCTTTATGTGGCATATTTGAAAAGTTTGTCTAAAAACCGTTTAGATTATATTTTGGTAGCTCGTTTGCATTGCTAATGAGCGAGCCCAGGGGTCCAGTCCAGAATTAATGGCCCCGACCATGTGAAAACTTCGTAAATACAATATTTGGCGTTTCGTATTAATTTATCAAAATCCGAAAACTACAGGCCATAAAAAGCACACATCAAATCGGCCGTTTACGTAAGTATATATGGTTATGTATGGTCATATAATATATCTGCTAGCGGGTTTCGGTCGTAAACTTGTTGACAACAACTTTTGTGCAAGTGCTTGTAGCTCATATTTGGGTGCTATTGCCGCTTGAGAATCGCCTGTTATTTAGTCTCCATATATAC	ATTAATTTATCAAAATCCGAAAACTACAGGCCATAAAAAGCACACATCAAATCGGCCGTTTACGTAAGTATATATGGTTATGTATGGTCATATAATATATC	FoSTeS	CG7720, intron	cic, intron	CG7720, cic	NA	bp2_rover_Gypsy=2; mh:0; ins:8; tup:3; tdown:3	0
B241R37	14	Control-Freec	DUP	4	542568	4	545232	-	-	somatic_tumour	-	2.7	4:542568-545232	Heterozygous duplication	0.45	0.63	-	-	-	-	-	Thd1, 3UTR	Thd1, 3UTR	Thd1	NA	snp_su:0; snp_op:0	0
B241R37	15	Control-Freec	DEL	X	3033408	X	3135528	-	-	somatic_tumour	-	102.1	X:3033408-3135528	Homozygous deletion	0.88	-1.63	-	-	-	-	-	kirre, intron	N, 5UTR	kirre, CG4116, N	NA	snp_su:0; snp_op:0	0
B241R37	15	lumpy	DEL	X	3033491	X	3135340	16	13	somatic_tumour	4318	101.8	X:3033491-3135340	5to3	0.78	-1.63	-	ACACTCC	-	CGCCCAGAAAAGCCGTCCAATAAAAGTCCAGATCTAGATTCAGATTCGGTTCCGGTACACTCCGATACACGAAAAGCGTTCTTTTTTTGCCACTTTTTTTTTA	FoSTeS	kirre, intron	N, 5UTR	kirre, CG4116, N	NA	mh:0; ins:7; tup:3; tdown:4; snp_su:0; snp_op:0	0
B241R37	15	novobreak	DEL	X	3033491	X	3135340	16	13	somatic_tumour	9	101.8	X:3033491-3135340	5to3	0.78	-1.63	-	ACACTCC	TTCCTACCCGAATATCTCTCGTATTTTCTCCACGCCCCACCATTCTCCTTGCCAATTCAACAAAAAACTGTCAACGCTGCTGTCGTCTGACTTTGTTTTCTCATTAGACAGTTGCCCTCGTGTTGTTTTTCCACTCGGAGCGCATTTCATAATTGTCAGCCCGCCCAGAAAAGCCGTCCAATAAAAGTCCAGATCTAGATTCAGATTCGGTTCCGGTACACTCCGATACACGAAAAGCGTTCTTTTTTTGCCACTTTTTTTTTATGTTTCAAAACGGAAAATGTCGCCGTCGTCGGGAGAGTGCCTCCTCTTAGTTTATCA	CGCCCAGAAAAGCCGTCCAATAAAAGTCCAGATCTAGATTCAGATTCGGTTCCGGTACACTCCGATACACGAAAAGCGTTCTTTTTTTGCCACTTTTTTTTTA	FoSTeS	kirre, intron	N, 5UTR	kirre, CG4116, N	NA	mh:0; ins:7; tup:3; tdown:4; snp_su:0; snp_op:0	0
B241R37	15	delly	DEL	X	3033491	X	3135340	16	13	somatic_tumour	DEL00000007	101.8	X:3033491-3135340	5to3	0.78	-1.63	-	ACACTCC	TTTCATAATTGTCAGCCCGCCCAGAAAAGCCGTCCAATAAAAGTCCAGATCTAGATTCAGATTCGGTTCCGGTACACTCCGATACACGAAAAGCGTTCTTTTTTTGCCACTTTTTTTTTATGTTTCAAAACGGAAAATGTC	CGCCCAGAAAAGCCGTCCAATAAAAGTCCAGATCTAGATTCAGATTCGGTTCCGGTACACTCCGATACACGAAAAGCGTTCTTTTTTTGCCACTTTTTTTTTA	FoSTeS	kirre, intron	N, 5UTR	kirre, CG4116, N	NA	mh:0; ins:7; tup:3; tdown:4; snp_su:0; snp_op:0	0
B241R39	7	novobreak	BND	2L	5318061	2L	5318184	4	0	somatic_tumour	1	0.1	2L:5318061-5318184	5to5	0.04	0	GCTGCGGCTGC	-	TGACGAGAAGATCGGCACCCGGAGAAGCGTGCGGGCCAGTGCGGCGGCCAACAAGATCATCTATAGTCGCAGCAATGCAGCCGCAGCGGTGGCTCCACGTGTTGCATGAACCACACTTGTGCCGCTGTTAACTTGGCTGGTGGTCACCACAGCTCCGCCTGGCATTGTTGTCGTCGTCACTGAGGAGGGCACAACACTGGCATTGTTGGCAGTGCTGCTGTTG	CAAGTTAACAGCGGCACAAGTGTGGTTCATGCAACACGTGGAGCCACCGCTGCGGCTGCATTGCTGCGACTATAGATGATCTTGTTGGCCGCCGCACTGGC	Alt-EJ	Ncoa6, exon_5	Ncoa6, exon_5	Ncoa6	NA	mh:11; ins:0; tup:0; tdown:0	0
B241R39	20	novobreak	DEL	3R	13698357	3R	23758748	13	0	somatic_tumour	6	10060.4	3R:13698357-23758748	5to3	0.07	-0.01	-	-	GATCCGGACGATGAGCTGGAACTGGACGATTCCGAACCTCCAACCCGCGCTTAGCTTCCACCATGCTCCTCCAGTCGACACCTGTTATTTCAGGCTGCCATGTTCGCACGCGTGTCCTTCTACCCCACCCTGCTGTACAATGTCCTGATGGAAAAGGCATCGGC	-	-	f-cup, exon_1	PTPMT1, 5UTR	f-cup, PTPMT1	NA	-	0
B241R39	29	Control-Freec	DEL	4	688224	4	690636	-	-	somatic_tumour	-	2.4	4:688224-690636	Heterozygous deletion	0.32	-0.56	-	-	-	-	-	CG11360, 3UTR	CG11360, 3UTR	CG11360	NA	snp_su:0; snp_op:0	0
B241R39	31	CNV-Seq	COMPLEX_DEL	X	3157127	X	3158876	-	-	somatic_tumour	-	1.8	X:3157127-3158876	31:31_32_33	0.91	-2.14	-	-	-	-	-	N, intron	N, intron	N	NA	snp_su:0; snp_op:0	0
B241R39	31	delly	COMPLEX_BND	X	3159064	X	3390026	19	19	somatic_tumour	INV00000007	231	X:3159064-3390026	32:31_32_33	0.7	-0.01	-	-	CCTTTCCCGTGTAGCCCGTGGGACACATGCACCTAGAACAGAAGCGAGAGGAGCAATTAAACGCGGGTTAAACGCGGCTGTTAATTGTTTGGATATATTTTTTAAGCATCACATAAAGTTTTCTGTTGGGT	-	-	N, intron	CG12535, 3UTR	N, Myc, CR44999, CG12535	NA	-	0
B241R39	31	lumpy	COMPLEX_BND	X	3159064	X	3390026	19	19	somatic_tumour	4784_1	231	X:3159064-3390026	32:31_32_33	0.7	-0.01	-	-	-	-	-	N, intron	CG12535, 3UTR	N, Myc, CR44999, CG12535	NA	-	0
B241R39	31	novobreak	COMPLEX_BND	X	3159064	X	3390026	19	19	somatic_tumour	46	231	X:3159064-3390026	32:31_32_33	0.7	-0.01	-	-	GTGTGTGTGTGTGTGTGTGAATTTGCCGGCTACTTCTGCCATTCGTGTACCCTTTCTATTTAACGCGGTATCCCCACTGTCATAATAAACTGCAAATTAAGTTTAATTCATCTGTTTTAGCTCTCCATTTTAAACTTTTAAACTTAAACGACCCAACAGAAAACTTTATGTGATGCTTAAAAAATATATCCAAACAATTAACAGCCGCGTTTAACCCGCGTTTAATTGCTCCTCTCGCTTCTGTTCTAGGTGCATGTGTCCCACGGGCTACACGGGAAAGGATTGCGACACCAAGTACAAGCCCTGCTCGCCATCGCCGTGCCAGAATGGCGGAATTTGCCGGTCGAACGGTCTGTCCTACGAGTGCAAGTGCCCCAAAGGTGAGTGCTAGTTATTAAGCTAAGCTAAAAATTTCATAACTACTTCTTCAGTAGGAACCAGATTAATCGAGTTAGAAAGATTGTAAATTATTACCAAAGAATGGGCACCTTTAATACAAATTCAAGTTACAATAG	-	-	N, intron	CG12535, 3UTR	N, Myc, CR44999, CG12535	NA	-	0
B241R39	31	CNV-Seq	COMPLEX_DUP	X	3392440	X	3393763	-	-	somatic_tumour	-	1.3	X:3392440-3393763	33:31_32_33	0.89	0.61	-	-	-	-	-	CG12535, 3UTR	CG12535, intron	CR44999, CG12535	NA	snp_su:0; snp_op:0	0
B241R41-1	83	Control-Freec	DUP	X	13949502	X	14039628	-	-	somatic_tumour	-	90.1	X:13949502-14039628	Homozygous duplication	0.8	0.61	-	-	-	-	-	mamo, intron	intergenic	mamo, CG11068, CR44655, ben, Ste12DOR, tRNA:Arg-TCG-2-1, tRNA:Ser-CGA-1-1, tRNA:Ser-CGA-1-2, tRNA:Arg-TCG-3-1, tRNA:Arg-TCG-3-2, tRNA:Arg-TCG-3-3, tRNA:Arg-TCG-3-4, tRNA:Ser-AGA-3-1, tRNA:Ser-AGA-2-1	NA	snp_su:0; snp_op:1	0
B241R41-1	77	CNV-Seq	COMPLEX_DEL	X	3005994	X	3239110	-	-	somatic_tumour	-	232	X:3005994-3239110	77:77_78_79	0.74	-0.64	-	-	-	-	-	kirre, intron	dnc, intron	kirre, CG4116, N, CG18508, Fcp3C, CG3939, CG14265, dnc	NA	snp_su:0; snp_op:0	0
B241R41-1	40	Control-Freec	DUP	3L	22785188	3L	22796871	-	-	somatic_tumour	-	11.7	3L:22785188-22796871	Heterozygous duplication	0.48	0.92	-	-	-	-	-	SPoCk, 3UTR	jim, 3UTR	SPoCk, CG14448, jim	NA	snp_su:0; snp_op:0	0
B241R41-1	49	Control-Freec	DUP	3R	25869500	3R	25874507	-	-	somatic_tumour	-	5	3R:25869500-25874507	Heterozygous triplication	0.48	1.32	-	-	-	-	-	CG5890, intron	Tsp96F, 3UTR	CG5890, Tsp96F	NA	snp_su:0; snp_op:0	0
B241R41-1	44	Control-Freec	DUP	3R	21309792	3R	21316468	-	-	somatic_tumour	-	6.7	3R:21309792-21316468	Heterozygous triplication	0.47	1.25	-	-	-	-	-	Hsromega, exon_2	Hsromega, ncRNA	Hsromega	NA	snp_su:2; snp_op:2	7.24
B241R41-1	65	Control-Freec	DUP	4	721008	4	746043	-	-	somatic_tumour	-	25	4:721008-746043	Heterozygous duplication	0.43	0.16	-	-	-	-	-	ey, 3UTR	bt, exon_23	ey, bt	TRUE	low FC; snp_su:5; snp_op:2; snp_ratio:2.49	10.29
B241R41-1	85	delly	BND	X	17074351	X	17132365	5	4	somatic_tumour	INV00000057	58	X:17074351-17132365	3to3	0.24	-0.19	-	-	ATTAAAATCCTTGTTTGTTGTCCATCGTAAATTTTGGGATCATCCATAAAATTCCAAAACATTAGTAAGAGATTCATCTGAAAGCTCTGAACAGCAAAATAAATAAAACCAAAGC	-	-	wcy, intron	CG5004, intron	wcy, CG5004	NA	-	0
B241R41-1	85	lumpy	BND	X	17074351	X	17132365	5	4	somatic_tumour	4494_1	58	X:17074351-17132365	3to3	0.24	-0.19	-	-	-	-	-	wcy, intron	CG5004, intron	wcy, CG5004	NA	-	0
B241R41-1	77	novobreak	COMPLEX_BND	X	3006006	X	3322256	5	3	somatic_tumour	64	316.2	X:3006006-3322256	78:77_78_79	0.21	-0.44	-	-	CTGACAGGGGAAGAGGGCCCTCCAAAGAGCCAGCTAAATTCGAAACGCACACAGAGGCGAAAAGTGCAACAACTTTGCTGGCATTTTAGGCTCCTACATATTTTTGAAAATAATCCTTTCTTACTGCCCGACTAGCTGAAATATGAAATATTGAATAGAAAAGGTACAAGT	-	-	kirre, intron	CR44886, ncRNA	kirre, CG4116, N, CG18508, Fcp3C, CG3939, CG14265, ng2, ng3, ng1, ng4, Pig1, Sgs4, CG10793, dnc, CR44886	NA	snp_su:0; snp_op:0	0
B241R41-1	25	novobreak	DEL	2R	11716582	2R	11717073	5	0	somatic_tumour	8	0.5	2R:11716582-11717073	5to3	0.06	0	-	-	AAACTTTCTTTTTATAAATATTTGCTAAGGCTTGAGCCTTCTTCGCAGTGGTAGATTCTCAAAAACTTTAAATTTAAATATATAAATATTATTTCCTGAATCGAGTACATTTTTTCTCAGTGCATCCATTGAATTTGTCTAGGGCTGTGAGCGGGCTACTCAAATATGACACC	-	-	pyr, intron	pyr, intron	pyr	NA	-	0
B241R41-1	48	novobreak	TANDUP	3R	25463643	3R	25485200	3	2	somatic_tumour	13	21.6	3R:25463643-25485200	3to5	0.06	0.14	-	-	GATACTGACCGCCACCGGGCGAAGAAAACTTAAGATGCGAGTGCCCAGCGGCGGTCCAGAAATGGCTTGGCTGTACAAAAGACAAAAGACAGCAGCCACGAAAATCAATTTGTGTTGCCTTCCCTTGTTTTTTTTTTTTAAATTTGGTGTACGTG	-	-	Fur1, intron	CG5116, exon	Fur1, CG42488, CG5116	NA	-	0
B241R41-2	3	Control-Freec	DUP	2L	4007322	2L	4056552	-	-	somatic_tumour	-	49.2	2L:4007322-4056552	Heterozygous duplication	0.35	0.45	-	-	-	-	-	intergenic	ed, intron	CG43773, CG43774, ed	NA	snp_su:57; snp_op:42; snp_ratio:1.36	12.79
B241R41-2	4	Control-Freec	DEL	2L	4460238	2L	4588236	-	-	somatic_tumour	-	128	2L:4460238-4588236	Heterozygous deletion	0.26	-0.44	-	-	-	-	-	CG15435, exon	dpy, intron	CG15435, CG15443, CG15436, FIG4, ine, HP6, CR43716, dpy	NA	snp_su:80; snp_op:81; snp_ratio:0.99	10.05
B241R41-2	5	novobreak	BND	2L	6821196	2L	16287254	2	2	somatic_tumour	4	9466.1	2L:6821196-16287254	5to5	0.14	0.07	-	-	GTTTTGATGGCAACCGGTACGGCGGACATGTTTAATCGTGTTTGTGTATTTGCTTACTATCGTGGCCAAAATGTCTGTGCCACGTGGTTTTTGTAAAATCAAACAGCCATGCGAAGTGGCAACCAACTTTGGCCCCCAGGAAATCACTTAGCCACCGTTCGCCGAGGC	-	NHEJ	intergenic	crp, 5UTR	crp	NA	mh:0; ins:0; tup:0; tdown:0	0
B241R41-2	8	novobreak	TRA	2L	10975938	Tomelloso	3575	3	0	somatic_tumour	7	10972.4	2L:10975938 Tomelloso:3575	8:8_57_78	0.51	0	-	-	TGATGTTGAAGGGGTTCCTCGATGCCTACCAAGTTACATTTTCACGCACTCGCCGATGTAGAACCAGAAGATGACCTCGGCGGTCACCAGGGTGTTAAGCCAGGCCTCGCGAACCGTGAGGTTCTTGTAGGCGCCGGTCTTGGCTCCCTTGATGATGTTGCCCAGTCCCTGGC	-	-	ATPsynG, exon	intergenic	ATPsynG	NA	bp1_Tomelloso_2	0
B241R41-2	8	novobreak	TRA	3R	6410416	Tomelloso	4015	3	0	somatic_tumour	29	6406.4	3R:6410416 Tomelloso:4015	57:8_57_78	0.34	0	-	-	CTGAGGCACCCACTACGGAATCGTCGAGTTCTTCCAGAAAGCTACAGTTGAGGATAATGCTGTAGTTGTACTTGGATACAGTTGGGAAAAGCAGATGGAGACAAGAAAATGATTAACCCATTTGTTTGAGAC	-	-	gpp, intron	intergenic	gpp	NA	-	0
B241R41-2	17	Control-Freec	DUP	2R	6158673	2R	6178365	-	-	somatic_tumour	-	19.7	2R:6158673-6178365	Heterozygous duplication	0.39	0.76	-	-	-	-	-	CR43904, exon_1	intergenic	EcR, CR43904, tRNA:Arg-ACG-1-2, tRNA:Asn-GTT-1-4, tRNA:Asn-GTT-1-5, tRNA:Asn-GTT-1-6, tRNA:Lys-CTT-1-2, tRNA:Lys-CTT-1-3, tRNA:Lys-CTT-1-4, tRNA:Ile-AAT-1-1, tRNA:Arg-ACG-1-3, tRNA:Lys-CTT-1-5, tRNA:Arg-ACG-1-4, Cyp6w1	NA	snp_su:0; snp_op:0	0
B241R41-2	18	novobreak	TRA	2R	6595948	3R	6939919	3	0	somatic_tumour	12	344	2R:6595948 3R:6939919	3to5	0.24	0	-	-	TTCATTTAGTGCTTATTTATTCCAAGTGCACGTGCGCGTGCCGACGGCTCAGGGTGCCCTGCCCTCCCCATCCGTATTGGACTACCCCCTTTTCAGCACTGCCGAAAATCGCATTTAAAT	-	-	jing, intron	Antp, intron	jing, Antp	NA	-	0
B241R41-2	20	Control-Freec	DUP	2R	10490913	2R	10574604	-	-	somatic_tumour	-	83.7	2R:10490913-10574604	Heterozygous duplication	0.27	0.51	-	-	-	-	-	lola, exon	psq, intron	lola, snoRNA:lola-a, snoRNA:lola-b, snoRNA:lola-c, snoRNA:lola-d, CR45135, acal, psq	NA	snp_su:50; snp_op:48; snp_ratio:1.04	10.22
B241R41-2	32	novobreak	BND	3L	7803668	3L	7804080	2	1	somatic_tumour	21	0.4	3L:7803668-7804080	3to3	0.11	0	-	-	CTCCTCGTAGGAATTCCCCCTGCTCGGCCTGATTTTGTTTGCCCTGATGGTGATATCTTGACCAGGGCATCATATCCAGTCTCTCCGATATTCTGGGGCTCTTCACAGCACCCTCCAACCACAATGCGAACCTCAGCCTGATCAGCTTCCCCGTGGGCTATGGCGTCCAGC	-	-	CG32369, exon_1	CG32369, exon_1	CG32369	NA	-	0
B241R41-2	33	novobreak	TANDUP	3L	8421440	3L	8422069	3	0	somatic_tumour	22	0.6	3L:8421440-8422069	3to5	0.12	0.19	-	-	GTCTTTCGGATTTCGATGCTGCTGCTACTGTTCTGCCTCGGCCGATGCCTCCGCTGACGCCTACTGCGACGCCGACTGCGACTGCAACTGCGGCGATTGCATTTCGTATTTCATTTCTTCTTTTTTATTGTTCTCGAATGAATGAATGAATGAATGGGCACTAACACACTCGCGCTCGCATCCGATTTGTACAATTCGTATTGTCGTCTTTGCCTCTCTCTCTCTCTTTAGCGCCCTTTTACGAGTTCATTCGTTTGCC	-	-	CG32354, 5UTR	CG32354, 5UTR	CG32354	NA	-	0
B241R41-2	34	Control-Freec	DUP	3L	8920476	3L	8940168	-	-	somatic_tumour	-	19.7	3L:8920476-8940168	Heterozygous duplication	0.25	0.43	-	-	-	-	-	Tsp66E, intron	orb2, 3UTR	Tsp66E, CG43783, orb2	NA	snp_su:29; snp_op:18; snp_ratio:1.61	12.4
B241R41-2	35	Control-Freec	DUP	3L	9914922	3L	9969075	-	-	somatic_tumour	-	54.2	3L:9914922-9969075	Heterozygous duplication	0.26	0.44	-	-	-	-	-	CG34356, intron	Dronc, exon_1	CG34356, CG6685, Dronc	NA	snp_su:71; snp_op:58; snp_ratio:1.22	10.45
B241R41-2	36	Control-Freec	DUP	3L	10338300	3L	10382607	-	-	somatic_tumour	-	44.3	3L:10338300-10382607	Heterozygous duplication	0.38	0.58	-	-	-	-	-	CR46006, ncRNA	intergenic	CR46006, mir-276a	NA	snp_su:43; snp_op:19; snp_ratio:2.26	15.5
B241R41-2	37	Control-Freec	DUP	3L	10500759	3L	10540143	-	-	somatic_tumour	-	39.4	3L:10500759-10540143	37:37_38	0.4	0.66	-	-	-	-	-	Rbfox1, intron	Rbfox1, intron	Rbfox1	NA	snp_su:53; snp_op:27; snp_ratio:1.96	15.41
B241R41-2	39	Control-Freec	DUP	3L	11229363	3L	11352438	-	-	somatic_tumour	-	123.1	3L:11229363-11352438	Heterozygous duplication	0.29	0.46	-	-	-	-	-	CR46050, exon_1	intergenic	CG42671, CR46050, CR45405, Ir68a, CR44718, CR44719, CR44714, CR44713, CR44715, CR44717, CR44716, scyl, CR44720, CR45404, CG6175, CG7573, CR44361, CR46240, CG6168, CR44721, CR44722, CR44723, CR45250, CR45251	NA	snp_su:131; snp_op:85; snp_ratio:1.54	13.81
B241R41-2	40	Control-Freec	DUP	3L	12076119	3L	12120426	-	-	somatic_tumour	-	44.3	3L:12076119-12120426	Heterozygous duplication	0.34	0.46	-	-	-	-	-	Sema-5c, intron	CG11560, exon_1	Sema-5c, CG17154, l(3)j2D3, ssp, CG11560	NA	snp_su:55; snp_op:43; snp_ratio:1.28	10.92
B241R41-2	43	Control-Freec	DUP	3L	14926536	3L	14960997	-	-	somatic_tumour	-	34.5	3L:14926536-14960997	Heterozygous duplication	0.29	0.46	-	-	-	-	-	DCX-EMAP, 5UTR	intergenic	DCX-EMAP, CG13465, BobA, CR45978	NA	snp_su:0; snp_op:0	0
B241R41-2	44	Control-Freec	DUP	3L	15989904	3L	16004673	-	-	somatic_tumour	-	14.8	3L:15989904-16004673	Heterozygous duplication	0.41	0.73	-	-	-	-	-	Hip14, exon_2	CG5830, exon_1	Hip14, CG5830	NA	snp_su:0; snp_op:0	0
B241R41-2	52	Control-Freec	DUP	3L	23325174	3L	23344866	-	-	somatic_tumour	-	19.7	3L:23325174-23344866	53:52_53	0.39	0.71	-	-	-	-	-	alpha-Cat, intron	ND-MLRQ, intron	alpha-Cat, mir-4942, ND-MLRQ	NA	snp_su:0; snp_op:0	0
B241R41-2	60	Control-Freec	DUP	3R	16275438	3R	16304976	-	-	somatic_tumour	-	29.5	3R:16275438-16304976	Heterozygous duplication	0.39	0.66	-	-	-	-	-	gish, intron	intergenic	gish	NA	snp_su:0; snp_op:0	0
B241R41-2	63	delly	TRA	3R	21272469	2L	1154922	3	0	somatic_tumour	BND00001934	20117.5	3R:21272469 2L:1154922	3to3	0.17	0	-	-	CCTCTGATGATCACAGGCGGAAGATTCTCGAATCTGCGCGGGGAACAATTTAAAGTTTTGTAAACCCTAGCGGCGACGCGGAGGAGGCG	-	-	CG3308, intron	capt, exon_2	CG3308, capt	NA	-	0
B241R41-2	63	novobreak	TRA	3R	21272469	2L	1154922	3	0	somatic_tumour	37	20117.5	3R:21272469 2L:1154922	3to3	0.17	0	-	-	TAGAACCTCCGGTCTAGGTACTTAAGCGCCTCCTCGGCGGTGCCCATAAAACCTCTGATGATCACAGGCGGAAGATTCTCGAATCTGCGCGGGGAACAATTTAAAGTTTTGTAAACCCTAGCGGCGACGCGGAGGAGGCGGACGAAGTGGGG	-	-	CG3308, intron	capt, exon_2	CG3308, capt	NA	-	0
B241R41-2	65	Control-Freec	DUP	4	127998	4	231381	-	-	somatic_tumour	-	103.4	4:127998-231381	Heterozygous duplication	0.31	0.12	-	-	-	-	-	Ank, intron	CG1674, intron	Ank, CG1674	TRUE	low FC; snp_su:24; snp_op:10; snp_ratio:2.4	16.46
B241R41-2	66	Control-Freec	DUP	4	231381	4	246150	-	-	somatic_tumour	-	14.8	4:231381-246150	Heterozygous duplication	0.48	0.58	-	-	-	-	-	CG1674, intron	intergenic	CG1674	NA	snp_su:3; snp_op:0; snp_ratio:301.0	29.43
B241R41-2	75	Control-Freec	DUP	4	1033830	4	1058445	-	-	somatic_tumour	-	24.6	4:1033830-1058445	Heterozygous duplication	0.44	0.55	-	-	-	-	-	ATPsynbeta, exon	Zyx, exon_5	ATPsynbeta, CaMKII, Zyx	NA	snp_su:1; snp_op:1	10
B241R41-2	77	Control-Freec	DUP	4	1092906	4	1156905	-	-	somatic_tumour	-	64	4:1092906-1156905	Heterozygous duplication	0.44	0.45	-	-	-	-	-	sv, intron	Kif3C, intron	sv, Cals, Arf102F, CG11155, CG32017, Kif3C	NA	snp_su:0; snp_op:3; snp_ratio:0.0	0
B241R43	9	lumpy	BND	2R	7381817	2R	7382003	1	3	somatic_tumour	2197_1	0.2	2R:7381817-7382003	3to3	0.11	0	-	-	-	-	-	Dscam1, exon_1	intergenic	Dscam1	NA	-	0
B241R43	22	lumpy	BND	3L	5322843	3L	5323023	2	1	somatic_tumour	4049	0.2	3L:5322843-5323023	5to5	0.09	0	-	-	-	-	-	intergenic	intergenic	-	NA	-	0
B241R43	54	Control-Freec	DUP	4	131794	4	138918	-	-	somatic_tumour	-	7.1	4:131794-138918	Heterozygous duplication	0.35	0.45	-	-	-	-	-	intergenic	CG32000, intron	CR43956, CG32000	NA	snp_su:1; snp_op:1	5.59
B241R43	56	Control-Freec	DUP	4	443469	4	454155	-	-	somatic_tumour	-	10.7	4:443469-454155	Heterozygous duplication	0.24	0.26	-	-	-	-	-	lgs, 5UTR	intergenic	lgs	TRUE	low FC; snp_su:4; snp_op:2; snp_ratio:2.0	13.83
B241R43	57	novobreak	BND	X	1219691	X	1219821	4	0	somatic_tumour	41	0.1	X:1219691-1219821	5to5	0.21	0	-	-	GTATCTACTGGCAGCGGAGGAGTTACTGGCGGAGGAGCCGCCATCAGCAACCAGAGCGATCTGTACTCGGTGACGGAGTTGTAGGAGTGCGCCTGCTGTTGCTGCTGCTGCTGTTCCAGCATTAGCTGTTGCTGCTGCTTCGATGAGAAGTTGTTGTTGTGCTGCCTTTGATAAAAGGCCTGCTGCTGCTGCTGCTGATGGTAGCTGCTGTCATAGG	-	-	CG3638, 3UTR	CG3638, exon	CG3638	NA	-	0
B241R43	58	lumpy	BND	X	16439367	X	16439415	4	0	somatic_tumour	8156_1	0	X:16439367-16439415	5to5	0.15	0	-	-	-	-	-	CG9947, intron	CG9947, intron	CG9947	NA	-	0
B241R45	2	lumpy	DEL	3R	28657288	3R	31057415	11	15	somatic_tumour	4555	2400.1	3R:28657288-31057415	5to3	0.21	0.01	-	AGGTTGCCCTTTTTTTTT	-	GATCACGTTCTGCAGCGCAGAAAGTTTCGACTTCCTATAAACACTTGAGATGCAGGTTGCCCTTTTTTTTTTACACCAGGTTGCCCTTTTTGCCAAGACCC	FoSTeS	intergenic	dco, exon	dco	NA	mh:0; ins:18; tup:3; tdown:14	0
B241R45	2	novobreak	DEL	3R	28657288	3R	31057415	11	15	somatic_tumour	1	2400.1	3R:28657288-31057415	5to3	0.21	0.01	-	AGGTTGCCCTTTTTTTTT	AATCTCGGCAAAATACTGCAGACTGTTTAAAAATTACAAACTCCGATCACGTTCTGCAGCGCAGAAAGTTTCGACTTCCTATAAACACTTGAGATGCAGGTTGCCCTTTTTTTTTTACACCAGGTTGCCCTTTTTGCCAAGACCCATGAGGAAGTTATCCGGCTTGATGTCGCGATGGATGAAGTCCCGCGAGTGTATGTAATCG	GATCACGTTCTGCAGCGCAGAAAGTTTCGACTTCCTATAAACACTTGAGATGCAGGTTGCCCTTTTTTTTTTACACCAGGTTGCCCTTTTTGCCAAGACCC	FoSTeS	intergenic	dco, exon	dco	NA	mh:0; ins:18; tup:3; tdown:14	0
B241R45	6	Control-Freec	DEL	X	2982420	X	3191076	-	-	somatic_tumour	-	208.7	X:2982420-3191076	6:6_7	0.85	-1.65	-	-	-	-	-	kirre, intron	dnc, intron	kirre, CG4116, N, CG18508, Fcp3C, CG3939, dnc	NA	snp_su:0; snp_op:0	0
B241R45	6	novobreak	DEL	X	2982553	X	3192604	3	2	somatic_tumour	3	210.1	X:2982553-3192604	7:6_7	0.24	-1.64	-	-	TTTCCAACTTGCCTGTTGAGTAATTCTACGAAAGATCGTCTCCGTCTGGGAATTGGGTTTCCCTGCTAAATTTTTTTGCTTTCCCTAACAAAAAAAAAAAATAAACAAACCCGTGAGTAGTTGGCTTCAAAAGGTATGCACCTTTTTACGGGAACTTACGCTAAATAT	-	NHEJ	kirre, intron	dnc, intron	kirre, CG4116, N, CG18508, Fcp3C, CG3939, dnc	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:0; snp_op:0	0
B241R49	4	Control-Freec	DUP	2R	9886142	2R	9907779	-	-	somatic_tumour	-	21.6	2R:9886142-9907779	Heterozygous duplication	0.28	0.3	-	-	-	-	-	CG1513, intron	FMRFa, intron	CG1513, FMRFa	TRUE	low FC; snp_su:21; snp_op:10; snp_ratio:2.1	13.83
B241R49	5	novobreak	BND	2R	15960557	2R	17016068	3	0	somatic_tumour	2	1055.5	2R:15960557-17016068	3to3	0.03	-0.01	-	-	CTATAAAGCAACTTTAAAGCACTCATGTATTTGTTTTAAAAACATCACAAACAGCAGCAATAGATCAACACAACGGTCGCGAGAGGAACAGCGGAGGACGCTCATCCTTCTCAGCTCCGACGGCCACATCGACGTTGACATTGGATTCGATGCGAC	-	NHEJ	Strn-Mlck, exon_5	intergenic	Strn-Mlck	NA	mh:0; ins:0; tup:0; tdown:0	0
B241R49	12	Control-Freec	DEL	3R	5137804	3R	5157474	-	-	somatic_tumour	-	19.7	3R:5137804-5157474	Heterozygous deletion	0.27	-0.41	-	-	-	-	-	CG12589, exon_1	dpr16, intron	CG12589, dpr16	NA	snp_su:11; snp_op:8; snp_ratio:1.37	12.58
B241R49	14	novobreak	TRA	Tomelloso	57648	3R	29824046	3	0	somatic_tumour	30	29766.4	Tomelloso:57648 3R:29824046	-	0.12	0	-	-	GTGTACGCCAAGGGATCGCCCAAGTCCTGCTCGGTGGACGTGAAGAGCGCGCTGGACTTCGGGCTGCAAGGAATTGATTGTGCGATGCCATCATTTTGACGAAGACACCCCATACATTGAGAATAATAT	-	-	intergenic	neo, exon_6	neo	NA	bp2_Tomelloso_2	0
B241R51	1	novobreak	BND	2L	16655322	2L	16655452	5	0	somatic_tumour	1	0.1	2L:16655322-16655452	5to5	0.05	0	TGCCCGCTGC	-	TGTCCAAGCTGGAATCCGAATTTCAGTGCAAGGCGGATGAAGTGGTTGCCCGCTGCTGGCAGCATTGTTGCTCAAAGACTCCGAATTGAACTCCACTTGAGCTGAACCTGGCTATCACAATTTTACATAACCCGCCAATCCC	TGTCCAAGCTGGAATCCGAATTTCAGTGCAAGGCGGATGAAGTGGTTGCCCGCTGCTGGCAGCATTGTTGCTCAAAGACTCCGAATTGAACTCCACTTGAGCTGAACCTGGCTAT	Alt-EJ	CG42389, intron	CG42389, intron	CG42389	NA	mh:10; ins:0; tup:0; tdown:0	0
B241R51	3	delly	DEL	3L	20444578	3L	20445608	17	21	somatic_tumour	DEL00000004	1	3L:20444578-20445608	5to3	0.46	-0.56	A	CT	AGCTTATTCAACACTTCTTCTGGCTACAATAAAATACCTATACGAGATTAGGTGAAATCTACCTAATGTTGTTCAAAATTTAATTAATGTTAGTCCAAAAAGGCACAATCCATCTTCCAAGTGATAACCAATTA	GGCTACAATAAAATACCTATACGAGATTAGGTGAAATCTACCTAATGTTGTTCAAAATTTAATTAATGTTAGTCCAAAAAGGCACAATCCATCTTCCAAGTGATAACCAATTACT	Alt-EJ	CG5910, intron	CG5910, intron	CG5910	NA	mh:1; ins:2; tup:0; tdown:0; snp_su:7; snp_op:0; snp_ratio:701.0	30.54
B241R51	3	lumpy	DEL	3L	20444578	3L	20445608	17	21	somatic_tumour	3184	1	3L:20444578-20445608	5to3	0.46	-0.56	A	CT	-	GGCTACAATAAAATACCTATACGAGATTAGGTGAAATCTACCTAATGTTGTTCAAAATTTAATTAATGTTAGTCCAAAAAGGCACAATCCATCTTCCAAGTGATAACCAATTACT	Alt-EJ	CG5910, intron	CG5910, intron	CG5910	NA	mh:1; ins:2; tup:0; tdown:0; snp_su:7; snp_op:0; snp_ratio:701.0	30.54
B241R51	6	Control-Freec	DUP	3R	29556129	3R	29558982	-	-	somatic_tumour	-	2.9	3R:29556129-29558982	Heterozygous duplication	0.31	0.49	-	-	-	-	-	intergenic	Dr, intron	Dr	NA	snp_su:0; snp_op:3; snp_ratio:0.0	0
B241R51	7	Control-Freec	DEL	X	3139251	X	3200115	-	-	somatic_tumour	-	60.9	X:3139251-3200115	Homozygous deletion	0.9	-2.07	-	-	-	-	-	N, intron	dnc, intron	N, CG18508, Fcp3C, CG3939, dnc	NA	snp_su:0; snp_op:0	0
B241R51	7	CNV-Seq	DEL	X	3139518	X	3200151	-	-	somatic_tumour	-	60	X:3139518-3200151	Homozygous deletion	0.9	-2.08	-	-	-	-	-	N, intron	dnc, intron	N, CG18508, Fcp3C, CG3939, dnc	NA	snp_su:0; snp_op:0	0
B241R53	1	novobreak	BND	2L	2692449	2L	15146570	3	0	somatic_tumour	1	12454.1	2L:2692449-15146570	5to5	0.03	-0.01	-	-	GCCCATCATCCTGTGGGTGTCCACACCAAGGACATGGCCAAGCTGCAGGATAAAGGAGGAGCACGCACAATATCTGATTGTTGCTATCAAAATTTGAGTTGGGTTTGACGCTTCGGTGGCCCAGCTGCTGATGTTTTTGGGGCTGCAT	CAACTCAAATTTTGATAGCAACAATCAGATATTGTGCGTGCTCCTCCTTTATCCTGCAGCTTGGCCATGTCCTTGGTGTGGACACCCACAGGATGATGGGC	NHEJ	CG31690, intron	intergenic	CG31690	NA	mh:0; ins:0; tup:0; tdown:0	0
B241R53	13	Control-Freec	DUP	3R	12903870	3R	12908385	-	-	somatic_tumour	-	4.5	3R:12903870-12908385	Heterozygous duplication	0.46	0.41	-	-	-	-	-	intergenic	intergenic	-	NA	snp_su:0; snp_op:0	0
B241R53	16	lumpy	DEL	X	3161667	X	3165215	12	28	somatic_tumour	3722	3.5	X:3161667-3165215	5to3	0.92	-2.6	-	-	-	-	NHEJ	N, intron	N, exon_6	N	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:0; snp_op:0	0
B241R55	9	Control-Freec	DEL	3L	0	3L	286520	-	-	somatic_tumour	-	286.5	3L:0-286520	Heterozygous deletion	0.24	-0.43	-	-	-	-	-	intergenic	RhoGEF3, intron	mthl8, CG43149, Lsp1gamma, CR44510, CR44511, CR43150, CR43988, CG13405, CG12483, CR45401, CR45402, CR45400, Pdk1, CR45805, CG6845, Dic61B, p130CAS, CR43151, CG7049, CR45806, Vdup1, CG13875, CG34140, Mkp, Mtch, rno, mri, Gk1, NitFhit, CG13876, CG7028, thoc7, CG16940, Kaz1-ORFB, Kaz1-ORFA, pyx, CG13877, CG33229, CR42862, CG42846, CG34454, CG34453, E(bx), mthl14, DIP2, wac, Tudor-SN, snoRNA:Tudor-SN-a, snoRNA:Psi18S-996, mRpL17, CG34263, miple1, miple2, CG32845, ttm2, RhoGEF3	NA	snp_su:118; snp_op:24; snp_ratio:4.92	21.23
B241R55	10	novobreak	BND	3L	284238	3L	286090	5	1	somatic_tumour	6	1.9	3L:284238-286090	5to5	0.06	-0.15	-	-	TCATAATGATCAGACTCATAATTATCGAATGGTAGGCTGCATGCAATTTATAGTAAATTAATGCAATTGCGAGTTTCCAGCCAACTTTTTATTTTATAAAAAACATTGACAGCTTTTCGAAATATCTGCCCCAACGAGAACACCGAAGACGCCCAAGTTTTACCAAAATTTGAGTTGCGATTGAGTTAGTGCT	-	-	RhoGEF3, intron	RhoGEF3, intron	RhoGEF3	NA	-	0
B241R55	11	Control-Freec	DEL	3L	326040	3L	532285	-	-	somatic_tumour	-	206.2	3L:326040-532285	Heterozygous deletion	0.24	-0.46	-	-	-	-	-	Atac3, exon_6	klar, intron	Atac3, Ptpmeg, mthl9, mthl10, mth, CG1231, Cdc5, Roc1b, CG1233, CG13884, trh, CR45378, CR43969, CG13891, snmRNA:438, CG34267, CG34268, CR46002, CR45118, CR45117, CG34269, klar	NA	snp_su:783; snp_op:114; snp_ratio:6.87	22.49
B241R55	11	delly	DEL	3L	326321	3L	532735	11	18	somatic_tumour	DEL00000004	206.4	3L:326321-532735	5to3	0.32	-0.46	TTT	-	GTGTTCAGCATTTCTTTCGAGTCCTCGTCATCGTTGTCCTGCACCATGTCTGCGATTTCGTGCGTCTTTCAGTTGGGTTGGGCCTTGCAACCGGACTCATGGGGAGAGTTATGCCCGCCTTGGGTTACTTGGGAAA	GTCCTGCACCATGTCTGCGATTTCGTGCGTCTTTCAGTTGGGTTGGGCCTTGCAACCGGACTCATGGGGAGAGTTATGCCCGCCTTGGGTTACTTGGGAAAATTA	Alt-EJ	Atac3, exon_6	klar, intron	Atac3, Ptpmeg, mthl9, mthl10, mth, CG1231, Cdc5, Roc1b, CG1233, CG13884, trh, CR45378, CR43969, CG13891, snmRNA:438, CG34267, CG34268, CR46002, CR45118, CR45117, CG34269, klar	NA	mh:3; ins:0; tup:0; tdown:0; snp_su:782; snp_op:114; snp_ratio:6.86	22.49
B241R55	11	lumpy	DEL	3L	326321	3L	532735	11	18	somatic_tumour	1834	206.4	3L:326321-532735	5to3	0.32	-0.46	TTT	-	-	GTCCTGCACCATGTCTGCGATTTCGTGCGTCTTTCAGTTGGGTTGGGCCTTGCAACCGGACTCATGGGGAGAGTTATGCCCGCCTTGGGTTACTTGGGAAAATTA	Alt-EJ	Atac3, exon_6	klar, intron	Atac3, Ptpmeg, mthl9, mthl10, mth, CG1231, Cdc5, Roc1b, CG1233, CG13884, trh, CR45378, CR43969, CG13891, snmRNA:438, CG34267, CG34268, CR46002, CR45118, CR45117, CG34269, klar	NA	mh:3; ins:0; tup:0; tdown:0; snp_su:782; snp_op:114; snp_ratio:6.86	22.49
B241R55	11	novobreak	DEL	3L	326321	3L	532735	11	18	somatic_tumour	7	206.4	3L:326321-532735	5to3	0.32	-0.46	TTT	-	ATTCTGCAACGCAGTGTTCAGCATTTCTTTCGAGTCCTCGTCATCGTTGTCCTGCACCATGTCTGCGATTTCGTGCGTCTTTCAGTTGGGTTGGGCCTTGCAACCGGACTCATGGGGAGAGTTATGCCCGCCTTGGGTTACTTGGGAAAATTATGAGCAAACATTTTGATAAAGTCCA	GTCCTGCACCATGTCTGCGATTTCGTGCGTCTTTCAGTTGGGTTGGGCCTTGCAACCGGACTCATGGGGAGAGTTATGCCCGCCTTGGGTTACTTGGGAAAATTA	Alt-EJ	Atac3, exon_6	klar, intron	Atac3, Ptpmeg, mthl9, mthl10, mth, CG1231, Cdc5, Roc1b, CG1233, CG13884, trh, CR45378, CR43969, CG13891, snmRNA:438, CG34267, CG34268, CR46002, CR45118, CR45117, CG34269, klar	NA	mh:3; ins:0; tup:0; tdown:0; snp_su:782; snp_op:114; snp_ratio:6.86	22.49
B241R55	21	CNV-Seq	DEL	X	3134274	X	3140118	-	-	somatic_tumour	-	5.8	X:3134274-3140118	Homozygous deletion	0.86	-1.85	-	-	-	-	-	kirre, 3UTR	N, intron	kirre, N	NA	snp_su:0; snp_op:0	0
B241R55	21	Control-Freec	DEL	X	3134430	X	3140605	-	-	somatic_tumour	-	6.2	X:3134430-3140605	Homozygous deletion	0.85	-1.75	-	-	-	-	-	kirre, 3UTR	N, intron	kirre, N	NA	snp_su:0; snp_op:0	0
B241R57	75	lumpy	BND	X	3084863	X	3143771	5	3	somatic_tumour	4793_1	58.9	X:3084863-3143771	75:75_76	0.2	0.41	-	-	-	-	-	kirre, intron	N, intron	kirre, N	NA	snp_su:1; snp_op:0	14.12
B241R57	75	novobreak	BND	X	3084863	X	3143771	5	3	somatic_tumour	66	58.9	X:3084863-3143771	75:75_76	0.2	0.41	-	-	AAGGTAAACTCTTCTTTAGTTGCAAGTTGTATACTTTTTTGTGTTATATTTAAGTGCAAGCTATCGAGAGGAGGAGTTCATTGACCCATAATCCTAGTTTTTTTTTTTTGTTGCTAAATTGAAAAGCATAGAGAAGGCAACGTAATGACCGCTGATGATGAGGTGTTTATGACCGCGGCCAGGTATCTCGAATATTTTGCATTAGTCACGCTTATTGTCTTCAGCCGAAACGGGGGCGTTTCTTGGCATTCGGTTATGGGTTATATGTGTATATAACTATAGGGCTTTATAGGTCGCGGATCGGCATTGCCCCTTTGTCTTTGCGCCGCATTTCCCGCCGTTTCGAACTCGGCGGCAGTCATTAGACACACAGCGAAACCGCTACAAAATCGAACCGCAAGATGAAACTGAAAACGTGAG	-	-	kirre, intron	N, intron	kirre, N	NA	snp_su:1; snp_op:0	14.12
B241R57	75	delly	BND	X	3084863	X	3143771	5	3	somatic_tumour	INV00000025	58.9	X:3084863-3143771	75:75_76	0.2	0.41	-	-	TCGAGATACCTGGCCGCGGTCATAAACACCTCATCATCAGCGGTCATTACGTTGCCTTCTCTATGCTTTTCAATTTAGCAACAAAAAAAAAAAACTAGGATTATGGG	-	-	kirre, intron	N, intron	kirre, N	NA	snp_su:1; snp_op:0	14.12
B241R57	75	novobreak	BND	X	3138400	X	3196544	4	3	somatic_tumour	67	58.1	X:3138400-3196544	76:75_76	0.2	0.14	-	-	TTTTTATTTCCATTAAATTTGGTTGCAACTTTATGTGGATGATCCATTCCGACCATAAAGTGCACACTTTACGATCCATATTATGTACATATTTATACTCGGTACTGTAAGCATACCTTTTTGTGAGCTTCAACTTATTAAACTTTTTAATTTCCATTTAAAC	-	-	N, intron	dnc, intron	N, dnc	NA	-	0
B241R57	23	novobreak	TRA	2R	5344709	3L	4352897	7	1	somatic_tumour	12	991.8	2R:5344709 3L:4352897	3to3	0.11	0	-	-	GGAGATCAGGGTCCGCAGAATCGATTTTAATGCAACTTCCTGCGGTTCAATGACTTCGCCCCTGCAACATGTTGCGGCAACACTTTCAGTGCACGAAGTAAAAATAAAGGATGATCAATCAGTCAAACAGCGGTATTACATGAAGAACCCGAAGTACAGGTAG	-	-	intergenic	Cip4, intron	Cip4	NA	bp1_INE-1_Helitron=4; bp2_gypsy8_Gypsy=2	0
B241R57	33	novobreak	TRA	3L	1862077	3R	9427693	3	0	somatic_tumour	20	7565.6	3L:1862077 3R:9427693	5to3	0.07	0	-	-	AATGCACCCGCATGTCGGGCGGCAGGGCAACTCTGGGCGGAGTTTTACCTATGCTTTTCACTCGCCGATAGATACAAAACTGCTGTCAGCGGATTTGTGTTGAGCCTATGAAAAGACGATAAA	-	-	Rap1, exon_1	ps, intron	Rap1, ps	NA	-	0
B241R57	40	novobreak	TRA	3L	12126856	2L	10898536	3	0	somatic_tumour	31	1228.3	3L:12126856 2L:10898536	5to3	0.05	0	-	-	GAGAAACGCAATGGGTAGCCGCGCAAGTCTTTCATCTTTCTTGGGTACGATGTCGCTGGGAATGAGACGATAATGGTCCCACAAGAATTGCGCCTCGTACG	-	-	Ir68b, exon	intergenic	Ir68b	NA	bp1_Stalker_Gypsy=2	0
B241R57	42	novobreak	BND	3L	15052420	3L	22264473	3	0	somatic_tumour	33	7212.1	3L:15052420-22264473	5to5	0.03	0.07	-	-	ATTCCTAATTGTCGTTGCTCTTGTGGCCTTTTTGGCTGTTGGTCTTGTGGCAGAGAATTGGCCGAGCAAACCTACAACCAGATCGAGAAGTTTAAATACCACCTGAGCAACCCAGAGGTTCGCTCCCTGCTGCTTATCGGTGGAGTGA	-	-	CG13461, exon	Ddx1, exon_3	Sytbeta, CG13461, Ddx1	NA	-	0
B241R57	58	novobreak	TANDUP	3R	14619449	3R	14625583	2	1	somatic_tumour	44	6.1	3R:14619449-14625583	3to5	0.03	0.22	-	-	ATTTTAAGCTAGAGGGGCACAGTTGAAAAAGTATATGCGCGCTGCACTTTTTCGTTTCTTATTATCTTCATTATCATTATGTTCGTCGTAATGATGTTTCAGCACCAATGGAAAATATAC	-	-	put, 3UTR	put, 5UTR	put	NA	-	0
B241R59	47	Control-Freec	DUP	3L	13503368	3L	13510140	-	-	somatic_tumour	-	6.8	3L:13503368-13510140	48:47_48	0.47	0.83	-	-	-	-	-	Spt20, exon_1	Spt20, 3UTR	Spt20	NA	snp_su:6; snp_op:2; snp_ratio:2.99	11.05
B241R59	56	Control-Freec	DEL	3L	22953694	3L	23348163	-	-	somatic_tumour	-	394.5	3L:22953694-23348163	Heterozygous deletion	0.19	-0.4	-	-	-	-	-	intergenic	intergenic	CG32461, CR45758, CG32457, nrm, RpL10, CkIIalpha, CG33217, CR41454, Vps11, CR45164, CG34031, CR43967, CR45735, nAChRalpha4, alpha-Cat, mir-4942, ND-MLRQ	NA	snp_su:6; snp_op:8; snp_ratio:0.75	6.43
B241R59	67	novobreak	TRA	3R	17628149	X	18565674	4	0	somatic_tumour	11	937.5	3R:17628149 X:18565674	3to5	0.09	0	-	-	AAATATGGGATATTATCGTAATTTGTCAAAAAAAAAAAGGTTCCAAGTTCCTTAAAATCGCTGGTTGAGATTCTAACCAAGACGGTGGGTTGCAATTACCAAATGGGCTGCAACCAACTGACTGTCAGGGATATTCTACACTTGACC	-	NHEJ	CG14325, exon_3	Bx, intron	CG14325, Bx	NA	mh:0; ins:0; tup:0; tdown:0	0
B241R59	68	Control-Freec	DUP	3R	17690157	3R	17718938	-	-	somatic_tumour	-	28.8	3R:17690157-17718938	Heterozygous duplication	0.32	0.4	-	-	-	-	-	osa, exon	intergenic	osa, CR46036, CR46035	NA	snp_su:50; snp_op:31; snp_ratio:1.61	12.54
B241R59	75	Control-Freec	DEL	3R	31933366	3R	32079331	-	-	somatic_tumour	-	146	3R:31933366-32079331	Heterozygous deletion	0.28	-0.54	-	-	-	-	-	heph, intron	intergenic	heph, CG2003, CR45556, CR45557, CG2053, krz, mod, Map205	NA	snp_su:105; snp_op:93; snp_ratio:1.13	10.46
B241R59	82	delly	DEL	X	3067156	X	3159711	9	16	somatic_tumour	DEL00000018	92.6	X:3067156-3159711	82:82_83	0.98	-2.7	-	-	GCTCCATTGGAAGTCGTGGTGACCAGGCCAGTTCCGGTTCCCGAAGTCGTTCCTGTTGTTCCCGTCGATGAAGTAGCTGCCACAAGGGGCAAACTCGTTTGTCAGCTAAGAAAAACCCCTTTGCCGACTCGACCGGCCCAGCATCATTCATC	-	-	CG4116, exon	N, intron	kirre, CG4116, N	NA	snp_su:0; snp_op:0	0
B241R59	82	lumpy	DEL	X	3067156	X	3159711	9	16	somatic_tumour	17624	92.6	X:3067156-3159711	82:82_83	0.98	-2.7	-	-	-	-	-	CG4116, exon	N, intron	kirre, CG4116, N	NA	snp_su:0; snp_op:0	0
B241R59	82	novobreak	DEL	X	3067156	X	3159711	9	16	somatic_tumour	55	92.6	X:3067156-3159711	82:82_83	0.98	-2.7	-	-	GGTTCACATAGATAGCTCCATTGGAAGTCGTGGTGACCAGGCCAGTTCCGGTTCCCGAAGTCGTTCCTGTTGTTCCCGTCGATGAAGTAGCTGCCACAAGGGGCAAACTCGTTTGTCAGCTAAGAAAAACCCCTTTGCCGACTCGACCGGCCCAGCATCATTCATCAGTTTTTGAC	-	-	CG4116, exon	N, intron	kirre, CG4116, N	NA	snp_su:0; snp_op:0	0
B241R59	82	Control-Freec	DEL	X	3067716	X	3160831	-	-	somatic_tumour	-	93.1	X:3067716-3160831	83:82_83	0.94	-2.67	-	-	-	-	-	kirre, intron	N, intron	kirre, N	NA	snp_su:0; snp_op:0	0
B241R59	84	Control-Freec	DEL	X	9170981	X	9191297	-	-	somatic_tumour	-	20.3	X:9170981-9191297	Homozygous deletion	0.66	-0.72	-	-	-	-	-	mei-P26, 3UTR	intergenic	mei-P26, CG12115	NA	snp_su:0; snp_op:0	0
B241R59	86	lumpy	DEL	X	19890758	X	19892413	7	0	somatic_tumour	18281	1.7	X:19890758-19892413	5to3	0.52	-2.64	-	-	-	-	-	Hers, intron	Hers, 5UTR	Hers	NA	bp1_roo_BEL=8; snp_su:0; snp_op:0	0
B241R59	86	novobreak	DEL	X	19890758	X	19892413	7	0	somatic_tumour	57	1.7	X:19890758-19892413	5to3	0.52	-2.64	-	-	ATATGATCTATACACTTATGTATATTACTTAATAATTAAAAGGAGAGGACGGCACTACGTTTAACTCGATGGCCAGCACAGGCGGCACAATGAATAATGAACTCACTCGAACCGAACTCCAAAACCGGAAGGCACCGAAACAATTTTGCCATGTGCCTATTATATGGTATTATTTTCATTGTGCTTTGCTTTTTTATGTATTTGTGCCGAAATCTGGACAGAAAGCTAGAAAATAAATAGGAG	-	-	Hers, intron	Hers, 5UTR	Hers	NA	bp1_roo_BEL=8; snp_su:0; snp_op:0	0
B241R61	9	novobreak	TRA	2L	7888676	2R	7170648	3	0	somatic_tumour	11	718	2L:7888676 2R:7170648	3to3	0.04	0	GCCAGC	-	CAGCCTAGAAAGTACAGTTGCCTCCGGCAAACTCTTTCGTCTTTCGAATGCTTAATTGCTGGCCGATCGAATGAAGGCAGCCTGGGCTATAAACGATTGGGTGCTCGATCAGACACTAGA	TCTAGTGTCTGATCGAGCACCCAATCGTTTATAGCCCAGGCTGCCTTCATTCGATCGGCCAGCAATTAAGCATTCGAAAGACGAAAGAGTTTGCCGGAGGC	Alt-EJ	Spn28Da, exon_2	pk, intron	Spn28Da, pk	NA	mh:6; ins:0; tup:0; tdown:0	0
B241R61	22	novobreak	TRA	2L	20336099	3L	2623731	3	0	somatic_tumour	25	17712.4	2L:20336099 3L:2623731	5to3	0.06	0	-	-	GGTTTTGGGTTATTCCCAGAATTTGTTATGAATAAATGTAGGTGAGATGGAACCGCAGAAAATAAATTAAACAAACCAGACTGAACGGCAAGGGCAAAAAACCGTAACAACAATATATATTATATTT	TATGAATAAATGTAGGTGAGATGGAACCGCAGAAAATAAATTAAACAAACCAGACTGAACGGCAAGGGCAAAAAACCGTAACAACAATATATATTATATTT	NHEJ	spir, intron	Pxn, intron	spir, Pxn	NA	mh:0; ins:0; tup:0; tdown:0	0
B241R61	28	delly	DEL	2R	8149322	2R	8149353	11	2	somatic_tumour	DEL00000002	0	2R:8149322-8149353	5to3	0.22	0	-	-	TACATGTGTAAGCACTTCCGCCGGAGAAAAGCCGCGGTTCATGAACCTTTTGAATCTCCGCTAATTATACGTACATGAGGGGAATGACGTTGCATTTACACACTTAAATTTTGATCGATTTAGAGAAGTCTCTTGAATAAAAAGGCCCAGAGAAATTTAAGGCACAGACTTGCT	-	NHEJ	kermit, exon_1	kermit, exon_1	Lpin, kermit	NA	mh:0; ins:0; tup:0; tdown:0	0
B241R61	34	novobreak	TRA	2R	16168568	3L	20283281	3	0	somatic_tumour	38	4114.7	2R:16168568 3L:20283281	3to3	0.04	0	GCCA	-	GACTTGGAGGCCCAGCAGGATCATTTGTCCAGCAAGGACTCGGGCACCGGTTCGGATGCGGCTGTGAAACGCACTCTGGATGACTTTGAGGTGGCCACCCAGTCCCAGTATTCCCTGCTCCGTACTCCGCGGAGTTTACGGCGAAGTCACCCCAAAATGTTGTTGGCCGAGTCCGAAC	GACTCGGGCACCGGTTCGGATGCGGCTGTGAAACGCACTCTGGATGACTTTGAGGTGGCCACCCAGTCCCAGTATTCCCTGCTCCGTACTCCGCGGAGTTT	Alt-EJ	lbk, exon	gogo, intron	lbk, gogo	NA	mh:4; ins:0; tup:0; tdown:0	0
B241R61	40	novobreak	TRA	2R	23886797	3R	31013782	3	0	somatic_tumour	50	7127	2R:23886797 3R:31013782	3to3	0.04	0	GGCAC	-	GGTGGTGGTGCCTGGCCAGCTGCGGAGCGATCTCCCCTCATGTCCATGCAAAGATCGTGCTTGTGCTCCGAGAGTCGCGCACAAGTCAAGTGGCACAATAATTGAGGAGCCGCCCGAGTTAGCAAATAGTCCAGCCTTACCATGCAGAAGAAAAC	TGCAAAGATCGTGCTTGTGCTCCGAGAGTCGCGCACAAGTCAAGTGGCACAATAATTGAGGAGCCGCCCGAGTTAGCAAATAGTCCAGCCTTACCATGCAGAAGAAAAC	Alt-EJ	intergenic	5-HT7, intron	5-HT7	NA	mh:5; ins:0; tup:0; tdown:0	0
B241R61	58	Control-Freec	DEL	3L	26370954	3L	26377602	-	-	somatic_tumour	-	6.6	3L:26370954-26377602	Heterozygous deletion	0.25	-0.54	-	-	-	-	-	CG42598, intron	intergenic	CG42598	NA	snp_su:0; snp_op:0	0
B241R61	84	CNV-Seq	COMPLEX_DEL	X	3170682	X	3194381	-	-	somatic_tumour	-	23	X:3170682-3194381	84:84_85	0.96	-3.84	-	-	-	-	-	N, exon	dnc, intron	N, CG18508, Fcp3C, CG3939, dnc	NA	snp_su:0; snp_op:0	0
B241R61	84	lumpy	COMPLEX_BND	X	3195652	X	3199676	25	5	somatic_tumour	5971_1	4	X:3195652-3199676	85:84_85	0.24	1.64	-	TATGAAATCCTA	-	TTGGCTGGATGAAGATGCACATTTTGTGGCTTAGTTGAAGCTTAGTGCTGAGTTATGTTAGGATTTCATATAATAGGATTCATATACATAAACTTGATGATATGGTATAAGTGCTTTTGCCT	FoSTeS	dnc, intron	dnc, intron	dnc	NA	mh:0; ins:12; tup:7; tdown:5; snp_su:0; snp_op:0	0
B241R61	84	novobreak	COMPLEX_BND	X	3195652	X	3199676	25	5	somatic_tumour	111	4	X:3195652-3199676	85:84_85	0.24	1.64	-	TATGAAATCCTA	GTAAACATTTTAAATTGCAATAGGAAAATATTTTTAGCCCTCCTATTTAACCCCTTGAAGGCCCATTGCCTCCTTAACCCCTATGTGTTCCTCTTGTTGACACTTGGCTGGATGAAGATGCACATTTTGTGGCTTAGTTGAAGCTTAGTGCTGAGTTATGTTAGGATTTCATATAATAGGATTCATATACATAAACTTGATGATATGGTATAAGTGCTTTTGCCTCTTCAATGGTCCTTCAATGGTATCAGTAGCCCCGGGATTTTGCCGCCTGGATGATGGCCTTGTATTTTGGGACACAGATTTACCATGCCACATTTTCCGCCATCCTGTTTAGTCC	TTGGCTGGATGAAGATGCACATTTTGTGGCTTAGTTGAAGCTTAGTGCTGAGTTATGTTAGGATTTCATATAATAGGATTCATATACATAAACTTGATGATATGGTATAAGTGCTTTTGCCT	FoSTeS	dnc, intron	dnc, intron	dnc	NA	mh:0; ins:12; tup:7; tdown:5; snp_su:0; snp_op:0	0
B241R61	84	Control-Freec	COMPLEX_DUP	X	3196026	X	3199350	-	-	somatic_tumour	-	3.3	X:3196026-3199350	85:84_85	0.8	1.6	-	-	-	-	-	dnc, intron	dnc, intron	dnc	NA	snp_su:0; snp_op:0	0
B241R63	13	novobreak	TRA	3L	3775419	X	19780138	3	0	somatic_tumour	8	16004.7	3L:3775419 X:19780138	3to3	0.1	0	ACGA	-	CTGCTGCTGCTGGTTGTTGCTGTTGTTGTTGGAAGCGTGCTGTGGTGAAGCGTTTGTCGTCAACGTCGTCGTCATTATCATCCTGTGCAGACATCCGACCAGAC	GTCTGGTCGGATGTCTGCACAGGATGATAATGACGACGACGTTGACGACAAACGCTTCACCACAGCACGCTTCCAACAACAACAGCAACAACCAGCAGCAGCAG	Alt-EJ	CG32264, intron	zld, exon_2	CG32264, zld	NA	mh:4; ins:0; tup:0; tdown:0	0
B241R63	24	delly	DEL	X	3162637	X	3165495	2	8	somatic_tumour	DEL00000023	2.9	X:3162637-3165495	5to3	0.35	-1.24	-	-	CTGTTGTGCGAGTGAGAACGGTGGAACCTGTCTGGATGG	-	NHEJ	N, intron	N, exon_6	N	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:0; snp_op:0	0
B241R63	24	novobreak	DEL	X	3162637	X	3165495	2	8	somatic_tumour	33	2.9	X:3162637-3165495	5to3	0.35	-1.24	-	-	TATTACAACTGTTTGCTGTTCTGAAATCCAAGATAACAGCAAACTTTCTTTTATGCTGCCCTCTGTTGTGCGAGTGAGAACGGTGGAACCTGTCTGGATGGGATCGGTGACTATAGCTGCCTGTGCGTGGATGGCTTCGATGGCAAGCACTGCGAGACGGACATCAATGAGTGCTTGAGTCAGCCGTGCCAGAA	-	NHEJ	N, intron	N, exon_6	N	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:0; snp_op:0	0
D050R01	2	Control-Freec	DUP	2L	166616	2L	177206	-	-	somatic_tumour	-	10.6	2L:166616-177206	Heterozygous duplication	0.32	0.43	-	-	-	-	-	spen, intron	spen, intron	spen	NA	snp_su:16; snp_op:0; snp_ratio:1601.0	40.11
D050R01	3	novobreak	BND	2L	273195	2L	273319	3	1	somatic_tumour	5	0.1	2L:273195-273319	3to3	0.14	0	-	-	GCACAGTAGGTTCTTCTGGCGTAACAGCCACATCAGGTGGTGCAACAGATACAGGTGGTGGTGGCGTCAAGTCCGCAGCGAAAGTAACAGGTGGCAGGCTCTCCTGTCTGAGAGAGGAGGGAGCAGGCGAGGATCGAGGCAGAGATTCCAATAGGCGTGGTGGCCGTAACAACTCGTGGCAACCTAAGGATCAGCATGTTAGTCCTGGCCAAAGTAACATGCTGTACTTCGATAATGTGGGGGACTTTACCGAAGACCCACC	-	NHEJ	mbm, exon_1	mbm, exon_1	mbm	NA	mh:0; ins:0; tup:0; tdown:0	0
D050R01	4	Control-Freec	DUP	2L	2407460	2L	2410284	-	-	somatic_tumour	-	2.8	2L:2407460-2410284	Heterozygous duplication	0.46	0.85	-	-	-	-	-	VGlut, intron	VGlut, 3UTR	VGlut	NA	snp_su:5; snp_op:0; snp_ratio:501.0	38.28
D050R01	8	Control-Freec	DUP	2L	7890962	2L	7893786	-	-	somatic_tumour	-	2.8	2L:7890962-7893786	Heterozygous duplication	0.48	0.89	-	-	-	-	-	intergenic	Snoo, 3UTR	Snoo	NA	snp_su:8; snp_op:0; snp_ratio:801.0	43.46
D050R01	9	Control-Freec	DUP	2L	8183952	2L	8189600	-	-	somatic_tumour	-	5.6	2L:8183952-8189600	Heterozygous duplication	0.37	0.47	-	-	-	-	-	Piezo, intron	Piezo, 3UTR	Piezo	NA	snp_su:33; snp_op:0; snp_ratio:3301.0	42.16
D050R01	10	Control-Freec	DUP	2L	8668268	2L	8670386	-	-	somatic_tumour	-	2.1	2L:8668268-8670386	Heterozygous duplication	0.48	0.96	-	-	-	-	-	Sema-1a, 3UTR	Sema-1a, 3UTR	Sema-1a	NA	snp_su:4; snp_op:0; snp_ratio:401.0	41.84
D050R01	11	Control-Freec	DUP	2L	8775580	2L	8777698	-	-	somatic_tumour	-	2.1	2L:8775580-8777698	Heterozygous duplication	0.45	0.68	-	-	-	-	-	LManV, exon_3	LManVI, 3UTR	LManV, LManVI	NA	snp_su:0; snp_op:1	0
D050R01	12	novobreak	TANDUP	2L	9669038	2L	9670576	2	0	somatic_tumour	14	1.5	2L:9669038-9670576	3to5	0.02	0.35	-	-	CATCTCTTAAAGTGCAGTTCCGACGGGATCACAATCCGAGCTGCGATGCATCTTTACGACTTGTTCGGGCAGCCAGAAATTCGTTATTAAGTGGCCGACACTTGAGTGCCATTTCGGGCACCATAGAAGATACGTGCAAAGTGCCCCAGCCGGCGCAACAAC	-	-	intergenic	CR44150, exon_2	CR44150	TRUE	low read support=2; snp_su:15; snp_op:0; snp_ratio:1501.0	41.63
D050R01	13	Control-Freec	DUP	2L	9711030	2L	9717384	-	-	somatic_tumour	-	6.4	2L:9711030-9717384	Heterozygous duplication	0.39	0.53	-	-	-	-	-	CG4364, intron	Nckx30C, 3UTR	CG4364, Nckx30C	NA	snp_su:25; snp_op:0; snp_ratio:2501.0	35.87
D050R01	14	Control-Freec	DEL	2L	11851622	2L	11856564	-	-	somatic_tumour	-	4.9	2L:11851622-11856564	Homozygous deletion	0.48	-2.55	-	-	-	-	-	Mal-B2, exon_3	Pde1c, intron	Pde1c, Mal-B2, CG42751	NA	snp_su:1; snp_op:0	77.5
D050R01	16	novobreak	TRA	2L	12806638	2R	21954163	3	0	somatic_tumour	17	9147.5	2L:12806638 2R:21954163	3to3	0.05	0	-	-	GTTTTCTCTTTTGCAGCGATTTAGCTAACCGCTCGCGGCATTTCCGCTGAGCCAGACACGAGGAGATGCCAGGATATGCCAGGAACACACTTACACACTCATACGCTCAGCGACTGTACTCTTAAAATTAAAAAAAAATCTATACCCAAAATAAAATTTCTGAAGGGTCAGGGTCAGCGAA	-	NHEJ	intergenic	intergenic	-	NA	mh:0; ins:0; tup:0; tdown:0	0
D050R01	17	Control-Freec	DUP	2L	14842238	2L	14998970	-	-	somatic_tumour	-	156.7	2L:14842238-14998970	Heterozygous duplication	0.2	0.16	-	-	-	-	-	intergenic	intergenic	-	TRUE	low FC; snp_su:486; snp_op:0; snp_ratio:48601.0	42.2
D050R01	20	Control-Freec	DUP	2L	16241530	2L	16252826	-	-	somatic_tumour	-	11.3	2L:16241530-16252826	Heterozygous duplication	0.28	0.35	-	-	-	-	-	intergenic	PRL-1, intron	CG42818, PRL-1	TRUE	low FC; snp_su:20; snp_op:0; snp_ratio:2001.0	39.67
D050R01	21	Control-Freec	DUP	2L	16459684	2L	16469568	-	-	somatic_tumour	-	9.9	2L:16459684-16469568	Heterozygous duplication	0.32	0.44	-	-	-	-	-	intergenic	dac, intron	dac	NA	snp_su:40; snp_op:0; snp_ratio:4001.0	40.31
D050R01	22	Control-Freec	DUP	2L	16940470	2L	17232048	-	-	somatic_tumour	-	291.6	2L:16940470-17232048	Heterozygous duplication	0.22	0.22	-	-	-	-	-	intergenic	beat-IIIc, intron	beat-IIIc	TRUE	low FC; snp_su:756; snp_op:1; snp_ratio:748.52	42.45
D050R01	25	Control-Freec	DUP	2L	19171430	2L	19179902	-	-	somatic_tumour	-	8.5	2L:19171430-19179902	Heterozygous duplication	0.35	0.46	-	-	-	-	-	brat, 3UTR	CG17568, 3UTR	brat, CG17568	NA	snp_su:18; snp_op:0; snp_ratio:1801.0	39.38
D050R01	27	Control-Freec	DUP	2L	19719286	2L	19725640	-	-	somatic_tumour	-	6.4	2L:19719286-19725640	Heterozygous duplication	0.39	0.53	-	-	-	-	-	CG46244, intron	CG46244, intron	Lar, CG46244	NA	snp_su:1; snp_op:0	49.51
D050R01	29	Control-Freec	DUP	2L	21390388	2L	21392506	-	-	somatic_tumour	-	2.1	2L:21390388-21392506	Heterozygous duplication	0.49	0.99	-	-	-	-	-	nrv3, 3UTR	nrv3, 3UTR	nrv3	NA	snp_su:0; snp_op:0	0
D050R01	30	Control-Freec	DUP	2R	325466	2R	331114	-	-	somatic_tumour	-	5.6	2R:325466-331114	Heterozygous duplication	0.47	0.94	-	-	-	-	-	intergenic	CG45781, intron	CG45781	NA	snp_su:0; snp_op:0	0
D050R01	43	Control-Freec	DUP	2R	10511634	2R	10515870	-	-	somatic_tumour	-	4.2	2R:10511634-10515870	Heterozygous duplication	0.44	0.81	-	-	-	-	-	lola, intron	lola, exon_6	lola	NA	snp_su:2; snp_op:2	9.73
D050R01	44	Control-Freec	DUP	2R	14622672	2R	14624790	-	-	somatic_tumour	-	2.1	2R:14622672-14624790	Heterozygous duplication	0.45	0.71	-	-	-	-	-	Uhg5, ncRNA	intergenic	Uhg5, snoRNA:Me18S-G1952, snoRNA:Me18S-A1061, snoRNA:Me28S-A992, snoRNA:Me28S-G2703a, snoRNA:Me28S-G2703b, snoRNA:Me28S-G2703c, snoRNA:Or-CD4	NA	snp_su:18; snp_op:11; snp_ratio:1.64	12.83
D050R01	46	novobreak	TRA	2R	17496576	3L	13324060	3	0	somatic_tumour	37	4172.5	2R:17496576 3L:13324060	3to5	0.05	0	C	-	GATTGAATGTTTGCTCGGGGTCGAGAGTTGCGATTGCCATTTTCCCCGTTTGATTTACGTTTTCCTTGCATCCGCATCCATTTTGTTGTGCTCAGCATTGCATGTTGCTTACTTCACTATTAAATTCCCCATGGTTAGGCTTTTCATGAGAAGTTCACGGCGCACCGACCCCGCCGACCTCTGCCCACA	ATTTTCCCCGTTTGATTTACGTTTTCCTTGCATCCGCATCCATTTTGTTGTGCTCAGCATTGCATGTTGCTTACTTCACTATTAAATTCCCCATGGTTAGGCTTTTCATGAGAAGTTCACGGCGCACCGACCCCGCCGACCTCTGCCCACA	Alt-EJ	intergenic	intergenic	-	NA	mh:1; ins:0; tup:0; tdown:0	0
D050R01	49	novobreak	DEL	2R	20844133	2R	20845979	13	5	somatic_tumour	40	1.8	2R:20844133-20845979	5to3	0.37	-0.55	-	-	TCGTGTAAAGTTAAGGTCCAACCGTGGGCGTTTTGTGGGCGTGCGATTGCGTGTTCAGTTGTAATTGTTCAGTAATTCATTGTTATCCCACCATCCCATCGACATGATAAGAAACAAGTTCCTAATTTCATTTGCAGGGAAATGAGGGCTGTTGCCAGTAGATTTTCCAACTCCCATAGTCCAGGTGCGCA	-	-	intergenic	intergenic	-	TRUE	contamination at bp1=3; snp_su:10; snp_op:0; snp_ratio:1001.0	37.71
D050R01	49	novobreak	DEL	2R	20844133	2R	20845979	13	5	somatic_tumour	41	1.8	2R:20844133-20845979	5to3	0.37	-0.55	-	-	CTCAAAAGCCCACAAAATGATGTTTTGGGTATATAAAATGTATGCCAAGCTTGTATGAATATATATTTATTTTTTATCGTGTAAAGTTAAGGTCCAAACGTGGGCGTTTTGTGGGCGTGCGATTGCGTGTTCAGTTGTAATTGTTCAGTAATTCATTGTTATCCCACCATCCCATCGACATGATAAGAAACAAGTTCCTAATTTCATTTGCAGGGAAATGAGGGCTGTTGCCAGTAGATTTTCCAAC	-	-	intergenic	intergenic	-	TRUE	contamination at bp1=3; snp_su:10; snp_op:0; snp_ratio:1001.0	37.71
D050R01	50	novobreak	DEL	2R	21042280	2R	21044184	4	2	somatic_tumour	42	1.9	2R:21042280-21044184	5to3	0.1	0.11	-	-	TGTTTACCTCAGCATATTTAGAACGCTCATTATGCCTCGAAATTGCCCCACAAATGGAGGGGGTGGACCCCCTGCCCCCGCACCATCAAAGTGGGTCGCTAGCTGCACTTTCTACGGGCAGCACTTTTGGGCCTGCATTTCCTTAGCCGCAAAGCCACTCAACTCG	-	NHEJ	intergenic	intergenic	-	NA	mh:0; ins:0; tup:0; tdown:0	0
D050R01	56	Control-Freec	DUP	3L	4091270	3L	4093388	-	-	somatic_tumour	-	2.1	3L:4091270-4093388	Heterozygous duplication	0.47	1	-	-	-	-	-	CG14989, 3UTR	CG14990, exon	CG14989, CG14990	NA	snp_su:0; snp_op:3; snp_ratio:0.0	0
D050R01	59	Control-Freec	DUP	3L	8937254	3L	8940784	-	-	somatic_tumour	-	3.5	3L:8937254-8940784	Heterozygous duplication	0.5	0.97	-	-	-	-	-	orb2, 3UTR	orb2, 3UTR	CG43783, orb2	NA	snp_su:1; snp_op:1	9.69
D050R01	63	Control-Freec	DUP	3L	16031848	3L	16033966	-	-	somatic_tumour	-	2.1	3L:16031848-16033966	Heterozygous duplication	0.47	0.82	-	-	-	-	-	Notum, 3UTR	CG42716, exon	Notum, CG42717, CG42716	NA	snp_su:5; snp_op:0; snp_ratio:501.0	22.18
D050R01	66	Control-Freec	DUP	3L	21619838	3L	21625486	-	-	somatic_tumour	-	5.6	3L:21619838-21625486	Heterozygous duplication	0.37	0.64	-	-	-	-	-	CG11307, 3UTR	CG7166, 5UTR	CG11307, CG7166	NA	snp_su:6; snp_op:4; snp_ratio:1.5	10.56
D050R01	68	Control-Freec	DUP	3L	24722002	3L	24730474	-	-	somatic_tumour	-	8.5	3L:24722002-24730474	Heterozygous duplication	0.43	0.65	-	-	-	-	-	intergenic	scro, intron	scro	NA	snp_su:1; snp_op:0	12.44
D050R01	70	novobreak	BND	3R	4185474	3R	4185746	3	0	somatic_tumour	65	0.3	3R:4185474-4185746	3to3	0.06	0	-	-	ATATACATATATACTATTGATCAATATCAATACCCGAGTCGATCTGGCCAAAGACGCTAGAATAACTAGTGTCTTTGACCTGGCCCTGTCCGTTTGTCTGTTCGTCCGTATTAACGTCGAAATCTCAGGAACAATAAAAGCTAGAAGCAGCTCAAGTTTGTTTCCAAATATTGC	-	NHEJ	CG12581, 3UTR	CG12581, 3UTR	CG12581	NA	bp1_INE-1_Helitron=7; mh:0; ins:0; tup:0; tdown:0	0
D050R01	71	delly	COMPLEX_DEL	3R	5455376	3R	5456532	13	5	somatic_tumour	DEL00006952	1.2	3R:5455376-5456532	72:71_72	0.3	-0.53	-	-	CACATCCTTGCCATCACACTTATCCTGAACTGGCCGAATGGCAGGAGCTCAAGGACATTTCCACGCTGGTGCGCAAACATTGGCGCTGCGGCTACGTCGAGTGCTCGGCGCAGTGAGTATGAAAATCCTCAACAGGCCAGCTCCATAATATCCATAAATATTCGCTCCGCAAT	-	NHEJ	CG14669, intron	CG14669, 3UTR	CG14669	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:1; snp_op:0	21.83
D050R01	71	lumpy	COMPLEX_DEL	3R	5455376	3R	5456532	13	5	somatic_tumour	5940	1.2	3R:5455376-5456532	72:71_72	0.3	-0.53	-	-	-	-	NHEJ	CG14669, intron	CG14669, 3UTR	CG14669	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:1; snp_op:0	21.83
D050R01	74	novobreak	TRA	3R	14142909	X	12048800	3	0	somatic_tumour	75	2094.1	3R:14142909 X:12048800	5to3	0.08	0	TTTATGCATTATTA	-	ACCCAACGCTGCGTGTGAATTTTCGTGCCCAGAGAACTCAATTCTTCTCGACAGAGCCCCATTTCCTTTATTTTATGCATTATTATTAGCCAGGTTTATTGCCAAATACTTACACGCCGTATTAGGCAACTCGAATAATTAATGAGAACGAAAATAAAGTTGAAAACATATT	ACCCAACGCTGCGTGTGAATTTTCGTGCCCAGAGAACTCAATTCTTCTCGACAGAGCCCCATTTCCTTTATTTTATGCATTATTATTAGCCAGGTTTATTGCCAAATACTTACACGCCGTATTAGGCAACTCGAATAATTAATGAGAACGAAAATAAAGTTGAAAACATATT	Alt-EJ	intergenic	CR43960, ncRNA	Ten-a, CR43960	NA	mh:14; ins:0; tup:0; tdown:0	0
D050R01	75	novobreak	BND	3R	14562649	3R	14564494	2	3	somatic_tumour	77	1.8	3R:14562649-14564494	3to3	0.06	0.25	-	-	GCCTCACGTTGACACGTCTGGAGTTGTTCCTGCGCCTCCGATTCCGGACGGTGGTGCTCCCCGATCCATTCCGGTTGACGCGGATGCGCCGAACGTTGGTGTAGCGCAGGTTGCTAACGCGGACGATCTTTCGGCTTCCGGTTCCGGTTCCGCTTGATGTCGTTGGCGCAGTGGTGGTGGTCGC	-	NHEJ	CG14851, exon	CG8087, exon	CG14851, CG8087	NA	mh:0; ins:0; tup:0; tdown:0	0
D050R01	76	novobreak	TRA	3R	14805358	2R	24566145	3	0	somatic_tumour	78	9760.8	3R:14805358 2R:24566145	5to3	0.04	0	-	-	GTTCAGTTGAATCCGAAATGCACGTACACAGTAAAAAGGTAAAAAGATCTCTCATAGTTCTAGCACAGAAAGCGAATGCGACAGCAAAAGCAGAAGGAGCGCCTCGAACGGGAGGCGGAACCTGTGAAGAAAGATAATGAAGTGCTGCGGAAGCTAGAAGAGCGAGAAATGATGGAGGA	GTTCAGTTGAATCCGAAATGCACGTACACAGTAAAAAGGTAAAAAGATCTCTCATAGTTCTAGCACAGAAAGCGAATGCGACAGCAAAAGCAGAAGGAGCGCCTCGAACGGGAGGCGGAACCTGTGAAGAAAGATAATGAAGTGCTGCGGAAGCTAGAAGAGCGAGAAA	NHEJ	btsz, 3UTR	uri, exon_3	btsz, uri	NA	mh:0; ins:0; tup:0; tdown:0	0
D050R01	95	Control-Freec	DUP	4	335350	4	349470	-	-	somatic_tumour	-	14.1	4:335350-349470	Heterozygous duplication	0.37	0.53	-	-	-	-	-	PMCA, intron	PMCA, intron	PMCA	NA	snp_su:0; snp_op:3; snp_ratio:0.0	0
D050R01	97	Control-Freec	DUP	4	866262	4	871204	-	-	somatic_tumour	-	4.9	4:866262-871204	Heterozygous duplication	0.43	0.68	-	-	-	-	-	Gyf, exon_2	CR43425, exon_2	Gyf, unc-13, CR43425	NA	snp_su:0; snp_op:3; snp_ratio:0.0	0
D050R01	103	Control-Freec	DUP	X	3664846	X	3666964	-	-	somatic_tumour	-	2.1	X:3664846-3666964	Heterozygous duplication	0.48	0.75	-	-	-	-	-	AstA-R1, exon_11	intergenic	AstA-R1	NA	snp_su:1; snp_op:3; snp_ratio:0.34	4.06
D050R01	110	Control-Freec	DUP	X	8046282	X	8049106	-	-	somatic_tumour	-	2.8	X:8046282-8049106	Heterozygous duplication	0.46	0.69	-	-	-	-	-	fs(1)h, 3UTR	fs(1)h, 3UTR	fs(1)h	NA	snp_su:0; snp_op:0	0
D050R01	112	Control-Freec	DUP	X	10705784	X	10712844	-	-	somatic_tumour	-	7.1	X:10705784-10712844	Heterozygous duplication	0.37	0.51	-	-	-	-	-	X11Lbeta, exon_8	CG32676, 3UTR	X11Lbeta, CG32676	NA	snp_su:0; snp_op:0	0
D050R01	114	Control-Freec	DUP	X	11806438	X	11809262	-	-	somatic_tumour	-	2.8	X:11806438-11809262	Heterozygous duplication	0.46	0.72	-	-	-	-	-	Hsc70-3, intron	CG1578, 3UTR	Hsc70-3, CG1578	NA	snp_su:0; snp_op:0	0
D050R01	116	Control-Freec	DUP	X	12679760	X	12685408	-	-	somatic_tumour	-	5.6	X:12679760-12685408	Heterozygous duplication	0.46	0.86	-	-	-	-	-	Tis11, 3UTR	Smr, 3UTR	Tis11, Smr	NA	snp_su:5; snp_op:2; snp_ratio:2.49	13.19
D050R01	121	lumpy	DEL	X	16426329	X	16426886	8	1	somatic_tumour	8979	0.6	X:16426329-16426886	5to3	0.2	0	-	-	-	-	NHEJ	hang, intron	hang, intron	hang	NA	mh:0; ins:0; tup:0; tdown:0	0
D050R01	121	novobreak	DEL	X	16426329	X	16426886	8	1	somatic_tumour	112	0.6	X:16426329-16426886	5to3	0.2	0	-	-	CCCAGAAGAGGAAAATGGCTTACGATGGATGGAACGATGATCCAGAATGAGACGAAAACATTAAATCGAGGAAACTATGCAAAATTGTGAAATTAGGAGTTTAAATCATTGTGAAATAGGGGGCAAGATAATATGAAATTTAAAAAACGGACAGGACAGGATGCTCTCTTTCTCTTGCCCACAGGCACAAATACATACATATATAGAG	-	NHEJ	hang, intron	hang, intron	hang	NA	mh:0; ins:0; tup:0; tdown:0	0
D050R05	2	Control-Freec	DEL	2L	11851140	2L	11856700	-	-	somatic_tumour	-	5.6	2L:11851140-11856700	Homozygous deletion	0.43	-1.74	-	-	-	-	-	Mal-B2, exon_2	Pde1c, intron	Pde1c, Mal-B2, CG42751	NA	snp_su:0; snp_op:0	0
D050R05	4	Control-Freec	DUP	2L	15982220	2L	16136232	-	-	somatic_tumour	-	154	2L:15982220-16136232	Heterozygous duplication	0.15	0.21	-	-	-	-	-	intergenic	intergenic	-	TRUE	low FC; snp_su:458; snp_op:12; snp_ratio:38.14	33.87
D050R05	5	Control-Freec	DUP	2L	16947992	2L	17285484	-	-	somatic_tumour	-	337.5	2L:16947992-17285484	Heterozygous duplication	0.17	0.25	-	-	-	-	-	CR44393, ncRNA	intergenic	CR44393	TRUE	low FC; snp_su:875; snp_op:16; snp_ratio:54.65	36.31
D050R05	12	novobreak	BND	3L	2191516	3L	3432011	2	1	somatic_tumour	6	1240.5	3L:2191516-3432011	5to5	0.05	-0.04	AAT	-	AGATAGGCTCGAGTCGAGTGCATTATTGTCGGGAAGTGAGGAACCGCACTATCATCGTTTTGGTGGGCATGTGTTTATGAATTGGACGGCAAAGTTTCTATTGTATCAGGTGTTTGTACTTTTGCCTTTATATTTACAAGTCCAGATTAATATCTTTATGATATGAAGCCATTATC	TCGGGAAGTGAGGAACCGCACTATCATCGTTTTGGTGGGCATGTGTTTATGAATTGGACGGCAAAGTTTCTATTGTATCAGGTGTTTGTACTTTTGCCTTTATATTTACAAGTCCAGATTAATATCTTTATGATATGAAGCCATTATC	Alt-EJ	CG5707, intron	eIF5B, intron	CG5707, eIF5B	NA	mh:3; ins:0; tup:0; tdown:0	0
D050R05	19	Control-Freec	DUP	3R	4163328	3R	4178896	-	-	somatic_tumour	-	15.6	3R:4163328-4178896	Heterozygous duplication	0.35	0.58	-	-	-	-	-	intergenic	CG12581, intron	CG12581	NA	snp_su:2; snp_op:1	8.67
D050R05	24	novobreak	TRA	3R	13534558	Tomelloso	60394	3	0	somatic_tumour	17	13474.2	3R:13534558 Tomelloso:60394	-	0.11	0	AA	-	TTTTGAAATGCCGTTTCAACCATTTTGTCGGAACAATCTATTATGGCTGCATCGAGCAATTGTGTAAATTGAAGAAGCCGACCACATTTACAACCATGATATGGAAGCAAATTCAACAATCGGTCATCAATGAGCAGTGGGAAATTAAAATTTGCACGCAGTGTGTGCGGTTTCGATGTATATTTAAACAAATGCGGTTAATGTTCATATTT	AAATATGAACATTAACCGCATTTGTTTAAATATACATCGAAACCGCACACACTGCGTGCAAATTTTAATTTCCCACTGCTCATTGATGACCGATTGTTGAATTTGCTTCCATATCATGGTTGTAAATGTGGTCGGCTTCTTCAATTTACAC	Alt-EJ	intergenic	intergenic	-	NA	mh:2; ins:0; tup:0; tdown:0	0
D050R05	28	Control-Freec	DUP	4	556	4	5004	-	-	somatic_tumour	-	4.4	4:556-5004	Heterozygous duplication	0.29	0.52	-	-	-	-	-	intergenic	JYalpha, 3UTR	JYalpha	NA	snp_su:1; snp_op:0	26.06
D050R07-1	1	Control-Freec	DEL	2L	11851125	2L	11856735	-	-	somatic_tumour	-	5.6	2L:11851125-11856735	Heterozygous deletion	0.42	-1.48	-	-	-	-	-	Mal-B2, exon_2	Pde1c, intron	Pde1c, Mal-B2, CG42751	NA	snp_su:0; snp_op:0	0
D050R07-1	2	Control-Freec	DUP	2L	14829474	2L	14955138	-	-	somatic_tumour	-	125.7	2L:14829474-14955138	Heterozygous duplication	0.15	0.16	-	-	-	-	-	intergenic	CG42313, intron	CG42313	TRUE	low FC; snp_su:374; snp_op:6; snp_ratio:62.23	35.49
D050R07-1	3	Control-Freec	DUP	2L	15918375	2L	16191021	-	-	somatic_tumour	-	272.6	2L:15918375-16191021	Heterozygous duplication	0.15	0.19	-	-	-	-	-	beat-Ib, intron	intergenic	beat-Ib	TRUE	low FC; snp_su:871; snp_op:10; snp_ratio:87.01	37.75
D050R07-1	4	Control-Freec	DUP	2L	16932102	2L	17268702	-	-	somatic_tumour	-	336.6	2L:16932102-17268702	Heterozygous duplication	0.15	0.18	-	-	-	-	-	intergenic	intergenic	-	TRUE	low FC; snp_su:833; snp_op:11; snp_ratio:75.66	36.14
D050R07-1	12	delly	DEL	2R	14340937	2R	14342082	9	5	somatic_tumour	DEL00000002	1.1	2R:14340937-14342082	5to3	0.27	-0.8	-	-	TGCCGATGCTGATGATGGGCCCAAAGTAGAAGGAAGATGATGGTAAACAATTTTCAATCAGCCCGGCAAAGTTGCAAGCGGCCAAATACAAATCCCTTGTCTCCACGAACAAACCAATTTCGGCCGTTTATTTGATTTATTTTGCGAGTCAATTTGTTCGTGCCCCAAACGATTCGCTTTTCAGATACAGATACAAAGTGCCGCGTGCT	-	NHEJ	Shroom, intron	Shroom, 5UTR	Shroom	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:2; snp_op:3; snp_ratio:0.67	5.33
D050R07-1	12	lumpy	DEL	2R	14340937	2R	14342082	9	5	somatic_tumour	3494	1.1	2R:14340937-14342082	5to3	0.27	-0.8	-	-	-	-	NHEJ	Shroom, intron	Shroom, 5UTR	Shroom	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:2; snp_op:3; snp_ratio:0.67	5.33
D050R07-1	15	delly	DEL	2R	21033949	2R	21034182	10	0	somatic_tumour	DEL00000003	0.2	2R:21033949-21034182	5to3	0.25	0	TTA	-	TTTTCGTTCGGAGATCTGGGTGTTAAAACTTTTGCGAAATGCTGTCACAAGAAATCCACATGTCACACGGCAGCACTCCATACCACTCCCGCCATCATCTTCTTGTTACAGTCGAGTGCGCTTGCTGAGCTCAGCATGAATTATTTGGCATTGGACGAAATCGAAAGACTTTTGCGTGACTGCGACACACGCACCCACGAGCATAAACTTTTTTTAAGCACGCGATTGCAAAGAAGATTCGCGGGAATTTTTTG	CCACTCCCGCCATCATCTTCTTGTTACAGTCGAGTGCGCTTGCTGAGCTCAGCATGAATTATTTGGCATTGGACGAAATCGAAAGACTTTTGCGTGACTGCGACACACGCACCCACGAGCATAAACTTTTTTTAAGCACGCGATTGCAAAGAAGATTCGCGGGAATTTTTTGT	Alt-EJ	intergenic	intergenic	-	NA	mh:3; ins:0; tup:0; tdown:0	0
D050R07-1	15	novobreak	DEL	2R	21033949	2R	21034182	10	0	somatic_tumour	4	0.2	2R:21033949-21034182	5to3	0.25	0	TTA	-	ACTACATGTAGTTCAATAAACCATTTACCAGTTCATATTCTCACTATTATAGAATGTAGCTGAAAAAGCGAAGGGATTGATTCATCGACTACCATCTTGAATTTTAAGCTTCTCCTTTGCTGACAATATTGTGGCCTCATATACCACCATATATTTATCTTATTTCTCAGAGTTATGTAAATAAACTCCGCTGCGAGGTGACTGAAATCGTCTTGGTTTTCGTTCGGAGATCTGGGTGTTAAAACTTTTGCGAAATGCTGTCACAAGAAATCCACATGTCACACGGCAGCACTCCATACCACTCCCGCCATCATCTTCTTGTTACAGTCGAGTGCGCTTGCTGAGCTCAGCATGAATTATTTGGCATTGGACGAAATCGAAAGACTTTTGCGTGACTGCGACACACGCACCCACGAGCATAAACTTTTTTTAAGCACGCGATTGCAAAGAAGATTCGCGGGAATTTTTTGTATTTCAATTTATACATAGCTGTAGTTATAATTACTAACAATTTAGGTTTTTACCATTTTACATCAATTTTAAGC	CCACTCCCGCCATCATCTTCTTGTTACAGTCGAGTGCGCTTGCTGAGCTCAGCATGAATTATTTGGCATTGGACGAAATCGAAAGACTTTTGCGTGACTGCGACACACGCACCCACGAGCATAAACTTTTTTTAAGCACGCGATTGCAAAGAAGATTCGCGGGAATTTTTTGT	Alt-EJ	intergenic	intergenic	-	NA	mh:3; ins:0; tup:0; tdown:0	0
D050R07-1	21	delly	BND	3L	15021983	3L	15023631	9	1	somatic_tumour	INV00000007	1.6	3L:15021983-15023631	5to5	0.13	0.05	-	TT	GTGCGGTTGGCTGCATTTCAATGGTATTATCGTTGATGTTTTCGCAGTTCTCCCCTCTAAAATGTGCAACAAAGTTGTCTGACACTCGAGGGGATCAAAGGATTCAGAGGAATGGCCAAAAAGAAGAGCCAAAGTCAAGGCACCGAAAAGGGCAAGAAAACCTGTAATAAGAATCAGTTCTTTGGCGGCTGCTTTAAGAG	CTTCAATAAGTGGGCAATCTCACTCTTAAAGCAGCCGCCAAAGAACTGATTCTTATTACAGGTTTTCTTGCCCTTTTCGGTGCCTTGACTTTGGCTCTTCTTTTTGGCCATTCCTCTGAATCCTTTGATCCCCTCGAGTGTCAGACAACTTTGTTGCACATTTTAGAGGGGAGAACTGCGA	NHEJ	Sytbeta, intron	CG32148, exon_1	Sytbeta, CG32148	NA	mh:0; ins:2; tup:0; tdown:0	0
D050R07-1	21	novobreak	BND	3L	15021983	3L	15023631	9	1	somatic_tumour	6	1.6	3L:15021983-15023631	5to5	0.13	0.05	-	TT	GAAAACCATTCACTTTAAAAAATGGAACCACTTCAATAAGTGGGCAATCTCACTCTTAAAGCAGCCGCCAAAGAACTGATTCTTATTACAGGTTTTCTTGCCCTTTTCGGTGCCTTGACTTTGGCTCTTCTTTTTGGCCATTCCTCTGAATCCTTTGATCCCCTCGAGTGTCAGACAACTTTGTTGCACATTTTAGAGGGGAGAACTGCGAAAACATCAACGATAATACCATTGAAATGCAGCCAACCGCACCGTTGCTAATTGACACCTATGTAAACTGCAATCAAAGCGACAATCAGCCAAGCCCACAGTTTTCCACGT	CTTCAATAAGTGGGCAATCTCACTCTTAAAGCAGCCGCCAAAGAACTGATTCTTATTACAGGTTTTCTTGCCCTTTTCGGTGCCTTGACTTTGGCTCTTCTTTTTGGCCATTCCTCTGAATCCTTTGATCCCCTCGAGTGTCAGACAACTTTGTTGCACATTTTAGAGGGGAGAACTGCGA	NHEJ	Sytbeta, intron	CG32148, exon_1	Sytbeta, CG32148	NA	mh:0; ins:2; tup:0; tdown:0	0
D050R07-1	24	Control-Freec	DUP	3L	19684368	3L	19687734	-	-	somatic_tumour	-	3.4	3L:19684368-19687734	Heterozygous duplication	0.43	0.7	-	-	-	-	-	CG8765, 3UTR	Gbeta76C, exon_1	CG8765, Gbeta76C	NA	snp_su:1; snp_op:1	10.44
D050R07-1	31	lumpy	DEL	3R	30472992	3R	30478842	10	2	somatic_tumour	6859	5.8	3R:30472992-30478842	5to3	0.32	-0.84	-	-	-	-	NHEJ	PH4alphaEFB, intron	spdo, 3UTR	PH4alphaEFB, spdo	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:65; snp_op:14; snp_ratio:4.64	21.25
D050R07-1	31	novobreak	DEL	3R	30472992	3R	30478842	10	2	somatic_tumour	13	5.8	3R:30472992-30478842	5to3	0.32	-0.84	-	-	GAGCAATTACCTGCTCAAGTGCGAGACAGCCTCTCTGTCTCGCCTTGGCAGAATTAATTACTGCTGATTAATTATTCAACGCCCACCGCCTACAAGAGCATGCATCAGCCTTAATTCGTCCTTGTGGTTTGTCGAAATACCAGCACAGCATTTTGTATCAATAAGGAAATGGTTAAAGTGTTCAATTAGGTTAGTTCTTTAACAA	-	NHEJ	PH4alphaEFB, intron	spdo, 3UTR	PH4alphaEFB, spdo	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:65; snp_op:14; snp_ratio:4.64	21.25
D050R07-1	39	lumpy	DEL	X	12752270	X	12754313	13	4	somatic_tumour	7527	2	X:12752270-12754313	5to3	0.36	-0.59	-	-	-	GACAAGCGACTGAGACGCCAGTCTGATGCGTGCAAAAGAGAGGGCAACATGCGAAACGAAAAACCAAACGAAAGCGTACAAATAAATAAAGCAGAAGCGGAGAAAGAAAGATGGTTGTCGGAGGAGAAGCCGAATAAGCGCAAAGTAGCGCAACTTGCGGTGACAACA	NHEJ	CR44619, exon_1	CR44619, exon_2	CR44619	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:3; snp_op:0; snp_ratio:301.0	33.57
D050R07-1	39	delly	DEL	X	12752270	X	12754313	13	4	somatic_tumour	DEL00000015	2	X:12752270-12754313	5to3	0.36	-0.59	-	-	CAAGCGACTGAGACGCCAGTCTGATGCGTGCAAAAGAGAGGGCAACATGCGAAACGAAAAACCAAACGAAAGCGTACAAATAAATAAAGCAGAAGCGGAGAAAGAAAGATGGTTGTCGGAGGAGAAGCCGAATAAGCGCAAAGTAGCGCAACTTGCGGTGACAACAAAAGCAACAACAATAACAAAAACGACAACTAGAACAACAATCGACGGTTACAGCAA	GACAAGCGACTGAGACGCCAGTCTGATGCGTGCAAAAGAGAGGGCAACATGCGAAACGAAAAACCAAACGAAAGCGTACAAATAAATAAAGCAGAAGCGGAGAAAGAAAGATGGTTGTCGGAGGAGAAGCCGAATAAGCGCAAAGTAGCGCAACTTGCGGTGACAACA	NHEJ	CR44619, exon_1	CR44619, exon_2	CR44619	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:3; snp_op:0; snp_ratio:301.0	33.57
D050R07-1	39	novobreak	DEL	X	12752270	X	12754313	13	4	somatic_tumour	80	2	X:12752270-12754313	5to3	0.36	-0.59	-	-	CACACACACGAAGAGGAATAAGATGATGATGATGAAGAGGGACAAGCGACTGAGACGCCAGTCTGATGCGTGCAAAAGAGAGGGCAACATGCGAAACGAAAAACCAAACGAAAGCGTACAAATAAATAAAGCAGAAGCGGAGAAAGAAAGATGGTTGTCGGAGGAGAAGCCGAATAAGCGCAAAGTAGCGCAACTTGCGGTGACAACAAAAGCAACAACAATAACAAAAACGACAACTAGAACAACAATCGACGGTTACAGCAACAATGAGGTACAGTGAGCACCAGAC	GACAAGCGACTGAGACGCCAGTCTGATGCGTGCAAAAGAGAGGGCAACATGCGAAACGAAAAACCAAACGAAAGCGTACAAATAAATAAAGCAGAAGCGGAGAAAGAAAGATGGTTGTCGGAGGAGAAGCCGAATAAGCGCAAAGTAGCGCAACTTGCGGTGACAACA	NHEJ	CR44619, exon_1	CR44619, exon_2	CR44619	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:3; snp_op:0; snp_ratio:301.0	33.57
D050R07-1	40	lumpy	DEL	X	13220924	X	13221024	5	1	somatic_tumour	7536	0.1	X:13220924-13221024	5to3	0.19	0	-	-	-	-	NHEJ	mew, intron	mew, intron	mew	NA	mh:0; ins:0; tup:0; tdown:0	0
D050R07-1	40	delly	DEL	X	13220924	X	13221024	5	1	somatic_tumour	DEL00000016	0.1	X:13220924-13221024	5to3	0.19	0	-	-	GCTACAAATATGTATGCATGTATGGTTATTTAGATAATATCGATTATTTTGAAGCAAACCTGAAGTAATTTAAATTGAAACACAAGCGATAAAATGCAAATTCCAAGCGACTTCAAACTCGGAACAATTGAATTATTTACAGATGATTTTC	-	NHEJ	mew, intron	mew, intron	mew	NA	mh:0; ins:0; tup:0; tdown:0	0
D050R07-2	1	Control-Freec	DEL	2L	11851125	2L	11856735	-	-	somatic_tumour	-	5.6	2L:11851125-11856735	Heterozygous deletion	0.44	-1.41	-	-	-	-	-	Mal-B2, exon_2	Pde1c, intron	Pde1c, Mal-B2, CG42751	NA	snp_su:0; snp_op:0	0
D050R07-2	3	Control-Freec	DUP	2L	17232237	2L	17233920	-	-	somatic_tumour	-	1.7	2L:17232237-17233920	Heterozygous duplication	0.46	0.74	-	-	-	-	-	beat-IIIc, intron	beat-IIIc, intron	beat-IIIc	NA	snp_su:0; snp_op:0	0
D050R07-2	6	lumpy	DEL	2R	14340937	2R	14342082	9	5	somatic_tumour	2279	1.1	2R:14340937-14342082	5to3	0.23	-0.87	-	-	-	-	NHEJ	Shroom, intron	Shroom, 5UTR	Shroom	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:2; snp_op:3; snp_ratio:0.67	10.09
D050R07-2	7	delly	DEL	2R	21033949	2R	21034182	10	0	somatic_tumour	DEL00000014	0.2	2R:21033949-21034182	5to3	0.22	0	TTA	-	TTTTCGTTCGGAGATCTGGGTGTTAAAACTTTTGCGAAATGCTGTCACAAGAAATCCACATGTCACACGGCAGCACTCCATACCACTCCCGCCATCATCTTCTTGTTACAGTCGAGTGCGCTTGCTGAGCTCAGCATGAATTATTTGGCATTGGACGAAATCGAAAGACTTTTGCGTGACTGCGACACACGCACCCACGAGCATAAACTTTTTTTAAGCACGCGATTGCAAAGAAGATTCGCGGGAATTTTTTG	CCACTCCCGCCATCATCTTCTTGTTACAGTCGAGTGCGCTTGCTGAGCTCAGCATGAATTATTTGGCATTGGACGAAATCGAAAGACTTTTGCGTGACTGCGACACACGCACCCACGAGCATAAACTTTTTTTAAGCACGCGATTGCAAAGAAGATTCGCGGGAATTTTTTGT	Alt-EJ	intergenic	intergenic	-	NA	mh:3; ins:0; tup:0; tdown:0	0
D050R07-2	7	novobreak	DEL	2R	21033949	2R	21034182	10	0	somatic_tumour	9	0.2	2R:21033949-21034182	5to3	0.22	0	TTA	-	ACTACATGTAGTTCAATAAACCATTTACCAGTTCATATTCTCACTATTATAGAATGTAGCTGAAAAAGCGAAGGGATTGATTCATCGACTACCATCTTGAATTTTAAGCTTCTCCTTTGCTGACAATATTGTGGCCTCATATACCACCATATATTTATCTTATTTCTCAGAGTTATGTAAATAAACTCCGCTGCGAGGTGACTGAAATCGTCTTGGTTTTCGTTCGGAGATCTGGGTGTTAAAACTTTTGCGAAATGCTGTCACAAGAAATCCACATGTCACACGGCAGCACTCCATACCACTCCCGCCATCATCTTCTTGTTACAGTCGAGTGCGCTTGCTGAGCTCAGCATGAATTATTTGGCATTGGACGAAATCGAAAGACTTTTGCGTGACTGCGACACACGCACCCACGAGCATAAACTTTTTTTAAGCACGCGATTGCAAAGAAGATTCGCGGGAATTTTTTGTATTTCAATTTATACATAGCTGTAGTTATAAT	CCACTCCCGCCATCATCTTCTTGTTACAGTCGAGTGCGCTTGCTGAGCTCAGCATGAATTATTTGGCATTGGACGAAATCGAAAGACTTTTGCGTGACTGCGACACACGCACCCACGAGCATAAACTTTTTTTAAGCACGCGATTGCAAAGAAGATTCGCGGGAATTTTTTGT	Alt-EJ	intergenic	intergenic	-	NA	mh:3; ins:0; tup:0; tdown:0	0
D050R07-2	9	Control-Freec	DUP	3L	71808	3L	77979	-	-	somatic_tumour	-	6.2	3L:71808-77979	Heterozygous triplication	0.5	1.02	-	-	-	-	-	intergenic	intergenic	CR43988, CG13405	NA	snp_su:6; snp_op:0; snp_ratio:601.0	74.39
D050R07-2	10	Control-Freec	DUP	3L	228888	3L	233937	-	-	somatic_tumour	-	5	3L:228888-233937	Heterozygous duplication	0.42	0.63	-	-	-	-	-	CR42862, exon_4	E(bx), 3UTR	CR42862, CG42846, CG34454, CG34453, E(bx)	NA	snp_su:1; snp_op:0	61.51
D050R07-2	11	novobreak	TRA	3L	475358	3R	29795810	2	1	somatic_tumour	13	29320.5	3L:475358 3R:29795810	5to5	0.04	0	GTGATCACA	-	CATCTGTGGGCAGATAGTCAGCTCCCAGTCCCCATCGATCCCCATAGAGTGTTGAAAACTTTATTATGCCTGTGATCACAGAACGCAACTGGGTGGTGGTGTCTAGAAGACATAGCCGCGACAGCGCTCGAACACAGCATCGTTGAGCAGCTGGAACCACTCGCTGGCATAGGT	GCTGCTCAACGATGCTGTGTTCGAGCGCTGTCGCGGCTATGTCTTCTAGACACCACCACCCAGTTGCGTTCTGTGATCACAGGCATAATAAAGTTTTCAACACTCTATGGGGATCGATGGGGACTGGGAGCTGACTATCTGCCCACAGATG	Alt-EJ	klar, intron	CG7837, 3UTR	klar, CG7837	NA	mh:9; ins:0; tup:0; tdown:0	0
D050R07-2	12	Control-Freec	DUP	3L	1037850	3L	1040655	-	-	somatic_tumour	-	2.8	3L:1037850-1040655	Heterozygous duplication	0.32	0.57	-	-	-	-	-	bab1, 3UTR	bab1, intron	bab1	TRUE	t_contamination: 378 n_contamination: 19; snp_su:11; snp_op:0; snp_ratio:1101.0; somatic_snvs:3	48.02
D050R07-2	15	novobreak	DEL	3L	1924997	3L	1925103	9	0	somatic_tumour	15	0.1	3L:1924997-1925103	5to3	0.44	0	-	ACTATTCAAAAAATATATTT	CCTTCACTCGTTGCTGGCGCACTGTCGCAATCCCTACATGAGTGGTAAGATATTCCAAAAGGATACTATTCAAAAAATATATTTATTTCCAAGTGTAATGCCCCTAATGGTCGAATATATCAAATGTCACATCCCCAACCAGAGTCCACAGCCACCCGCTGTGCCCATTAACAAGTGTTTTGGTCTAATGCATTTCCTCTTTCCTCTTCCCCTCCCTCCAC	CCGCACCTTCACTCGTTGCTGGCGCACTGTCGCAATCCCTACATGAGTGGTAAGATATTCCAAAAGGATACTATTCAAAAAATATATTTATTTCCAAGTGTAATGCCCCTAATGGTCGAATATATCAAATGTCACATCCCCAACCAGAGTCCACAG	FoSTeS	Dbx, intron	Dbx, intron	Dbx	NA	mh:0; ins:20; tup:5; tdown:7	0
D050R07-2	16	novobreak	DEL	3L	2181268	3L	2181408	16	2	somatic_tumour	16	0.1	3L:2181268-2181408	5to3	0.32	0	-	-	AATGTTCATTTCCGGTCAAAGACTTCTCCAACTTCTCAAATTTCCTTTGCCATCCAAGCCATCAACGTTACTTAAAATGCCAAATGAGCTTCCGTTGGGCCATCCCAAGTCTGTTCCATCTCCTTGTCGATTTTCTTGGCCGCAACTGGAGTGGCTGAGCGGAATCCCAATCCCAAAGCCAAATAGAATCCGGGCTCAGCAAATGTGGGTGGCTTCCCTGGGTTTCCATGGCCGTCCATGGCCAGAAATCAATGTGTGAAACGTGCTAATTGCGGCAGCTGTGCAAATGTGTGCCTGGCCATTTGATAGTTGACCATCATTTTGATGACCCACAAG	-	NHEJ	intergenic	intergenic	-	NA	mh:0; ins:0; tup:0; tdown:0	0
D050R07-2	18	novobreak	DEL	3L	4398351	3L	4398478	11	1	somatic_tumour	19	0.1	3L:4398351-4398478	5to3	0.23	0	T	-	GTGCAATTCCGATCGCTCTGTTCTGGAATTGTGCATTTGCTGGCCGGGCCAATTTAAATTCTAATTTCATGTAGCAAATCAGATTAGCTGCCCAGTTTGCCGGACCACAAATGGCCCAAACAGTTAGCCAAAGTTTCATTTTACGACCCTGACAACAATATTTTTATGTTTTTATAAATTTATTTCACATTTTCATCTGGAAACCAGATACGCGAAGCTAGACTTGCACTTTTCTCCGGTATATCTTGAATGTTTACAGCCGTTAAGTGTC	GGCCAATTTAAATTCTAATTTCATGTAGCAAATCAGATTAGCTGCCCAGTTTGCCGGACCACAAATGGCCCAAACAGTTAGCCAAAGTTTCATTTTACGACCCTGACAACAATATTTTTATGTTTTTATAAATTTATTTCACATTTTCATCTGTAAACCAGAT	Alt-EJ	slow, intron	slow, intron	slow	NA	mh:1; ins:0; tup:0; tdown:0	0
D050R07-2	20	novobreak	DEL	3L	4755736	3L	4756178	10	4	somatic_tumour	22	0.4	3L:4755736-4756178	5to3	0.29	0	-	CAATTC	GTGTGGGGACTGCTGCATTTGTGTCTCCCATTGTTTTGTCACCATATATCTGGGTTAAATCCTGCCAAGTTGGGTAAGGCTTTAAGCACTTCTACATTCAATTCAATTCAATTCAATAATAATTTGTTCCAAGAGATATCTTCTATGAAATGCAGTGGATGTTTCTGTGTCAATTACACGGCTAAAATGTTCACACCTAGCGTTAATAATGCAGCTGCGAAATTGATATGCATCCAGCGGATAAA	CTCCCATTGTTTTGTCACCATATATCTGGGTTAAATCCTGCCAAGTTGGGTAAGGCTTTAAGCACTTCTACATTCAATTCAATTCAATTCAATAATAATTTGTTCCAAGAGATATCTTCTATGAAATGCAGTGGATGTTTCTGTGTCAATTACACGGCTAAAATGTTCACACCTAGCGTTAATAATGCAGC	FoSTeS	CR43881, ncRNA	RhoGEF64C, intron	RhoGEF64C, CR43881	NA	mh:0; ins:6; tup:6; tdown:5	0
D050R07-2	21	novobreak	DEL	3L	5901977	3L	5902395	18	10	somatic_tumour	23	0.4	3L:5901977-5902395	5to3	0.33	0	-	-	CTGCAGATACGCGCCCAAGGTCTTGGCGGTGTTCAACAGAATGGCACAGGGCACGGCGGAGTCAGTGGCGCCCACGAACCCGGGATCATTGGGGAAGTACTTGCTGTCGTAGTGGCAGGCCAGAGCGAGAAAGTTCTGAGCCTGGGCAAAAACTACGGAACCGATCGCCATCTATACGCTTCAGAGCTCGGCGACGCACTAAAGCCCGATCGGTGGCTGAAAAATCGATCTTTACCGTAGTTGATGTTGTGGTTTCCGATGCTGATGGCTTTTGTTTTCGTTTTCCGCTGCCT	-	NHEJ	QC, exon_3	QC, exon_1	QC	NA	mh:0; ins:0; tup:0; tdown:0	0
D050R07-2	22	novobreak	DEL	3L	7865604	3L	7865704	15	0	somatic_tumour	25	0.1	3L:7865604-7865704	5to3	0.42	0	-	CTGTGTCCTTTC	TCCCCGACCTGACCATGTGATCCGATCGCTGGAAAAAAAAACAACCGAACCCCAGATCGTGAGAGTTGTTTCTGTGAGGAAAACACGATCGTGAGTCTCGCACTCTCGCGAGCTTTTAATGAGAGCTTTGTCGATTCGATCCAGAAGTTGCTAGAAAACAATGAATATCAGGGTACAACAGGCTGTGTCCTTTCAATCCTTTTCATTATTATTATTTTTCAGGTTCATAATT	AACACGATCGTGAGTCTCGCACTCTCGCGAGCTTTTAATGAGAGCTTTGTCGATTCGATCCAGAAGTTGCTAGAAAACAATGAATATCAGGGTACAACAGGCTGTGTCCTTTCAATCCTTTTCATTATTATTATTTTTCAGGTTCATAATTTTGTTAGCTTATAAACCAATATCTAAGATC	FoSTeS	Pdp1, intron	Pdp1, intron	Pdp1	NA	mh:0; ins:12; tup:4; tdown:6	0
D050R07-2	25	delly	BND	3L	15021983	3L	15023631	9	1	somatic_tumour	INV00000067	1.6	3L:15021983-15023631	5to5	0.11	0.09	-	AA	GTGCGGTTGGCTGCATTTCAATGGTATTATCGTTGATGTTTTCGCAGTTCTCCCCTCTAAAATGTGCAACAAAGTTGTCTGACACTCGAGGGGATCAAAGGATTCAGAGGAATGGCCAAAAAGAAGAGCCAAAGTCAAGGCACCGAAAAGGGCAAGAAAACCTGTAATAAGAATCAGTTCTTTGGCGGCTGCTTTAAGAG	GCAGCCGCCAAAGAACTGATTCTTATTACAGGTTTTCTTGCCCTTTTCGGTGCCTTGACTTTGGCTCTTCTTTTTGGCCATTCCTCTGAATCCTTTGATCCCCTCGAGTGTCAGACAACTTTGTTGCACATTTTAGAGGGGAGAACTGCGAAAACATCAACGATAATACCATTGAAATGCAGCCAACCGCACC	NHEJ	Sytbeta, intron	CG32148, exon_1	Sytbeta, CG32148	NA	mh:0; ins:2; tup:0; tdown:0	0
D050R07-2	25	novobreak	BND	3L	15021983	3L	15023631	9	1	somatic_tumour	28	1.6	3L:15021983-15023631	5to5	0.11	0.09	-	AA	GTTTACATAGGTGTCAATTAGCAACGGTGCGGTTGGCTGCATTTCAATGGTATTATCGTTGATGTTTTCGCAGTTCTCCCCTCTAAAATGTGCAACAAAGTTGTCTGACACTCGAGGGGATCAAAGGATTCAGAGGAATGGCCAAAAAGAAGAGCCAAAGTCAAGGCACCGAAAAGGGCAAGAAAACCTGTAATAAGAATCAGTTCTTTGGCGGCTGCTTTAAGAGTGAGATTGCCCACTTATTGAAGTGGTTCCATTTTTTAAAGTGAATGGTTTTC	GCAGCCGCCAAAGAACTGATTCTTATTACAGGTTTTCTTGCCCTTTTCGGTGCCTTGACTTTGGCTCTTCTTTTTGGCCATTCCTCTGAATCCTTTGATCCCCTCGAGTGTCAGACAACTTTGTTGCACATTTTAGAGGGGAGAACTGCGAAAACATCAACGATAATACCATTGAAATGCAGCCAACCGCACC	NHEJ	Sytbeta, intron	CG32148, exon_1	Sytbeta, CG32148	NA	mh:0; ins:2; tup:0; tdown:0	0
D050R07-2	30	lumpy	DEL	3R	30472992	3R	30478842	10	2	somatic_tumour	5717	5.8	3R:30472992-30478842	5to3	0.28	-0.79	-	-	-	-	NHEJ	PH4alphaEFB, intron	spdo, 3UTR	PH4alphaEFB, spdo	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:83; snp_op:5; snp_ratio:16.57	27.29
D050R07-2	30	novobreak	DEL	3R	30472992	3R	30478842	10	2	somatic_tumour	40	5.8	3R:30472992-30478842	5to3	0.28	-0.79	-	-	CCTGCTCAAGTGCGAGACAGCCTCTCTGTCTCGCCTTGGCAGAATTAATTACTGCTGATTAATTATTCAACGCCCACCGCCTACAAGAGCATGCATCAGCCTTAATTCGTCCTTGTGGTTTGTCGAAATACCAGCACAGCATTTTGTATCAATAAGGAAATGGTTAAAGTGTTCAATTAGGTTAGTTCTTTAACAA	-	NHEJ	PH4alphaEFB, intron	spdo, 3UTR	PH4alphaEFB, spdo	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:83; snp_op:5; snp_ratio:16.57	27.29
D050R07-2	32	Control-Freec	DEL	3R	31112499	3R	31134939	-	-	somatic_tumour	-	22.4	3R:31112499-31134939	Heterozygous deletion	0.38	-0.68	-	-	-	-	-	intergenic	Gycbeta100B, intron	Prosalpha3T, CG15554, CG15556, CR46207, CR43458, Gycbeta100B	NA	snp_su:131; snp_op:2; snp_ratio:65.18; somatic_snvs:7	30.2
D050R07-2	34	Control-Freec	DUP	4	561	4	5049	-	-	somatic_tumour	-	4.5	4:561-5049	Heterozygous duplication	0.4	0.55	-	-	-	-	-	intergenic	intergenic	JYalpha	NA	snp_su:1; snp_op:0	70.03
D050R07-2	37	Control-Freec	DEL	X	705738	X	710787	-	-	somatic_tumour	-	5	X:705738-710787	Heterozygous deletion	0.42	-0.99	-	-	-	-	-	sdk, intron	sdk, intron	sdk	NA	snp_su:0; snp_op:0	0
D050R07-2	38	Control-Freec	DUP	X	1446258	X	1482723	-	-	somatic_tumour	-	36.5	X:1446258-1482723	Heterozygous duplication	0.25	0.28	-	-	-	-	-	futsch, exon_6	sta, exon_2	futsch, Gr2a, CG14785, Lrpprc2, CG14787, Ns3, O-fut2, CG14777, CG14778, CG32808, pck, CG14780, Rab27, mei-38, rush, snoRNA:M, snoRNA:Me28S-G980, sta	TRUE	low FC; snp_su:114; snp_op:0; snp_ratio:11401.0; somatic_snvs:42	46.7
D050R07-2	40	Control-Freec	DUP	X	4097544	X	4125594	-	-	somatic_tumour	-	28.1	X:4097544-4125594	Heterozygous duplication	0.27	0.31	-	-	-	-	-	intergenic	tyf, exon_7	CG6379, CG15375, Xpac, brn, cib, Nsun2, dgt4, Tip60, tyf	TRUE	low FC; snp_su:96; snp_op:17; snp_ratio:5.64; somatic_snvs:38	35.14
D050R07-2	41	novobreak	DEL	X	6979579	X	6979975	14	1	somatic_tumour	174	0.4	X:6979579-6979975	5to3	0.39	0	-	ATAGAA	CATATCTACATATAGGTTAACCTTATGATATTTCTAAAGTAAGATATGTACCTAAATGCAACCCCGTAGCCAAAACCAAGTAAAGTATTGCAACCAATAGAATAGAATGCAGAAACCGCAACGTAGCGTGCTCATAATAGGGATACCGGGAATGGGAAAGAGCGAAGGTGGCTGGCTAGGTATAGTAGTGGCCACTACGTGCTCCTCCCCCTATTTGATTCCGTCATTGGAGACACATGCTCGGAAACAATGAGTCGCCACTGTTCTGCGTCACTTAAATTGACCATTTCCGTTTGGTGGGGGC	AGTAAGATATGTACCTAAATGCAACCCCGTAGCCAAAACCAAGTAAAGTATTGCAACCAATAGAATAGAATGCAGAAACCGCAACGTAGCGTGCTCATAATAGGGATACCGGGAATGGGAAAGAGCGAAGGTGGCTGGCTAGGTATAGTAGTGGCCACTACGTGCTCCT	FoSTeS	ogre, intron	ogre, intron	ogre	NA	mh:0; ins:6; tup:3; tdown:5	0
D050R07-2	42	Control-Freec	DEL	X	7034379	X	7046160	-	-	somatic_tumour	-	11.8	X:7034379-7046160	Heterozygous deletion	0.35	-0.58	-	-	-	-	-	CG12541, intron	CG12541, intron	CG12541, CG14427	NA	snp_su:53; snp_op:2; snp_ratio:26.37; somatic_snvs:6	32.34
D050R07-2	43	Control-Freec	DUP	X	11110605	X	11127435	-	-	somatic_tumour	-	16.8	X:11110605-11127435	Heterozygous duplication	0.22	0.29	-	-	-	-	-	Hsp60A, exon_2	Gtp-bp, exon	Hsp60A, CG11122, Rpt3, Gtp-bp	TRUE	t_contamination: 1389 n_contamination: 178; low FC; snp_su:12; snp_op:0; snp_ratio:1201.0; somatic_snvs:4	47.97
D050R07-2	44	novobreak	DEL	X	11165921	X	11166208	8	0	somatic_tumour	181	0.3	X:11165921-11166208	5to3	0.29	0	-	TTGTTCG	CCAAATGCCGCGAGCTGGTTGCAAACTCGTATCAAAGATACTTTTCATATTAAAATTATATGAGTTTCAATACTTATGCCACTTTTGGGCATTTCAAATTGATATAACTGCAAGTTAAATCCGCCAATTTGGTGCATATTTAAAGTAAATATATTAAATTAAATTACAGATGGATGCTAGAATGTATCTTTGGTAATTTGTTGTTGTTCGCGGCGCTGCAGCGAATAAAATGCAAATCAAATTTTACACAATGTAATTAAGTTGCATTTTTCATTTTTGTTGTTGTTTTCGTTTGGTTCTATACAAATCTAATAATAATTAAGCATGCCAGAGATGTGTGTATCG	TGCAAGTTAAATCCGCCAATTTGGTGCATATTTAAAGTAAATATATTAAATTAAATTACAGATGGATGCTAGAATGTATCTTTGGTAATTTGTTGTTGTTCGCGGCGCTGCAGCGAATAAAATGCAAATCAAATTTTACACAATGTAATTAAGTTG	FoSTeS	intergenic	intergenic	-	NA	mh:0; ins:7; tup:5; tdown:3	0
D050R07-2	46	lumpy	DEL	X	12752270	X	12754313	13	4	somatic_tumour	6418	2	X:12752270-12754313	5to3	0.32	-0.81	-	-	-	GACAAGCGACTGAGACGCCAGTCTGATGCGTGCAAAAGAGAGGGCAACATGCGAAACGAAAAACCAAACGAAAGCGTACAAATAAATAAAGCAGAAGCGGAGAAAGAAAGATGGTTGTCGGAGGAGAAGCCGAATAAGCGCAAAGTAGCGCAACTTGCGGTGACAACAAAAGCAACAACAATAACAA	NHEJ	CR44619, exon_1	CR44619, exon_2	CR44619	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:3; snp_op:1; snp_ratio:2.98	23.5
D050R07-2	46	delly	DEL	X	12752270	X	12754313	13	4	somatic_tumour	DEL00000163	2	X:12752270-12754313	5to3	0.32	-0.81	-	-	CAAGCGACTGAGACGCCAGTCTGATGCGTGCAAAAGAGAGGGCAACATGCGAAACGAAAAACCAAACGAAAGCGTACAAATAAATAAAGCAGAAGCGGAGAAAGAAAGATGGTTGTCGGAGGAGAAGCCGAATAAGCGCAAAGTAGCGCAACTTGCGGTGACAACAAAAGCAACAACAATAACAAAAACGACAACTAGAACAACAATCGACGGTTACAGCAA	GACAAGCGACTGAGACGCCAGTCTGATGCGTGCAAAAGAGAGGGCAACATGCGAAACGAAAAACCAAACGAAAGCGTACAAATAAATAAAGCAGAAGCGGAGAAAGAAAGATGGTTGTCGGAGGAGAAGCCGAATAAGCGCAAAGTAGCGCAACTTGCGGTGACAACAAAAGCAACAACAATAACAA	NHEJ	CR44619, exon_1	CR44619, exon_2	CR44619	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:3; snp_op:1; snp_ratio:2.98	23.5
D050R07-2	46	novobreak	DEL	X	12752270	X	12754313	13	4	somatic_tumour	185	2	X:12752270-12754313	5to3	0.32	-0.81	-	-	TATATTTTTGAATGCGAAGATGAAGCAGAAGTGGAAGAGCAAGAAGAAGCACAACAGCATGCCAAATAACTAGCGCAGACGTAAAAGGGGCAAGAGAGAGCGAGAGAGGGAGAGCTCACCAGTTAACATGACACGACCAACGTCAACAACAACAACGACAGCAACAACAAGTCAACAGAACAAACCGGCACATTCAACTTAAGCACACACACACACGAAGAGGAATAAGATGATGATGATGAAGAGGGACAAGCGACTGAGACGCCAGTCTGATGCGTGCAAAAGAGAGGGCAACATGCGAAACGAAAAACCAAACGAAAGCGTACAAATAAATAAAGCAGAAGCGGAGAAAGAAAGATGGTTGTCGGAGGAGAAGCCGAATAAGCGCAAAGTAGCGCAACTTGCGGTGACAACAAAAGCAACAACAATAACAAAAACGACAACTAGAACAACAATCGACGGTTACAGCAACAATGAGGTACAGTG	GACAAGCGACTGAGACGCCAGTCTGATGCGTGCAAAAGAGAGGGCAACATGCGAAACGAAAAACCAAACGAAAGCGTACAAATAAATAAAGCAGAAGCGGAGAAAGAAAGATGGTTGTCGGAGGAGAAGCCGAATAAGCGCAAAGTAGCGCAACTTGCGGTGACAACAAAAGCAACAACAATAACAA	NHEJ	CR44619, exon_1	CR44619, exon_2	CR44619	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:3; snp_op:1; snp_ratio:2.98	23.5
D050R07-2	47	lumpy	DEL	X	13220924	X	13221024	5	1	somatic_tumour	6428	0.1	X:13220924-13221024	5to3	0.17	0	-	-	-	-	NHEJ	mew, intron	mew, intron	mew	NA	mh:0; ins:0; tup:0; tdown:0	0
D050R07-2	47	delly	DEL	X	13220924	X	13221024	5	1	somatic_tumour	DEL00000165	0.1	X:13220924-13221024	5to3	0.17	0	-	-	GCTACAAATATGTATGCATGTATGGTTATTTAGATAATATCGATTATTTTGAAGCAAACCTGAAGTAATTTAAATTGAAACACAAGCGATAAAATGCAAATTCCAAGCGACTTCAAACTCGGAACAATTGAATTATTTACAGATGATTTTC	-	NHEJ	mew, intron	mew, intron	mew	NA	mh:0; ins:0; tup:0; tdown:0	0
D050R07-2	48	Control-Freec	DUP	X	14200593	X	14202276	-	-	somatic_tumour	-	1.7	X:14200593-14202276	Heterozygous duplication	0.35	0.67	-	-	-	-	-	CG11590, exon	l(1)G0007, exon_1	CG11590, l(1)G0007	TRUE	t_contamination: 373 n_contamination: 44; snp_su:4; snp_op:1; snp_ratio:3.97	41.71
D050R07-2	50	lumpy	DEL	X	19160794	X	19162573	7	2	somatic_tumour	6702	1.8	X:19160794-19162573	5to3	0.27	-0.4	-	-	-	-	-	RhoGAP18B, intron	RhoGAP18B, intron	RhoGAP18B	TRUE	contamination at bp1=3; snp_su:20; snp_op:0; snp_ratio:2001.0	49.73
D050R07-2	50	delly	DEL	X	19160794	X	19162573	7	2	somatic_tumour	DEL00000176	1.8	X:19160794-19162573	5to3	0.27	-0.4	-	-	ATCTAATCTTAAATGTGTAGTATATCCTAAATGTATAATAATATCTAATAGTGTGCATAAATAAAGTGTTTCCCTCATTCGCATCAGAGAAATTCGCTTGACAATTGCTTGCTAATGAGACCCAGCTTATAATGGTTATATTCTATTTTTCCTGGTTTAATTTCTTTCCCCATTTCGCAATGC	-	-	RhoGAP18B, intron	RhoGAP18B, intron	RhoGAP18B	TRUE	contamination at bp1=3; snp_su:20; snp_op:0; snp_ratio:2001.0	49.73
D050R10	5	Control-Freec	DEL	3L	9102625	3L	9106160	-	-	somatic_tumour	-	3.5	3L:9102625-9106160	Heterozygous deletion	0.47	-0.94	-		-		-	bol, 3UTR	bol, intron	bol	NA	snp_su:18; snp_op:2; snp_ratio:8.96	26.53
D050R10	10	Control-Freec	DEL	X	11195850	X	11199385	-	-	somatic_tumour	-	3.5	X:11195850-11199385	Heterozygous deletion	0.47	-0.9	-		-		-	intergenic	intergenic	-	NA	snp_su:0; snp_op:0	0
D050R12	4	Control-Freec	DEL	3R	32031456	3R	32079331	-	-	somatic_tumour	-	47.9	3R:32031456-32079331	Heterozygous deletion	0.44	-0.48	-		-		-	intergenic	intergenic	CG2053, krz, mod, Map205	NA	snp_su:25; snp_op:19; snp_ratio:1.32	10.77
D050R12	6	Control-Freec	DUP	X	6268144	X	6274032	-	-	somatic_tumour	-	5.9	X:6268144-6274032	Heterozygous duplication	0.46	0.44	-		-		-	Spt6, exon_2	Spt6, exon	Spt6	NA	snp_su:0; snp_op:0	0
D050R12	7	Control-Freec	DEL	X	11196032	X	11199344	-	-	somatic_tumour	-	3.3	X:11196032-11199344	Heterozygous deletion	0.48	-0.86	-		-		-	intergenic	intergenic	-	NA	snp_su:0; snp_op:2	0
D050R14	5	Control-Freec	DEL	3L	9102666	3L	9106596	-	-	somatic_tumour	-	3.9	3L:9102666-9106596	Heterozygous deletion	0.48	-0.94	-		-		-	bol, 3UTR	bol, 3UTR	bol	NA	snp_su:20; snp_op:2; snp_ratio:9.96	22.8
D050R14	9	Control-Freec	DUP	4	328941	4	330120	-	-	somatic_tumour	-	1.2	4:328941-330120	Heterozygous duplication	0.47	0.44	-		-		-	PMCA, 3UTR	PMCA, 3UTR	CG32850, PMCA	NA	snp_su:0; snp_op:0	0
D050R16	7	Control-Freec	DUP	2R	21820177	2R	21830291	-	-	somatic_tumour	-	10.1	2R:21820177-21830291	Heterozygous duplication	0.37	0.41	-		-		-	intergenic	CG13492, intron	CG13492	NA	snp_su:0; snp_op:0	0
D050R16	15	Control-Freec	DUP	X	9363230	X	9373733	-	-	somatic_tumour	-	10.5	X:9363230-9373733	Heterozygous duplication	0.41	0.53	-		-		-	mgl, exon_12	mgl, exon_7	mgl	NA	snp_su:0; snp_op:0	0
D050R16	17	Control-Freec	DUP	X	20392158	X	20410830	-	-	somatic_tumour	-	18.7	X:20392158-20410830	Heterozygous duplication	0.38	0.42	-		-		-	l(1)G0004, exon	HERC2, exon_9	l(1)G0004, Syx16, HERC2	NA	snp_su:0; snp_op:0	0
D050R18	3	Control-Freec	DUP	2L	8538675	2L	8543670	-	-	somatic_tumour	-	5	2L:8538675-8543670	Heterozygous duplication	0.35	0.57	-	-	-	-	-	CG17834, intron	Sema-1a, exon_1	CG17834, tRNA:Asp-GTC-1-4, tRNA:Asp-GTC-1-5, Sema-1a	NA	snp_su:0; snp_op:0	0
D050R18	4	Control-Freec	DUP	2L	10278600	2L	10281930	-	-	somatic_tumour	-	3.3	2L:10278600-10281930	Heterozygous duplication	0.43	0.48	-	-	-	-	-	Utx, intron	intergenic	Utx, CG34043	NA	snp_su:0; snp_op:0	0
D050R18	5	Control-Freec	DUP	2L	10291920	2L	10293585	-	-	somatic_tumour	-	1.7	2L:10291920-10293585	Heterozygous duplication	0.46	0.6	-	-	-	-	-	CG5604, intron	Hand, intron	CG5604, Hand	NA	snp_su:0; snp_op:0	0
D050R18	6	Control-Freec	DUP	2L	10995660	2L	10997880	-	-	somatic_tumour	-	2.2	2L:10995660-10997880	Heterozygous duplication	0.48	0.78	-	-	-	-	-	CG16833, 3UTR	aub, 3UTR	CG16833, aub	NA	snp_su:0; snp_op:0	0
D050R18	8	novobreak	BND	2L	11516068	2L	11516283	6	0	somatic_tumour	2	0.2	2L:11516068-11516283	5to5	0.12	0	-	TGCA	CTTCCCTTTTTTCTACACTTCGCCACCTATCCCCATTCTCCCTACTGCCAACCCACTGCATTTTATCTAAAATAAACTGTAACTTTTTGTTAACTTTACTAGTAATACTATTTTGACCATTGCTGTATTTTTTGAAGTGTGCGAGTAAGTATGAAAAGCAAGGCATTGGAAAAACGAAACTTTCACAATTTTTGTGAAACCGCGA	CTTCCCTTTTTTCTACACTTCGCCACCTATCCCCATTCTCCCTACTGCCAACCCACTGCATTTTATCTAAAATAAACTGTAACTTTTTGTTAACTTTACTAGTAATACTATTTTGACCATTGCTGTATTTTTTGAAGTGTGCGAGTAAGTA	NHEJ	Dlg5, intron	Dlg5, intron	Dlg5	NA	mh:0; ins:4; tup:3; tdown:3	0
D050R18	9	Control-Freec	DUP	2L	11793750	2L	11795970	-	-	somatic_tumour	-	2.2	2L:11793750-11795970	Heterozygous duplication	0.43	0.62	-	-	-	-	-	CG14937, exon	crol, 3UTR	CG14937, crol	NA	snp_su:0; snp_op:1	0
D050R18	10	Control-Freec	DUP	2L	14517690	2L	14528790	-	-	somatic_tumour	-	11.1	2L:14517690-14528790	Heterozygous duplication	0.4	0.47	-	-	-	-	-	intergenic	intergenic	tRNA:Gly-GCC-1-4, tRNA:Gly-GCC-1-5, tRNA:Gly-GCC-1-6, CG33648	NA	snp_su:8; snp_op:9; snp_ratio:0.89	10.44
D050R18	11	Control-Freec	DUP	2L	15032730	2L	15034950	-	-	somatic_tumour	-	2.2	2L:15032730-15034950	Heterozygous duplication	0.43	0.57	-	-	-	-	-	GABA-B-R1, 3UTR	intergenic	GABA-B-R1	NA	snp_su:1; snp_op:0	12.4
D050R18	12	Control-Freec	DUP	2L	17457525	2L	17461410	-	-	somatic_tumour	-	3.9	2L:17457525-17461410	Heterozygous duplication	0.41	0.5	-	-	-	-	-	CG18563, exon	BicD, exon_8	CG5050, CG18563, BicD	NA	snp_su:1; snp_op:1	5.88
D050R18	18	Control-Freec	DUP	3L	16197675	3L	16202115	-	-	somatic_tumour	-	4.4	3L:16197675-16202115	Heterozygous duplication	0.44	0.67	-	-	-	-	-	intergenic	intergenic	CG33687, CG33688, CG33689, CG33690	NA	snp_su:6; snp_op:3; snp_ratio:2.0	15.54
D050R18	21	Control-Freec	DUP	3R	14618145	3R	14620920	-	-	somatic_tumour	-	2.8	3R:14618145-14620920	Heterozygous duplication	0.47	0.73	-	-	-	-	-	CG14853, 3UTR	put, 3UTR	CG14853, put	NA	snp_su:0; snp_op:0	0
D050R18	22	novobreak	BND	3R	20367342	3R	20367486	3	0	somatic_tumour	14	0.1	3R:20367342-20367486	3to3	0.04	0	-	-	CCTTAGTGGAGTTCCATACCCCGCAGACCCTTCCCCAGGAAGCTCAGAAATTCCCCCCCAAACCCCAAAACAGTTCGCAAGTTTTCACAAGAGTGCCTAGCCAAAAAAGGGGGGAAGGACGCACAAGCGCCAAACGAGGCTGGCAAAACGTCGAAAACAAGAAATCAGAAAATCAGATGTAGCTGCGATTCTCACAATCGGACGCACTGATGTGTATAATGATCTTTAGCTGGGATTTAAAACG	-	NHEJ	intergenic	intergenic	-	NA	mh:0; ins:0; tup:0; tdown:0	0
D050R18	23	Control-Freec	DUP	4	235875	4	253635	-	-	somatic_tumour	-	17.8	4:235875-253635	Heterozygous duplication	0.39	0.46	-	-	-	-	-	CG1674, intron	intergenic	CG1674, dpr7	NA	snp_su:0; snp_op:0	0
D050R18	24	Control-Freec	DUP	4	570540	4	572205	-	-	somatic_tumour	-	1.7	4:570540-572205	Heterozygous duplication	0.47	0.64	-	-	-	-	-	ND-49, intron	Ephrin, intron	ND-49, Ephrin	NA	snp_su:0; snp_op:0	0
D050R18	26	Control-Freec	DUP	4	810855	4	812520	-	-	somatic_tumour	-	1.7	4:810855-812520	Heterozygous duplication	0.47	0.67	-	-	-	-	-	Sox102F, intron	Sox102F, intron	Sox102F	NA	snp_su:0; snp_op:0	0
D050R18	27	Control-Freec	DUP	4	812520	4	831945	-	-	somatic_tumour	-	19.4	4:812520-831945	Heterozygous duplication	0.37	0.43	-	-	-	-	-	Sox102F, intron	Sox102F, intron	Sox102F	NA	snp_su:0; snp_op:0	0
D050R18	28	Control-Freec	DUP	4	892995	4	897435	-	-	somatic_tumour	-	4.4	4:892995-897435	Heterozygous duplication	0.44	0.56	-	-	-	-	-	unc-13, intron	unc-13, intron	unc-13	NA	snp_su:0; snp_op:0	0
D050R18	31	Control-Freec	DUP	X	13071915	X	13074690	-	-	somatic_tumour	-	2.8	X:13071915-13074690	Heterozygous duplication	0.44	0.54	-	-	-	-	-	rad, intron	rad, intron	rad	NA	snp_su:0; snp_op:0	0
D050R20	1	novobreak	BND	2L	15334268	2L	15343758	7	0	somatic_tumour	2	9.5	2L:15334268-15343758	5to5	0.07	0.17	CT	-	GCTCTAGGCATCCTCTGCACCTGAAAAAATTATTCAGTATCCTAGAATACGCTGTATAAATGGTATATGCAAGCTAGAAGTAATCAAAACAGTTAGGCTGATCAACGTCAGCGATTGTTGCGAGGACGAGGGTGTGGATGTGGATCATACAGATGATGAACACATCGAGGAAGAGGACGAGGACGTCGATGTGGATGTGGACTCGGACCCCAATCAGACCCAGGCTGCGGCT	GCTCTAGGCATCCTCTGCACCTGAAAAAATTATTCAGTATCCTAGAATACGCTGTATAAATGGTATATGCAAGCTAGAAGTAATCAAAACAGTTAGGCTGATCAACGTCAGCGATTGTTGCGAGGACGAGGGTGTGGATGTGGATCATACAGATGATGAACACATCG	Alt-EJ	esg, exon	intergenic	esg	NA	mh:2; ins:0; tup:0; tdown:0	0
D050R20	5	novobreak	BND	3L	12212180	3L	12212290	4	0	somatic_tumour	7	0.1	3L:12212180-12212290	3to3	0.04	0	CGGCGCCAGCGGC	-	GTTGCGGCGAATAGTATTTGAAGTCCGTGGGCGCCGGCGCTTGCGGCGCCGCAGTGTGTATGGTGGTCAGAGTGCTGTTGCTGGCGGAGATTGCTCCGCTGGCCTGCAGCTGCAGCGTCGACGGGCGTCGTGGCGCCAGCGGCACCAATACCGGTACCGGCACTGGTACGGGTGGTTCCTCCTCCTCCGCCACCACCACCG	CCGCAGTGTGTATGGTGGTCAGAGTGCTGTTGCTGGCGGAGATTGCTCCGCTGGCCTGCAGCTGCAGCGTCGACGGGCGTCGCGGCGCCAGCGGCACCAATACCGGTACCGGCACTGGTACGGGTGGTTCCTCCTCCTCCGCCACCACCACCG	Alt-EJ	app, exon	app, exon	app	NA	mh:13; ins:0; tup:0; tdown:0	0
D050R20	6	lumpy	DEL	3L	21411443	3L	21412383	11	2	somatic_tumour	4949	0.9	3L:21411443-21412383	5to3	0.12	-0.2	-	-	-	-	NHEJ	rgn, intron	rgn, intron	rgn	NA	mh:0; ins:0; tup:0; tdown:0	0
D050R20	7	Control-Freec	DUP	3R	5147556	3R	5151408	-	-	somatic_tumour	-	3.9	3R:5147556-5151408	Heterozygous duplication	0.43	0.71	-	-	-	-	-	intergenic	dpr16, intron	dpr16	NA	snp_su:0; snp_op:2	0
D050R20	13	Control-Freec	DUP	4	798220	4	799504	-	-	somatic_tumour	-	1.3	4:798220-799504	Heterozygous duplication	0.39	0.49	-	-	-	-	-	intergenic	intergenic	-	NA	snp_su:0; snp_op:1	0
D050R20	15	Control-Freec	DUP	X	10435068	X	10436352	-	-	somatic_tumour	-	1.3	X:10435068-10436352	Heterozygous duplication	0.44	0.44	-	-	-	-	-	CG32683, intron	CG32683, intron	CG32683	NA	snp_su:0; snp_op:0	0
D050R20	17	novobreak	TRA	X	10822149	3R	22494715	3	0	somatic_tumour	52	11672.6	X:10822149 3R:22494715	5to5	0.07	0	C	-	GAGTTGTCACCTACACAAAAATCAATAACGAAACCCAATAAAATAAAATCCCACTAAATACTGTTCCATATATCAAGGCTTAACCGTAGAAGCAACAGCCATAAAGTCCGGCTGATTGCAAACAATTCCGATTGATTTATTGTGGCAATGGTTAATAC	GAGTTGTCACCTACACAAAAATCAATAACGAAACCCAATAAAATAAAATCCCACTAAATACTGTTCCATATATCAAGGCTTAACCGTAGAAGCAACAGCCATAAAGTCCGGCTGATTGCAAACAATTCCGATTGATTTATTGTGGCAATGGTTAATAC	Alt-EJ	Imp, intron	intergenic	Imp	NA	mh:1; ins:0; tup:0; tdown:0	0
D050R20	21	Control-Freec	DEL	X	21557932	X	21571200	-	-	somatic_tumour	-	13.3	X:21557932-21571200	Heterozygous deletion	0.32	-0.55	-	-	-	-	-	intergenic	intergenic	-	NA	snp_su:0; snp_op:0	0
D050R22	1	novobreak	DEL	2L	140255	2L	144791	3	0	somatic_tumour	1	4.5	2L:140255-144791	5to3	0.01	-0.12	-	-	AAAGGCCCATCGGGTCTATCTGGGGCGGCTGCTAAGAATTCAAAAAACTGGTCCGACAACTCTTTCATTCGGGCTACAAGTCTGGAGTCTACCAAGTCGTCACATTCCTGCTGAAGGCTGGTGGACTTCAGCGAGAACAGCTCCGCAGCTGCTTGGCAGGAAGCTCGAGCTACTTGGG	-	NHEJ	CG31975, exon_1	CG42399, exon	ND-15, CG31976, CG31975, CG42399	NA	bp1_roo_BEL=13; mh:0; ins:0; tup:0; tdown:0	0
D050R22	2	delly	DEL	2L	3788744	2L	3790516	12	1	somatic_tumour	DEL00000000	1.8	2L:3788744-3790516	5to3	0.12	-0.03	-	-	GGGCAATAATTAGACCTCAAACGAGCATAAAATTGTTTAGCCAATTGGCATTATTCTAACAACATTAGTTCAGAGGGTTGTTGAACTCTTCGGTAGAACGGAAACTAAACCTTTTCCCCCAAACAGCTGTTAAATAATCACGAAACTGCCATGGCGAATGTGTAATAAAAACCGTTAGTGAAGTAGTTAATTGAAAGCAAAAATAAACCA	-	NHEJ	bark, intron	bark, intron	bark	NA	mh:0; ins:0; tup:0; tdown:0	0
D050R22	2	lumpy	DEL	2L	3788744	2L	3790516	12	1	somatic_tumour	512	1.8	2L:3788744-3790516	5to3	0.12	-0.03	-	-	-	-	NHEJ	bark, intron	bark, intron	bark	NA	mh:0; ins:0; tup:0; tdown:0	0
D050R22	3	Control-Freec	DUP	2R	3897936	2R	3943296	-	-	somatic_tumour	-	45.4	2R:3897936-3943296	Heterozygous duplication	0.26	0.28	-	-	-	-	-	intergenic	uex, exon_3	uex	TRUE	low FC; snp_su:10; snp_op:4; snp_ratio:2.5	11.97
D050R22	4	Control-Freec	DUP	2R	10492776	2R	10499832	-	-	somatic_tumour	-	7.1	2R:10492776-10499832	Heterozygous duplication	0.38	0.51	-	-	-	-	-	lola, intron	lola, intron	lola	NA	snp_su:0; snp_op:5; snp_ratio:0.0	0
D050R22	10	Control-Freec	DUP	4	71568	4	75600	-	-	somatic_tumour	-	4	4:71568-75600	Heterozygous duplication	0.4	0.56	-	-	-	-	-	pan, intron	pan, intron	pan	NA	snp_su:1; snp_op:1	5.01
D050R22	11	Control-Freec	DUP	4	553392	4	577584	-	-	somatic_tumour	-	24.2	4:553392-577584	Heterozygous duplication	0.31	0.33	-	-	-	-	-	Thd1, exon_2	Ephrin, 3UTR	Thd1, CR43958, Pur-alpha, ND-49, Ephrin	TRUE	low FC; snp_su:6; snp_op:2; snp_ratio:2.99	14.3
D050R22	12	Control-Freec	DUP	4	983808	4	988848	-	-	somatic_tumour	-	5	4:983808-988848	Heterozygous duplication	0.34	0.41	-	-	-	-	-	intergenic	intergenic	-	NA	snp_su:0; snp_op:1	0
D050R22	13	Control-Freec	DUP	4	1051848	4	1054368	-	-	somatic_tumour	-	2.5	4:1051848-1054368	Heterozygous duplication	0.4	0.52	-	-	-	-	-	CaMKII, intron	intergenic	CaMKII	NA	snp_su:0; snp_op:0	0
D050R22	15	Control-Freec	DUP	X	3335976	X	3354624	-	-	somatic_tumour	-	18.6	X:3335976-3354624	Heterozygous duplication	0.39	0.53	-	-	-	-	-	CR44886, ncRNA	intergenic	dnc, CR44886	NA	snp_su:0; snp_op:0	0
D050R22	17	novobreak	BND	X	15470322	X	15495936	7	0	somatic_tumour	8	25.6	X:15470322-15495936	5to5	0.1	0.02	-	CAACACCAC	ATATAACTTCATATATAGCTAGTTATATTGATAATATACCATATAAAAAAAGGTTAACCAATGCAGGGATATAACAGTTACTATTTTAAGACCACTTTTCCATTGATCATTGATCGTTTTGGAAAAATACCACAAATAGTTTTACCAACACCACCAGCTGGCTAAAATGTTCCCTGAACTCAATCGTAAAACGGATCAGTGTATTTTTCGCTGGATCCTTATTGACACGATCCTCGTAAGCGATGAGGAGCTGGCAAATGGGCTGGACAAGATCTCTCAGGCCGTATGCAAAGA	ATCGTTTTGGAAAAATACCACAAATAGTTTTACCAACACCACCAGCTGGCTAAAATGTTCCCTGAACTCAATCGTAAAACGGATCAGTGTATTTTTCGCTGGATCCTTATTGACACGATCCTCGTAAGCGATGAGGAGCTGGCAAATGGGC	FoSTeS	Grip128, exon_4	Gmap, intron	Grip128, Gmap	NA	mh:0; ins:9; tup:4; tdown:5	0
D050R24	17	Control-Freec	DEL	3L	0	3L	106488	-	-	somatic_tumour	-	106.5	3L:0-106488	Heterozygous deletion	0.37	-0.53	-		-		-	intergenic	intergenic	mthl8, CG43149, Lsp1gamma, CR44510, CR44511, CR43150, CR43988, CG13405, CG12483	NA	snp_su:46; snp_op:38; snp_ratio:1.21	10.51
D050R24	31	Control-Freec	DUP	3R	11371248	3R	11376990	-	-	somatic_tumour	-	5.7	3R:11371248-11376990	Heterozygous duplication	0.47	0.74	-		-		-	pros, intron	pros, exon_5	pros	NA	snp_su:0; snp_op:1	0
D050R24	34	Control-Freec	DUP	3R	24318414	3R	24329376	-	-	somatic_tumour	-	11	3R:24318414-24329376	Heterozygous duplication	0.42	0.54	-		-		-	Nab2, 5UTR	CG5728, exon_3	Nab2, CR46093, BRWD3, CG5728	NA	snp_su:1; snp_op:1	9.28
D050R24	40	Control-Freec	DEL	4	266220	4	292320	-	-	somatic_tumour	-	26.1	4:266220-292320	Heterozygous deletion	0.35	-0.41	-		-		-	intergenic	Syt7, intron	NfI, CR44023, Syt7	NA	snp_su:0; snp_op:0	0
D050R24	41	Control-Freec	DEL	4	728190	4	729756	-	-	somatic_tumour	-	1.6	4:728190-729756	Heterozygous deletion	0.41	-0.71	-		-		-	bt, exon_5	bt, intron	bt	NA	snp_su:0; snp_op:0	0
D050R24	42	Control-Freec	DEL	4	898362	4	903582	-	-	somatic_tumour	-	5.2	4:898362-903582	Heterozygous deletion	0.34	-0.42	-		-		-	unc-13, intron	unc-13, intron	unc-13	NA	snp_su:0; snp_op:0	0
D050R24	44	Control-Freec	DUP	X	2724840	X	2737890	-	-	somatic_tumour	-	13.1	X:2724840-2737890	Heterozygous duplication	0.43	0.51	-		-		-	fs(1)Ya, exon	crm, intron	fs(1)Ya, vilya, dwg, ttm50, CG2712, crm	NA	snp_su:0; snp_op:0	0
D050R24	45	Control-Freec	DUP	X	4619700	X	4660416	-	-	somatic_tumour	-	40.7	X:4619700-4660416	Heterozygous duplication	0.41	0.48	-		-		-	peb, intron	CG3009, exon_2	peb, CG12184, CG12179, pon, CG3081, CG3062, HLH4C, mRpL30, Torsin, Cbp80, CG15473, CG3009	NA	snp_su:1; snp_op:0	21.43
D050R24	48	Control-Freec	DUP	X	5312916	X	5329098	-	-	somatic_tumour	-	16.2	X:5312916-5329098	Heterozygous duplication	0.43	0.55	-		-		-	dhd, 3UTR	CG3309, exon_1	dhd, CG4198, CG15930, Sas10, Rnp4F, Mcm3, CG3309	NA	snp_su:0; snp_op:0	0
D050R24	49	Control-Freec	DUP	X	6083388	X	6114708	-	-	somatic_tumour	-	31.3	X:6083388-6114708	Heterozygous duplication	0.41	0.5	-		-		-	Mipp2, 3UTR	Ca-alpha1T, exon_19	raptor, Mipp2, CR44959, Nep1, Ca-alpha1T	NA	snp_su:0; snp_op:1	0
D050R24	50	Control-Freec	DUP	X	8125452	X	8168256	-	-	somatic_tumour	-	42.8	X:8125452-8168256	Heterozygous duplication	0.41	0.47	-		-		-	cyr, intron	CG2278, exon	cyr, CG2116, CG10958, CG2120, Smox, CG17982, alpha-PheRS, CG2129, CG15336, CG10959, Gbeta5, CG18262, Traf6, GIIIspla2, CG15337, CG10761, CR45536, Or7a, CG2278	NA	snp_su:0; snp_op:0	0
D050R24	51	Control-Freec	DUP	X	10465578	X	10470798	-	-	somatic_tumour	-	5.2	X:10465578-10470798	Heterozygous duplication	0.47	0.75	-		-		-	nocte, intron	nocte, exon_4	nocte	NA	snp_su:0; snp_op:0	0
D050R24	52	Control-Freec	DUP	X	11110248	X	11128518	-	-	somatic_tumour	-	18.3	X:11110248-11128518	Heterozygous duplication	0.46	0.67	-		-		-	Hsp60A, exon_2	Gtp-bp, exon_2	Hsp60A, CG11122, Rpt3, Gtp-bp	NA	snp_su:0; snp_op:0	0
D050R24	54	Control-Freec	DUP	X	15453288	X	15474690	-	-	somatic_tumour	-	21.4	X:15453288-15474690	Heterozygous duplication	0.4	0.46	-		-		-	intergenic	mh, exon_3	CG11655, shtd, CG6299, CG6294, CG15642, CG15641, Grip128, CG6308, mh	NA	snp_su:0; snp_op:0	0
D050R24	56	Control-Freec	DUP	X	17661870	X	17667090	-	-	somatic_tumour	-	5.2	X:17661870-17667090	Heterozygous duplication	0.49	0.94	-		-		-	beta-Spec, exon_2	beta-Spec, exon_2	beta-Spec	NA	snp_su:0; snp_op:0	0
D050R24	59	Control-Freec	DUP	X	19855314	X	19864188	-	-	somatic_tumour	-	8.9	X:19855314-19864188	Heterozygous duplication	0.49	0.83	-		-		-	Nup205, exon_6	CG15618, exon_4	Nup205, CG15618	NA	snp_su:1; snp_op:1	5.12
D050R24	60	Control-Freec	DUP	X	20392452	X	20442564	-	-	somatic_tumour	-	50.1	X:20392452-20442564	Heterozygous duplication	0.41	0.43	-		-		-	Syx16, exon	CG1695, exon_5	Syx16, HERC2, CG15459, CG15458, Obp19a, Obp19b, Obp19c, Obp19d, Pp4-19C, cactin, CG15456, CG11710, mal, CG1695	NA	snp_su:0; snp_op:0	0
D106R11	12	Control-Freec	DUP	2L	5118828	2L	5150856	-	-	somatic_tumour	-	32	2L:5118828-5150856	Heterozygous duplication	0.17	0.23	-	-	-	-	-	Msp300, intron	Msp300, intron	Msp300	TRUE	low FC; snp_su:132; snp_op:19; snp_ratio:6.94	20.67
D106R11	13	novobreak	TRA	2L	5230062	3R	21956534	3	0	somatic_tumour	14	16726.5	2L:5230062 3R:21956534	5to3	0.03	0	TTTTTTTTT	-	GCCAAAAGTCACTCAAGCCGAGATCAAGATGATCAGACGATTTGCTCCACAGTAGCGAAATGGAGGAGCATTCTTTTTTTTTTTTTTTGTACTTTTTTCTTGGCCGTTTTTGTAGGTGAGCTGGGCCATGAACGAGGGGCAGGCTCGACCTTACTAACCAGGCTCAATGGAGTGCTTGGG	GCCAAAAGTCACTCAAGCCGAGATCAAGATGATCAGACGATTTGCTCCACAGTAGCGAAATGGAGGAGCATTCTTTTTTTTTTTTTTTGTACTTTTTTCTTGGCCGTTTTTGTAGGTGAGCTGGGCCATGAACGAGGGGCAGGCTCGACCT	Alt-EJ	tkv, intron	Eip93F, intron	tkv, Eip93F	NA	mh:9; ins:0; tup:0; tdown:0	0
D106R11	25	Control-Freec	DEL	2L	11850988	2L	11857268	-	-	somatic_tumour	-	6.3	2L:11850988-11857268	Heterozygous deletion	0.3	-0.88	-	-	-	-	-	Mal-B2, exon_2	Pde1c, intron	Pde1c, Mal-B2, CG42751	NA	snp_su:0; snp_op:0	0
D106R11	31	novobreak	TRA	2L	15863763	X	1326498	3	0	somatic_tumour	34	14537.3	2L:15863763 X:1326498	5to5	0.04	0	GCTGCAGGTC	-	AATGTCCGGATCTCCGTTTACTTGACCATTTAGCTGCAGGTCTTGTTGCCCAAAAATGTCCACGCCTGCCACAAAATGGTAACGAAGAATTTTCCCGTCGCCTTCCGATCAAGTTTCCTTTTGAGCGTGAAATTCGGCATTTGATTTGCGGCAAAGAGGGC	AATGTCCGGATCTCCGTTTACTTGACCATTTAGCTGCAGGTCTTGTTGCCCAAAAATGTCCACGCCTGCCACAAAATGGTAACGAAGAATTTTCCCGTCGCCTTCCGATCAAGTTTCCTTTTGAGCGTGAAATTCGGCATTTGATTTGCGGCAAAGAGGGC	Alt-EJ	intergenic	fs(1)N, exon_5	fs(1)N	NA	mh:10; ins:0; tup:0; tdown:0	0
D106R11	35	novobreak	TRA	2L	18708428	3R	24261982	3	0	somatic_tumour	38	5553.6	2L:18708428 3R:24261982	3to3	0.03	0	-	-	GTGCTTGTGTGGGTGCCAATGGCCCGTGACTGTCTCCCTGGTGTTGTTTTTGTTGTAAGCTGGCCTTTGTCCAGTGGCTCAGCCGCTGCGGCGGGGGACGGGGGATGAGTAGCGTGCCGTCAAGTCATTTGCCGCTTCCACACTTGGTTGCCTGCTCTTCACTCAGAGAAAATCGTGTCCAAAAACAATCGGAAACTAAAGATTTATGCTCTATGGTACAT	-	NHEJ	Faf2, 5UTR	jar, intron	Faf2, jar	NA	mh:0; ins:0; tup:0; tdown:0	0
D106R11	60	novobreak	TRA	2R	20068550	2L	15733420	6	0	somatic_tumour	65	4335.1	2R:20068550 2L:15733420	3to5	0.1	0	GGACAC	-	GTCCAGGGAGATGGCTTCTTAGGCCATTGCACGCTTTGATTTTAATTACATTGCATCTGGGTGCCTTGACATGTGTCCTGATGTATTGTTCTGAAGCCAAAGACCTCACCACGTGTTGGATAAACATAGAGCTCTCGTTTTTTTTTTCACGAAATTCGCCAAACATCTGTCCAAAATGCAGAAA	TTTCTGCATTTTGGACAGATGTTTGGCGAATTTCGTGAAAAAAAAAACGAGAGCTCTATGTTTATCCAACACGTGGTGAGGTCTTTGGCTTCAGAAAAATAAATCAGGACACATGTCAAGGCACCCAGATGCAATGTAATTAAAATCAAAG	Alt-EJ	intergenic	CycE, intron	CycE	NA	mh:6; ins:0; tup:0; tdown:0	0
D106R11	111	novobreak	TRA	3R	20897730	2R	14485369	5	0	somatic_tumour	125	6412.4	3R:20897730 2R:14485369	3to5	0.08	0	TCAG	-	AGGCCCACTGGGCGCCCAAAAGAGAGGGAGTTGCTCCAAGAGGCGCTCACTCGAAGAAACTCCAAACGATATCAGCTGGCGTAAGGTGGGTTCCCCTATTTGGGGCAAAGTTCGCTGCCATGTCATAGCAAATTATGGCACATGGCATACTTTAAGGCGTCGCACATACTTTGTGCCTCGGCATGCCAACTATCCTGGTT	AGGCCCACTGGGCGCCCAAAAGAGAGGGAGTTGCTCCAAGAGGCGCTCACTCGAAGAAACTCCAAACGATATCAGCTGGCGTAAGGTGGGTTCCCCTATTTGGGGCAAAGTTCGCTGCCATGTCATAGCAAATTATGGCACATGGCATACT	Alt-EJ	intergenic	PRAS40, intron	PRAS40	NA	mh:4; ins:0; tup:0; tdown:0	0
D106R11	125	Control-Freec	DEL	4	357332	4	360472	-	-	somatic_tumour	-	3.1	4:357332-360472	Heterozygous deletion	0.3	-0.66	-	-	-	-	-	PMCA, intron	Hcf, intron	PMCA, Hcf	NA	snp_su:0; snp_op:3; snp_ratio:0.0	0
D106R11	127	Control-Freec	DEL	4	578388	4	580272	-	-	somatic_tumour	-	1.9	4:578388-580272	Heterozygous deletion	0.31	-0.62	-	-	-	-	-	Ephrin, 3UTR	intergenic	Ephrin	NA	snp_su:0; snp_op:0	0
D106R11	128	Control-Freec	DEL	4	1144216	4	1148612	-	-	somatic_tumour	-	4.4	4:1144216-1148612	Heterozygous deletion	0.29	-0.53	-	-	-	-	-	CG32017, intron	Kif3C, intron	CG32017, Kif3C	NA	snp_su:1; snp_op:3; snp_ratio:0.34	3.43
D106R11	137	novobreak	DEL	X	3770729	X	3773147	3	0	somatic_tumour	158	2.4	X:3770729-3773147	5to3	0.06	-0.38	-	-	CCATATTATTTCGCTCAGTATTTTCGGGTTTTGCTTCTCAGTTTGCTCTTTATTTGCCTTAGCGCTGCATTGTTTGTTCTAATTAAATCTTATCTAAACAATTTTAAGCACAAATTGTTTCAATGGCAATAAAAAGTAGAAAAAATCACAAAAGCTCGGCGAGAGCTCACAGCAAAGTCGAGGGCAATGTTCTAAAGCAAAGGCTATATATGATTGTTTTTGCATTTCGCGTTTGCTCAAA	-	NHEJ	Tlk, intron	Tlk, intron	Tlk	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:0; snp_op:0	0
D106R11	140	novobreak	BND	X	9564384	X	21258536	2	1	somatic_tumour	162	11694.2	X:9564384-21258536	3to3	0.03	-0.03	-	-	GTCCTCGTTGTGTATATCCTCTTGTCACATCTGTGCCAATCCAAAAATGATTCTTTTCACGAAAGTTTCGCTCGGCCATAAGTTTGTGCAGCGGCCATAGCAACACAACAACAATGGCAAGAGCAACGACGGACATTGGAGCTCGTATCGAGGTGACTGATCCCGACGAAACCATCATCTCCAGCACGAATGTGGTTTACTTCACGAGCAATCGAGGTCCTTTCAAGTTAAATTGGAA	-	NHEJ	Cubn, exon_11	CG32521, intron	Cubn, CG32521	NA	mh:0; ins:0; tup:0; tdown:0	0
D106R11	149	novobreak	TRA	X	13784021	3R	30001930	4	0	somatic_tumour	172	16217.9	X:13784021 3R:30001930	5to5	0.06	0	-	-	GGCTAGGTCTTCTCCCGGGAGTACAGCCACAAAGACTTTTGCCTTGCCCATCTCTTTACCGATCTCAAGTTCGAAGGCGGCATTTTGGGCCTGGCCTACGTGGGTGCAAATTCCATGGGGAAAAAGCTAAGGAAGGAAGAGGACGCAGCAGTGTACAAGAAGTACAAGAACAACAACATGAGGACGCCGACGTCGAAGCAGACAGCGACTGCGACGCCGGCAGCGGTAGCGGCAAGACAATTCGAA	-	NHEJ	inaE, exon_1	Tace, exon_5	inaE, Tace	NA	mh:0; ins:0; tup:0; tdown:0	0
D106R13	2	Control-Freec	DUP	2L	0	2L	139486	-	-	somatic_tumour	-	139.5	2L:0-139486	Heterozygous duplication	0.17	0.28	-	-	-	-	-	intergenic	CG31975, exon	ND-15, CG31976, CG31975	TRUE	low FC; snp_su:138; snp_op:66; snp_ratio:2.09	14.38
D106R13	4	Control-Freec	DUP	2L	4191770	2L	4572121	-	-	somatic_tumour	-	380.4	2L:4191770-4572121	Heterozygous duplication	0.08	0.14	-	-	-	-	-	CG3714, intron	dpy, intron	CG3714, dpy	TRUE	low FC; snp_su:1285; snp_op:427; snp_ratio:3.01	15.61
D106R13	8	lumpy	DEL	2L	9526676	2L	9528115	9	10	somatic_tumour	846	1.4	2L:9526676-9528115	5to3	0.22	-0.3	-	-	-	CTTCTGGCTTCCCAGAGCCATATATTCATTTCCTTTATCCAAAACCTTGCAACAACCACGAAGCTAAGCCTTTGGGGCTTTGGAAACTTGAAAGTTGCATTCGAGTGGCCCAAAAGAACCCGTTGAGTACTCACAAAACCATTTGGCAGTATCGGGAACA	NHEJ	Oatp30B, intron	Oatp30B, intron	Oatp30B	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:0; snp_op:0	0
D106R13	8	novobreak	DEL	2L	9526676	2L	9528115	9	10	somatic_tumour	9	1.4	2L:9526676-9528115	5to3	0.22	-0.3	-	-	TATATAATGACTATAAAGGAATATGGCCAAGCTTTGGGAACTGGTACGTGAAATGATTTCAGCTAAATGTTGGCTTAATAACTGTTTTTGTTTGCTTCTGGCTTCCCAGAGCCATATATTCATTTCCTTTATCCAAAACCTTGCAACAACCACGAAGCTAAGCCTTTGGGGCTTTGGAAACTTGAAAGTTGCATTCGAGTGGCCCAAAAGAACCCGTTGAGTACTCACAAAACCATTTGGCAGTATCGGGAACAAAGCAATATTTCAAAGAAACGTTACACCCAATGAAGCCATTTTGTATG	CTTCTGGCTTCCCAGAGCCATATATTCATTTCCTTTATCCAAAACCTTGCAACAACCACGAAGCTAAGCCTTTGGGGCTTTGGAAACTTGAAAGTTGCATTCGAGTGGCCCAAAAGAACCCGTTGAGTACTCACAAAACCATTTGGCAGTATCGGGAACA	NHEJ	Oatp30B, intron	Oatp30B, intron	Oatp30B	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:0; snp_op:0	0
D106R13	9	Control-Freec	DUP	2L	10197577	2L	10515375	-	-	somatic_tumour	-	317.8	2L:10197577-10515375	Heterozygous duplication	0.09	0.17	-	-	-	-	-	Sur, intron	Fatp, intron	Sur, Fatp	TRUE	low FC; snp_su:1124; snp_op:417; snp_ratio:2.7	15.58
D106R13	11	Control-Freec	DEL	2L	17524906	2L	17882968	-	-	somatic_tumour	-	358.1	2L:17524906-17882968	Heterozygous deletion	0.19	-0.3	-	-	-	-	-	Dhc36C, intron	intergenic	Dhc36C	TRUE	low FC; snp_su:878; snp_op:212; snp_ratio:4.14	18.55
D106R13	23	novobreak	TANDUP	3R	17310383	3R	20277308	6	2	somatic_tumour	20	2966.9	3R:17310383-20277308	3to5	0.11	0.18	-	-	TTGCTAAGTGGTGTCAAATATTTACATGATATTATATTTCGATTTTCTATTTACCTCTAACAAGTTCACTTTTGACTGGATATTCGTGTTCTAAAAGCTCTTTTATCTTTTGCATATTTTTTTTGGAAATAACTTGCTTAGAAATCAGGACCAAGGCCAAAGGACTTCAGTGCAGCCACACAATCCAGTGTCAGCGCAATAAAGTCCATAACTCGCCGCACAACAACACGGCACACAAAAAAACACAGGCCGAAAACGCTGAGGATGTG	-	-	intergenic	cic, intron	cic	NA	-	0
D106R13	27	Control-Freec	DUP	3R	21317631	3R	21320507	-	-	somatic_tumour	-	2.9	3R:21317631-21320507	Heterozygous duplication	0.38	0.84	-	-	-	-	-	Hsromega, exon_1	CG16791, 3UTR	Hsromega, CG16791	NA	snp_su:4; snp_op:0; snp_ratio:401.0	15.54
D106R13	37	Control-Freec	DUP	4	357343	4	359500	-	-	somatic_tumour	-	2.2	4:357343-359500	Heterozygous duplication	0.43	0.83	-	-	-	-	-	PMCA, intron	intergenic	PMCA	NA	snp_su:1; snp_op:2	5.41
D106R13	45	Control-Freec	DUP	X	11933962	X	11964879	-	-	somatic_tumour	-	30.9	X:11933962-11964879	Heterozygous duplication	0.26	0.44	-	-	-	-	-	cac, exon_33	cac, intron	cac	NA	snp_su:1; snp_op:0	17.31
D106R15	1	Control-Freec	DEL	2L	166370	2L	185365	-	-	somatic_tumour	-	19	2L:166370-185365	Heterozygous deletion	0.18	-0.35	-	-	-	-	-	spen, intron	spen, exon_4	spen	TRUE	low FC; snp_su:16; snp_op:6; snp_ratio:2.66	20.64
D106R15	2	Control-Freec	DUP	2L	4484785	2L	4581070	-	-	somatic_tumour	-	96.3	2L:4484785-4581070	Heterozygous duplication	0.21	0.3	-	-	-	-	-	dpy, exon_43	dpy, intron	dpy	TRUE	low FC; snp_su:302; snp_op:9; snp_ratio:33.52	29.97
D106R15	3	Control-Freec	DUP	2L	6974440	2L	6987540	-	-	somatic_tumour	-	13.1	2L:6974440-6987540	Heterozygous duplication	0.22	0.31	-	-	-	-	-	uif, exon_11	uif, intron	uif, CR44326	TRUE	low FC; snp_su:87; snp_op:1; snp_ratio:86.15	31.22
D106R15	4	Control-Freec	DEL	2L	8531375	2L	8556265	-	-	somatic_tumour	-	24.9	2L:8531375-8556265	Heterozygous deletion	0.2	-0.38	-	-	-	-	-	CG17834, intron	Sema-1a, intron	CG17834, tRNA:Asp-GTC-1-4, tRNA:Asp-GTC-1-5, Sema-1a	TRUE	low FC; snp_su:130; snp_op:11; snp_ratio:11.81	28.55
D106R15	5	Control-Freec	DUP	2L	8978085	2L	8980050	-	-	somatic_tumour	-	2	2L:8978085-8980050	Heterozygous duplication	0.47	0.79	-	-	-	-	-	CG13101, exon	CG13101, exon_3	CG13101	NA	snp_su:27; snp_op:0; snp_ratio:2701.0	34.79
D106R15	7	Control-Freec	DEL	2L	11850915	2L	11856810	-	-	somatic_tumour	-	5.9	2L:11850915-11856810	Heterozygous deletion	0.37	-1.27	-	-	-	-	-	Mal-B2, exon_2	Pde1c, intron	Pde1c, Mal-B2, CG42751	NA	snp_su:0; snp_op:0	0
D106R15	8	Control-Freec	DUP	2L	12912670	2L	12942145	-	-	somatic_tumour	-	29.5	2L:12912670-12942145	Heterozygous duplication	0.25	0.32	-	-	-	-	-	ACXC, exon_1	intergenic	ACXC, ACXB, ACXA, ACXE, CR44183	TRUE	low FC; snp_su:90; snp_op:2; snp_ratio:44.78	28.78
D106R15	15	Control-Freec	DUP	3L	21333350	3L	21341210	-	-	somatic_tumour	-	7.9	3L:21333350-21341210	Heterozygous duplication	0.33	0.5	-	-	-	-	-	CR46068, exon_1	CG7324, exon_6	Rab26, CR46068, Tsr1, CG7324	NA	snp_su:0; snp_op:1	0
D106R15	16	Control-Freec	DUP	3R	4173005	3R	4184795	-	-	somatic_tumour	-	11.8	3R:4173005-4184795	Heterozygous duplication	0.33	0.4	-	-	-	-	-	intergenic	CG12581, 3UTR	CG12581	NA	snp_su:3; snp_op:1; snp_ratio:2.98	14.8
D106R15	25	Control-Freec	DUP	3R	24234345	3R	24243515	-	-	somatic_tumour	-	9.2	3R:24234345-24243515	Heterozygous duplication	0.31	0.45	-	-	-	-	-	mask, intron	mask, exon_15	mask, scaRNA:MeU2-G25	NA	snp_su:0; snp_op:0	0
D106R15	27	Control-Freec	DEL	4	94320	4	107420	-	-	somatic_tumour	-	13.1	4:94320-107420	Heterozygous deletion	0.25	-0.45	-	-	-	-	-	pan, intron	pan, exon_13	pan	NA	snp_su:9; snp_op:2; snp_ratio:4.48	16.28
D106R15	39	lumpy	DEL	X	19569630	X	19570265	12	4	somatic_tumour	5693	0.6	X:19569630-19570265	5to3	0.26	-0.32	-	-	-	-	NHEJ	intergenic	Tao, 3UTR	Tao	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:0; snp_op:0	0
D106R15	39	delly	DEL	X	19569630	X	19570265	12	4	somatic_tumour	DEL00000019	0.6	X:19569630-19570265	5to3	0.26	-0.32	-	-	AGCATACCCTTTAACTCGAGCAACCATATATGCATTGCCATCCTTTAGCAGTTTGTCGTCCCAATCCCAACTTCTTCGCTTGAACAGCACGGGCGTGGAGTTTGTTGTGGGTGCAGTGTATCCGTGGGTTTGGGAGCAGCATGCGAGTGAGGGAAAACTAATATTTCCATGTGAA	-	NHEJ	intergenic	Tao, 3UTR	Tao	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:0; snp_op:0	0
D106R15	39	novobreak	DEL	X	19569630	X	19570265	12	4	somatic_tumour	60	0.6	X:19569630-19570265	5to3	0.26	-0.32	-	-	AACATACCCGTTAATCTGCCGAATGATGATCTGCCTGTTGGGTAATCCCTAACGAATCTAGCATACCCTTTAACTCGAGCAACCATATATGCATTGCCATCCTTTAGCAGTTTGTCGTCCCAATCCCAACTTCTTCGCTTGAACAGCACGGGCGTGGAGTTTGTTGTGGGTGCAGTGTATCCGTGGGTTTGGGAGCAGCATGCGAGTGAGGGAAAACTAATATTTCCATGTGAACATAATCTTTGAATAATTAAACGTTTCGAGGCTTTAATTTTCTATACAATTTTTATTGTTTTGACTAAGCATTTTGCAATTTGCATTAATTAACTCTAAAATAGGCTTACTTTAGTTTTATG	-	NHEJ	intergenic	Tao, 3UTR	Tao	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:0; snp_op:0	0
D106R17	9	Control-Freec	DEL	2L	11851728	2L	11856432	-	-	somatic_tumour	-	4.7	2L:11851728-11856432	Homozygous deletion	0.47	-2.8	-	-	-	-	-	Mal-B2, exon_3	Pde1c, intron	Pde1c, Mal-B2, CG42751	NA	snp_su:0; snp_op:0	0
D106R17	11	Control-Freec	DUP	2L	16595712	2L	16598848	-	-	somatic_tumour	-	3.1	2L:16595712-16598848	Heterozygous duplication	0.42	0.66	-	-	-	-	-	CG42389, intron	CG42389, intron	CG42389	NA	snp_su:0; snp_op:0	0
D106R17	17	lumpy	DEL	2R	9551429	2R	9551538	10	0	somatic_tumour	1510	0.1	2R:9551429-9551538	5to3	0.7	0	TATT	-	-	CATACATATGTAAAATAGGTGGTTTATATAAAGGAAGGGTTTCAAAAGACATTTTGTTGACGTACAAATGTAAATATTGAGCCATCTTGTATTTGGGAAATAACGATTTTTAAGCTAAATTTGTATTCTAAAGTGAAGATACATACATACATACCCTTTTTGGCATTTGTGCGTGTCCCGTGTAATTG	Alt-EJ	intergenic	intergenic	-	NA	mh:4; ins:0; tup:0; tdown:0	0
D106R17	25	novobreak	TRA	2R	18795929	3R	21957221	3	0	somatic_tumour	27	3161.3	2R:18795929 3R:21957221	3to3	0.05	0	-	-	ATCCGATGGTCTCCTCGCCTGTCCAGAAGATTCAATGAACCTTCGCTCATTTGGCGTTATCGTTGGATGTTGCGCCGGCGTACTGGAACATAGGTATAGCCACACGAATGACCAAACGATACCAACGCATCCGGGTATGTAAAAAGTGCTGGGCCAGCCCAGTGAGGATGAGGCAATGTATCCGCTAACTGACAGCATTACGACGGTGCCAAACTGGGAGCCAGAGTACGTGTAGCCCACCAGTCGTCCACGTTCCTCAGCCGGCGCCCACTTCGATAGGAACGTATGTGTCGAAGGGAAAATTCTATTTAATTTTTGCTTATTTTCCGGTGTTTCCCTGCAACGACTTAAGAACAACATTTTATT	-	NHEJ	MFS15, exon_3	Eip93F, intron	MFS15, Eip93F	NA	mh:0; ins:0; tup:0; tdown:0	0
D106R17	36	novobreak	TANDUP	3L	4552985	3L	4577242	8	0	somatic_tumour	41	24.3	3L:4552985-4577242	3to5	0.14	0.25	-	-	GGCGTTACAAATAAATCCTCAGATCCTGAAATCCTTTCATCTCGGCGCAAAACTCTTGGCACTCCTGTGCCAGTGGCACATTCAAATCGCAATTATTCTGAAATCAATTTCAATAAAAGTTTGCTGCGGTGCGATGCGATGCGAAGAGTTTGAAGGTGGTGAGGAATTGCCCAGAATGTTTAAACTGCTGAAATCAGTGAATAACCAAACCAAATATTGATTTCGATGTAGATCGCGTAACAGTGGACGGAAATATTTATTAAAAAGTATATATACGT	TGCTGCGGTGCGATGCGATGCGAAGAGTTTGAAGGTGGTGAGGAATTGCCCAGAATGTTTAAACTGCTGAAATCAGTGAATAACCAAACCAAATATTGATTTCGATGTAGATCGCGTAACAGTGGACGGAAATATTTATTAAAAAGTATATATACGT	NHEJ	CG11357, 3UTR	CG42540, intron	CG11357, CG42540	NA	mh:0; ins:0; tup:0; tdown:0	0
D106R17	39	Control-Freec	DUP	3L	7082656	3L	7095984	-	-	somatic_tumour	-	13.3	3L:7082656-7095984	Heterozygous duplication	0.33	0.44	-	-	-	-	-	intergenic	form3, intron	Cpr65Ea, Cpr65Eb, Cpr65Ec, form3	NA	snp_su:41; snp_op:37; snp_ratio:1.11	10.93
D106R17	42	lumpy	DEL	3L	9499706	3L	9502865	8	1	somatic_tumour	2765	3.2	3L:9499706-9502865	5to3	0.2	-0.1	TA	-	-	AACCTCCTCTAATGAGTTTTATTTTTAGTCGCTTGGATGCCGCAAGTACAGCTCCCAATAGGTTTCTAAAAAGTCTCCTTATCAAAATTAAGACACGCGTCAAAAAAAAAAAAAAATAATGAAATGGTAGTAACTATCTGTTGTTTCGTCTTATCTACAGAGATA	Alt-EJ	path, intron	path, intron	path	NA	mh:2; ins:0; tup:0; tdown:0	0
D106R17	42	novobreak	DEL	3L	9499706	3L	9502865	8	1	somatic_tumour	46	3.2	3L:9499706-9502865	5to3	0.2	-0.1	TA	-	CCTCACAATTGATGCAATTGAATTCGTTTCAAAAAGGCGAAGACATTTTTGGTCATTTGTATGCAAATTGAACATAATTTGGATTCATTTAAAACCTCCTCTAATGAGTTTTATTTTTAGTCGCTTGGATGCCGCAAGTACAGCTCCCAATAGGTTTCTAAAAAGTCTCCTTATCAAAATTAAGACACGCGTCAAAAAAAAAAAAA	AACCTCCTCTAATGAGTTTTATTTTTAGTCGCTTGGATGCCGCAAGTACAGCTCCCAATAGGTTTCTAAAAAGTCTCCTTATCAAAATTAAGACACGCGTCAAAAAAAAAAAAAAATAATGAAATGGTAGTAACTATCTGTTGTTTCGTCTTATCTACAGAGATA	Alt-EJ	path, intron	path, intron	path	NA	mh:2; ins:0; tup:0; tdown:0	0
D106R17	50	Control-Freec	DUP	3R	3076416	3R	3078768	-	-	somatic_tumour	-	2.4	3R:3076416-3078768	Heterozygous duplication	0.45	0.8	-	-	-	-	-	Pzl, intron	Pzl, intron	Pzl	NA	snp_su:1; snp_op:0	12.25
D106R17	51	Control-Freec	DUP	3R	4172448	3R	4177936	-	-	somatic_tumour	-	5.5	3R:4172448-4177936	Heterozygous duplication	0.47	0.69	-	-	-	-	-	intergenic	CG12581, intron	CG12581	NA	snp_su:0; snp_op:0	0
D106R17	72	Control-Freec	DUP	3R	29498784	3R	29502704	-	-	somatic_tumour	-	3.9	3R:29498784-29502704	Heterozygous duplication	0.36	0.56	-	-	-	-	-	CG2010, 3UTR	Trc8, intron	CG2010, Trc8	NA	snp_su:11; snp_op:6; snp_ratio:1.83	10.01
D106R17	75	Control-Freec	DUP	4	784	4	4704	-	-	somatic_tumour	-	3.9	4:784-4704	Heterozygous duplication	0.36	0.51	-	-	-	-	-	intergenic	JYalpha, exon_5	JYalpha	NA	snp_su:0; snp_op:1	0
D106R17	76	Control-Freec	DUP	4	62720	4	98000	-	-	somatic_tumour	-	35.3	4:62720-98000	Heterozygous duplication	0.25	0.23	-	-	-	-	-	CR43957, ncRNA	pan, intron	CR43957, pan	TRUE	low FC; snp_su:12; snp_op:4; snp_ratio:3.0	15.18
D106R17	77	Control-Freec	DUP	4	214032	4	221088	-	-	somatic_tumour	-	7.1	4:214032-221088	Heterozygous duplication	0.31	0.47	-	-	-	-	-	intergenic	CG31999, intron	CG31999	NA	snp_su:2; snp_op:2	8.42
D106R17	78	Control-Freec	DUP	4	495488	4	497840	-	-	somatic_tumour	-	2.4	4:495488-497840	Heterozygous duplication	0.38	0.58	-	-	-	-	-	intergenic	intergenic	-	NA	snp_su:1; snp_op:1	6.44
D106R17	88	Control-Freec	DUP	X	7423696	X	7426048	-	-	somatic_tumour	-	2.4	X:7423696-7426048	Heterozygous duplication	0.43	0.65	-	-	-	-	-	intergenic	intergenic	CG15036, CG32726	NA	snp_su:0; snp_op:0	0
D106R17	89	Control-Freec	DUP	X	7574224	X	7582848	-	-	somatic_tumour	-	8.6	X:7574224-7582848	Heterozygous duplication	0.31	0.4	-	-	-	-	-	intergenic	intergenic	CG11369	NA	snp_su:0; snp_op:0	0
D106R17	92	Control-Freec	DUP	X	9041088	X	9045008	-	-	somatic_tumour	-	3.9	X:9041088-9045008	Heterozygous duplication	0.44	0.7	-	-	-	-	-	Nost, intron	Nost, intron	CR43836, Nost	NA	snp_su:0; snp_op:0	0
D106R17	111	Control-Freec	DUP	X	22638784	X	22643488	-	-	somatic_tumour	-	4.7	X:22638784-22643488	Heterozygous duplication	0.37	0.61	-	-	-	-	-	intergenic	intergenic	-	NA	snp_su:10; snp_op:15; snp_ratio:0.67	11.43
D106R19	2	novobreak	BND	2L	1056682	2L	2942451	4	2	somatic_tumour	3	1885.8	2L:1056682-2942451	3to3	0.07	-0.02	-	-	ACATGCGGGTGGTGGCTCTGCGGAAAGAAGGCAGGCGGGCGGAGTAAGTACCTCATAAGAAGTGGTTCCTCTAGTCATCGTGAGTCGCCGTGGCGCATGCTGTGATAATGCCGTTTGAGCTTTGCTTTTCAAATTGAGCACTCGCTGCGCTTTAGCAAAAGTTCAAGTAACAAGTTAAGTTACTTTTAAGCTATTGGAAACAGTAATTTGAACACTACTGTTTGCTAAATGCCTCGTATTGTATTCCAT	-	NHEJ	S, intron	lilli, intron	S, lilli	NA	mh:0; ins:0; tup:0; tdown:0	0
D106R19	4	novobreak	DEL	2L	7017540	2L	7025093	5	0	somatic_tumour	6	7.6	2L:7017540-7025093	5to3	0.05	0.09	C	-	ATGCCAACACAATAGCCTGCCATGTCGTGCTGACCGGGAGCATATAGAGAAGGCATCTCTGCAGTTTCGCCGCCTAAAGAGAAATTTCAAATTAATCGATGGATTTCAGAGGAGCTCGGTCATGTGCATGCATTTGGAATCGAAGTACCAAGTTGAAAATTAGAAGTTATTGAAATAGACAGGACTTGCTCCATTGCCGCAGTCTGTTACCGGCGCATCTGAAAGCCAATGGAGCCATTCGGACAGGGACCCTTGGGCAGCGCAGGACTAGGTCGTTGAACGGATGCGGATGCTGGCCGAGCTGCTGCGCCTGATGATTCTGATGCTGCTGCTGATGCTGGTGCTGCTGCTGATG	CTGACCGGGAGCATATAGAGAAGGCATCTCTGCAGTTTCGCCGCCTAAAGAGAAATTTCAAATTAATCGATGGATTTCAGAGGAGCTCGGTCATGTGCATGCATTTGGAATCGAAGTACCAAGTTGAAAATTAGAAGTTATTGAAATAGACAGGAC	Alt-EJ	ade3, intron	CG31908, 3UTR	ade3, CG31908	NA	mh:1; ins:0; tup:0; tdown:0	0
D106R19	5	novobreak	BND	2L	11925026	2L	14218708	3	0	somatic_tumour	9	2293.7	2L:11925026-14218708	5to5	0.06	-0.07	TTGTGG	-	GACTTAAGTATTATGAGTATTTCATTTGGGCATTGTTCCATATCAAAAACATTGAAATTTCTACTCAAGAGCACACCTTCCACAATCCATTAGCCCCATCAGAGGTCTGTTCTTAAGCCGTGTCTGGAATCGCCTTGAACCCGGGCCAAGCCCCATGTCTTATGTCAGCTCAAGTTACTTCGCAGCTAGCCCCACTCATCTTGTAAGCGATCAATCTCCAAC	GCTTGGCCCGGGTTCAAGGCGATTCCAGACACGGCTTAAGAACAGACCTCTGATGGGGCTAATGGATTGTGGAAGGTGTGCTCTTGAGTAGAAATTTCAATGTTTTTGATATGGAACAATGCCCAAATGAAATACTCATAATACTTAAGTC	Alt-EJ	Pde1c, intron	Dyrk2, intron	Pde1c, Dyrk2	NA	mh:6; ins:0; tup:0; tdown:0	0
D106R19	7	novobreak	TANDUP	2R	1919579	2R	1920108	5	0	somatic_tumour	19	0.5	2R:1919579-1920108	3to5	0.12	0	T	-	GAATTACTATCAATGAATGCACTGCCTCGAAAAGGCTAACACCAAAAATATTTTCTATGCTTTTGGGTAACATTATGACAAAAAAATTTTATCGTAAATAAGATAGGCAAGGTAGGCACGATAATATATGTACATGAATATGAATATCGGCCCGCTCGTAATCCTCTTTTGCCAAGGCTGTCCGTCAAATGTTATGTCATTGTTTCTGATCTATACTTCACGTCTCTTTACGTCTCAGTACCTCTATTGAA	ATGCTTTTGGGTAACATTATGACAAAAAAATTTTATCGTAAATAAGATAGGCAAGGTAGGCACGATAATATATGTACATGAATATGAATATCGGCCCGCTCGTAATCCTCTTTTGCCAAGGCTGTCCGTCAAATGTTATGTCATTGTTTCTGA	Alt-EJ	CG17684, intron	CG17684, intron	CG17684	NA	mh:1; ins:0; tup:0; tdown:0	0
D106R19	9	novobreak	BND	2R	11179140	2R	11179338	7	0	somatic_tumour	23	0.2	2R:11179140-11179338	5to5	0.24	0	AGTTCCTCATTAAGTA	-	GTATAAATGTAGGCAATGGTTTCTGAAATATTCGAATGTTATCTGAAATATTCGAATTATGCAGTTCATGCAGTTCAAAGGTCAAATTAACAATTTCAATATATTGTAAAACTTTTCAAACCTTTTTAAACCTACTCGAACTATTTAAAACAAAAGCTTCTGAGTGCTTAAGATACCTTTTGGTTTATGTGATTTTCGTAGAAAATAGTTCCTCATTAAGTATTAATGAACTCGACTAATTTCTCTC	TCAATATATTGTAAAACTTTTCAAACCTTTTTAAACCTACTCGAACTATTTAAAACAAAAGCTTCTGAGTGCTTAAGATACCTTTTGGTTTATGTGATTTTCGTAGAAAATAGTTCCTCATTAAGTATTAATGAACTCGACTAATTTCTCTC	Alt-EJ	shn, intron	shn, intron	shn	NA	mh:16; ins:0; tup:0; tdown:0	0
D106R19	10	novobreak	DEL	2R	15560674	2R	23484819	8	0	somatic_tumour	27	7924.1	2R:15560674-23484819	5to3	0.1	-0.01	-	C	CTCATAGCCACTTTCTTTTTACGCCTGCTGATCGGCATCGTGGCCTATGCAGCCCTACAGGTGATCCTTAGATTCAGCAAATCCCTTCGATGGTGATTGGTAACCAAGTTCTGTTCTTATTCCCCCAAAGTTCGCTGTTGTTTGGATCTTGAAATGCTGGTGTTATAGACATCGAAACCATCGAATAGATTCTCGTAAGTCACACTGGCTTTCTGGTTTGATGGTTCGGGGTTTTCGTGAACTGCGGCTTGAATGACAAACGCTTGCTTGCACTTGTGTTTGGAAGAATCATCCGGAAAAATACCGCCTAGTACTTTTCCAAAG	GAAACCATCGAATAGATTCTCGTAAGTCACACTGGCTTTCTGGTTTGATGGTTCGGGGTTTTCGTGAACTGCGGCTTGAATGACAAACGCTTGCTTGCACTTGTGTTTGGAAGAATCATCCGGAAAAATACCGCCTAGTACTTTTCCAAAG	NHEJ	CG12963, 5UTR	CG43795, intron	CG12963, CG43795	NA	mh:0; ins:1; tup:0; tdown:0	0
D106R19	15	novobreak	DEL	3L	4629662	3L	4629779	11	1	somatic_tumour	37	0.1	3L:4629662-4629779	5to3	0.37	0	-	-	AAATACTTACGTTTCCACATTTAGGTTTCTTAGTAACAAACAAAACAATAATTTTTAACAATTTATTTGTATTTTAACTAGGTCTAGCTAACAATTTTTAAGTTTTTATTGCAGTGGGCGGAGAACTGGAAACTGGCTGCGGTGCTAATCCAGCGATAATATCGAGTCGATGCTGGTGCGATTACTGCGCGGCTGCAGACGCGGTCCACCCAAGTAACTAATTGGATTCGC	-	NHEJ	axo, 3UTR	axo, 3UTR	axo	NA	mh:0; ins:0; tup:0; tdown:0	0
D106R19	15	novobreak	DEL	3L	4629662	3L	4629779	11	1	somatic_tumour	38	0.1	3L:4629662-4629779	5to3	0.37	0	-	-	GAATTGAGCTGCTATCTTTAGATTTATATTTTCTTTTGGAAGTATTCGATTTCTCTTTTATAGCAAAATACTTACGTTTCCACATTTAGGTTTCTTAGTAACAAACAAAACAATAATTTTTAACAATTTATTTGTATTTTAACTAGGTCTAGCTAACAATTTTTAAGTTTTTATTGCAGTGGGCGGAGAACTGGAAACTGGCTGCGGTGCTAATCCAGCGATAATATCGAGTCGATGCTGGTGCGATTACTGCGCGGCTGCAGACGCGGTCCACCCAAGTAACTAATTGGATTCGC	-	NHEJ	axo, 3UTR	axo, 3UTR	axo	NA	mh:0; ins:0; tup:0; tdown:0	0
D106R19	17	novobreak	DEL	3L	6592718	3L	6593027	6	0	somatic_tumour	43	0.3	3L:6592718-6593027	5to3	0.23	0	-	-	CAGCATAAAGACGTCGTAGTTAGTAAAGTTAATAGTAGGTTAGATATGTAAATATATAAACTGCTGTGTTTCAAGACAACGTAAACGAAATGTAAGAATCACATACAATTTATTTGCCCTGCGCGAATCGAGACGAACAAAATCGAAAGGTTTTACAGTATTGCAGAAAGTATGTAAGGTAAACTCGTATTCCACATCAATGTCCGACTTTTTGCTGATTTGTAATGGTTTTTTAATACTTTATTGAATCGGAGTACTGGGTATGAAAACG	-	NHEJ	CG18769, 3UTR	CG18769, 3UTR	CG18769	NA	mh:0; ins:0; tup:0; tdown:0	0
D106R19	24	novobreak	BND	3L	23476221	3L	25458394	19	0	somatic_tumour	62	1982.2	3L:23476221-25458394	3to3	0.22	0.34	-	ATGATCTTGTTTCAGCCG	GAACTACAGAATTTGACACTATCACACTCGCCAAAATTAACGTAGTCAGTCCAAGCATCTTGGATCATGCAGATCTGGAGCAATTTTGGGTCGAGGAGCCCACCGACACCCCCATAAGGGAAATTTTATCCGTTGCGTCTGTTAAAGTTTTACACTCCCCTAACATATTGCATTACATAATTAAGTTCCCCAAGATTAAAATCGGCTGAAACAAGATCATCATTCTTCCGGTGGCACACCACGATACGGTGTTAAAGTTAGAGGATAATTTGGTGGCGGAGTGTAACGGATAAGTCCGCACCGTCAAGAACTGCTCCATGTCACCCGGTGCAACGTTCTGCCAGTTATCTTCGGTGAGCTCATGCGCCTAAGAACTCTACAGAAGAGCAATCTTCATCCGATCACCTATGTCGACGAAGGAATTGTAGTAATCAACCAGCACTTGTGCGCGTGGATAATGG	CCCCTAACATATTGCATTACATAATTAAGTTCCCCAAGATTAAAATCGGCTGAAACAAGATCATCATTCTTCCGGTGGCACACCACGATACGGTGTTAAAGTTAGAGGATAATTTGGTGGCGGAGTGTAACGGATAAGTCCGCACCGTCAAGAACTGCTC	FoSTeS	intergenic	CG45782, intron	AGO3, CR45174, CG17454, CG40298, CR45736, CG17698, CG43968, CG40470, CR43941, CR43942, CR40053, CG40045, Snap25, CR45159, nvd, CR12460, mRpS5, CR42722, CR42723, CR41597, scro, CG40472, ND-AGGG, Set1, MED21, UQCR-11, CR40354, CR40450, CG45782	NA	bp1_Stalker4_Gypsy=6; bp2_springer_Copia=4; mh:0; ins:18; tup:6; tdown:4; snp_su:88; snp_op:95; snp_ratio:0.93	8.73
D106R19	24	novobreak	BND	3L	23476221	3L	25458394	19	0	somatic_tumour	63	1982.2	3L:23476221-25458394	3to3	0.22	0.34	-	ATGATCTTGTTTCAGCCG	GTCCAAGCATCTTGGATCATGCAGATCTGGAGCAATTTTGGGTCGAGGAGCCCACCGACACCCCCATAAGGGAAATTTTATCCGTTGCGTCTGTTAAAGTTTTACACTCCCCTAACATATTGCATTACATAATTAAGTTCCCCAAGATTAAAATCGGCTGAAACAAGATCATCATTCTTCCGGTGGCACACCACGATACGGTGTTAAAGTTAGAGGATAATTTGGTGGCGGAGTGTAACGGATAAGTCCGCACCGTCAAGAACTGCTCCATGTCACCCGGTGCAACGTTCTGCCAGTTATCTTCGGTGAGCTCATGCGCCTAAGAACTCTACAGAAGAGCAATCTTCATCCGATCACCTA	CCCCTAACATATTGCATTACATAATTAAGTTCCCCAAGATTAAAATCGGCTGAAACAAGATCATCATTCTTCCGGTGGCACACCACGATACGGTGTTAAAGTTAGAGGATAATTTGGTGGCGGAGTGTAACGGATAAGTCCGCACCGTCAAGAACTGCTC	FoSTeS	intergenic	CG45782, intron	AGO3, CR45174, CG17454, CG40298, CR45736, CG17698, CG43968, CG40470, CR43941, CR43942, CR40053, CG40045, Snap25, CR45159, nvd, CR12460, mRpS5, CR42722, CR42723, CR41597, scro, CG40472, ND-AGGG, Set1, MED21, UQCR-11, CR40354, CR40450, CG45782	NA	bp1_Stalker4_Gypsy=6; bp2_springer_Copia=4; mh:0; ins:18; tup:6; tdown:4; snp_su:88; snp_op:95; snp_ratio:0.93	8.73
D106R19	34	lumpy	DEL	X	16289160	X	16289225	7	0	somatic_tumour	4463	0.1	X:16289160-16289225	5to3	0.12	0	-	-	-	-	NHEJ	caz, intron	caz, intron	caz	NA	mh:0; ins:0; tup:0; tdown:0	0
D106R1	247	novobreak	TRA	3R	14796796	2L	17053333	17	0	somatic_tumour	299	2256.5	3R:14796796 2L:17053333	3to5	0.46	0	GGATGAGCAGAA	-	CCATGCACCTTAGCCTTCGAATTTCACAAGCCCTTGCTGCCAAAAGTTTTGGCTTGAATTTAATTTGTTGTAAAGTTTCGGATGAGCAGAACCACACGCTCAGTAGGGAGCGCTGCAATCGGTGGATCTATAAGTACGACTTTGGGTACAAAAGTATGAATACAGAGGTAAG	TTTCACAAGCCCTTGCTGCCAAAAGTTTTGGCTTGAATTTAATTTGTTGTAAAGTTTCGGATGAGCAGAACCACACGCTCAGTAGGGAGCGCTGCAATCGGTGGATCTATAAGTACGACTTTGGGTACAAAAGTATGAATACAGAGGTAAG	Alt-EJ	CG14855, exon_1	intergenic	CG14855	NA	mh:12; ins:0; tup:0; tdown:0	0
D106R1	75	Control-Freec	DUP	2R	7531149	2R	7537800	-	-	somatic_tumour	-	6.7	2R:7531149-7537800	Heterozygous duplication	0.39	0.57	-	-	-	-	-	Drat, intron	CG2137, exon	Drat, CR44209, Cyt-b5, CG2137	NA	snp_su:1; snp_op:1	10.66
D106R1	313	Control-Freec	DUP	4	376890	4	393148	-	-	somatic_tumour	-	16.3	4:376890-393148	Heterozygous duplication	0.39	0.58	-	-	-	-	-	dati, intron	dati, intron	dati, CR45125	NA	snp_su:2; snp_op:2	5.99
D106R1	316	Control-Freec	DUP	4	854284	4	874976	-	-	somatic_tumour	-	20.7	4:854284-874976	Heterozygous duplication	0.38	0.59	-	-	-	-	-	Gyf, intron	unc-13, intron	Gyf, CR43425, unc-13	NA	snp_su:0; snp_op:2	0
D106R1	291	Control-Freec	DUP	3R	26026102	3R	26033492	-	-	somatic_tumour	-	7.4	3R:26026102-26033492	Heterozygous duplication	0.37	0.53	-	-	-	-	-	intergenic	E(spl)m6-BFM, 3UTR	E(spl)m5-HLH, E(spl)m6-BFM	NA	snp_su:0; snp_op:0	0
D106R1	200	Control-Freec	DUP	3L	22036980	3L	22046587	-	-	somatic_tumour	-	9.6	3L:22036980-22046587	Heterozygous duplication	0.34	0.45	-	-	-	-	-	Oct-TyrR, intron	Oct-TyrR, intron	Oct-TyrR	NA	snp_su:4; snp_op:1; snp_ratio:3.97	17.11
D106R1	248	Control-Freec	DUP	3R	15170192	3R	15182755	-	-	somatic_tumour	-	12.6	3R:15170192-15182755	Heterozygous duplication	0.34	0.5	-	-	-	-	-	Gyc88E, intron	Gyc88E, intron	Gyc88E, Mf	NA	snp_su:0; snp_op:0	0
D106R1	360	Control-Freec	DUP	X	17733783	X	17743390	-	-	somatic_tumour	-	9.6	X:17733783-17743390	Heterozygous duplication	0.34	0.45	-	-	-	-	-	CG42684, intron	CG42684, intron	CG42684	NA	snp_su:0; snp_op:0	0
D106R1	179	Control-Freec	DUP	3L	15782823	3L	15801298	-	-	somatic_tumour	-	18.5	3L:15782823-15801298	Heterozygous duplication	0.32	0.45	-	-	-	-	-	intergenic	intergenic	-	NA	snp_su:23; snp_op:28; snp_ratio:0.82	10.25
D106R1	275	Control-Freec	DUP	3R	21879573	3R	21889180	-	-	somatic_tumour	-	9.6	3R:21879573-21889180	Heterozygous duplication	0.32	0.48	-	-	-	-	-	CR45046, exon_2	CG6678, exon_4	P5CDh2, CR45046, CG31465, fit, CG17819, dnd, CG6678	NA	snp_su:40; snp_op:36; snp_ratio:1.11	10.41
D106R1	164	Control-Freec	DUP	3L	6324362	3L	6334708	-	-	somatic_tumour	-	10.3	3L:6324362-6334708	Heterozygous duplication	0.31	0.43	-	-	-	-	-	intergenic	CG13300, intron	Or65b, Or65c, CG13300	NA	snp_su:31; snp_op:19; snp_ratio:1.63	11.37
D106R1	39	Control-Freec	DUP	2L	11866123	2L	11880164	-	-	somatic_tumour	-	14	2L:11866123-11880164	Heterozygous duplication	0.3	0.41	-	-	-	-	-	Pde1c, intron	Pde1c, intron	Pde1c	NA	snp_su:52; snp_op:3; snp_ratio:17.28	29.85
D106R1	28	Control-Freec	DUP	2L	8762323	2L	8784493	-	-	somatic_tumour	-	22.2	2L:8762323-8784493	Heterozygous duplication	0.29	0.36	-	-	-	-	-	intergenic	intergenic	LManIII, LManIV, LManV, LManVI, CG42710	TRUE	low FC; snp_su:57; snp_op:8; snp_ratio:7.12	24.54
D106R1	117	novobreak	TRA	2R	19616497	X	21243323	10	0	somatic_tumour	138	1626.8	2R:19616497 X:21243323	3to5	0.25	0	-	-	AAATGAACGTTAAGAAATGAAAAAGTTCGGCCACTTGAGCCACTTAAATGCTCGTGAAAACAAACAAATTGAGTGAACTTGGCTGGCGCTTGTCTGCAGTTGCGACTGTAGCGCTATATGTACATATACTTACGTATTTTACTATTCGAGTCGAACAAATGATCCGTCGTTTGACTAAGATC	-	NHEJ	sm, intron	CG32521, intron	sm, CG32521	NA	bp2_rover_Gypsy=12; mh:0; ins:0; tup:0; tdown:0	0
D106R1	20	novobreak	TRA	2L	7217971	2R	22650610	3	1	somatic_tumour	24	15432.6	2L:7217971 2R:22650610	5to5	0.13	0	CCGAATA	-	TGGGCCACCTCGTTCAGTCGCGGCTGGTAGGTAGGTTGGTCCTGGGTAGGTTGGTCTTGGTTCTGTTTCTCAGTTAACTCGCTTGGGGTTTCCATTTTTATCACAATAATCTTTACCGAATACCTAAATACCGCTGGGAGTACAATAAAGATAAAACCAGTACGCTGGTCCTTCGTCCAAATTGTGGAAGTCGTCTATCGACTATGGTGAGCAAAATCGACCAGAAATCATGACATAGC	TGGGCCACCTCGTTCAGTCGCGGCTGGTAGGTAGGTTGGTCCTGGGTAGGTTGGTCTTGGTTCTGTTTCTCAGTTAACTCGCTTGGGGTTTCCATTTTTATCACAATAATCTTTACCGAATACCTAAATACCGCTGGGAGTACAATAAAGA	Alt-EJ	CG13784, intron	nsr, 5UTR	CG13784, nsr	NA	mh:7; ins:0; tup:0; tdown:0	0
D106R1	120	novobreak	TRA	2R	20274536	3R	21246770	4	0	somatic_tumour	141	972.2	2R:20274536 3R:21246770	3to3	0.12	0	-	-	CTTACGCAAGTGCCAGCACTTACGGGCACTTCATTCAGGTTGCGTCATAGACCTCGGTAGTGATTACCCCGTGATTCTACGCACTCCCCCCCGCACACCCTGCAAGGGCACACTCACCGCTCAGCTGATCAGTTATTTAACGGTCGTAGCCTTGGCGAGAACGTTTCTT	AAGAAACGTTCTCGCCAAGGCTACGACCGTTAAATAACTGATCAGCTGAGCGGTGAGTGTGCCCTTGCAGGGTGTGCGGGGGGGAGTGCGTAGAATCACGGGGTAATCACTACCGAGGTCTATGACGCAACCTGAATGAAGTGCCCGTAAGTGCTGGCACTTGCGTAAG	NHEJ	intergenic	intergenic	-	NA	mh:0; ins:0; tup:0; tdown:0	0
D106R1	194	novobreak	TRA	3L	20006935	3R	24241046	3	0	somatic_tumour	228	4234.1	3L:20006935 3R:24241046	3to5	0.12	0	-	-	GAGACAGCTCCAGCAGCAGTTGGCAGCAGCCTCCGCGGCAGCGGCGCACGCCAAAGCGTCTGTAGTCCACCAGAAGCAGCAGCATGGAGAGGGAGATCAGCAATGCGGTGCTATGTAAAAATTGGAGTTAGTGCTCGTAATGGTGTGACTTCTGTCTC	-	NHEJ	kug, intron	mask, intron	kug, mask	NA	mh:0; ins:0; tup:0; tdown:0	0
D106R1	225	novobreak	TRA	3R	10454305	X	11008343	3	0	somatic_tumour	272	554	3R:10454305 X:11008343	3to5	0.11	0	AAAT	-	CCCAAACCGTTTGCCACTTACCATTTACCAACTAGAAAACTTCTGGCCCCAAAACTTTGTGATGTCACTTTCAATCTGGCTGGAATGTAAATTATACAAAGTGTCCAGCTTCCCTACAGGATGCGGTTTTGGACTTGTATTCGTATTCGTATTCGTATTC	CCCAAACCGTTTGCCACTTACCATTTACCAACTAGAAAACTTCTGGCCCCAAAACTTTGTGATGTCACTTTCAATCTGGCTGGAATGTAAATTATACAAAGTGTCCAGCTTCCCTACAGGATGCGGTTTTGGACTTGTATTCGTATTCGTATTCGTATTC	Alt-EJ	intergenic	CG42339, intron	CG42339	NA	mh:4; ins:0; tup:0; tdown:0	0
D106R1	118	lumpy	BND	2R	19864564	2R	21577542	3	0	somatic_tumour	1827_1	1713	2R:19864564-21577542	3to3	0.1	-0.04	AAA	-	-	CTGTCGTGTTGCGTGTCCTTTGTGCATTTAACGGCTATTCGAAGGCTAAGGCAAAAATATACAAGTTTTTCATAGCTAATTAGTATTATACAAATATTTAAAGTCTTGAATGCTAGGTATTCATGCAAATTGCTTTTCTTTCTACCATTTG	Alt-EJ	intergenic	intergenic	-	NA	mh:3; ins:0; tup:0; tdown:0	0
D106R1	4	novobreak	TRA	2L	1102719	3R	17589417	3	0	somatic_tumour	6	16486.7	2L:1102719 3R:17589417	5to3	0.09	0	-	-	CGCCAACGCCGCCGGTCGCCGGTGGCAGAGGCAGCAGCAGCAGCAGCAGCAGCAGAGATAGTACCAGTAGCCAAAGTGGGCGCATGTAATAAGGGGGAGTGGACCCGAACAACGTGGGCGTGCTCCCATGAACATCTGTTCGTCCTATTTACGTTTAGTTTAGTTTTTCCTTTGGGTTTGTTTTTTTTTTTTCACTGCACGCACCGTGAGAACACAAGAGTCTTTGGTAGTTCAAGAGCTCGCAGCCTCTTTCAGGTGAATAATCGAGACC	GGGCGCATGTAATAAGGGGGAGTGGACCCGAACAACGTGGGCGTGCTCCCATGAACATCTGTTCGTCCTATTTACGTTTAGTTTAGTTTTTCCTTTGGGTTTGTTTTTTTTTTTTCACTGCACGCACCGTGAGAACACAAGAGTCTTTGGTAGTTCAAGA	NHEJ	intergenic	intergenic	-	NA	mh:0; ins:0; tup:0; tdown:0	0
D106R1	11	novobreak	TRA	2L	4052951	2R	15686210	3	0	somatic_tumour	14	11633.3	2L:4052951 2R:15686210	5to3	0.09	0	-	-	TTCGGAAGATTGACTGAGTTTAGAGTGGCATGAAGTTGGGCAACACCTAGTGGAAAATTGCCATTCTCTTACTTTTTAGTTGAAGATTTCTTTTTTTCGCACAGCAACCCTCGCACGTCTACCTCATCGAAGATGGTATCATGCTCTGGCTGGCGGTGATTGGGAACTCGAC	TTCGGAAGATTGACTGAGTTTAGAGTGGCATGAAGTTGGGCAACACCTAGTGGAAAATTGCCATTCTCTTACTTTTTAGTTGAAGATTTCTTTTTTTCGCACAGCAACCCTCGCACGTCTACCTCATCGAAGATGGTATCATGCTCTGGCTGGCGGTGATTGGGAACTCGAC	NHEJ	ed, intron	Ranbp11, intron	ed, Ranbp11	NA	mh:0; ins:0; tup:0; tdown:0	0
D106R1	49	novobreak	TRA	2L	14824598	3R	6580568	3	0	somatic_tumour	56	8244	2L:14824598 3R:6580568	5to3	0.09	0	-	-	ATACGCCAAACTCAAAAATTCACCGATGGAGAGGCGCTGGACTGCAAAGGAATTTAAAGCGGTTGTGGTTGAAAAATTGTGGCCAATAGTACGAGCTGAAATTTGGGCCCACAATAAGGTCGTTGGGGGCAGCCTTCGATGGGCGGTCAACTGCACAAGTCAAGTGTGAATGAGTGTGATTTGATAAATCACTGCGATATAACAAGGCTCAACGTATCTGAAACTTAGATACCGA	-	NHEJ	intergenic	dpr11, intron	dpr11	NA	mh:0; ins:0; tup:0; tdown:0	0
D106R1	102	novobreak	TRA	2R	15578842	3R	27432774	3	0	somatic_tumour	119	11853.9	2R:15578842 3R:27432774	3to3	0.09	0	AGGA	-	GCATTTAATTAAGATTTGCCACAAAAATCCACATTCAGCGGTTCGCTGCGATTCGAGGCGGCTGGGGAGCGAGTGCCGGGGCAAATAGCGATTCATCGATTCCATTTCCATTTTCCCCAAAATTTTCCTGCCCTGCACCGCCCTGGCCATTTTTTTTTTTTCGCCCGGCACCTCGTAAGA	TCTTACGAGGTGCCGGGCGAAAAAAAAAAAATGGCCAGGGCGGTGCAGGGCAGGAAAATTTTGGGGAAAATGGAAATGGAATCGATGAATCGCTATTTGCCCCGGCACTCGCTCCCCAGCCGCCTCGAATCGCAGCGAACCGCTGAATGTG	Alt-EJ	intergenic	side, intron	side	NA	mh:4; ins:0; tup:0; tdown:0	0
D106R1	135	novobreak	TRA	2R	24804025	3L	10449427	3	0	somatic_tumour	161	14354.6	2R:24804025 3L:10449427	5to5	0.09	0	-	-	GTTTTAAAGATTGGTATTGATAGATAAATGCTAAATGTTGTAAAGAATTTAACTCGAAGTAAGATTACCTTTTATAGTTTATGGCTGAAGTTCCCATGCCAACTGATTGATTTCGCTCTGATCTTTGCTTTTCAGCTGAATCAAATCCCTCCATCCGATGGATGTGGATTCGAACTCGTTTCGCTAGTAACTCGAACTACGGCAGACTCCCAGTTGAGTCATGGGAAGTATTAAGC	GTTTTAAAGATTGGTATTGATAGATAAATGCTAAATGTTGTAAAGAATTTAACTCGAAGTAAGATTACCTTTTATAGTTTATGGCTGAAGTTCCCATGCCAACTGATTGATTTCGCTCTGATCTTTGCTTTTCAGCTGAATCAAATCCCTCCATCCGATGGATGTGGA	NHEJ	intergenic	intergenic	-	NA	mh:0; ins:0; tup:0; tdown:0	0
D106R1	196	novobreak	TRA	3L	20393522	4	626084	3	0	somatic_tumour	231	19767.4	3L:20393522 4:626084	5to3	0.09	0	CCCAC	-	GTCGAATATGAGGAGCAGGCATTCGATGGTCAGATCCTTCAAGCTCATGCGGGAGCTCATCATATCTTTCAACGCCAATTCGTGAGATTAGCTCATATTCCCACACACACCCACACATCTGCAGTGGACTCATGCACGTCTTACAAACACAAGATTTTCTGGGTGTTGCGTTGTGT	ATGGTCAGATCCTTCAAGCTCATGCGGGAGCTCATCATATCTTTCAACGCCAATTCGTGAGATTAGCTCATATTCCCACACACACCCACACATCTGCAGTGGACTCATGCACGTCTTACAAACACAAGATTTTCTGGGTGTTGCGTTGTGT	Alt-EJ	CG33969, 5UTR	intergenic	CG33969	NA	mh:5; ins:0; tup:0; tdown:0	0
D106R1	337	novobreak	TRA	X	7541977	3R	15395074	3	0	somatic_tumour	402	7853.1	X:7541977 3R:15395074	5to3	0.08	0	CGTTTGAA	-	GCGCGTGAAGTGAACAAGAAAATCCGTGCAAAAAAAAAAAAAAAGAAAAAATGAGAGGCAACCCCTTGGCCCGTTTGAACGAGTACGAGTATCTGCTTTTCGAATCAAATATTTCTTTTAGCGTTGATTCCTCTCGTTGATTTCTCGTTTT	GCGCGTGAAGTGAACAAGAAAATCCGTGCAAAAAAAAAAAAAAAGAAAAAATGAGAGGCAACCCCTTGGCCCGTTTGAACGAGTACGAGTATCTGCTTTTCGAATCAAATATTTCTTTTAGCGTTGATTCCTCTCGTTGATTTCTCGTTTT	Alt-EJ	CG32719, intron	Rbp, intron	CG32719, Rbp	NA	mh:8; ins:0; tup:0; tdown:0	0
D106R1	355	novobreak	TRA	X	15672636	3L	20809241	3	0	somatic_tumour	422	5136.6	X:15672636 3L:20809241	5to3	0.08	0	-	CAG	AAGCAGAAGGTGAGGGAGCAGAGGAGCTCGCCTAGCCGTGCTAATCCCCGAGCGAACAGCTGTCCGGCCCAAGGATTGTGCATTGTGGGTCCCTATGTGTGATTCCTCGGATTTCCTCAAAACTCGGCCGCTCTGTCCTGGCGCCAGTACCAGCGCAACGTGACCGTTTCTCGTCGCCTTCTAAATGCCGCTGAACGTACTG	GCGAACAGCTGTCCGGCCCAAGGATTGTGCATTGTGGGTCCCTATGTGTGATTCCTCGGATTTCCTCAAAACTCGGCCGCTCTGTCCTGGCGCCAGTACCAGCGCAACGTGACCGTTTCTCGTCGCCTTCTAAATGCCGCTGAACGTACTG	NHEJ	intergenic	CG3634, 5UTR	CG3634	NA	mh:0; ins:3; tup:3; tdown:3	0
D106R1	3	novobreak	TRA	2L	1075651	3R	30198906	3	0	somatic_tumour	5	29123.3	2L:1075651 3R:30198906	5to3	0.07	0	GACGGCA	-	GTTTCAGTTGGGTTAGAGGCAACACAACTGGGGGAAGTTCGAGACCGCTCTTTATCGGGCCTCTCTATTTACGTTTCCAGAGTGGGACGGCATAGTCGGTTTTAGCATAATTTGATGACTTTTATGTAAACTGAGACCCGTCATGAGTAATGCCAAAGCAAACAACCAAAGGC	GTTTCAGTTGGGTTAGAGGCAACACAACTGGGGGAAGTTCGAGACCGCTCTTTATCGGGCCTCTCTATTTACGTTTCCAGAGTGGGACGGCATAGTCGGTTTTAGCATAATTTGATGACTTTTATGTAAACTGAGACCCGTCATGAGTAATGCCAAAGCAAACAACCAAAGGC	Alt-EJ	S, intron	CG9743, intron	S, CG9743	NA	mh:7; ins:0; tup:0; tdown:0	0
D106R1	185	novobreak	TRA	3L	17193889	2R	20632242	3	0	somatic_tumour	217	3438.4	3L:17193889 2R:20632242	3to5	0.07	0	GGGCTGT	-	GTGACTGTGACTTTCTTCAATGGCCGGAAAGAATTGCAAGCCAAGTTTGTTTTATTGCTAATTAGCTGGACACACTCATTCTTGGCTGGGCTGTTAGTTGGCGTGGAGGGGGCGTGGCCCGGCCTTTGCATACCCGGCACACAATTTATATTTGCCAAAGCTGCCGCTGACGCTGATGCTCGGGCATCGGAGCTTCGGAGCATCGGGGCTTCCAGGCAGACAGGCAGT	GTGACTGTGACTTTCTTCAATGGCCGGAAAGAATTGCAAGCCAAGTTTGTTTTATTGCTAATTAGCTGGACACACTCATTCTTGGCTGGGCTGTTAGTTGGCGTGGAGGGGGCGTGGCCCGGCCTTTGCATACCCGGCACACAATTTATAT	Alt-EJ	Rbp6, intron	Rcd6, intron	Rbp6, Rcd6	NA	mh:7; ins:0; tup:0; tdown:0	0
D106R1	193	novobreak	TRA	3L	19691046	3R	9825857	3	0	somatic_tumour	227	9865.2	3L:19691046 3R:9825857	3to3	0.07	0	-	-	GCCGAGATGTTGCACGTGTGTGCCCCTATGCGTTGGCTTCTGGTGCCTCCACCAGCGATGGATGCCTTTGATTTCATTTCACTTCATTTCATTTTGTTGCCGGTGGAGGCAAACTCGCGGCTGCCCATCGAGGAGCCACCCCGTGTGGGAGATGGTCATGAACGAGCTGGACCGGCGCGACGATCCCACCTTCGACGAGTCCCTGCCCGGTTGCCATATGG	-	NHEJ	verm, exon	intergenic	verm	NA	mh:0; ins:0; tup:0; tdown:0	0
D106R1	288	novobreak	TRA	3R	24323979	2R	14690066	3	0	somatic_tumour	342	9633.9	3R:24323979 2R:14690066	5to3	0.07	0	GCAA	-	GCTCGGAGCCGTGGAACTTTCACACACTGCGCGACCACGAGCTGGTGCGTGTGATTGGAATCAAGTACGAAATCCGCCCACCCCGATTATGTTGCTTGAAGTTGGCCATCATCGATGAGGAGGGCAAACTAATGAATGACTGGAAAATTGTGTACCAAATTCTGTGTGCTTGTATCAACTGAAG	ACCACGAGCTGGTGCGTGTGATTGGAATCAAGTACGAAATCCGCCCACCCCGATTATGTTGCTTGAAGTTGGCCATCATCGATGAGGAGGGCAAACTAATGAATGACTGGAAAATTGTGTACCAAATTCTGTGTGCTTGTATCAACTGAAG	Alt-EJ	BRWD3, exon_9	mspo, intron	BRWD3, mspo	NA	mh:4; ins:0; tup:0; tdown:0	0
D106R1	298	lumpy	BND	3R	28446465	3R	28789522	3	0	somatic_tumour	3930_1	343.1	3R:28446465-28789522	3to3	0.07	0	TGGCGTATGCGTAAT	-	-	CCGCACAATCAAACGCACACAGGCAGGAACACTCAGTCCGCAATGTATCTCAGCTGTAACATGTGGCGTATGCGTAATCAAAATGTTTTGCCTGCTAAATGGCAAACATAAACAGATGACGGCTGTCAGTTGTTGGCAGTTGTTGCGTGTTGACAA	Alt-EJ	beat-VI, intron	intergenic	beat-VI	NA	mh:15; ins:0; tup:0; tdown:0	0
D106R1	298	novobreak	BND	3R	28446465	3R	28789522	3	0	somatic_tumour	354	343.1	3R:28446465-28789522	3to3	0.07	0	TGGCGTATGCGTAAT	-	TTGTCAACACGCAACAACTGCCAACAACTGACAGCCGTCATCTGTTTATGTTTGCCATTTAGCAGGCAAAACATTTTGATTACGCATACGCCACATGTTACAGCTGAGATACATTGCGGACTGAGTGTTCCTGCCTGTGTGCGTTTGATTGTGCGG	CCGCACAATCAAACGCACACAGGCAGGAACACTCAGTCCGCAATGTATCTCAGCTGTAACATGTGGCGTATGCGTAATCAAAATGTTTTGCCTGCTAAATGGCAAACATAAACAGATGACGGCTGTCAGTTGTTGGCAGTTGTTGCGTGTTGACAA	Alt-EJ	beat-VI, intron	intergenic	beat-VI	NA	mh:15; ins:0; tup:0; tdown:0	0
D106R1	319	novobreak	TRA	X	1709179	3L	24938100	3	0	somatic_tumour	381	23228.9	X:1709179 3L:24938100	5to3	0.07	0	-	-	GACCAGCACCGCCCGTGGAACGAATCGCGGAGCAGGCGGGCGCAGGATATCCCAGTGAGCAGGAGCAGCAGCAGCAGAAACAGCGTCCACACGGACCGTGTGCCTAGGGGGCAGGAGTTCTCGGTGATCCAAACTACAATTCTCAACGGCATCCGGTTTCATATTGGAGGACAATTTGTTGACACACAATTATGCAGATTAACAA	GGCGGGCGCTAGGATATCCCAGTGAGCAGGAGCAGCAGCAGCAGAAACAGCGTCCACACGGACCGTGTGCCTAGGGGGCAGGAGTTCTCGGTGATCCAAACTACAATTCTCAACGGCATCCGGTTTCATATTGGAGGACAATTTGTTGACACCCAATTATGCAGATTAACAA	NHEJ	CG3795, exon	intergenic	CG3795	NA	mh:0; ins:0; tup:0; tdown:0	0
D106R1	339	novobreak	TRA	X	8160492	2R	24310150	3	0	somatic_tumour	404	16149.7	X:8160492 2R:24310150	5to3	0.07	0	-	-	GTCTGAGGTTCGGGACGCGCTGCGAGCTCAGCCTCAGGCCAGTGACATTCGCCTGTTGATCTTCACGGCGGCGGCCAGCAGTGTGGAGCACGAGAGAACTCTCATTCCGGTGCCTCTCTATGTTTTTTTTTTTTTTTTTGGATTTTGGGCGGATTCTGTGGCTGCGGCCATATGTCAG	-	-	CG15337, exon	betaTub60D, intron	CG15337, betaTub60D	NA	-	0
D106R1	349	novobreak	TRA	X	13751782	2L	22725958	3	0	somatic_tumour	417	8974.2	X:13751782 2L:22725958	3to5	0.07	0	CC	-	GGGATATGCATTGACATGAGGCTGGCCAACAAGGCAATCTTAAGAGAAAATTATCCACTGCCGGTTTTTGAAACGTTTATGACAAAATTGGGAGGCGCATCAGTTGGAGCTAGATGAATCCACCCCCGCCTCGATCTCTTCGTTCAGCTCCCGCTCGACGGAACTCTCCTTGGAATCGGAGTCCGACGGTGGAGTGA	AAAATTATCCACTGCCGGTTTTTGAAACGTTTATGACAAAATTGGGAGGCGCATCAGTTGGAGCTAGATGAATCCACCCCCGCCTCGATCTCTTCGTTCAGCTCCCGCTCGACGGAACTCTCCTTGGAATCGGAGTCCGACGGTGGAGTGA	Alt-EJ	Pdcd4, exon_2	CG40006, intron	Pdcd4, CG40006	NA	mh:2; ins:0; tup:0; tdown:0	0
D106R1	136	novobreak	TRA	2R	25011229	3L	8873017	3	0	somatic_tumour	163	16138.2	2R:25011229 3L:8873017	5to5	0.06	0	TTTC	-	GAGTTCTTTTTTCGAATGTCCCCCCCTTCCGTTTTCACATTTTTCAGCTGGCGGCGTCCCGACGCCGGCGAATAGGTCGCTGCATCCGCTGGATGCCTGTGCACATTTCCGATTTTTTTTTACCGATTTTAATGCAAGCCAGGCGCTTTTCATTTGTTTGGCGACAGCTGCACCCACACAC	GAGTTCTTTTTTCGAATGTCCCCCCCTTCCGTTTTCACATTTTTCAGCTGGCGGCGTCCCGACGCCGGCGAATAGGTCGCTGCATCCGCTGGATGCCTGTGCACATTTCCGATTTTTTTTTACCGATTTTAATGCAAGCCAGGCGCTTTTC	Alt-EJ	zip, intron	dally, intron	zip, dally	NA	mh:4; ins:0; tup:0; tdown:0	0
D106R1	285	novobreak	TRA	3R	23882161	X	795002	3	0	somatic_tumour	338	23087.2	3R:23882161 X:795002	3to3	0.06	0	-	-	ACTTAATTTCTTGCCAATTACAGTTGGTTGGCACATCTGAAACGAATTCTCAGAACGGATTTGCCAACCTACAAAGCCTTAGTTAACAAGGCTAACGAGCCTCCGCTCCTCCTCTGCAAAACTGAACTGAACTCCAACTGCGCAGCAGGCCTATGTGTGTGGCCATGGCCTGAAGCACCTGGAAACACTCCAAGCGCACGGCGGATGGAATTCTCATGCCCTCCAGACAGCGGA	TAACAAGGCTAACGAGCCTCCGCTCCTCCTCTGCAAAACTGAACTGAACTCCAACTGCGCAGCAGGCCTATGTGTGTGGCCATGGCCTGAAGCACCTGGAAACACTCCAAGCGCACGGCGGATGGAATTCTCATGCCCTCCAGACAGCGGA	NHEJ	Pli, intron	CG16989, exon	Pli, CG16989	NA	mh:0; ins:0; tup:0; tdown:0	0
D106R21	19	Control-Freec	DUP	2L	18303896	2L	19171464	-	-	somatic_tumour	-	867.6	2L:18303896-19171464	Heterozygous deletion	0.12	0.09	-	-	-	-	-	intergenic	brat, 3UTR	brat	TRUE	low FC; snp_su:1798; snp_op:594; snp_ratio:3.03	21.39
D106R21	25	lumpy	TRA	2R	3573532	3L	12392168	3	0	somatic_tumour	7521_1	8818.6	2R:3573532 3L:12392168	3to3	0.27	0	AATAAGACG	-	-	CAGCGGCGGTTATTGTTCTGCGAGCGGGGCAGTTCCTACTCCACCTCTATCGCAGCGTCAGAATAAGACGTCGCGGAAAAACAACTGTCATGTTTGAAAAATTACTTTTTGAGTCTTTCGTTCAATAGGCACTTTTCTCTTCTCCAAGTTG	Alt-EJ	intergenic	intergenic	-	NA	mh:9; ins:0; tup:0; tdown:0	0
D106R21	26	Control-Freec	DUP	2R	5250128	2R	5771116	-	-	somatic_tumour	-	521	2R:5250128-5771116	Heterozygous deletion	0.11	0.15	-	-	-	-	-	Nipped-A, intron	Gp210, intron	Nipped-A, Gp210	TRUE	low FC; snp_su:298; snp_op:132; snp_ratio:2.26	18.67
D106R21	30	novobreak	TRA	2R	8504388	3R	8522427	3	0	somatic_tumour	22	18	2R:8504388 3R:8522427	3to3	0.21	0	-	-	GTTTAAAGCCAGCTGCGTGAAACTATTCATGACACTTTTGCTATGTGTTGGTAAAAATGTTTTTTAAGCTTGCGTTGGCATTTTTTCCCTACACATTACAAATTAACTTTTAATATACAACACATTTCGATAAAAACGCAGGCAACCATGCGGCGGTAGCGAAGTAGAAACCACCGAGAAACTGGCGCACCAGGCAAATGGCGAGGACAAAGA	TTTAAGCTTGCGTTGGCATTTTTTCCCTACACATTACAAATTAACTTTTAATATACAACACATTTCGATAAAAACGCAGGCAACCATGCGGCGGTAGCGAAGTAGAAACCACCGAGAAACTGGCGCACCAGGCAAATGGCGAGGACAAAGA	NHEJ	mtt, intron	CG31454, exon_2	mtt, CG31454	NA	mh:0; ins:0; tup:0; tdown:0	0
D106R21	60	Control-Freec	DUP	3L	9145240	3L	9172072	-	-	somatic_tumour	-	26.8	3L:9145240-9172072	Heterozygous duplication	0.32	0.67	-	-	-	-	-	nwk, 3UTR	Rdl, intron	nwk, Rdl	TRUE	t_contamination: 912 n_contamination: 12; snp_su:38; snp_op:13; snp_ratio:2.92	18.22
D106R21	68	Control-Freec	DUP	3L	18751096	3L	18889728	-	-	somatic_tumour	-	138.6	3L:18751096-18889728	Heterozygous duplication	0.07	0.35	-	-	-	-	-	ftz-f1, 3UTR	CG3961, intron	ftz-f1, CR45938, CR45939, CG14073, HipHop, Cat, Indy, CR32027, CR45388, CR45387, CR45912, mir-315, CG6865, CG14074, Dysb, CG6852, Rad9, Blos3, Ugt, CG3961	TRUE	t_contamination: 3661 n_contamination: 130; low FC; snp_su:326; snp_op:146; snp_ratio:2.23	17.94
D106R21	91	novobreak	TRA	3R	11525767	X	16884059	3	0	somatic_tumour	80	5358.3	3R:11525767 X:16884059	5to3	0.24	0	CTC	-	TTCGAATTTTTTCTGTGTGTTTGTGTATGACTCACCTGGCAGCTTATCTTGCAGCCCGCCGTCGCATGAAACTCGCTGAGGAAGATGCACCGGATCTTGCCCTCCGTGCTGCCATGGGCACCCGCTGCTCCAGCTCCTGATCCGCCTGCTCCAT	TTCGAATTTTTTCTGTGTGTTTGTGTATGACTCACCTGGCAGCTTATCTTGCAGCCCGCCGTCGCATGAAACTCGCTGAGGAAGATGCACCGGATCTTGCCCTCCGTGCTGCCATGGGCACCCGCTGCTCCAGCTCCTGATCCGCCTGCTCCAT	Alt-EJ	intergenic	Nprl2, intron	Nprl2	NA	mh:3; ins:0; tup:0; tdown:0	0
D106R21	98	Control-Freec	DUP	3R	21311316	3R	21340384	-	-	somatic_tumour	-	29.1	3R:21311316-21340384	Heterozygous duplication	0.18	0.53	-	-	-	-	-	Hsromega, ncRNA	CG16791, intron	Hsromega, mir-4951, CG16791	TRUE	t_contamination: 975 n_contamination: 47; snp_su:50; snp_op:14; snp_ratio:3.57	17.09
D106R21	100	lumpy	TRA	3R	29459288	X	15810979	7	0	somatic_tumour	7816_1	13648.3	3R:29459288 X:15810979	3to5	0.45	0	TTGGT	-	-	AACTAAGGTCACTAAAATGTCAATCCAATTAATATATGTGAATTTCTGAGGATGCGAACTGCATTGGAATTGGTTTGCAGGTAGTGGGATTGCAGCACGCGAGTGCTTCCAGGAAAAGGCATTCCATTTCGTTTGGGAATTGGAAAATTGTTCGAAATATTAGCGCTAATAA	Alt-EJ	Ptp99A, intron	sd, intron	Ptp99A, sd	NA	mh:5; ins:0; tup:0; tdown:0	0
D106R21	105	Control-Freec	DUP	4	93912	4	114036	-	-	somatic_tumour	-	20.1	4:93912-114036	Heterozygous duplication	0.41	1.16	-	-	-	-	-	pan, intron	pan, 3UTR	pan	TRUE	t_contamination: 644 n_contamination: 11; snp_su:15; snp_op:3; snp_ratio:4.99	21.44
D106R21	106	Control-Freec	DUP	4	114036	4	565708	-	-	somatic_tumour	-	451.7	4:114036-565708	Heterozygous duplication	0.05	0.36	-	-	-	-	-	pan, 3UTR	Pur-alpha, exon	pan, Ank, CG32000, CR43956, CG32006, CG31997, CG33978, CR45198, Arl4, CG2316, CR44441, CG31998, Crk, CG31999, yellow-h, CR46065, CG1674, dpr7, RhoGAP102A, NfI, CR44023, Syt7, Rad23, Zip102B, CG32850, PMCA, Hcf, dati, CR45125, CR44027, mir-9385, CR43437, CR44024, lgs, CaMKI, CR45126, bip2, pncr013:4, Asator, zfh2, Thd1, CR43958, Pur-alpha	TRUE	t_contamination: 9495 n_contamination: 236; low FC; snp_su:237; snp_op:115; snp_ratio:2.06	17.56
D106R21	107	Control-Freec	DUP	4	608192	4	1348131	-	-	somatic_tumour	-	739.9	4:608192-1348131	Heterozygous duplication	0.05	0.36	-	-	-	-	-	intergenic	intergenic	Eph, mav, mir-954, Gat, Ekar, CR44028, gw, Slip1, CG11360, myo, ey, bt, CR45200, MED26, Sox102F, fd102C, CR33797, CR45123, Gyf, CR43425, unc-13, CR44029, CR43361, eIF4G, mGluR, 4E-T, CR45201, CR44030, fuss, sphinx, toy, PlexA, CR44031, CG11077, CG11076, ATPsynbeta, CaMKII, Zyx, apolpp, Actbeta, sv, Cals, Arf102F, CG11155, CG32017, Kif3C, pho, CG33521, PIP4K, Mitf, Dyrk3, Cadps	TRUE	t_contamination: 15098 n_contamination: 489; low FC; snp_su:419; snp_op:175; snp_ratio:2.39	17.89
D106R21	111	Control-Freec	DUP	X	3454620	X	3700580	-	-	somatic_tumour	-	246	X:3454620-3700580	Heterozygous deletion	0.15	0.13	-	-	-	-	-	CR44999, ncRNA	Mnt, intron	CR44999, Mnt	TRUE	low FC; snp_su:322; snp_op:161; snp_ratio:2.0	16.75
D106R21	114	Control-Freec	DUP	X	4702308	X	5388760	-	-	somatic_tumour	-	686.5	X:4702308-5388760	Heterozygous deletion	0.17	0.12	-	-	-	-	-	l(1)G0334, intron	SK, intron	l(1)G0334, SK	TRUE	low FC; snp_su:922; snp_op:456; snp_ratio:2.02	17.44
D106R21	115	Control-Freec	DUP	X	5393232	X	5402176	-	-	somatic_tumour	-	8.9	X:5393232-5402176	Heterozygous duplication	0.42	0.96	-	-	-	-	-	SK, intron	SK, 3UTR	SK	TRUE	t_contamination: 489 n_contamination: 4; snp_su:14; snp_op:6; snp_ratio:2.33	14.87
D106R21	121	Control-Freec	DUP	X	9172072	X	9183252	-	-	somatic_tumour	-	11.2	X:9172072-9183252	Heterozygous duplication	0.43	1.06	-	-	-	-	-	mei-P26, 3UTR	mei-P26, 3UTR	mei-P26	TRUE	t_contamination: 533 n_contamination: 25; snp_su:15; snp_op:5; snp_ratio:3.0	21.06
D106R21	122	Control-Freec	DUP	X	11931296	X	11967072	-	-	somatic_tumour	-	35.8	X:11931296-11967072	Heterozygous duplication	0.34	0.66	-	-	-	-	-	cac, 3UTR	cac, intron	cac	TRUE	t_contamination: 1057 n_contamination: 35; snp_su:59; snp_op:23; snp_ratio:2.56	17.21
D106R21	127	Control-Freec	DUP	X	13834132	X	13885560	-	-	somatic_tumour	-	51.4	X:13834132-13885560	Heterozygous duplication	0.26	0.69	-	-	-	-	-	AMPdeam, exon_3	mamo, intron	AMPdeam, mamo	TRUE	t_contamination: 2617 n_contamination: 45; snp_su:55; snp_op:18; snp_ratio:3.05	19.4
D106R23	3	lumpy	COMPLEX_TRA	2L	7831964	2R	11894390	23	0	somatic_tumour	6115_1	4062.4	2L:7831964 2R:11894390	4:3_4	0.19	0	-	-	-	-	-	mts, 3UTR	Ef1alpha48D, exon	mts, Ef1alpha48D	NA	bp2_rDNA_2	0
D106R23	12	Control-Freec	DUP	2L	21641064	2L	21644502	-	-	somatic_tumour	-	3.4	2L:21641064-21644502	Heterozygous duplication	0.41	0.49	-	-	-	-	-	Ac3, intron	Ac3, intron	Ac3	NA	snp_su:0; snp_op:3; snp_ratio:0.0	0
D106R23	18	delly	DEL	2R	13582874	2R	13584102	29	11	somatic_tumour	DEL00000007	1.2	2R:13582874-13584102	5to3	0.35	-0.78	-	-	ACCTCGCAATGCCATGATTCTTAAGCGCCGCTGTGCTCGTGATCTCCATTTGGTTCTCAAAGATGGAAGGATTCGCCGCCCGCAGAAACGGAGAGAAAAATCAGCGGAGGCAGAAAGATTTTCCCTTGTGCATTTAAAGGGCGATCAGGCCCGCTGCTTATCGCTT	-	-	CG45088, exon_5	CG45088, intron	CG6191, CG45088	NA	snp_su:2; snp_op:0	42.73
D106R23	18	lumpy	DEL	2R	13582874	2R	13584102	29	11	somatic_tumour	2234	1.2	2R:13582874-13584102	5to3	0.35	-0.78	-	-	-	-	-	CG45088, exon_5	CG45088, intron	CG6191, CG45088	NA	snp_su:2; snp_op:0	42.73
D106R23	18	novobreak	DEL	2R	13582874	2R	13584102	29	11	somatic_tumour	6	1.2	2R:13582874-13584102	5to3	0.35	-0.78	-	-	TCAACAAAAATGATACGAAAGATGATCCAAAATATGCTGGCAAACAGGAAGCCGGCACCAACCTCGCAATGCCATGATTCTTAAGCGCCGCTGTGCTCGTGATCTCCATTTGGTTCTCAAAGATGGAAGGATTCGCCGCCCGCAGAAACGGAGAGAAAAATCAGCGGAGGCAGAAAGATTTTCCCTTGTGCATTTAAAGGGCGATCAGGCCCGCTGCTTATCGCTTGTGTATTTTTGGAAATCAAACAAACACATCAACACAAACACACACACGCATACACATTCACACGCTCGTTGGCACACACATGTGCAATGCCGAAGGGCAGCCGCAACGCAAGTCAATTAGCCAACTGAAGTCAACATCTTCACGGCATCTGTGCGCCTGGTTGATTACC	-	-	CG45088, exon_5	CG45088, intron	CG6191, CG45088	NA	snp_su:2; snp_op:0	42.73
D106R23	28	Control-Freec	DUP	4	91680	4	126633	-	-	somatic_tumour	-	35	4:91680-126633	28:28_29	0.25	0.22	-	-	-	-	-	pan, exon_1	Ank, intron	pan, Ank	TRUE	low FC; snp_su:12; snp_op:6; snp_ratio:2.0	10.76
D106R23	30	Control-Freec	COMPLEX_DUP	4	410268	4	413706	-	-	somatic_tumour	-	3.4	4:410268-413706	30:30_31_40	0.41	0.57	-	-	-	-	-	intergenic	intergenic	-	NA	snp_su:2; snp_op:2	8.57
D106R23	33	Control-Freec	DUP	4	1013637	4	1015356	-	-	somatic_tumour	-	1.7	4:1013637-1015356	33:33_34_35	0.45	0.64	-	-	-	-	-	PlexA, exon_10	PlexA, intron	PlexA	NA	snp_su:0; snp_op:0	0
D106R23	36	Control-Freec	DUP	X	2791083	X	2793375	-	-	somatic_tumour	-	2.3	X:2791083-2793375	Homozygous duplication	0.91	1.28	-	-	-	-	-	w, exon	w, intron	kirre, w	NA	snp_su:12; snp_op:0; snp_ratio:1201.0	38.11
D106R23	37	lumpy	DEL	X	3135343	X	3140437	9	2	somatic_tumour	5415	5.1	X:3135343-3140437	5to3	0.53	-1.56	-	-	-	-	-	N, 5UTR	N, intron	N	NA	snp_su:0; snp_op:0	0
D106R23	37	delly	DEL	X	3135343	X	3140437	9	2	somatic_tumour	DEL00000009	5.1	X:3135343-3140437	5to3	0.53	-1.56	-	-	CGAGTGCAAGAAGCGCAAGAGGAAGAGAGCAATACGCAAGCGTGCGGCGTCGGTTTGAATTTGAATTTGTGGCTCGATCCTCGCGAAGAGAAAAGCAAGCAAAAGATAAAAAAATCCCCCTATGTTGCCCATGCGATTTACTCCGATACTCTTATACAGACCGATCTCTCATTTGG	-	-	N, 5UTR	N, intron	N	NA	snp_su:0; snp_op:0	0
D106R23	37	Control-Freec	DEL	X	3135456	X	3140040	-	-	somatic_tumour	-	4.6	X:3135456-3140040	Homozygous deletion	0.9	-1.55	-	-	-	-	-	N, 5UTR	N, intron	N	NA	snp_su:0; snp_op:0	0
D106R25	6	novobreak	TRA	2L	720533	2R	19579841	6	0	somatic_tumour	5	18859.3	2L:720533 2R:19579841	5to5	0.17	0	CTTC	-	CAATTAAATGTTAATGGCAATATTTTATGGCTGACACTCAGCTTCTCGTTATTACAGTCGCATATCATTTAAACATGGCCAATTATAGCAAGAATCCTTAAATGATGCACGCATTTTCTTTCTGTGTACCGCTCATAAGATTTCATCTGATTTCAAC	CAATTAAATGTTAATGGCAATATTTTATGGCTGACACTCAGCTTCTCGTTATTACAGTCGCATATCATTTAAACATGGCCAATTATAGCAAGAATCCTTAAATGATGCACGCATTTTCTTTCTGTGTACCGCTCATAAGATTTCATCTGATTTCAAC	Alt-EJ	intergenic	sm, intron	sm	NA	mh:4; ins:0; tup:0; tdown:0	0
D106R25	13	novobreak	BND	2L	2163585	2L	2461707	4	2	somatic_tumour	9	298.1	2L:2163585-2461707	3to3	0.12	0.16	-	-	AAAAGTTGGAGTCGGTGGCACGTAGTAAAATGACAAATGAATGCTCATCAGCCAGCAACAGAAACAAAAAAAAGAAAAAGAAAAGGAAGGCAGGGCAGCAGACCCAGGAAGAGGGAGAGTTGGGGAAGTTCAAAAAAGGTTGGCCAAGAAGTGCATCAGAGGAAGCGGAGCGAAAAAACTGACAGCTTACGGATAATTACCGAGGAAAACACACAGATGCAGGGCTGCTGGGATGAGG	-	NHEJ	aop, intron	intergenic	aop	NA	mh:0; ins:0; tup:0; tdown:0	0
D106R25	23	novobreak	DEL	2L	3809700	2L	15393453	2	1	somatic_tumour	16	11583.8	2L:3809700-15393453	5to3	0.1	0.27	-	-	ATCTAACGAAAGAAACAAAAGAGATCACAGCAAGTTAAACCCATATTCAATTCAAGGAAAACCAAATGAAACGCAAAAACTAAGAACTAAAAAAAAAACCAATAACGTGTGCAACCATAGCAAAGCAAAAGTAAACGAAACAAACAAACTTCCTAATCGCTGCATCGCCTCTTATCCCAACATGACATTAGCTAATGG	-	-	Reph, 3UTR	intergenic	Reph	NA	snp_su:21464; snp_op:23903; snp_ratio:0.9; somatic_snvs:1	8.82
D106R25	59	lumpy	COMPLEX_TRA	2L	10250421	3L	1679928	3	0	somatic_tumour	5945_1	8570.5	2L:10250421 3L:1679928	59:59_60_83	0.12	0	-	-	-	-	-	bsk, exon_1	CG7991, intron	bsk, CG7991	NA	-	0
D106R25	59	novobreak	COMPLEX_TRA	2L	10250421	3L	1679928	3	0	somatic_tumour	38	8570.5	2L:10250421 3L:1679928	59:59_60_83	0.12	0	-	-	GGTCACATCGATTTAAGTAACTTTGTTGTGATCGAATATTCCAATAGATTTTCGTATATTGTATTGTATCCATGTACAATTATTCTCATGCGAAAGTGCCGTTTGGCACCAGGTCGGCTACTCGGTGTCTCTCGGGGATGGGACATAAATTGACTACCAGGAGCAGGAGTCGATTGTTTCCTGTTCGGTGCAGGTGTGCGCCCAACTGCGGAGATTTAATGTCATTTTCTGGGGCTGCCTAC	-	-	bsk, exon_1	CG7991, intron	bsk, CG7991	NA	-	0
D106R25	59	Control-Freec	COMPLEX_DUP	2L	16916480	2L	17451008	-	-	somatic_tumour	-	534.5	2L:16916480-17451008	83:59_60_83	0.37	0.59	-	-	-	-	-	tweek, exon	CR46204, exon_1	tweek, CR43053, CR44393, CR45285, beat-IIIb, CG44406, CR44408, CG31806, CR45356, CR45357, CG6304, CR45462, CR43802, CG15136, CR43819, CG12620, CR45448, CG31784, CG34106, beat-IIIa, CG34169, CR44394, Gr36a, Gr36b, Gr36c, CG31750, beat-IIIc, CR44396, CR44395, CR45729, CG15140, CG6380, CG34170, CR45696, CG45691, CR43239, CR44345, CR44346, CG31804, Lrch, CLIP-190, Rpb11, CG15141, CG31803, Dif, CR44409, CG5043, CG33928, dl, CR46204	NA	snp_su:663; snp_op:609; snp_ratio:1.09	10.18
D106R25	68	Control-Freec	DUP	2L	12454912	2L	12617728	-	-	somatic_tumour	-	162.8	2L:12454912-12617728	68:68_69	0.41	0.71	-	-	-	-	-	CR17024, exon_1	Ref2, intron	CR17024, bun, mir-967, t-cup, CR43051, snoRNA:CG43051-a, CR42746, CR44598, CR44597, CR44596, CR44595, nub, Ref2	NA	snp_su:296; snp_op:281; snp_ratio:1.05	10.07
D106R25	72	novobreak	TRA	2L	13148395	3R	29965289	3	0	somatic_tumour	44	16816.9	2L:13148395 3R:29965289	5to3	0.12	0	GCTG	-	TCTTGCCGGCAATCAAATTATAGAGCAATTCGAGACAAGTCAAGACCACTTTTGGCTGGCTTAAACGAGCGTTTTTAATTTCCCCACAAGCACACACACTGGCGAAACAATTAGGCACAAAACGAGCATTAAATATATGGGGCTGCAAATT	TCTTGCCGGCAATCAAATTATAGAGCAATTCGAGACAAGTCAAGACCACTTTTGGCTGGCTTAAACGAGCGTTTTTAATTTCCCCACAAGCACACACACTGGCGAAACAATTAGGCACAAAACGAGCATTAAATATATGGGGCTGCAAATTGGCCACATGCGCTG	Alt-EJ	intergenic	TkR99D, intron	TkR99D	NA	mh:4; ins:0; tup:0; tdown:0	0
D106R25	85	Control-Freec	DUP	2L	17531904	2L	18123776	-	-	somatic_tumour	-	591.9	2L:17531904-18123776	Heterozygous duplication	0.29	0.43	-	-	-	-	-	CG15145, exon_2	CG5758, exon_2	CG15145, CR43304, CR45697, CG7094, CR45919, mir-124, mir-287, CR45358, CR45698, CR45111, CR45112, CR44411, Oli, CR44410, CG6870, Sytalpha, CR44412, CR44413, CG15147, CG43054, CR45699, CadN, CG43231, CadN2, CR43419, CG42830, CR43420, CR45332, CR45333, CG43271, CR43274, CR44399, CR44398, CR44397, btv, CG5674, CG5681, Prosbeta5R2, CR44767, CR44604, CR44605, CG5693, CG42659, CG42634, CG42635, CG31740, elfless, rdo, Arr1, ninaD, CG31741, CG15153, CG5755, CG44476, CG15152, CG5758	NA	snp_su:723; snp_op:726; snp_ratio:1.0	10.11
D106R25	94	Control-Freec	DUP	2L	19593216	2L	19696640	-	-	somatic_tumour	-	103.4	2L:19593216-19696640	Heterozygous duplication	0.37	0.53	-	-	-	-	-	Lar, intron	CG46244, intron	Lar, CR44978, CR44979, CG46244	NA	snp_su:4; snp_op:3; snp_ratio:1.33	12.7
D106R25	97	lumpy	TRA	2L	22747975	2R	23173956	3	0	somatic_tumour	5935_1	426	2L:22747975 2R:23173956	5to5	0.13	0	-	-	-	-	-	CG40006, intron	CG34371, intron	CG40006, CG34371	NA	bp2_INE-1_Helitron=2	0
D106R25	97	novobreak	TRA	2L	22747975	2R	23173956	3	0	somatic_tumour	59	426	2L:22747975 2R:23173956	5to5	0.13	0	-	-	CTTTAAAGCTACTTAAAAAGAGGCAGAACAAATAAAAAAAAAAAAAAGAGTCCACAAAGAATTTAATTCATTCGGAAAACAAACCTTCTGCCTGTTGCATACTTTTAACGAATCTAGTATACTCTTTTACTCTACGAGTAACAAAAGAGGTTTCTCTAGAGTAAGAATGGGCGTAGCAAAAATGATTTTGGCATATGGGCCTTGGCCTTGCGTTCCGT	-	-	CG40006, intron	CG34371, intron	CG40006, CG34371	NA	bp2_INE-1_Helitron=2	0
D106R25	101	novobreak	TRA	2R	6605795	X	9629822	3	0	somatic_tumour	64	3024	2R:6605795 X:9629822	3to3	0.11	0	-	-	ATTCATAGGTGTCGCCTTTTTCGACACTTTTCCCAAATAATTTCTAATCAAACTTCACACTCGAACGAGAACTGGTAAAAAGCGCAGCGAGTGCAAGCTAAACAACGAGCACACACACTCGCGCGTGATGGAGCGCGGACGCGTGAAATGCGGCCAGTACTGGGAGCCGACTGAAGAAAGTTCCTTAGAGTTTGGCG	-	-	jing, intron	Ptpmeg2, exon_6	jing, Ptpmeg2	NA	-	0
D106R25	111	lumpy	TRA	2R	11135623	X	17792512	3	0	somatic_tumour	6411_1	6656.9	2R:11135623 X:17792512	3to5	0.14	0	-	-	-	-	-	intergenic	OdsH, intron	OdsH	NA	-	0
D106R25	116	novobreak	TRA	2R	12259479	3R	18928294	3	0	somatic_tumour	79	6668.8	2R:12259479 3R:18928294	3to5	0.1	0	-	-	CCCCAGTTGGCCACCGGGCCCCAGAAGTGGGTACTGTGGATATAAAAAGCAATATTTACAATAAGTCATATAAGGCCAATTGATAACCAACAAACAGACCTCATAAAGTAATCCCGCCACTCCTTTGAGGCCGTTGTGGACATAGCTCTCCTGATCGACATGATGCTACCGATTTGCTAATTGAATATATCTGACCAGACATTGCATATAGAGAGCAGTATTGGGCCAACAAAAAAAAAAAAAAAAATACAAAAAAAGCGAAAAG	-	-	CR43900, ncRNA	Mpc1, 5UTR	Cam, CR43900, Mpc1	NA	-	0
D106R25	125	lumpy	TRA	2R	14509830	3R	15589099	4	0	somatic_tumour	6326_1	1079.3	2R:14509830 3R:15589099	3to5	0.11	0	-	-	-	-	-	Asx, intron	intergenic	Asx	NA	-	0
D106R25	125	novobreak	TRA	2R	14509830	3R	15589099	4	0	somatic_tumour	87	1079.3	2R:14509830 3R:15589099	3to5	0.11	0	-	-	GTTATGGGCTGGCCTGGGCTGGAGTGGAATGGTACGGTATTCTAGGTTATTGGACCGCGTATGAGTGGTTTCCCAAGAAAGAAATATGTCCAACGGAAGCCGTCACCCACAACGCTCATCCGGCATTTGTTTAGTCCCGGACCTGGAGGAGCTACAG	-	-	Asx, intron	intergenic	Asx	NA	-	0
D106R25	129	novobreak	BND	2R	15499236	2R	23013562	3	1	somatic_tumour	92	7514.3	2R:15499236-23013562	5to5	0.1	0.16	-	-	CCAAGTGCATTCCCATTTCGATGCATGTTTTAAGATTTTGCAAATCTAAGCCAGACTGCGGGGAAATGCCAATTGAAGAGCAGAAAAAGGGAACCAGCTGGCCGGGAAAACTTTTGCCTGTCAGTCGGGAGTCTTTACACAATTTCCTAAT	-	-	intergenic	CG42741, intron	twi, CG42741	NA	-	0
D106R25	132	novobreak	BND	2R	16385221	2R	17989583	1	2	somatic_tumour	95	1604.4	2R:16385221-17989583	3to3	0.06	0.23	-	-	GTATAGATATATTTTGTTATGTTTTGCAGTGCCTCGGATTTTTTCCTGTGCACTGAAAGAACAATTTCTTCGTCTTTAGTTTCAATGGCCCCCACGACGGACCGAAAACCATTTTAAATGGAACGTAAGCCGAGAACTCGACGGTGGTCACCACGCAGATCGGGGCCACCGCCCACGTTCCCTGCACCGTGCACCACATCGG	-	-	CG43187, 3UTR	dpr13, exon_2	CG43187, dpr13	NA	-	0
D106R25	146	novobreak	TRA	2R	18951192	3L	9705332	3	0	somatic_tumour	102	9245.9	2R:18951192 3L:9705332	3to5	0.07	0	-	-	CGCTCAATCCTCCGTTGCCGGAGGAGCCGACGTTAGCCAAATCCTTGCCGCGAACGGCGGCCGTAAAATTGGAAACCAAAACGCACGTCACATCCACAGCCACTGCATCCAATGTGGCGGCACCCAAGCTGCAACAGCCAGTGAGTTTTGAAATATTCCTTTAAGGACTTGCAACTAATTTTGTTAGCCCTGATGGAGTTGCGTCTACAG	-	-	sano, intron	CG16711, exon_1	sano, CG16711	NA	-	0
D106R25	147	novobreak	TRA	2R	18970697	3R	32039211	3	0	somatic_tumour	103	13068.5	2R:18970697 3R:32039211	147:147_148	0.09	0	-	-	GGTCATCGAGATGTCCTTTTCCGTGGACAGAAGGCTGCGTCTGTACTTGCTGATCCTTAAGCTATTGCCGGCTCAGATTCGGAACGGCTATTTTTGCCAGGAAGGTTTAGTGGGCTTCGAGAGCGCTTCTCTAGAGCTAGCTGATCTTAACCGTAAGC	-	-	prod, exon_2	CG2053, exon_1	prod, CG2053	NA	-	0
D106R25	151	delly	DEL	2R	19856257	2R	19860148	6	3	somatic_tumour	DEL00000016	3.9	2R:19856257-19860148	5to3	0.19	0.07	-	-	AAAATATTTAATTACCGCAGAGAGTCAAAATTAATTATGACAGCTGTCAGCTGAGTGTGCCAGACCGAAGACCAAAACCAAGCCAAGCCAAAGCTCGGTTCACAATGGCAGGTCAATATGCCAGTTGTTTGCATGTTTCGTGTGGCCCGAGACATGCATTAATTATGTAGATAACTGGCGACTGCGAATGCAC	-	-	intergenic	intergenic	-	NA	-	0
D106R25	151	lumpy	DEL	2R	19856257	2R	19860148	6	3	somatic_tumour	2274	3.9	2R:19856257-19860148	5to3	0.19	0.07	-	-	-	-	-	intergenic	intergenic	-	NA	-	0
D106R25	151	novobreak	DEL	2R	19856257	2R	19860148	6	3	somatic_tumour	109	3.9	2R:19856257-19860148	5to3	0.19	0.07	-	-	TCATGCAACACTTCAAAGGGCTAATCAGAGCTGGCACTGGCCTGAAATTCAAAACGCAGGCCGACGACCACCCGACGACTGCTTCCATTGTCTGGCACTTGAAGAACCTGCACGAAAATATTTAATTACCGCAGAGAGTCAAAATTAATTATGACAGCTGTCAGCTGAGTGTGCCAGACCGAAGACCAAAACCAAGCCAAGCCAAAGCTCGGTTCACAATGGCAGGTCAATATGCCAGTTGTTTGCATGTTTCGTGTGGCCCGAGACATGCATTAATTATGTAGATAACTGGCGACTGCGAATGCACGGTGCCCCAAAAGAAATCCAAAATCCGAGTCGAAACCAAACCAGTTGCCCCCAAACCAAATC	-	-	intergenic	intergenic	-	NA	-	0
D106R25	170	Control-Freec	COMPLEX_DUP	3L	0	3L	141312	-	-	somatic_tumour	-	141.3	3L:0-141312	170:170_172	0.31	0.52	-	-	-	-	-	intergenic	Pdk1, exon_1	mthl8, CG43149, Lsp1gamma, CR44510, CR44511, CR43150, CR43988, CG13405, CG12483, CR45401, CR45402, CR45400, CR45805, Pdk1	NA	snp_su:33; snp_op:24; snp_ratio:1.37	13.57
D106R25	176	novobreak	TRA	3L	662392	2L	5435490	3	0	somatic_tumour	120	4773.1	3L:662392 2L:5435490	3to5	0.1	0	-	-	GGAGTTAGCGCCCAATTTATCATATTTTCCCTGGCTTTCAACTATGGTCGAATGACTATGTCATGAGGTTGACTTAGCTGGCCAATCGAAGCGTCAGAAATAAATTACAAAATCGTGTAAAGTGCAAACTGGACTCGGACATGGATGGGGTTTTTCTATTTCTTGCGCCGCATTTTGTCTTTTGACG	-	-	intergenic	intergenic	-	NA	-	0
D106R25	181	CNV-Seq	COMPLEX_DEL	3L	1018999	3L	1056277	-	-	somatic_tumour	-	37.3	3L:1018999-1056277	179:179_180_181_413_414	0.47	-1.92	-	-	-	-	-	trio, exon_2	bab1, intron	trio, CG9205, bab1	NA	snp_su:0; snp_op:0	0
D106R25	181	lumpy	COMPLEX_DEL	3L	1019000	3L	1563588	6	1	somatic_tumour	2664	544.6	3L:1019000-1563588	180:179_180_181_413_414	0.36	-0.7	-	-	-	-	-	trio, exon_2	CG7879, intron	trio, CG9205, bab1, bab2, CG13912, Trh, LysX, Aplip1, mwh, CG32335, CG9119, LysB, LysC, LysD, LysE, LysP, LysS, CG33965, CG33966, CR45747, CG9194, CG9192, Klp61F, CG32318, Psf1, Sac1, CG9129, CG9130, CG9133, tfc, CG32333, Rabex-5, scf, Rac1, CG9149, CG2277, CG2469, CG9186, Sherpa, Myo61F, CG9184, CR45166, ND-ACP, msd1, msd5, CG2211, l(3)02640, CG2199, Ptp61F, 312, ru, tRNA:Glu-CTC-3-1, tRNA:Glu-CTC-3-2, tRNA:Glu-CTC-3-3, tRNA:Glu-CTC-3-4, tRNA:Glu-CTC-3-5, tRNA:Glu-CTC-3-6, tRNA:Glu-CTC-3-7, CG32320, tRNA:Glu-CTC-3-8, tRNA:Glu-CTC-3-9, CG9168, FucTD, CG9173, SA-2, CR44842, rho, CG32319, stet, robl62A, CR43701, snoRNA:Psi28S-2622, CG12084, CR45812, hfp, scaRNA:MeU2-48, Psa, cue, Iml1, Ir62a, CG12091, pns, CG32313, Cct1, CR45813, Cct2, CG12099, Pex10, CG7879	NA	snp_su:10; snp_op:3; snp_ratio:3.33	24.03
D106R25	181	delly	COMPLEX_DEL	3L	1019000	3L	1563588	6	1	somatic_tumour	DEL00000019	544.6	3L:1019000-1563588	180:179_180_181_413_414	0.36	-0.7	-	-	GCGAAGGATCGCCAACGGCGATTGGTGCGCTCGTGGGCAGCGGTGTATTGGGCAGGGATACGTAGCCCTTGGTCGGTGTGTCCTCGCCGCACTTGAGCAACATTTTCCGATTTTGCCGCTTTCTGAATTTAAATCTATCGATATTTGAAATATATATGAAATTATAGGGTTTTTG	-	-	trio, exon_2	CG7879, intron	trio, CG9205, bab1, bab2, CG13912, Trh, LysX, Aplip1, mwh, CG32335, CG9119, LysB, LysC, LysD, LysE, LysP, LysS, CG33965, CG33966, CR45747, CG9194, CG9192, Klp61F, CG32318, Psf1, Sac1, CG9129, CG9130, CG9133, tfc, CG32333, Rabex-5, scf, Rac1, CG9149, CG2277, CG2469, CG9186, Sherpa, Myo61F, CG9184, CR45166, ND-ACP, msd1, msd5, CG2211, l(3)02640, CG2199, Ptp61F, 312, ru, tRNA:Glu-CTC-3-1, tRNA:Glu-CTC-3-2, tRNA:Glu-CTC-3-3, tRNA:Glu-CTC-3-4, tRNA:Glu-CTC-3-5, tRNA:Glu-CTC-3-6, tRNA:Glu-CTC-3-7, CG32320, tRNA:Glu-CTC-3-8, tRNA:Glu-CTC-3-9, CG9168, FucTD, CG9173, SA-2, CR44842, rho, CG32319, stet, robl62A, CR43701, snoRNA:Psi28S-2622, CG12084, CR45812, hfp, scaRNA:MeU2-48, Psa, cue, Iml1, Ir62a, CG12091, pns, CG32313, Cct1, CR45813, Cct2, CG12099, Pex10, CG7879	NA	snp_su:10; snp_op:3; snp_ratio:3.33	24.03
D106R25	181	novobreak	COMPLEX_DEL	3L	1019000	3L	1563588	6	1	somatic_tumour	122	544.6	3L:1019000-1563588	180:179_180_181_413_414	0.36	-0.7	-	-	GTGCAGAGTGGCGTATTTTGAGCAGAGTCTGCAATGGACGGCGACGGCGAAGGATCGCCAACGGCGATTGGTGCGCTCGTGGGCAGCGGTGTATTGGGCAGGGATACGTAGCCCTTGGTCGGTGTGTCCTCGCCGCACTTGAGCAACATTTTCCGATTTTGCCGCTTTCTGAATTTAAATCTATCGATATTTGAAATATATATGAAATTATAGGGTTTTTGAGATATGCATTCTGGAATGCTTATTATGGA	-	-	trio, exon_2	CG7879, intron	trio, CG9205, bab1, bab2, CG13912, Trh, LysX, Aplip1, mwh, CG32335, CG9119, LysB, LysC, LysD, LysE, LysP, LysS, CG33965, CG33966, CR45747, CG9194, CG9192, Klp61F, CG32318, Psf1, Sac1, CG9129, CG9130, CG9133, tfc, CG32333, Rabex-5, scf, Rac1, CG9149, CG2277, CG2469, CG9186, Sherpa, Myo61F, CG9184, CR45166, ND-ACP, msd1, msd5, CG2211, l(3)02640, CG2199, Ptp61F, 312, ru, tRNA:Glu-CTC-3-1, tRNA:Glu-CTC-3-2, tRNA:Glu-CTC-3-3, tRNA:Glu-CTC-3-4, tRNA:Glu-CTC-3-5, tRNA:Glu-CTC-3-6, tRNA:Glu-CTC-3-7, CG32320, tRNA:Glu-CTC-3-8, tRNA:Glu-CTC-3-9, CG9168, FucTD, CG9173, SA-2, CR44842, rho, CG32319, stet, robl62A, CR43701, snoRNA:Psi28S-2622, CG12084, CR45812, hfp, scaRNA:MeU2-48, Psa, cue, Iml1, Ir62a, CG12091, pns, CG32313, Cct1, CR45813, Cct2, CG12099, Pex10, CG7879	NA	snp_su:10; snp_op:3; snp_ratio:3.33	24.03
D106R25	181	novobreak	COMPLEX_TRA	3L	1056277	X	2955861	10	0	somatic_tumour	123	1899.6	3L:1056277 X:2955861	181:179_180_181_413_414	0.8	0	-	-	AAATTGAGTTTGCCAAAAGTGTGATGCCCAAAGCTATATTATTGACTTATGGAAATTCACAAATATCTCGGGGGAACGATTCAAAGGAGAGGCGCTGCTAAAGCGCCGAGGAAAAATCAGGAGGAGGAGGAGGAGGAGGAGCGCCACTTACCATCTCTGTCTTCTGGCCGCCGATGATCGGTTCGTCGTTTATGAACCAGCGGTACCGGACATCGCTGGGATTCGCATCTGCCCGGCACTCCAAGCGCACCTGCGAATGCTCCACAATACGGGAACCGGTGCTCATGTGGACACTGCCACCGCCTGCACCACCAACAGTTCAGTTCGTTAATCTATGCAGGCGGCGGCGAGGAAAGT	-	-	bab1, intron	rst, intron	bab1, kirre, rst	NA	-	0
D106R25	181	lumpy	COMPLEX_TRA	3L	1056277	X	2956112	8	0	somatic_tumour	6598_1	1899.8	3L:1056277 X:2956112	181:179_180_181_413_414	0.68	0	-	-	-	-	-	bab1, intron	rst, exon_5	bab1, kirre, rst	NA	-	0
D106R25	181	CNV-Seq	COMPLEX_DEL	X	2955393	X	2955861	-	-	somatic_tumour	-	0.5	X:2955393-2955861	413:179_180_181_413_414	0.96	-3	-	-	-	-	-	rst, intron	rst, intron	kirre, rst	TRUE	low FC; snp_su:0; snp_op:0	0
D106R25	181	CNV-Seq	COMPLEX_DEL	X	2956113	X	3275824	-	-	somatic_tumour	-	319.7	X:2956113-3275824	414:179_180_181_413_414	0.91	-1.5	-	-	-	-	-	rst, exon_5	dnc, intron	kirre, rst, CG4116, N, CG18508, Fcp3C, CG3939, CG14265, ng2, ng3, ng1, ng4, Pig1, Sgs4, dnc	NA	snp_su:0; snp_op:0	0
D106R25	195	Control-Freec	DUP	3L	5309440	3L	5559296	-	-	somatic_tumour	-	249.9	3L:5309440-5559296	197:195_197	0.28	0.45	-	-	-	-	-	intergenic	intergenic	CR45741, CR45742, tRNA:Ser-AGA-2-5, lama, tRNA:Val-TAC-1-1, tRNA:Val-TAC-1-2, Klp64D, Cyt-c1, Uev1A, Membrin, CG10635, CR44515, CR44516, CR45743, Ir64a, DIP-delta, CG4835, CR44520, blanks, CR44518, CR44519, CG34342, Lkr, CG13285, frm	NA	snp_su:559; snp_op:451; snp_ratio:1.24	10.79
D106R25	196	novobreak	BND	3L	5258479	3L	11002401	2	1	somatic_tumour	137	5743.9	3L:5258479-11002401	3to3	0.06	0.28	-	-	TAATATATCCTTCTATATGTATGCTCATTCGGCCGATAAACAACGCCGGATATTCAATATTAAATCGTCATTGCGCATTAAAAATTAATGTTTATTTAAAAAGGCACAAAGTCCGGGCCGCAATCGGCTTGACAAATTCGAGACCCAGGAACGCAAAGGGCTGAGGTCTCGAAATTCCAAGGCGTTTTACCTTCCCTGTCCG	-	-	shep, intron	klu, intron	shep, klu	NA	bp1_rDNA_2; snp_su:9559; snp_op:10320; snp_ratio:0.93	9.01
D106R25	242	Control-Freec	DUP	3L	16144384	3L	16224256	-	-	somatic_tumour	-	79.9	3L:16144384-16224256	Heterozygous duplication	0.41	0.72	-	-	-	-	-	CG5151, intron	intergenic	CG5151, CG33796, CG33795, CR45754, CR45755, CR45437, CG33687, CG33688, CG33689, CG33690, CG13073, CR43891, tRNA:Met-CAT-1-3	NA	snp_su:125; snp_op:104; snp_ratio:1.2	10.92
D106R25	252	Control-Freec	DUP	3L	19934208	3L	19956736	-	-	somatic_tumour	-	22.5	3L:19934208-19956736	Heterozygous duplication	0.49	0.96	-	-	-	-	-	intergenic	Ac76E, intron	CG32219, CG34258, CG33710, CG42655, CG42654, CG42263, Ac76E	NA	snp_su:0; snp_op:0	0
D106R25	285	novobreak	BND	3R	7480141	3R	10531342	3	0	somatic_tumour	210	3051.2	3R:7480141-10531342	5to5	0.05	0.2	-	-	CCCAAAAGCCGAGAAGACGAAAGAAACTCATGAAACACCAGAGACCAGAAGAAGGGGAGCAGCGATCTTGTTCGAAAAAATGTTTGCTTGTTGCATTTGGGCAAGGGGAGGCATTTCTGTGTTGTTTACTTTTTATTGCAACGATTTCGTAATGAGAAAAGTTTTTGGCGTGGCAAAAATGTTGCTGACTGCC	-	-	intergenic	hth, intron	hth	NA	-	0
D106R25	287	novobreak	DEL	3R	8430479	3R	18030144	4	0	somatic_tumour	211	9599.7	3R:8430479-18030144	5to3	0.07	0.25	-	-	GCTGGCATTCGGGGTCCCAAAAACATTCTCACGCAACGAGGAGAGGCTTGGTCTTGGCTCTTTTGGCCATAAGTGAGACATTAAGCACAGTTTGCAGCAGCAGCAAAGCAGAAGTCGCCTCACAGCCCGCTTGTTGCGCCCCACATCCGCTAGCGTTTAGCAGCGGTTTCCGGCCATTTTCCACCCTACAAAACCCTGTGTGTGCAAATA	-	-	CG45263, intron	intergenic	CG45263	NA	-	0
D106R25	291	Control-Freec	DUP	3R	8841216	3R	8980480	-	-	somatic_tumour	-	139.3	3R:8841216-8980480	Heterozygous duplication	0.35	0.54	-	-	-	-	-	pyd, intron	intergenic	pyd, tRNA:Arg-TCG-2-3, tRNA:Arg-TCG-2-4, CR44020, osk, skap, CG11964, CG11966	NA	snp_su:167; snp_op:130; snp_ratio:1.28	10.8
D106R25	299	Control-Freec	DUP	3R	9591808	3R	9621504	-	-	somatic_tumour	-	29.7	3R:9591808-9621504	Heterozygous duplication	0.43	0.78	-	-	-	-	-	CG8312, exon_1	CG8312, intron	CG8312	NA	snp_su:33; snp_op:26; snp_ratio:1.27	10.9
D106R25	300	novobreak	TANDUP	3R	9821735	3R	30528249	2	1	somatic_tumour	220	20706.5	3R:9821735-30528249	3to5	0.07	0.21	-	-	CGTTTGTCCGTCACGCACACAGAGAAGAAGAGGCAACGCAACCAGCAAATCGAGTGGGACAAAGTTGTCGACTGAAAGATGTTCAGTAACTGCAATCTCGAAAGCCACCCGAAAAGCAGCCAAGAGTCACCCAACTACTCCGTTCCTCCTTGCCGTTCCACTCCATGCCACTCACATGCCAATGCCCGTGTAAATAAAAGTCAAGTG	-	-	CR45790, exon_1	intergenic	CR45790	NA	-	0
D106R25	309	Control-Freec	DUP	3R	10895360	3R	11339776	-	-	somatic_tumour	-	444.4	3R:10895360-11339776	Heterozygous duplication	0.25	0.4	-	-	-	-	-	Leash, 3UTR	pros, intron	Leash, CR45577, CR45578, Tengl4, CR45561, CG34114, CR46007, CR44940, CG43449, CR45579, CG6629, Ugt86Dd, CG4706, CheA86a, Ugt86Di, Ugt86Dc, Ugt86Da, CG4757, Ugt86Dg, Ugt86De, Ugt35b, Ugt35a, Ugt86Dj, Ugt86Dh, CG18577, cu, SdhC, Tctp, ZnT86D, RpS25, CG4820, CG6689, CG6693, RpL3, snoRNA:Me18S-C1096, CR31144, snoRNA:Me18S-A425, snoRNA:Psi28S-291, snoRNA:Me28S-G2017, scpr-C, CG17726, GCC88, CG17187, CG14701, Arfip, CG17721, CG31441, CG31388, scpr-B, scpr-A, CG17734, CG5214, CR43283, CR31386, CR45055, CR46008, pros	NA	snp_su:215; snp_op:192; snp_ratio:1.12	10.8
D106R25	311	novobreak	BND	3R	11452075	3R	17385817	3	0	somatic_tumour	227	5933.7	3R:11452075-17385817	5to5	0.09	0.25	-	-	GTATTCTAATCAGCTGAGTATAACGAATGGGAAATGTGTTGAAAAGGTTTAAGTCGTGGCCTTTCGCCAGCTGGTCACACCAATTTGCTGCCGCCGAAATCAATCCAATAGCTGCAACAGAGCGAAAACAAATGATTAAGTCTATGCCACTGCCGCAAATATTTATTTAACGTGCAATGTAGGTTATCAATGGCA	-	-	CG17230, intron	lute, intron	CG17230, Brf, lute	NA	-	0
D106R25	313	Control-Freec	DUP	3R	12721152	3R	12940288	-	-	somatic_tumour	-	219.1	3R:12721152-12940288	Heterozygous duplication	0.38	0.64	-	-	-	-	-	Men, intron	intergenic	Men, CR44231, CG5724, CG5999, CR46238, beat-Vc, CR44233, CR44232, CG31345, CR46217, beat-Va, CR45587, CR44234, CG10126, CR46218, CR44235, d-cup, CR33929, CG10909, beat-Vb, CR44236	NA	snp_su:267; snp_op:259; snp_ratio:1.03	10.09
D106R25	316	Control-Freec	DUP	3R	15148032	3R	15185920	-	-	somatic_tumour	-	37.9	3R:15148032-15185920	323:316_323	0.48	0.97	-	-	-	-	-	intergenic	Gyc88E, intron	Mf, Gyc88E	NA	snp_su:0; snp_op:0	0
D106R25	321	novobreak	TRA	3R	13855558	2L	4704205	3	0	somatic_tumour	234	9151.4	3R:13855558 2L:4704205	321:33_321	0.08	0	-	-	CAGTTGCATTTACGGTGGAGCAGGCGTTAATGTGGCATCGCATTTAGTTGGTCACGCCGGATGCCTAAGCCACGCTTGTGTGCCTAAAAATTGTGTGCGAATTTCATTTTCCATTTCCCATTTTTCTTGTTTTTGATAAACGCCGTTCAAGATCTGTTAAGATTAGGGTCTAGACCTCATTTTATGCGTTAGTTGTCTTTTACGATCGTGTAC	-	-	intergenic	CG34351, intron	CG34351	NA	bp2_rDNA_2	0
D106R25	322	novobreak	BND	3R	14992522	3R	30290266	3	0	somatic_tumour	235	15297.7	3R:14992522-30290266	5to5	0.06	0.19	-	-	ATAACTAGTCAACATTTTCTCCTAGTGTTTAAATTCATTATGTCAGTCAGCAAAAGTTTGCGCTGCCAGCGGTCGAGTGTGACTCACTGCCTCGGATTCAGTTTCAGTTTCAGCTTCAGCTTCAGCTTTCGCCTGCCGCATAAATCATCTTTCTCTCTCCGTGCAC	-	-	intergenic	hdc, intron	hdc	NA	-	0
D106R25	324	Control-Freec	DUP	3R	15278080	3R	15311872	-	-	somatic_tumour	-	33.8	3R:15278080-15311872	Heterozygous duplication	0.36	0.58	-	-	-	-	-	l(3)neo43, 3UTR	Tm2, intron	MRG15, l(3)neo43, Tm1, CG45218, Tm2	NA	snp_su:0; snp_op:0	0
D106R25	335	novobreak	TRA	3R	17120013	2R	18162537	3	0	somatic_tumour	244	1042.5	3R:17120013 2R:18162537	5to5	0.11	0	-	-	CCAATCGCTGGGGTGCGAGCGTGCGGGGTGGACGTGCGGATGCGTGATCTTTGGGTTGGTGCAACGTGAGGTGCACGACGTCGGCCAGACAAGTGAATGAGCCAAGCAAATGGGGCTGACAACCAGCGACCTTCTCGATATGGTTAGGAATTGTTAATTTTAGCCAAATGAGTCAAAGTCAAAACGGGTAGCTATGTACATACATATGA	-	-	cher, intron	CG10915, intron	cher, CG10915	NA	-	0
D106R25	338	Control-Freec	DUP	3R	17898496	3R	18158592	-	-	somatic_tumour	-	260.1	3R:17898496-18158592	Heterozygous duplication	0.27	0.41	-	-	-	-	-	Rim, intron	CR45104, exon_1	Rim, CG12347, CG43445, cpo, DNaseII, CG7785, CG7794, htl, CG14317, sr, tRNA:Gly-TCC-1-3, tRNA:Gly-TCC-1-4, CG14316, CR45103, CR45104	NA	snp_su:459; snp_op:439; snp_ratio:1.05	10.06
D106R25	355	novobreak	TRA	3R	22464852	2L	14023950	4	0	somatic_tumour	257	8440.9	3R:22464852 2L:14023950	3to3	0.13	0	-	-	AGACAGGTAATTGCCACTTATGCGGCTGACCAGTCGGTTCCGATGGAGGGGCAAAGATATAGAACCAGAATCGGGGAGAGCGAGTAAGACAGAGAGCGAGAGTGAGCGAGGTCTGGGTTGCGAGTGTTAGTTGGGGCGGGGTGTATAGAAACTAGTTTTCACTTCGTTGAACATCATTAATAATTGTGACGTTAATT	-	-	intergenic	CR31840, ncRNA	CR31840	NA	-	0
D106R25	366	novobreak	TRA	3R	25052198	3L	7654700	6	0	somatic_tumour	266	17397.5	3R:25052198 3L:7654700	3to5	0.16	0	-	-	GTTTTTGATGGCAGAAATTGCATAGGGCCCAGCCAAGGAGTTTTTTGGCCAGTTGACGATTTTCACGGTTCGGTTATCCGTTTTTCCTCGGCCCAGCTCATCTGCGTTGCTGCTATCACTTGACCGAAAACCACATTTTCCCATAAAACGTACAAGGACTTTTTGGCGAAACACTTACA	-	-	CG11791, intron	CG7492, exon_1	CG11791, CG32373, CG7492	NA	-	0
D106R25	379	novobreak	TRA	3R	29152675	2L	2923810	6	0	somatic_tumour	278	26228.9	3R:29152675 2L:2923810	3to3	0.13	0	-	-	CCTTGTGGGCGCGGAAGTTGCCAGACTTTTTTGAGTTCCTCGAATGGGGATTGTTGCCGCCTTTGGGCGCAGCTGCATCTCCGTTGGCCGAGGAGTTGCAGCTGAAAGTTCTTTTCATGCTCAATTTATCGGAATAAGTGTCATTTTAGTTTGAAGCACAGTTG	-	-	Slbp, exon	lilli, intron	Slbp, lilli	NA	-	0
D106R25	381	novobreak	TRA	3R	29357981	3L	9040826	3	0	somatic_tumour	279	20317.2	3R:29357981 3L:9040826	3to3	0.07	0	-	-	TTCCCAGCCTGTCTGAGCCCCTACATGACATTAATAATTCACTTTGCGCAGTCAATTTGGCCAAATCGCTTTGGCTATTCGAGATGGCGAAAGTCCGGCCATTTTTTTTTTTTTTTGTCTCTTCCGTCGCTGTCGGAAAATGTCCGTTGCCATTTCCATTGCAGCCGTCTTCCGTTTGGGCGCTGTCCCTCCGTCGTTTGCCA	-	-	intergenic	intergenic	-	NA	-	0
D106R25	385	novobreak	TRA	3R	30426360	3L	874623	4	0	somatic_tumour	282	29551.7	3R:30426360 3L:874623	3to5	0.06	0	-	-	GAGTACCAGTATGTACCCGAAGACGCTGGTCAGCCGGGAGTGGATGAACGTGGAGCTCAGCCGGACGGCGGAATGACCCAGATCTGGCACCAGGGCCCCATGTACGCAGAGGACTTCGAACTACCGTGTTGGCTGTGCCTTGCTCTTTTGGCCGCCGGCGGCGAGTGCGGGGATCCGCCGAAGGATGCCGCCGATGAGGATGTGGCCGTAGCAGTGGCCCTGCTCTTACGCTGCTGCTGCTTGTAGG	-	-	CG2218, exon	Usp10, exon_3	CG2218, Usp10	NA	-	0
D106R25	390	Control-Freec	DUP	4	0	4	374784	-	-	somatic_tumour	-	374.8	4:0-374784	Heterozygous duplication	0.36	0.64	-	-	-	-	-	intergenic	Hcf, 3UTR	JYalpha, CR32011, CR32010, CR32009, PlexB, CR45124, CR44440, ci, CR43957, RpS3A, snoRNA:CD-24, pan, Ank, CG32000, CR43956, CG32006, CG31997, CG33978, CR45198, Arl4, CG2316, CR44441, CG31998, Crk, CG31999, yellow-h, CR46065, CG1674, dpr7, RhoGAP102A, NfI, CR44023, Syt7, Rad23, Zip102B, CG32850, PMCA, Hcf	NA	snp_su:127; snp_op:100; snp_ratio:1.27	11.34
D106R25	397	Control-Freec	DUP	4	535552	4	545792	-	-	somatic_tumour	-	10.2	4:535552-545792	396:396_397_398_399	0.49	1.22	-	-	-	-	-	zfh2, exon_11	Thd1, exon	zfh2, Thd1	NA	snp_su:3; snp_op:2; snp_ratio:1.5	9.1
D106R25	397	Control-Freec	DUP	4	599040	4	746496	-	-	somatic_tumour	-	147.5	4:599040-746496	399:396_397_398_399	0.28	0.57	-	-	-	-	-	onecut, 3UTR	bt, exon_24	onecut, Eph, mav, mir-954, Gat, Ekar, CR44028, gw, Slip1, CG11360, myo, ey, bt	NA	snp_su:47; snp_op:35; snp_ratio:1.34	11.33
D106R25	400	Control-Freec	DUP	4	769024	4	786432	-	-	somatic_tumour	-	17.4	4:769024-786432	Heterozygous duplication	0.42	0.77	-	-	-	-	-	bt, exon_35	MED26, exon_3	bt, CR45200, MED26	NA	snp_su:4; snp_op:3; snp_ratio:1.33	11.08
D106R25	402	Control-Freec	DUP	4	905216	4	1006592	-	-	somatic_tumour	-	101.4	4:905216-1006592	Heterozygous duplication	0.38	0.74	-	-	-	-	-	CR43361, exon_1	toy, 3UTR	unc-13, CR43361, eIF4G, mGluR, 4E-T, CR45201, CR44030, fuss, sphinx, toy	NA	snp_su:51; snp_op:49; snp_ratio:1.04	10.74
D106R25	404	Control-Freec	DUP	4	1006592	4	1013760	-	-	somatic_tumour	-	7.2	4:1006592-1013760	403:403_404_405_406	0.46	1.55	-	-	-	-	-	toy, 3UTR	PlexA, exon_10	toy, PlexA	NA	snp_su:3; snp_op:2; snp_ratio:1.5	13.23
D106R25	404	Control-Freec	DUP	4	1031168	4	1065984	-	-	somatic_tumour	-	34.8	4:1031168-1065984	405:403_404_405_406	0.46	1.03	-	-	-	-	-	CG11076, intron	apolpp, exon_4	CG11076, ATPsynbeta, CaMKII, Zyx, apolpp	NA	snp_su:14; snp_op:1; snp_ratio:13.87	17.77
D106R25	411	Control-Freec	DUP	X	2501632	X	2567168	-	-	somatic_tumour	-	65.5	X:2501632-2567168	Homozygous duplication	0.78	0.65	-	-	-	-	-	trol, exon_2	Pdfr, intron	trol, mir-4955, Pdfr	NA	snp_su:0; snp_op:0	0
D106R25	412	Control-Freec	DUP	X	2738176	X	2955264	-	-	somatic_tumour	-	217.1	X:2738176-2955264	Homozygous duplication	0.67	0.64	-	-	-	-	-	crm, exon_2	rst, intron	crm, Syx4, CR43494, CG32795, w, CG12498, CG14416, CG14417, CG14418, CG14419, CG3526, CG3588, CG14424, CG32793, CG3592, CG3598, CG14420, CG14421, CG14422, CG14423, CG17959, CG3603, kirre, rst	NA	snp_su:3; snp_op:17; snp_ratio:0.18	2.24
D106R25	415	novobreak	COMPLEX_TRA	3L	3454007	X	3275824	8	0	somatic_tumour	131	178.2	3L:3454007 X:3275824	190:190_415_416_417	0.54	0	-	-	CTCTATTAATTCTCAATTAATAAATTGATTATTAATGCAAACATCTCAACTTCTCAGCTGTTCCAGAGGTTTAATTGAATAATCCTATAAAAATGGTCTGATTGATTGTTCTGTTCTCATTCGGCGGGTGAATTTATGCTTAAAGCTTCTAACATTTCAGTTTTCTTTCTCTCGCCTTTCATT	-	-	eIF5B, intron	dnc, intron	eIF5B, dnc	NA	-	0
D106R25	415	Control-Freec	COMPLEX_DUP	X	4973568	X	5035008	-	-	somatic_tumour	-	61.4	X:4973568-5035008	416:190_415_416_417	0.99	1.03	-	-	-	-	-	CR44833, ncRNA	CR44833, ncRNA	CR44833, CR45792, CG12680	NA	snp_su:0; snp_op:0	0
D106R25	422	Control-Freec	DUP	X	8176640	X	9061376	-	-	somatic_tumour	-	884.7	X:8176640-9061376	422:422_423	0.63	0.61	-	-	-	-	-	slpr, exon_2	CG15365, intron	slpr, sdt, CG2147, sni, Trxr-1, ND-75, CG1632, Corp, CG15343, CG1636, nAChRalpha3, CR43695, CG1387, CR15345, CG10555, CG11190, lawc, Trf2, CG32712, Miga, CG1440, CG12123, org-1, CG32713, CG15347, Es2, Sptr, CG33223, CG12116, Cp7Fa, Cp7Fb, Cp7Fc, Cp36, Cp38, CR43834, otu, CG33181, Nrg, PIP82, IntS4, CG12112, Trf4-1, CR46195, CG12111, spirit, CG12065, CG12081, CG12659, Crag, Caf1-180, oc, CG12772, CG11284, Ppt1, Ogg1, CG11294, CR44507, CR44508, Hexo2, CG2004, CG1785, l(1)G0020, CG1789, CR43297, Lim1, CR45537, CG12075, Moe, CG1885, Rbm13, e(r), rdgA, CR44111, CG12661, CG43255, mir-4964, CR43836, CG10962, CG12662, mir-31b, Nost, CG15365	NA	snp_su:8; snp_op:3; snp_ratio:2.66	17.27
D106R25	422	Control-Freec	DUP	X	9061376	X	9068544	-	-	somatic_tumour	-	7.2	X:9061376-9068544	423:422_423	0.9	1.63	-	-	-	-	-	CG15365, intron	intergenic	CG15365	NA	snp_su:0; snp_op:0	0
D106R25	425	Control-Freec	DUP	X	9377792	X	9551872	-	-	somatic_tumour	-	174.1	X:9377792-9551872	Homozygous duplication	0.96	1.03	-	-	-	-	-	mgl, intron	l(1)G0320, 3UTR	mgl, CG44815, CG32700, CG34028, CG34026, l(1)G0320	NA	snp_su:0; snp_op:0	0
D106R25	426	Control-Freec	DUP	X	10289152	X	10315776	-	-	somatic_tumour	-	26.6	X:10289152-10315776	428:426_428_429	0.97	1.23	-	-	-	-	-	alpha-Man-Ia, intron	alpha-Man-Ia, intron	alpha-Man-Ia	NA	snp_su:0; snp_op:0	0
D106R25	438	Control-Freec	DUP	X	18903040	X	19117056	-	-	somatic_tumour	-	214	X:18903040-19117056	Homozygous duplication	0.7	0.63	-	-	-	-	-	CG7378, intron	intergenic	CG7378, CR44708, CG43759, Diedel3, CG14190, CG34330, CG7406, CG14191, CG7423, CR45503	NA	snp_su:0; snp_op:1	0
D106R25	441	novobreak	TRA	X	20129197	2R	14604361	3	0	somatic_tumour	324	5524.8	X:20129197 2R:14604361	3to3	0.17	0	-	-	CCCTGCTATATTGCACACCCAATCAGTGTTTACCAATTAATTGATAGCCTTTGGCAGGTTTTATTTATTCTGTCTGCGTTTAGAAAGACGCACGCTTCGACAGGGGTGGCGATAGGTGAGGACGTGCGTTATCGATTGGCACTTTATATTCGCGTTGCTCTCCTTTTCTTTTTTTTTTGCTTACGCAGCTTATCAGGCATTCAACGCGATATATTG	-	-	intergenic	intergenic	-	NA	-	0
D106R27	4	Control-Freec	DUP	2L	10994008	2L	10997840	-	-	somatic_tumour	-	3.8	2L:10994008-10997840	Heterozygous duplication	0.48	0.97	-	-	-	-	-	CG16833, exon_10	aub, 3UTR	CG16833, aub	NA	snp_su:3; snp_op:0; snp_ratio:301.0	15.54
D106R27	5	Control-Freec	DUP	2L	16177746	2L	16182536	-	-	somatic_tumour	-	4.8	2L:16177746-16182536	Heterozygous duplication	0.42	0.71	-	-	-	-	-	Ca-alpha1D, exon_17	Ca-alpha1D, intron	Ca-alpha1D, CR43806	NA	snp_su:4; snp_op:2; snp_ratio:2.0	10.89
D106R27	8	Control-Freec	DUP	2L	21298256	2L	21307836	-	-	somatic_tumour	-	9.6	2L:21298256-21307836	Heterozygous duplication	0.38	0.61	-	-	-	-	-	Mondo, intron	Mondo, intron	Mondo	NA	snp_su:0; snp_op:1	0
D106R27	13	Control-Freec	DUP	2R	4693242	2R	4701864	-	-	somatic_tumour	-	8.6	2R:4693242-4701864	Heterozygous duplication	0.41	0.69	-	-	-	-	-	Nipped-B, intron	Nipped-B, intron	Nipped-B	NA	snp_su:1; snp_op:4; snp_ratio:0.25	2.7
D106R27	16	novobreak	BND	2R	14379013	2R	22170535	2	1	somatic_tumour	6	7791.5	2R:14379013-22170535	3to3	0.03	0.03	-	-	CCATGCACTTGACCACTCTAATAAACTAACTGCTAACCAGGAAGGACTTGTTGCCATGGCCTTAAGGACTTCCCTTTGCAAGCCAAGTAAATCTCCGGCAATCTCCGTGGCATTTCGGCCACCCAGCGACACGGGAGCACTGCAGATGCTGCTGTTTCTCGTCGATGGGGCACCCAGTCCCAGACTCATGCCCATGCC	-	-	Dh44-R1, intron	a, exon_6	Dh44-R1, a	NA	-	0
D106R27	23	Control-Freec	DUP	3L	15551214	3L	15554088	-	-	somatic_tumour	-	2.9	3L:15551214-15554088	Heterozygous duplication	0.48	1.15	-	-	-	-	-	CrebA, exon	intergenic	CrebA	NA	snp_su:0; snp_op:0	0
D106R27	27	Control-Freec	DUP	3L	24728854	3L	24748014	-	-	somatic_tumour	-	19.2	3L:24728854-24748014	Heterozygous duplication	0.36	0.53	-	-	-	-	-	scro, intron	scro, intron	scro	NA	snp_su:3; snp_op:2; snp_ratio:1.5	11.59
D106R27	28	Control-Freec	DUP	3L	26002036	3L	26014490	-	-	somatic_tumour	-	12.5	3L:26002036-26014490	Heterozygous duplication	0.38	0.6	-	-	-	-	-	CG40178, intron	intergenic	CG40178	NA	snp_su:2; snp_op:1	14.37
D106R27	29	Control-Freec	DUP	3R	4078206	3R	4081080	-	-	somatic_tumour	-	2.9	3R:4078206-4081080	Heterozygous duplication	0.5	0.94	-	-	-	-	-	CG42402, exon_1	CG42402, intron	CG42402	NA	snp_su:0; snp_op:1	0
D106R27	30	Control-Freec	DUP	3R	4168258	3R	4171132	-	-	somatic_tumour	-	2.9	3R:4168258-4171132	Heterozygous duplication	0.47	0.93	-	-	-	-	-	intergenic	intergenic	-	NA	snp_su:1; snp_op:0	13.81
D106R27	34	Control-Freec	DUP	3R	15299260	3R	15310756	-	-	somatic_tumour	-	11.5	3R:15299260-15310756	Heterozygous duplication	0.34	0.5	-	-	-	-	-	Tm1, intron	Tm2, exon_1	Tm1, Tm2	NA	snp_su:0; snp_op:0	0
D106R27	37	Control-Freec	DUP	3R	22071362	3R	22079026	-	-	somatic_tumour	-	7.7	3R:22071362-22079026	Heterozygous duplication	0.32	0.51	-	-	-	-	-	how, exon_6	how, exon_9	how	NA	snp_su:0; snp_op:0	0
D106R27	38	Control-Freec	DUP	3R	24062086	3R	24067834	-	-	somatic_tumour	-	5.7	3R:24062086-24067834	Heterozygous duplication	0.39	0.77	-	-	-	-	-	SMC1, exon_9	4EHP, 3UTR	SMC1, 4EHP	NA	snp_su:1; snp_op:1	5.91
D106R27	39	Control-Freec	DUP	3R	25493338	3R	25496212	-	-	somatic_tumour	-	2.9	3R:25493338-25496212	Heterozygous duplication	0.45	0.66	-	-	-	-	-	intergenic	CR44948, exon_2	CG33494, CR44948	NA	snp_su:1; snp_op:2	12.05
D106R27	44	Control-Freec	DUP	4	558514	4	571926	-	-	somatic_tumour	-	13.4	4:558514-571926	Heterozygous duplication	0.41	0.75	-	-	-	-	-	Pur-alpha, intron	Ephrin, exon_1	Pur-alpha, ND-49, Ephrin	NA	snp_su:1; snp_op:0	24.51
D106R27	46	Control-Freec	DUP	4	1190794	4	1198458	-	-	somatic_tumour	-	7.7	4:1190794-1198458	49:45_46_47_48_49	0.47	0.88	-	-	-	-	-	CG33521, intron	intergenic	CG33521, PIP4K	NA	snp_su:3; snp_op:3; snp_ratio:1.0	13.75
D106R27	50	CNV-Seq	DEL	X	3146021	X	3245519	-	-	somatic_tumour	-	99.5	X:3146021-3245519	Homozygous deletion	0.95	-1.77	-	-	-	-	-	N, intron	dnc, exon_3	N, CG18508, Fcp3C, CG3939, CG14265, ng2, ng3, ng1, ng4, dnc	NA	snp_su:0; snp_op:0	0
D106R27	50	Control-Freec	DEL	X	3146072	X	3245704	-	-	somatic_tumour	-	99.6	X:3146072-3245704	Homozygous deletion	0.95	-1.77	-	-	-	-	-	N, intron	dnc, exon_3	N, CG18508, Fcp3C, CG3939, CG14265, ng2, ng3, ng1, ng4, dnc	NA	snp_su:0; snp_op:0	0
D106R29	2	novobreak	TRA	2R	16271743	3R	26322116	3	0	somatic_tumour	60	10050.4	2R:16271743 3R:26322116	56:2_56	0.04	0	-	-	GTTCACTGTGTTGTTGTGCCGATTCTGGTACTCCGTTTTGCCCCTTTTGTTCCGATTCTCTGCTGATTCCGACACACTCGCGAAAATTGGGTTGGGGGCGGCTCAAATAAGAAGATGCAGTGAAATGAAATGCAAATGGGGAGCCCTAAAAAAGCGTTGCAATGTCGGAATG	-	-	Khc, 5UTR	CG33970, intron	Khc, CG33970	NA	bp2_rover_Gypsy=5	0
D106R29	18	Control-Freec	DEL	2L	11851245	2L	11856915	-	-	somatic_tumour	-	5.7	2L:11851245-11856915	Homozygous deletion	0.5	-4	-	-	-	-	-	Mal-B2, exon_2	Pde1c, intron	Pde1c, Mal-B2, CG42751	NA	snp_su:0; snp_op:0	0
D106R29	23	novobreak	TRA	2L	13830336	3L	11165569	4	0	somatic_tumour	23	2664.8	2L:13830336 3L:11165569	5to3	0.06	0	-	-	TTTAAATGCCATCGAATGCTACACCACCAAGATAATGCTGGAGATCCTGTTAGACTCGCTGGCACCCGATCAAGGTGATGCGCTGAAGGTCGACAACTATTGGCAGCAGGAGGCGCACCTGCCGGCGGCGGTCTTTGGGGCTGCCAGTGTGCTTATGCGCCAGACGAATATCGTGTGGG	-	-	Orc5, exon_1	Alg10, exon_2	Orc5, Alg10	NA	-	0
D106R29	28	novobreak	DEL	2L	16657137	2L	16657673	7	0	somatic_tumour	30	0.5	2L:16657137-16657673	5to3	0.11	0	-	-	ATGCGTTTTAAAAAATACTGTTAGAGTGGTGGTATTTTTTCAACTCAGTGAACGCAGCCCCACTGAAAACGTTTAATTTGTTGTTCCTTGAACCCACAGCAACAACAACAACAGCAGCAGCAGGTGGCACCACCTGCGGTCCAAGGAGCACCAAGCACTGGAAGTGTAGGAGCTGCCCAAGGAGCACCAGCCACTGCGACAGCCACCCATACACACGCCCATTCGCACTCCCACTCACACGCCCACTCGCACACACATCCCCAGCCACATGCAC	-	-	CG42389, 5UTR	CG42389, exon_4	CG42389	NA	-	0
D106R29	29	Control-Freec	DUP	2L	16981650	2L	17007165	-	-	somatic_tumour	-	25.5	2L:16981650-17007165	Heterozygous duplication	0.31	0.33	-	-	-	-	-	beat-IIIb, intron	intergenic	beat-IIIb, CG44406, CR44408, CG31806, CR45356, CR45357	TRUE	low FC; snp_su:60; snp_op:0; snp_ratio:6001.0	43.63
D106R29	40	novobreak	TRA	2R	5423581	3R	26700737	3	0	somatic_tumour	43	21277.2	2R:5423581 3R:26700737	3to5	0.08	0	-	-	CTGTTAATGGAAATGGTCCACATGGAGGCGGCATAGCCGTCACAGTTGCAGTCATCCTCCTCGCCGCCGTCGCCGGATGCCCAAACATATATGTTGCCCAGGCCATTTCGGCTTTGATCCTGATCAAGAATATATATACTTTATACCGCTTCCTTCTACATGTTACCTATTTTTCAACGAATCTAGTATACCTTTTTACTGTACGATTTATGGG	-	-	laccase2, intron	amon, exon_8	laccase2, amon	NA	bp2_INE-1_Helitron=6	0
D106R29	42	Control-Freec	DUP	2R	5720085	2R	5722920	-	-	somatic_tumour	-	2.8	2R:5720085-5722920	Heterozygous duplication	0.46	0.66	-	-	-	-	-	ap, intron	ap, intron	ap	NA	snp_su:0; snp_op:0	0
D106R29	70	novobreak	TRA	3L	1013729	3R	14926092	3	0	somatic_tumour	78	13912.4	3L:1013729 3R:14926092	5to5	0.05	0	-	-	ATGAAACCTTGATGACGCCAAAATGAATGCGTCCTGCCATAACGGAAATGGAACAAAAACCGAACGGAGTGGGCGGAAACGGAAGTGGGGGTACGAGTGGAACTCTTCGTTCGATCTACGTGCTTTGAACCAAGATATTGAGTGGAAGGGAGAAATTTTAGACAGATTTCGTATGCCAGTTGATGCCTGGCTGGAATTTGTTCGCCTAAATGCCCTCATGGGCGCCATAAATC	-	-	trio, intron	intergenic	trio	NA	-	0
D106R29	77	delly	DEL	3L	3450239	3L	3450565	8	0	somatic_tumour	DEL00000002	0.3	3L:3450239-3450565	5to3	0.23	0	-	-	CAAGAAAATGCCGCACGTTGCTCGAGAACTTCCGTTTTGCTTTGGGGCTCTTTCAGTGCAAACACATATCTATTATTTTCAACTTCCTTTCCTTCCAAAAATACGGCCGCTACGTGTTTAAATTTATATCCCAAACTTATATTTCTTACTCGGACCAAATACTTTTATAT	-	-	eIF5B, intron	eIF5B, intron	eIF5B	NA	-	0
D106R29	77	novobreak	DEL	3L	3450239	3L	3450565	8	0	somatic_tumour	86	0.3	3L:3450239-3450565	5to3	0.23	0	-	-	TCGAATTCAAGAAAATGCCGCACGTTGCTCGAGAACTTCCGTTTTGCTTTGGGGCTCTTTCAGTGCAAACACATATCTATTATTTTCAACTTCCTTTCCTTCCAAAAATACGGCCGCTACGTGTTTAAATTTATATCCCAAACTTATATTTCTTACTCGGACCAAATACTTTTATATAACTTCATTTCAATAACTTAATGAATGTAGCAGTGCTTCGAAAAAAAATTCTACTTCTCTCTGGTTTCAACATCAAGGGTATGAAA	-	-	eIF5B, intron	eIF5B, intron	eIF5B	NA	-	0
D106R29	85	novobreak	TRA	3L	6774868	X	918170	2	1	somatic_tumour	97	5856.7	3L:6774868 X:918170	5to5	0.06	0	-	-	GCCCCTCCCCCGCCTGCAGGAGTTTGTGTGTGTTTGCATAACAAAACTAACATTTAACAATAACATTTATTTTTGTGGTTGCGTTTTAGTTGGGTTTTGTGTGTTTATTTTTATATTTTGGTGTTTCGCTTCAAAAATTTATTTGTCGCCGACAATTGACGGACTGCCATGTAC	-	-	intergenic	CG43867, intron	CG43867	NA	-	0
D106R29	115	novobreak	TRA	3L	19887596	X	15186910	4	0	somatic_tumour	124	4700.7	3L:19887596 X:15186910	5to5	0.07	0	-	-	CTCTTAAGATTAAGCTGCTCGGCAAGCGCAAACGCGATAGTTCGGATGAGGAGCAAATTATTTCGGAAAAGGAGGTAGCCAAACCTCTCCAGAAAGAGGTAGCTACTCCACCTGATTATGAGGTGAAAACCACTCCGGAAGAGGCGGTAGATGTAAAACAAGAAGAGTCAGTTGTTCCGGAAAA	-	-	Mi-2, exon_4	CG43737, exon	Mi-2, CG43737	NA	bp2_211000022278137_3	0
D106R29	119	novobreak	TRA	3L	20870098	3R	25477350	3	0	somatic_tumour	127	4607.3	3L:20870098 3R:25477350	3to3	0.04	0	-	-	ATCGCTTCATAGACGTCGCCCGCCAAATGGAGGCGTTCTTCCTGCAGAAGCGTTTTCTCGTCTCCACGCTGAAGCCCTACATGCTGATCAAGGACGAGAATCAGTGTGTTTTCCTGATTGATGGCTCTACTTGGTGCTAACTAAACGGATT	-	-	CG32432, intron	MED28, exon	CG32432, MED28	NA	-	0
D106R29	123	Control-Freec	DUP	3L	23446395	3L	23449230	-	-	somatic_tumour	-	2.8	3L:23446395-23449230	Heterozygous duplication	0.42	0.47	-	-	-	-	-	intergenic	intergenic	-	NA	snp_su:0; snp_op:1	0
D106R29	125	Control-Freec	DUP	3L	24230745	3L	24236415	-	-	somatic_tumour	-	5.7	3L:24230745-24236415	Heterozygous duplication	0.41	0.55	-	-	-	-	-	Snap25, intron	Snap25, intron	Snap25	NA	snp_su:0; snp_op:1	0
D106R29	126	Control-Freec	DUP	3L	25605720	3L	25610445	-	-	somatic_tumour	-	4.7	3L:25605720-25610445	Heterozygous duplication	0.42	0.52	-	-	-	-	-	CG45782, intron	CG45782, intron	CG45782	NA	snp_su:1; snp_op:0	16.76
D106R29	132	Control-Freec	DUP	3R	4163670	3R	4180680	-	-	somatic_tumour	-	17	3R:4163670-4180680	132:132_133	0.45	0.82	-	-	-	-	-	intergenic	CG12581, intron	CG12581	NA	snp_su:1; snp_op:3; snp_ratio:0.34	6.82
D106R29	149	novobreak	BND	3R	17750912	3R	18341929	3	0	somatic_tumour	169	591	3R:17750912-18341929	3to3	0.08	-0.02	-	-	CTTTCTCGCAGTGTGTTCGGGCAATCTGACAATAAGCGAGCGTACATCTGTTACGCTGATTGATTTATCACTCGATTGAAACAATTTGATCTGCATGCGCTTGACAGTCGCTTGATTTACATTTGAAGGTACTGAAATCAGTGGAACATCTGGGGGCTGGGATCAAGTTGAGAATTAGCTTTAATCATCTTTATCGGA	-	-	TyrR, 3UTR	CG15803, intron	TyrR, CG15803	NA	-	0
D106R29	159	novobreak	TRA	4	385213	3L	6045215	3	0	somatic_tumour	187	5660	4:385213 3L:6045215	5to3	0.05	0	-	-	GTACCAATTCCATAAGTACTGAAGCTTGGAAATTAAAAAGAAAACATAAAATCGTAACGAGAGAGGAAGATAATTGTATAATGAAATCCAAACAACACTTGGGTCTTGGTGTGGCTCTGCTGGTGGCTCCACTTGAACCACCAACGCCCGAAAACAAGTTCACTCAGCATCCACCACAATGACTTGACGGCAAAGTTCGCTGCACCAGCA	-	-	dati, intron	intergenic	dati	NA	-	0
D106R29	178	novobreak	TRA	X	20667011	3R	26146683	3	0	somatic_tumour	211	5479.7	X:20667011 3R:26146683	5to5	0.1	0	-	-	ACAGAAAGGAATCGCTAATCATGCCGGCAGATAAAAACAAGTGGGAGTGTCATATGTGACCCGTTATTTTTTCTATGGGTTGTCGCCTGTTGTTAATGATGATGACAACCAAAGTTGGTTGTGCTCCTGTCACCCATCCACTTGATATGTTCAGAGCCCGCTTTGTCCTCGTACTG	-	-	CG1835, intron	intergenic	CG1835	NA	-	0
D106R31	2	novobreak	COMPLEX_DEL	2L	729105	2L	1531070	9	2	somatic_tumour	3	802	2L:729105-1531070	1:1_2_3	0.1	-0.27	-	-	TAGCCACCCTCTCCGCGAACGGGGATACTGAAATTGGGCGGCTCATTGGGGAGGCCACCGACAAAGTGGGTCCAAGAGGAACTATTACTGTAAAGGATGGCAAGCTCATAATGGACGAAAAGGTCGAGTTCAAATGAGAGAAATGAGAGGAGTAAGAGCTGCAGCCAAACGGTGGCCAACAACTGAATGTGTGGCAATTGGGGTTGCATCCTGGTGGGCCCACGGATGGGGAAAGCCAGGATCAGGACACGTGTGAGAGCAAAGAACAACACGTGGCCACAGCCCAGTTTTCTGGGCCTAATCAACATCAATTGCGCTTTTTGGTCTCCTCTGCGG	-	NHEJ	Hsp60B, exon	intergenic	Hsp60B	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:1953; snp_op:1418; snp_ratio:1.38	10.51
D106R31	2	novobreak	COMPLEX_TANDUP	2L	1440862	2L	1444311	18	0	somatic_tumour	5	3.4	2L:1440862-1444311	3:1_2_3	0.13	-0.1	-	ACT	TGGTGGCCAGCTGTCTCTGGCCATGTATCCTGATTTTCCACCCCCCCCCAGAAGCCAAAGGATATTCGCAAACAATGCGAATGGAATTGGTACATGCAATTTTCAATCTTTGGAGTGCCGTGCAAATTGACTTCCGTCAAAAGGCATGAGCATCATTTCAATTGCCTTCTGACTTGGCCAGTCCAAAATTGCTACTAAACATTAATCAAACTCCCGTTTAGACCTCCCAATGACGACCCGAACAAATGCAGACATCAGCAGCCCCAGTTTCAATGT	GGGAGTTTGATTAATGTTTAGTAGCAATTTTGGACTGGCCAAGTCAGAAGGCAATTGAAATGATGCTCATGCCTTTTGACGGAAGTCAATTTGCACGGCACTCCAAAGATTGAAAATTGCATGTACCAATTCCATTCGCATTGTTTGCGAATATCCTTTGGCT	NHEJ	intergenic	intergenic	-	NA	mh:0; ins:3; tup:2; tdown:3	0
D106R31	2	novobreak	COMPLEX_BND	2L	1440908	2L	1444311	0	6	somatic_tumour	6	3.4	2L:1440908-1444311	3:1_2_3	0.05	-0.1	-	ACT	GTCAGATGTGTATAAGAGACAGGAATTGGTACATGCAATTTTCAATCTTTGGAGTGCCGTGCAAATTGACTTCCGTCAAAAGGCATGAGCATCATTTCAATTGCCTTCTGACTTGGCCAGTCCAAAATTGCTACTAAACATTAATCAAACTCTGTCTCTTATACACATCTCCG	GGGAGTTTGATTAATGTTTAGTAGCAATTTTGGACTGGCCAAGTCAGAAGGCAATTGAAATGATGCTCATGCCTTTTGACGGAAGTCAATTTGCACGGCACTCCAAAGATTGAAAATTGCATGTACCAATTCCATTCGCATTGTTTGCGAATATCCTTTGGCT	NHEJ	intergenic	intergenic	-	NA	mh:0; ins:3; tup:2; tdown:3	0
D106R31	10	novobreak	DEL	3L	157613	3L	158064	6	4	somatic_tumour	9	0.5	3L:157613-158064	5to3	0.09	0	-	-	TTTGTTATTTATCTGTAAACGTTCTACCTCGTCGTTAGCTTGGTTAAATCGCAGACCAAACATTATCTCCGCTTACCGTTTTAATTACCATTTTATAGCAACGCATTCTTTTGGCTTATGACAAAGCCGAAAATTTTCTTTTGTTGGGCATTCTTGGGACCAACTACTCCGCAGGAGGTTTCATTCCGCACTTCGAGATCCTCGCGTAAGAACCAAATGATTCGGCTACTGTTACGCAAATTCATTATACAATATTATGGAATCGAAAGTTCATTTTAGTGTTATGC	-	-	p130CAS, intron	CR43151, exon_1	p130CAS, CR43151	NA	-	0
D106R31	11	novobreak	DEL	3L	3818450	3L	3819947	5	3	somatic_tumour	10	1.5	3L:3818450-3819947	5to3	0.1	-0.01	-	-	GCTCGAATTATCAATGCGAATTGTATCTGAATGTGTAATAAATATGCATAAAAACAGGATAGATGTGGTGAATTTTCGTGGTTTTGCTATACAAGCCATATCCTTTGAAAATATGAATTTTCAGGTTTTTGCGAATTATCCGACCAGCCCGGCTATATCCCCCCTCACTCCACTTCCCTGGGCCTTTCTCACATTTGTCTCCAATTCTCTTACATCGCTGGCGTCGCAATAATGTCGTC	-	-	intergenic	enc, intron	enc	NA	-	0
D106R31	13	novobreak	DEL	3R	8801755	3R	8801863	11	1	somatic_tumour	13	0.1	3R:8801755-8801863	5to3	0.14	0	-	-	TTTATTGTTTTAAACTGTAATACGTGCTAAAGGCCAACCCCATCACATAAATATGGTAAGTCCGGCCGGAAATAATCCGAGGATAACCAAGTGAATCCAATCATGGACTCGTCCGCGAGCGGCATGAGACGCAAATCGTGCTCCTCAAAGAAGGCACTGACTCGTCGCAGGGCAAGCCGCAACTGGTGTCCAACATCAATGCCTGCCAGTCGATCGTGGACGCAGTGCGGACCACTCTGGGTCCCCGCGGCATGGACAAGCTGATTGTGGATGCCCACGGCAAGGCGACGATTTCCAACGATGGAGCCACCATCATGAAGCTGCTGGAGATCATCCACCCGGCGGCCAAGACCCTGGTGGACATTGCCAAGTCACAAGACGCCGAGGTAAG	TGTAATAAATATGCATAAAAACAGGATAGATGTGGTGAATTTTCGTGGTTTTGCTATACAAGCCATATCCTTTGAAAATATGAATTTTCAGGTTTTTGCGAATTATCCGACCAGCCCGGCTATATCCCCCCTCACTCCACTTCCCTGGGCCTTTCTCACATTTGTCTCCAATTC	NHEJ	Tcp-1eta, intron	Tcp-1eta, exon_2	Tcp-1eta	NA	mh:0; ins:0; tup:0; tdown:0	0
D106R31	17	novobreak	DEL	3R	28621620	3R	28624106	3	1	somatic_tumour	16	2.5	3R:28621620-28624106	5to3	0.02	0.13	-	-	CTTTCATTACTCTGACTTGCAATCTAATTGAACTGAATACGGAAAGCTGACAGAATGTCTGAATGGATGAAAGGCCATTGGCAAGTAGCTTTTTCGGTTCTGGCCAAAGAAAATGGAATTAATGTTTCTTTGCCAACACAATTGCATTTTCCGTACGGCTCTTGTTTTTTCTTTCGCACTTGGCCGGCAGATGTTATTCATGGCTTTGGGCTAATTAATGCGAGTAAGGAGCAAATTAAAATGCTGTTTAGCCACTGCCACTTGCAGCTGTCTCTTAAAAC	-	-	CG10011, intron	CG10011, intron	CG10011	NA	-	0
D106R31	18	novobreak	BND	X	3121806	X	3145610	4	1	somatic_tumour	23	23.8	X:3121806-3145610	5to5	0.12	-0.01	-	-	GGCACAAAGTTCCCTAACCAGTAGGACGAAATAAAAAAGGGTTAGAACAAGGAGGGGGATTTTCTAATGCTTTTGTGCACATGAAAAAAACATATCGTTGAGCAAGTTTAATTAGGTCTTAACTCGATTTGAGCCAACTCAAGCAATTAACAGCTCATTTGTCGGTAAAGAAGCATCTGCCTAAGC	-	-	kirre, intron	N, intron	kirre, N	NA	-	0
D106R31	20	Control-Freec	DEL	Y	498296	Y	500174	-	-	somatic_tumour	-	1.9	Y:498296-500174	Homozygous deletion	0.84	-1.26	-	-	-	-	-	kl-3, intron	kl-3, intron	kl-3	NA	snp_su:0; snp_op:0	0
D106R33	7	Control-Freec	DUP	2L	21257798	2L	21260456	-	-	somatic_tumour	-	2.7	2L:21257798-21260456	Heterozygous duplication	0.42	0.61	-	-	-	-	-	Hr39, exon	intergenic	Hr39	NA	snp_su:3; snp_op:2; snp_ratio:1.5	7.34
D106R33	8	Control-Freec	DUP	2L	21304756	2L	21307414	-	-	somatic_tumour	-	2.7	2L:21304756-21307414	Heterozygous duplication	0.42	0.78	-	-	-	-	-	Mondo, intron	Mondo, intron	Mondo	NA	snp_su:7; snp_op:7; snp_ratio:1.0	12.08
D106R33	9	Control-Freec	DUP	2L	21390698	2L	21393356	-	-	somatic_tumour	-	2.7	2L:21390698-21393356	Heterozygous duplication	0.46	0.96	-	-	-	-	-	nrv3, 3UTR	intergenic	nrv3	NA	snp_su:0; snp_op:0	0
D106R33	16	novobreak	DEL	2R	8396835	2R	8406450	5	2	somatic_tumour	2	9.6	2R:8396835-8406450	5to3	0.11	-0.63	-	-	GAACCAGTGCTTTCCCACAGGCGAAAGTTGCTATAAGCGGCAATCATAAATACGGCCGAAGCCGAGTCCTGGCCGGAACAACTTGGCACTTAGCCGCACATGTTGGCCTCGTCAGGCATTAATGTCTCGCAATTAACTTTAGATCAATTATGTGGCTGCGGAGTCTGGAGTTTTGCCTGTTAATTAGGCAGCAAGCCGGCCAAAACGGCCAAATGAGTGTTTTTCCACAGGAATAGAGGCAAACTTGACTAGGCAGCAGAACAGCCGGGAAC	-	-	CG2121, exon_5	CG2121, intron	CG2121	NA	snp_su:12; snp_op:14; snp_ratio:0.86	7.54
D106R33	20	Control-Freec	DUP	3L	8937082	3L	8941512	-	-	somatic_tumour	-	4.4	3L:8937082-8941512	Heterozygous duplication	0.39	0.58	-	-	-	-	-	CG43783, intron	orb2, 3UTR	CG43783, orb2	NA	snp_su:2; snp_op:1	21.08
D106R33	23	novobreak	BND	3R	10985943	3R	19145997	9	1	somatic_tumour	7	8160.1	3R:10985943-19145997	5to5	0.15	0.15	-	-	CTCTACGAGTAAAGGGTATAACCACCACGAGCATTTAACCCCAGTTTTTGAACATGAAAATTTAATAGAGAATAGAATTTAAAAGTTGCTTTAATTGCAACATAACGATTAGGAAACAGAATAATCAATATTAAATATTGATATTGAACTCAGCGAACGGGACACAATGCGCCTGTACTATCACCCCCTTTTTCGTGGTTACTGGGGTTTGCAGAAGGCAGCCTGGGCAACTGGGTTGCTGAGAGATTTGGCCCAAGACCTTGTTCGTGTCCGTGTCCAGGGTCTGACACTTA	-	-	CG34114, intron	Ppcs, intron	CG34114, Ppcs	NA	-	0
D106R33	24	novobreak	BND	3R	13797050	3R	20999372	6	2	somatic_tumour	8	7202.3	3R:13797050-20999372	3to3	0.08	0.22	-	-	CCATATAGCTTAGTTGTGCAGCTCAGACAATCTGGGTCACATTTTGCCATTGAACCGGTGACGTCACGGCGGGGCAACGACCGCAAAGCACGACCAGCTACAGCAACAACAATAATATCTAGCTACAACAACGACAACAAAAAAATTCCTTGGAATTCATAATTAGCTGGGCGACAGGTCGCCTTGAGTCTTCAAACGTGCCTTTCGCCCACCAAATTTCCCCGACATTTTCTTCGTTTTCCCGCCATGAGTCAAATTTAGGTGACGTTTTAATGAAGAAACC	-	-	intergenic	Calx, intron	Calx	NA	-	0
D106R33	25	Control-Freec	DUP	3R	15301220	3R	15304764	-	-	somatic_tumour	-	3.5	3R:15301220-15304764	26:25_26	0.38	0.62	-	-	-	-	-	Tm1, intron	Tm1, 3UTR	Tm1	NA	snp_su:0; snp_op:0	0
D106R33	30	Control-Freec	DUP	3R	24064646	3R	24067304	-	-	somatic_tumour	-	2.7	3R:24064646-24067304	Heterozygous duplication	0.5	1.01	-	-	-	-	-	4EHP, 3UTR	4EHP, 3UTR	4EHP	NA	snp_su:1; snp_op:1	7.32
D106R33	31	Control-Freec	DUP	3R	25084432	3R	25087976	-	-	somatic_tumour	-	3.5	3R:25084432-25087976	31:31_32_33	0.41	0.81	-	-	-	-	-	fd96Ca, exon	intergenic	fd96Ca	NA	snp_su:0; snp_op:3; snp_ratio:0.0	0
D106R33	31	Control-Freec	DUP	3R	25134934	3R	25137592	-	-	somatic_tumour	-	2.7	3R:25134934-25137592	33:31_32_33	0.45	0.87	-	-	-	-	-	Bili, intron	intergenic	Bili	NA	snp_su:2; snp_op:0	19.87
D106R33	38	Control-Freec	DUP	4	110750	4	114294	-	-	somatic_tumour	-	3.5	4:110750-114294	Heterozygous duplication	0.47	0.82	-	-	-	-	-	pan, 3UTR	intergenic	pan	NA	snp_su:1; snp_op:2	6.67
D106R33	40	Control-Freec	DUP	4	239220	4	242764	-	-	somatic_tumour	-	3.5	4:239220-242764	Heterozygous duplication	0.44	0.83	-	-	-	-	-	CG1674, intron	CG1674, intron	CG1674	NA	snp_su:0; snp_op:2	0
D106R33	44	Control-Freec	DUP	4	484642	4	487300	-	-	somatic_tumour	-	2.7	4:484642-487300	43:42_43_44_45_46	0.48	0.91	-	-	-	-	-	Asator, intron	Asator, intron	Asator	NA	snp_su:2; snp_op:1	8.38
D106R33	44	Control-Freec	DUP	4	878912	4	881570	-	-	somatic_tumour	-	2.7	4:878912-881570	45:42_43_44_45_46	0.46	0.86	-	-	-	-	-	unc-13, exon_9	CR44029, exon_1	unc-13, CR44029	NA	snp_su:0; snp_op:0	0
D106R33	47	Control-Freec	DUP	4	1034848	4	1065858	-	-	somatic_tumour	-	31	4:1034848-1065858	47:47_48_49	0.32	0.53	-	-	-	-	-	ATPsynbeta, 3UTR	apolpp, exon_3	ATPsynbeta, CaMKII, Zyx, apolpp	NA	snp_su:18; snp_op:7; snp_ratio:2.57	14.75
D106R33	47	Control-Freec	DUP	4	1195214	4	1199644	-	-	somatic_tumour	-	4.4	4:1195214-1199644	49:47_48_49	0.47	0.84	-	-	-	-	-	PIP4K, intron	Mitf, intron	PIP4K, Mitf	NA	snp_su:3; snp_op:2; snp_ratio:1.5	12.66
D106R33	50	delly	DEL	X	3143402	X	3150528	4	1	somatic_tumour	DEL00000085	7.1	X:3143402-3150528	5to3	0.24	-0.58	-	-	CAAACAAAAGGGGTTAGCAGAGATAGAGATAGAGGGCCGAAAGAGATGGAGGCAGATGGAGTGACAAAGACGGGTAGAGTGGGTTGGAAAGAGAATTTCTGGCAACTTGAATTGAATGGCAATTAAACATTATGCCCAGACGTATTTAATCATCAGAAAGTGAATTAAGCGTCGAGTGAGAAAAGTTCGTTGC	-	-	N, intron	N, intron	N	NA	snp_su:0; snp_op:0	0
D106R33	50	lumpy	DEL	X	3143402	X	3150528	4	1	somatic_tumour	7559	7.1	X:3143402-3150528	5to3	0.24	-0.58	-	-	-	-	-	N, intron	N, intron	N	NA	snp_su:0; snp_op:0	0
D106R33	51	lumpy	DEL	X	15495519	X	15496834	4	0	somatic_tumour	7872	1.3	X:15495519-15496834	5to3	0.21	0.37	-	-	-	-	-	Gmap, intron	Gmap, intron	Gmap	NA	snp_su:0; snp_op:0	0
D106R33	51	novobreak	DEL	X	15495519	X	15496834	4	0	somatic_tumour	40	1.3	X:15495519-15496834	5to3	0.21	0.37	-	-	TTGCCAGGTAACTAGTATCTACCCATCCGGAGATACTCGCACCTAGCAGATCGCCGATCTCCAAGTGCTATGTATGTTTGTGGCATGCTCTGCCCATTTACCTCTTCCTGCCCAACCAAAAAGGTGCGAAAGAGATGGCCACTATGGGCTTGGGGTCTAGACGATTGTGTGTGCTGTGTGTATTTCTACCTTCATGGGTTGACTGTATTTTTATCTGCTAATTAAACACAGACGCTC	-	-	Gmap, intron	Gmap, intron	Gmap	NA	snp_su:0; snp_op:0	0
D106R3	4	novobreak	BND	2L	9879541	2L	11236361	6	0	somatic_tumour	5	1356.8	2L:9879541-11236361	5to5	0.05	-0.13	TGTTGTTGTTGTTGTT	-	ATAAATAACTGCTTATCTTGTTATGATTACTGCTCTCGGCATTATTGTTGTTATTGTTATTGTTGTTGCTCAGGCTGTTGTTGCTGCTACTGTTGTTGTTGTTGTTGTTGGTGTTGCTGCTTTTTGCCTGTTGTTGGTAGACAACGTTGTTATTTATGACAATTTCATTGTCTTGTCCACTTGCTGCCCTTTTTATTTCCGTC	ATAAATAACTGCTTATCTTGTTATGATTACTGCTCTCGGCATTATTGTTGTTATTGTTATTGTTGTTGCTCAGGCTGTTGTTGCTGCTACTGTTGTTGTTGTTGTTGTTGGTGTTGCTGCTTTTTGCCTGTTGTTGGTAGACAACGTTGTT	Alt-EJ	nAChRalpha6, intron	ab, exon_5	nAChRalpha6, ab	NA	bp1_211000022279740_2; bp1_hobo_hAT=71; mh:16; ins:0; tup:0; tdown:0	0
D106R3	5	novobreak	TANDUP	2L	11347915	2L	11348073	7	0	somatic_tumour	6	0.2	2L:11347915-11348073	3to5	0.24	0	-	-	ATATTACAAGTTGTATTCTTCCAAGTTAATCTTGTGATCATGCCCAATTTAAAAACTTTAATTTATTCCTTCGAATTGGTAGGAAAACAGATGAATTACTCAAAACTTAACCATCGCATAATGCATATGTAACTTAATGCATCAACTAAACTTAAATTCTTATACAAGTATATTACAAGTTGTATTCTTCCAAGTTAATCTTGTGATCATGCCCAATTTAAAAACTTTAATTTATTCCTTCGAATTGGTAGGAAAACAGATGAATTACTCAAAACTTAACCATCGCATAATGCATATGTACAAATGCAAATTTTCACTTCCATCCACACACACACTCACATGAAT	-	NHEJ	intergenic	intergenic	-	NA	mh:0; ins:0; tup:0; tdown:0	0
D106R3	7	delly	DEL	2L	16897868	2L	16904445	22	4	somatic_tumour	DEL00000002	6.6	2L:16897868-16904445	5to3	0.32	-0.69	-	-	CTGCCCCACTTTGATCTCTACTCTTGTTGGCGGGAGATTAAAGTGGTTCCTCGATACGAAAACGCCACTGGGAGCAACAGCTCGGCTACATTTATGTTATACATTACATTTTTTATAGGGAATCATTGTGCTAAGCCGGCAGTGGAAGAATACGCTGTACAATCCAATTCTGTTTGAGCATCAGTACAAGAA	-	NHEJ	tweek, exon_8	tweek, intron	tweek, CG31805, CG12288	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:5; snp_op:0; snp_ratio:501.0	37.94
D106R3	7	lumpy	DEL	2L	16897868	2L	16904445	22	4	somatic_tumour	1237	6.6	2L:16897868-16904445	5to3	0.32	-0.69	-	-	-	-	NHEJ	tweek, exon_8	tweek, intron	tweek, CG31805, CG12288	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:5; snp_op:0; snp_ratio:501.0	37.94
D106R3	7	novobreak	DEL	2L	16897868	2L	16904445	22	4	somatic_tumour	8	6.6	2L:16897868-16904445	5to3	0.32	-0.69	-	-	CTTCTCGGAGAACGAAGACGGGGGATTGACCTATATTGGCAGCAAGATGCTGCCCCACTTTGATCTCTACTCTTGTTGGCGGGAGATTAAAGTGGTTCCTCGATACGAAAACGCCACTGGGAGCAACAGCTCGGCTACATTTATGTTATACATTACATTTTTTATAGGGAATCATTGTGCTAAGCCGGCAGTGGAAGAATACGCTGTACAATCCAATTCTGTTTGAGCATCAGTACAAGAACAAGCTGTCGCGACCCATCAACGTGACCTTTTCGTTCCCGCAGAACGAGGAGGATGCGGAGAACGATGAGTGCGAAGGTGATGTTGAAATGGGCGCCTTTGCGGGCGTCGGCGAGAATCCGGAAGAGAGTGAGAATGCATTATTACTTGGGCAAACACAGCATCATCGAACTCACATTGGTATTTTTTTGATTAACGCTCCCCACCCG	-	NHEJ	tweek, exon_8	tweek, intron	tweek, CG31805, CG12288	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:5; snp_op:0; snp_ratio:501.0	37.94
D106R3	8	lumpy	DEL	2R	9599307	2R	9600112	55	15	somatic_tumour	2192	0.8	2R:9599307-9600112	5to3	0.56	-0.48	-	-	-	-	NHEJ	CG1902, intron	CG30340, exon	clos, CG30338, CG1902, CG30340	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:2; snp_op:0	60.02
D106R3	8	novobreak	DEL	2R	9599307	2R	9600112	55	15	somatic_tumour	10	0.8	2R:9599307-9600112	5to3	0.56	-0.48	-	-	CCCGACAGTTGGAGCTCACAGGATTCAGTAGACCCGGTAAACCGGGCATCATATGCGTGGAAGGTGATTCGGCAAATGTACAGGAATTCTGGCGCACCATCAAGGCCCTGCGCTGGCAGAAGATCAGCGTGGTGCGGACGGAGCCTCATTTGGGTGGCGTCTCGCCATCGGCGAACCCAAGAAATTTGGTAGTAGGCCCTTCTAAAGTTCTCATTGTTGAAGCCATAGATCAGCGGATTGACGGCGGCGTTCAGAAACATCAAATACTGTGATATGTACCAGAATAGCTGC	-	NHEJ	CG1902, intron	CG30340, exon	clos, CG30338, CG1902, CG30340	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:2; snp_op:0	60.02
D106R3	9	novobreak	TRA	2R	14995760	2L	8422318	11	0	somatic_tumour	11	6573.4	2R:14995760 2L:8422318	3to3	0.15	0	-	-	GCAACAACAATGGCAACAACATTAAACGTGTTTACACCATGTCCGACCAGTTGATATGCCAACTGCCCCCCGACCTGTCCTGCACCCCACCACACACACACACACTCACTGGCACACACACATACACACTCCTCCTTTGCACACACACACACATG	-	NHEJ	intergenic	Akap200, intron	Akap200	NA	mh:0; ins:0; tup:0; tdown:0	0
D106R3	14	novobreak	DEL	3L	13710637	3L	13710841	6	0	somatic_tumour	16	0.2	3L:13710637-13710841	5to3	0.22	0	A	-	GTTCCTGTATGCTCTGCTGCATGCTTATTACTGTTTGCTACGTGTTTGTGTCCCATGTTCCCCCTGATCCTTCTGCTCCTTTTGCCAGCTTGTTTGTTTTAACGTTTTTATCTTTTGATACACTCAAATATGACACACACACACTTGTCCCCTCAAACATACACGCACGCTCACACATATACACACACACACAGACATAAACAGGCAAAATATCTTGTGTTAATTGCAAATGAGACTCTTCTTAATGAATTCAAATGTGGAATATTGAGAAATAATCATTGCAGCAAAGTTATTTCACTTATAATTTATTTTTTTAAAATCACTGACTAGCTCATATATTTTTTGAAACAATAGTCAGAATTGGAATCATATTTTATTAATGGATCGTAAGGCATGTCAACTAATGCCAATTATTACAAATGTAGGAGCACCTGCTCTAATTTATAACTAAAAGTACAAAAATCCGCTTAGATAACTG	TTGATACACTCAAATATGACACACACACACTTGTCCCCTCAAACATACACGCACGCTCACACATATACACACACACACAGACATAAACAGGCAAAATATCTTGTGTTAATTGCAAATGAGACTCTTCTTAATGAATTCAAATGTGGAATATTGAGAAATAATCATTGCAGCAAAGTTATTTCAC	Alt-EJ	bru3, intron	bru3, intron	bru3	NA	mh:1; ins:0; tup:0; tdown:0	0
D106R3	16	lumpy	DEL	3R	5736314	3R	5737069	56	17	somatic_tumour	5580	0.8	3R:5736314-5737069	5to3	0.62	-0.53	-	-	-	-	NHEJ	CG2100, 5UTR	CG1236, exon	CG2100, CG1236	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:2; snp_op:0	38.77
D106R3	16	delly	DEL	3R	5736314	3R	5737069	56	17	somatic_tumour	DEL00000016	0.8	3R:5736314-5737069	5to3	0.62	-0.53	-	-	TTTACGAGGAGGCTTGGTCCATTCATGTAAGATATTCGAGCCCGCCCGGCAAAACTTCTAAGCAATGTCGAAAAATTTAAGATCGCCGGAAAAGATGCCCTTTACTGCGCTCTAACGGACAAGGTTGACAAGGAAGTCTTGGATGCTGCCGGTCCTCAGTTG	-	NHEJ	CG2100, 5UTR	CG1236, exon	CG2100, CG1236	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:2; snp_op:0	38.77
D106R3	16	novobreak	DEL	3R	5736314	3R	5737069	56	17	somatic_tumour	21	0.8	3R:5736314-5737069	5to3	0.62	-0.53	-	-	GGGGTAAATATGCTTTTGAACTCAGGAGTTGCCACCTTCCGGAATGCCGGGTTTGTGCGCATCCTAGGTGGTTTTCCCAGCTGGGCAATCAATTCTGGAGAGACGCCTCGCGAGCAAACCATACTATTGGCCATCGACTTTAGCCAGCGATTCTGGGGGCGACCGTTGAATAACAGGAAGGCACGTGTGGTCAACTTTACGAGGAGGCTTGGTCCATTCATGTAAGATATTCGAGCCCGCCCGGCAAAACTTCTAAGCAATGTCGAAAAATTTAAGATCGCCGGAAAAGATGCCCTTTACTGCGCTCTAACGGACAAGGTTGACAAGGAAGTCTTGGATGCTGCCGGTCCTCAGTTGAAGTGCGTGGCAACTATTTCGGTGGGTTACGATCACATCGACGTGGAGGAGTGCAGGAAACGTGGAATTCGAGTGGGCTTCACACCGGACGTCCTAACGG	-	NHEJ	CG2100, 5UTR	CG1236, exon	CG2100, CG1236	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:2; snp_op:0	38.77
D106R3	17	novobreak	DEL	3R	13812118	3R	13813511	33	10	somatic_tumour	22	1.4	3R:13812118-13813511	5to3	0.4	-0.71	-	-	CCGGTGGCCTTTGTGAGTGGACCTGCCTCCGGTGTCGCATTTCGCGGAAGCACCCGTCGTTTCGGTGGGTCGTCCAGCACCGACTGACTGCTGACTCATGCCGAGCGTTTATCCTTTTTATGAGTCGGCAGTTGCGGCCTAAGCCCTTTGAGTCCTCAGCCTTCGAGTTGGCCCGGCTTAGGCTACCACAAATGTCACGTAAAGTGGGCAGTGGCCGTCGCGCCGCCGGCTCAAAGACCATTAATTTGGGACTTATGGCACATAAGGATATTAGCATTTTGGCAAGGATCTTCGTCTTGTCGTCTCTGTTACACGGCATACGAAATGGCAGCCTACTTGGATCCCACTGGCCAGTACTAAAGAAGCAACACGACGACAGCAAGACATCGTAATCGTAGACCTCTTTTAGAAAATCCAATAAATCACAGATCTTCGCCATGGCCGCC	-	NHEJ	intergenic	tal-3A, 5UTR	tal-AA, tal-2A, tal-1A, tal-3A	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:16; snp_op:0; snp_ratio:1601.0	40.32
D106R5	5	Control-Freec	DUP	2L	19852051	2L	19856905	-	-	somatic_tumour	-	4.9	2L:19852051-19856905	Heterozygous duplication	0.41	0.69	-	-	-	-	-	sick, intron	sick, intron	sick	NA	snp_su:0; snp_op:0	0
D106R5	6	Control-Freec	DUP	2R	8044696	2R	8053595	-	-	somatic_tumour	-	8.9	2R:8044696-8053595	Heterozygous duplication	0.37	0.6	-	-	-	-	-	intergenic	CG12769, 3UTR	CG12769	NA	snp_su:23; snp_op:8; snp_ratio:2.87	16.11
D106R5	16	Control-Freec	DUP	3R	4164732	3R	4195474	-	-	somatic_tumour	-	30.7	3R:4164732-4195474	Heterozygous duplication	0.44	0.71	-	-	-	-	-	intergenic	CR33294, exon_4	CG12581, Dsk, CR33294	NA	snp_su:1; snp_op:2	6.03
D106R5	17	novobreak	DEL	3R	6352663	3R	6353455	5	0	somatic_tumour	19	0.8	3R:6352663-6353455	5to3	0.09	0.06	-	-	TTTTCTCATTAGGGAATAATTTTGCATGGGCCCCTGCAGAAAGAAAAACATTTTTTATCGATTTTACCTAAAGTTCGACCGTCAATGAAATCAAACACAATGCGGTACATCGTTAACCCAGTTCTGGGCGCCCACACGCGCGATGCCGCCCACTCGAGTGTGTTTATGTTGTTGTTGTCCTCGCTGCTTAATTTCCTCATTTGTGTTGCTGTAATTCCCAATGCGTGAGCTGCTTTGTTTTTATTATGAGTGCAATCGAAGCCACTCTTGTTATCGCAACGAATTTTTTATGGCTCTCGAT	-	NHEJ	Pak, intron	Pak, exon_1	Pak	NA	mh:0; ins:0; tup:0; tdown:0	0
D106R5	20	Control-Freec	DUP	3R	8914371	3R	8940259	-	-	somatic_tumour	-	25.9	3R:8914371-8940259	Heterozygous duplication	0.34	0.48	-	-	-	-	-	pyd, intron	skap, intron	pyd, CR44020, osk, skap	NA	snp_su:26; snp_op:16; snp_ratio:1.62	11.84
D106R5	25	Control-Freec	DUP	3R	18879633	3R	18882060	-	-	somatic_tumour	-	2.4	3R:18879633-18882060	Heterozygous duplication	0.45	0.98	-	-	-	-	-	intergenic	intergenic	-	TRUE	t_contamination: 212 n_contamination: 2; snp_su:7; snp_op:3; snp_ratio:2.33	12.42
D106R5	26	Control-Freec	DUP	4	355151	4	359196	-	-	somatic_tumour	-	4	4:355151-359196	Heterozygous duplication	0.45	0.71	-	-	-	-	-	PMCA, exon_3	intergenic	PMCA	NA	snp_su:2; snp_op:2	10.88
D106R5	27	Control-Freec	DUP	4	423916	4	432006	-	-	somatic_tumour	-	8.1	4:423916-432006	Heterozygous duplication	0.43	0.66	-	-	-	-	-	intergenic	intergenic	CR43437, CR44024	NA	snp_su:6; snp_op:2; snp_ratio:2.99	11.54
D106R5	30	Control-Freec	DUP	4	1003160	4	1009632	-	-	somatic_tumour	-	6.5	4:1003160-1009632	Heterozygous duplication	0.44	0.88	-	-	-	-	-	toy, intron	intergenic	toy	NA	snp_su:7; snp_op:2; snp_ratio:3.49	18.13
D106R5	31	Control-Freec	DUP	4	1062217	4	1066262	-	-	somatic_tumour	-	4	4:1062217-1066262	Heterozygous duplication	0.46	0.95	-	-	-	-	-	apolpp, intron	apolpp, exon_4	Zyx, apolpp	NA	snp_su:0; snp_op:1	0
D106R5	32	Control-Freec	DUP	4	1242624	4	1245051	-	-	somatic_tumour	-	2.4	4:1242624-1245051	Heterozygous duplication	0.46	0.77	-	-	-	-	-	Cadps, intron	Cadps, intron	Cadps	NA	snp_su:0; snp_op:1	0
D106R5	36	Control-Freec	DUP	X	7081986	X	7088458	-	-	somatic_tumour	-	6.5	X:7081986-7088458	Heterozygous duplication	0.37	0.62	-	-	-	-	-	Sxl, intron	Sxl, intron	Sxl, mir-4956	NA	snp_su:0; snp_op:0	0
D106R5	37	Control-Freec	DUP	X	10334166	X	10339829	-	-	somatic_tumour	-	5.7	X:10334166-10339829	Heterozygous duplication	0.4	0.66	-	-	-	-	-	CG43740, intron	CG43740, intron	CG43740	NA	snp_su:1; snp_op:4; snp_ratio:0.25	2.63
D106R5	38	Control-Freec	DUP	X	10706306	X	10711160	-	-	somatic_tumour	-	4.9	X:10706306-10711160	Heterozygous duplication	0.37	0.56	-	-	-	-	-	X11Lbeta, intron	intergenic	X11Lbeta	NA	snp_su:0; snp_op:3; snp_ratio:0.0	0
D106R5	42	Control-Freec	DUP	X	17040776	X	17043203	-	-	somatic_tumour	-	2.4	X:17040776-17043203	Heterozygous duplication	0.49	0.93	-	-	-	-	-	CG45002, intron	CG45002, intron	CG45002	NA	snp_su:3; snp_op:1; snp_ratio:2.98	24.05
D106R5	43	Control-Freec	DUP	X	17723572	X	17727617	-	-	somatic_tumour	-	4	X:17723572-17727617	Heterozygous duplication	0.48	0.95	-	-	-	-	-	CG42684, intron	CG42684, intron	CG42684	NA	snp_su:0; snp_op:1	0
D106R5	45	Control-Freec	DUP	X	19043860	X	19050332	-	-	somatic_tumour	-	6.5	X:19043860-19050332	Heterozygous duplication	0.5	1.04	-	-	-	-	-	intergenic	intergenic	-	NA	snp_su:0; snp_op:0	0
D106R7	2	Control-Freec	DUP	2L	11557238	2L	11593890	-	-	somatic_tumour	-	36.7	2L:11557238-11593890	Heterozygous duplication	0.3	0.39	-	-	-	-	-	intergenic	kek2, intron	CR44495, Mst33A, CR44496, Acp33A, kek2	TRUE	low FC; snp_su:71; snp_op:5; snp_ratio:14.17	32.84
D106R7	3	Control-Freec	DEL	2L	11851532	2L	11856922	-	-	somatic_tumour	-	5.4	2L:11851532-11856922	Homozygous deletion	0.45	-1.65	-	-	-	-	-	Mal-B2, exon_2	Pde1c, intron	Pde1c, Mal-B2, CG42751	NA	snp_su:0; snp_op:0	0
D106R7	4	lumpy	TRA	2L	15039622	2R	6222315	7	0	somatic_tumour	4791_1	8817.3	2L:15039622 2R:6222315	5to3	0.3	0	-	-	-	-	NHEJ	Su(H), 5UTR	bin3, intron	Su(H), bin3	NA	mh:0; ins:0; tup:0; tdown:0	0
D106R7	4	novobreak	TRA	2L	15039622	2R	6222315	7	0	somatic_tumour	2	8817.3	2L:15039622 2R:6222315	5to3	0.3	0	-	-	ACATATCGCCGGTAGGCAGGGACTATCATAAATAAGCGCCTATCGGACTATCGATACAACATCAACATCCTCAGTCGCTTTTTTAGTTGTAGCATATTATAAATATAACTCGAGCGCTAGTTGCAGCCTTAAACAGAAGCCAGCCGCCACTACCGCTAGTCGCTAGTCAAGATCTGACTTCATGTAAAAGGGCGTGGATTGAAAAAAGTAGGTGTAACTGAGCACGTTTTCTATGTTTCCAAATATTAA	-	NHEJ	Su(H), 5UTR	bin3, intron	Su(H), bin3	NA	mh:0; ins:0; tup:0; tdown:0	0
D106R7	5	Control-Freec	DUP	2L	21300202	2L	21358414	-	-	somatic_tumour	-	58.2	2L:21300202-21358414	Heterozygous duplication	0.16	0.29	-	-	-	-	-	Mondo, intron	intergenic	Mondo	TRUE	low FC; snp_su:91; snp_op:8; snp_ratio:11.36	28.48
D106R7	12	Control-Freec	DUP	2R	18238682	2R	18245150	-	-	somatic_tumour	-	6.5	2R:18238682-18245150	Heterozygous duplication	0.34	0.47	-	-	-	-	-	intergenic	intergenic	-	NA	snp_su:19; snp_op:9; snp_ratio:2.11	12.71
D106R7	13	Control-Freec	DUP	2R	19452510	2R	19461134	-	-	somatic_tumour	-	8.6	2R:19452510-19461134	Heterozygous duplication	0.32	0.46	-	-	-	-	-	CG7744, 5UTR	par-1, intron	CG7744, mei-W68, par-1	NA	snp_su:2; snp_op:3; snp_ratio:0.67	9.66
D106R7	17	lumpy	DEL	3L	6701362	3L	6701401	6	0	somatic_tumour	2256	0	3L:6701362-6701401	5to3	0.35	0	-	CC	-	CAAATCCCACACGCATAACTTTGCTACTTTTGGGCTACTTGGGGTGATGATCCAAGGATCTGGGTCAAAGATGTAGAGAAAATTTTCATACATAAAAAATCATTGCCCTCATATTTTGTTTTTTTATCATTTTGAAATTTGATATGTGACC	NHEJ	SP1173, intron	SP1173, intron	SP1173	NA	mh:0; ins:2; tup:0; tdown:0	0
D106R7	23	Control-Freec	DUP	3L	16154908	3L	16159220	-	-	somatic_tumour	-	4.3	3L:16154908-16159220	Heterozygous duplication	0.42	0.69	-	-	-	-	-	CG5151, intron	CG5151, intron	CG5151	NA	snp_su:1; snp_op:4; snp_ratio:0.25	6.39
D106R7	24	lumpy	DEL	3L	17032291	3L	17032333	8	0	somatic_tumour	2705	0	3L:17032291-17032333	5to3	0.25	0	-	-	-	-	NHEJ	CR45756, exon_1	CR45756, exon_1	CR45756	NA	mh:0; ins:0; tup:0; tdown:0	0
D106R7	25	delly	DEL	3L	18265550	3L	18266427	10	0	somatic_tumour	DEL00000021	0.9	3L:18265550-18266427	5to3	0.32	-0.22	AA	-	GTCAAGTACAAAAAAAAAACACATATAAATTACGAAAAAAGTGGGAAGACGCAGCATGTATATTTGCGTAAAAAAACCCCTTATCGCGATGCGGATAGAAAGAGTTGACTTGTGTAAATAAACATGGCAGCCAGATCGGATCAGATCAGCATTTACTAGGCACAAGACTCTGGCGTAGAAAAACCTGCCCCTCCAGCGGCAGTTTGTCCGTCAGTCTGTCA	GTATATTTGCGTAAAAAAACCCCTTATCGCGATGCGGATAGAAAGAGTTGACTTGTGTAAATAAACATGGCAGCCAGATCGGATCAGATCAGCATTTACTAGGCACAAGACTCTGGCGTAGAAAAACCTGCCCCTCCAGCGGCAGTTTGTCCGTCAGTCTGTCAGC	Alt-EJ	intergenic	intergenic	-	NA	mh:2; ins:0; tup:0; tdown:0	0
D106R7	25	lumpy	DEL	3L	18265550	3L	18266427	10	0	somatic_tumour	2744	0.9	3L:18265550-18266427	5to3	0.32	-0.22	AA	-	-	GTATATTTGCGTAAAAAAACCCCTTATCGCGATGCGGATAGAAAGAGTTGACTTGTGTAAATAAACATGGCAGCCAGATCGGATCAGATCAGCATTTACTAGGCACAAGACTCTGGCGTAGAAAAACCTGCCCCTCCAGCGGCAGTTTGTCCGTCAGTCTGTCAGC	Alt-EJ	intergenic	intergenic	-	NA	mh:2; ins:0; tup:0; tdown:0	0
D106R9	1	novobreak	DEL	2L	4123965	2L	4124094	5	0	somatic_tumour	2	0.1	2L:4123965-4124094	5to3	0.32	0	-	-	ATGCGACTCCGATAACGACGATGTAGAGTATTTCGAGGAAATGGGCGTGGACATACGCCATAGGACCGATCTATGAGGGTAATCCCCAGTGATACCAAAAAACGCTCAGGCCTGTGCCTATTGTATAGGATGTTTCTAAAAATAAATAAAATGTGCCAAACAACTGATACGAGATCCCTTACAGAACATATGCCCTTGGAATACCAAATACTAAAGAATTGCGTCATTTGTTGATTTGTTTATTTAAATGGGTA	-	NHEJ	Sr-CI, 3UTR	Sr-CI, 3UTR	Sr-CI	NA	mh:0; ins:0; tup:0; tdown:0	0
D106R9	2	Control-Freec	DUP	2L	5299264	2L	5318112	-	-	somatic_tumour	-	18.8	2L:5299264-5318112	Heterozygous duplication	0.39	0.63	-	-	-	-	-	vri, intron	Ncoa6, exon_5	vri, CG14024, Ncoa6	NA	snp_su:38; snp_op:5; snp_ratio:7.59	24.06
D106R9	4	Control-Freec	DUP	2L	8166144	2L	8236576	-	-	somatic_tumour	-	70.4	2L:8166144-8236576	Heterozygous duplication	0.16	0.22	-	-	-	-	-	Piezo, intron	Pvr, intron	Piezo, Pvr	TRUE	low FC; snp_su:251; snp_op:81; snp_ratio:3.1	20.06
D106R9	5	Control-Freec	DUP	2L	10477504	2L	10493376	-	-	somatic_tumour	-	15.9	2L:10477504-10493376	Heterozygous duplication	0.32	0.47	-	-	-	-	-	RluA-2, exon_2	Myo31DF, exon_8	RluA-2, Grip75, CG7456, CG6144, CG13144, Myo31DF	NA	snp_su:63; snp_op:7; snp_ratio:8.99	26.46
D106R9	10	Control-Freec	DUP	2L	15242080	2L	15257952	-	-	somatic_tumour	-	15.9	2L:15242080-15257952	Heterozygous duplication	0.34	0.51	-	-	-	-	-	ZnT35C, intron	yuri, exon_11	ZnT35C, dao, Pol32, l(2)35Cc, yuri	NA	snp_su:47; snp_op:23; snp_ratio:2.04	14.07
D106R9	15	Control-Freec	DUP	2L	17088192	2L	17114976	-	-	somatic_tumour	-	26.8	2L:17088192-17114976	Heterozygous duplication	0.08	0.15	-	-	-	-	-	CG12620, exon	intergenic	CG12620	TRUE	low FC; snp_su:26; snp_op:13; snp_ratio:2.0	13.05
D106R9	16	Control-Freec	DEL	2L	17114976	2L	17154656	-	-	somatic_tumour	-	39.7	2L:17114976-17154656	Heterozygous deletion	0.31	-0.5	-	-	-	-	-	intergenic	CG34106, intron	CG31784, beat-IIIa, CG34106	NA	snp_su:21; snp_op:20; snp_ratio:1.05	11.39
D106R9	22	Control-Freec	DUP	2R	19894560	2R	19911424	-	-	somatic_tumour	-	16.9	2R:19894560-19911424	Heterozygous duplication	0.36	0.58	-	-	-	-	-	intergenic	CR44573, exon_1	CR44572, CR44573	NA	snp_su:31; snp_op:21; snp_ratio:1.48	13.18
D106R9	23	novobreak	TRA	2R	21040110	X	17507089	5	0	somatic_tumour	8	3533	2R:21040110 X:17507089	3to3	0.13	0	-	-	TTCGATTCCAGTATTCTCAACGATTTGGCACGAATGCAGTTGCACTTGAACGCAACCGTTTTTCAAAAATATTCAAACGCAGACGCGCGCGAAACAGCGAACGAACCGCTCACGACGAAAGTTCGAAAGCAACGACCAAGTTGTATAAAATTTCAGTTAAATTTAATGAATATATCGAAGCTTTTTTAAATAATACCCTGTCACTGTGCATCAAACAGTGTGCTCAAACGCTTGGACTTCGAC	-	NHEJ	intergenic	CG43658, exon_1	CG43658	NA	mh:0; ins:0; tup:0; tdown:0	0
D106R9	25	Control-Freec	DUP	2R	22627520	2R	22662240	-	-	somatic_tumour	-	34.7	2R:22627520-22662240	Heterozygous duplication	0.32	0.47	-	-	-	-	-	CG33143, intron	CG42566, intron	CG33143, CG17807, Cdk9, bonsai, CG3732, RpS24, Ugt58Fa, CG2852, CG30195, CG34446, CG34445, CG3746, nsr, Cyp6d2, CG30196, CG43325, CG43326, CR45268, CG13510, CG13511, CG42565, CG42566	NA	snp_su:53; snp_op:40; snp_ratio:1.32	10.5
D106R9	28	Control-Freec	DUP	3L	68448	3L	72416	-	-	somatic_tumour	-	4	3L:68448-72416	Heterozygous duplication	0.5	1.12	-	-	-	-	-	Lsp1gamma, exon	CR43988, exon_2	Lsp1gamma, CR44510, CR44511, CR43150, CR43988	NA	snp_su:0; snp_op:0	0
D106R9	36	novobreak	TANDUP	3L	12594292	3L	12594408	8	0	somatic_tumour	12	0.1	3L:12594292-12594408	3to5	0.23	0	-	-	ACCATGGACAGCGGCACGCGGCGCAAGAACGCCACGCGCGAGACCACCAGCACGCTCAAGGCCTGGCTGCAGGAGCACCGCAAGAACCCCTACCCCACCAAGGGCGAGAAGATCATGCTGGCCATCATCACCAAGATGACCCTCACACAGGTCTCCACCTGGTTCGCCAACGCGCGCCGGCGCCTCAAGAAGGAGAACAAGATGACGTGGCCGCCGCGGAACAAGTGCGCAGACGAGAAGCGGCCCTACGCGGAGGGCGAGGAGGAGGAGGGGGGCGAGGAGGAGGCGCGGGAGG	-	NHEJ	ara, exon_4	ara, exon_4	ara	NA	mh:0; ins:0; tup:0; tdown:0	0
D106R9	42	Control-Freec	DUP	3L	24566880	3L	24573824	-	-	somatic_tumour	-	6.9	3L:24566880-24573824	Heterozygous duplication	0.36	0.54	-	-	-	-	-	intergenic	intergenic	-	NA	snp_su:0; snp_op:1	0
D106R9	43	Control-Freec	DEL	3R	4132672	3R	4173344	-	-	somatic_tumour	-	40.7	3R:4132672-4173344	Heterozygous deletion	0.32	-0.51	-	-	-	-	-	Gfat1, intron	intergenic	Gfat1, CR41601, CG40198	NA	snp_su:4; snp_op:2; snp_ratio:2.0	14.78
D106R9	48	Control-Freec	DUP	3R	7472736	3R	7486624	-	-	somatic_tumour	-	13.9	3R:7472736-7486624	Heterozygous duplication	0.36	0.58	-	-	-	-	-	CG1142, exon	alpha-Est10, 3UTR	CG1142, scaRNA:MeU5-C46, snRNA:7SK, tRNA:Val-CAC-2-4, alpha-Est10	NA	snp_su:10; snp_op:9; snp_ratio:1.11	13.93
D106R9	56	Control-Freec	DUP	3R	20892512	3R	20906400	-	-	somatic_tumour	-	13.9	3R:20892512-20906400	Heterozygous duplication	0.36	0.56	-	-	-	-	-	intergenic	CG5621, exon_8	CR44947, Ktl, TotX, CG5621	NA	snp_su:5; snp_op:6; snp_ratio:0.83	15.88
D106R9	60	novobreak	TANDUP	3R	27123619	3R	27175379	4	0	somatic_tumour	24	51.8	3R:27123619-27175379	3to5	0.09	0.22	-	AAAA	ATCTGTTACTGTGTCTAAACTGTGGCCAAATCTATTTTCATTTTCTATATCTGTGTCTGTGACAAAAAAGCAAAACGCGTGAAATATGCAAAAAAAAAAGACGATCGCTGCGCTGCTTTAGTGCTTCGTTGGTGGCAGCCAGCTCCATAAAATCCTTCTCGGCCGCCTGGAGTTCCTCGTTTTGCTGCACAACGG	ATCTGTTACTGTGTCTAAACTGTGGCCAAATCTATTTTCATTTTCTATATCTGTGTCTGTGACAAAAAAGCAAAACGCGTGAAATATGCAAAAAAAAAAGACGATCGCTGCGCTGCTTTAGTGCTTCGTTGGTGGCAGCCAGCTCCATAAA	NHEJ	CG6059, exon_2	Ser, intron	CG6059, Ser	NA	mh:0; ins:4; tup:3; tdown:4	0
D106R9	63	Control-Freec	DUP	3R	28990208	3R	29014016	-	-	somatic_tumour	-	23.8	3R:28990208-29014016	Heterozygous duplication	0.28	0.41	-	-	-	-	-	intergenic	wat, intron	mir-4947, wat	NA	snp_su:41; snp_op:26; snp_ratio:1.58	12.64
D106R9	67	Control-Freec	DUP	3R	31034720	3R	31055552	-	-	somatic_tumour	-	20.8	3R:31034720-31055552	Heterozygous duplication	0.3	0.43	-	-	-	-	-	intergenic	dco, 3UTR	CG33773, CanA1, CG33920, Alp4, mir-4948, l(3)03670, dco	NA	snp_su:62; snp_op:35; snp_ratio:1.77	12.65
D106R9	70	Control-Freec	DUP	4	42656	4	46624	-	-	somatic_tumour	-	4	4:42656-46624	Heterozygous duplication	0.42	0.74	-	-	-	-	-	PlexB, intron	intergenic	PlexB, CR45124, CR44440	NA	snp_su:1; snp_op:2	16.71
D106R9	74	Control-Freec	DUP	4	461280	4	487072	-	-	somatic_tumour	-	25.8	4:461280-487072	Heterozygous duplication	0.33	0.5	-	-	-	-	-	bip2, intron	Asator, intron	CR45126, bip2, pncr013:4, Asator	NA	snp_su:4; snp_op:6; snp_ratio:0.67	11.46
D106R9	83	Control-Freec	DUP	X	10596544	X	10626304	-	-	somatic_tumour	-	29.8	X:10596544-10626304	Heterozygous duplication	0.26	0.41	-	-	-	-	-	CG2124, exon_1	CG9806, exon_2	CG2124, CG1628, CG43347, Rab9Db, CG9806	NA	snp_su:21; snp_op:18; snp_ratio:1.17	10.34
D197R01	16	novobreak	TRA	2R	6268113	3L	24250729	1	2	somatic_tumour	3	17982.6	2R:6268113 3L:24250729	3to3	0.03	0	-	-	GGATACGTAAAAGCTGACCCTTCTGCCTTCAATTTCAGCTGTAATTGCCCCAGTCGAAAATTGGGGTTAAGTTTACGGAGAGTTATAGCGTGATTGGTAGTCCGAAATGGACATTGAAATTAAATTAAAGCGATTTTAAATTGATCTAAATTCGTTACAGCACCTTTTCAGAAATAATAGGAAGTGAACTAGCCGATCAAGC	-	-	intergenic	Snap25, intron	Snap25	NA	bp1_copia_Copia=12; bp2_Y_mapped_Scaffold_20_D1762_D1719_2	0
D197R01	34	novobreak	TRA	3L	11879024	2R	21463775	5	0	somatic_tumour	6	9584.8	3L:11879024 2R:21463775	3to5	0.08	0	-	-	CACTGAAATCACACGAAGAGCAAATAAATTTTCACCGAACAGCTGCTGTAAATTATTTGCGATTAATTGGGCGTGCAATTAAAATGCGAAATAAATGCTCAACACAAAAAAAAAAAAAGACAAATACAACAACTCCAATGGTAATGAACAAATAATTAC	-	-	CG44837, intron	Sdc, intron	CG44837, Sdc	NA		0
D197R01	63	Control-Freec	DEL	X	2785056	X	3337404	-	-	somatic_tumour	-	552.3	X:2785056-3337404	63:63_64	0.61	-0.63	-	-	-	-	-	CG32795, exon_4	CR44886, ncRNA	kirre, CG32795, w, CG12498, CG14416, CG14417, CG14418, CG14419, CG3526, CG3588, CG14424, CG32793, CG3592, CG3598, CG14420, CG14421, CG14422, CG14423, CG17959, CG3603, rst, CG4116, N, CG18508, Fcp3C, CG3939, CG14265, ng2, ng3, ng1, ng4, Pig1, Sgs4, CG10793, dnc, CR44886	NA	snp_su:2; snp_op:22; snp_ratio:0.09	1.15
D197R01	63	lumpy	DEL	X	2785301	X	3336717	4	1	somatic_tumour	8782	551.4	X:2785301-3336717	64:63_64	0.21	-0.63	-	-	-	-	-	CG32795, intron	CR44886, ncRNA	kirre, CG32795, w, CG12498, CG14416, CG14417, CG14418, CG14419, CG3526, CG3588, CG14424, CG32793, CG3592, CG3598, CG14420, CG14421, CG14422, CG14423, CG17959, CG3603, rst, CG4116, N, CG18508, Fcp3C, CG3939, CG14265, ng2, ng3, ng1, ng4, Pig1, Sgs4, CG10793, dnc, CR44886	NA	snp_su:2; snp_op:22; snp_ratio:0.09	1.15
D197R01	63	novobreak	DEL	X	2785301	X	3336717	4	1	somatic_tumour	12	551.4	X:2785301-3336717	64:63_64	0.21	-0.63	-	-	GGATCGGGTGGGCCAATATACACTTTGCGTCATCGAATACAGATAAGATTACTTTCTCATAAATTGAGTGTAAAGATAATTTGGAATTTGAAATGAATATTAATTTATGCACAGGCAATTTGAATTTGAATTTGCTCTCCATGCCACAAACAGCGACAAACAAACAAAAACAAAAACAAAAGCAAAAACAATTGGGCTGCGAGGGTTTAAGGGCTGCGGCCCCAAAA	-	-	CG32795, intron	CR44886, ncRNA	kirre, CG32795, w, CG12498, CG14416, CG14417, CG14418, CG14419, CG3526, CG3588, CG14424, CG32793, CG3592, CG3598, CG14420, CG14421, CG14422, CG14423, CG17959, CG3603, rst, CG4116, N, CG18508, Fcp3C, CG3939, CG14265, ng2, ng3, ng1, ng4, Pig1, Sgs4, CG10793, dnc, CR44886	NA	snp_su:2; snp_op:22; snp_ratio:0.09	1.15
D197R01	65	novobreak	DEL	X	3134156	X	3136185	9	2	somatic_tumour	13	2	X:3134156-3136185	5to3	0.65	-1.56	-	-	TTCACTAAGCCAATACTGTAATTAATTAACTAATTTATTGTTTCATATTTTATTTTTTGTTTCTTTCGAGAATATACATATGTATGTATTTATCTAAAGTAATTCTGAAAATGCTTAAAAATAATGCCCGTTCGTTTAAACTTGCATAGCTAGGAAATGTTGGTCTATAAAATCGGATGCATTCGCAACACATATAAGTGACTGAGCAAATCCATGCAACTGTAATCCAAAAAGGAAGTGGTGCTACTTAATCTGCTTAATAAGCCCATAGGATTGTTGCAAATC	-	-	kirre, 3UTR	N, intron	kirre, N	NA	snp_su:0; snp_op:0	0
D197R03	19	lumpy	DEL	3R	29320606	3R	29376068	14	8	somatic_tumour	7090	55.5	3R:29320606-29376068	5to3	0.23	-0.23	-	-	-	-	-	intergenic	intergenic	-	NA		0
D197R03	19	novobreak	DEL	3R	29320606	3R	29376079	12	4	somatic_tumour	7	55.5	3R:29320606-29376079	5to3	0.17	-0.23	-	-	ACTCGTAATCGAACTCCCCTTCCAACCAAAATCAAATTTTGGAAAAAAAATTTTGAGCCAAATTTTGCAAAAAATGATGATGGTACCCCTTACAAAAAATTCAAAAATGGCCAAAATATGGATTTTGGAAAAACGGTGATGGACTGGCAGTTTTGTCAGATGGCAAATTTAATGCGAAAGAAATCGTGTTCTATGTTCAATTAAATTGACGGTAAATAATACCATTAGAATATATTT	-	-	intergenic	intergenic	-	NA		0
D197R03	33	Control-Freec	DEL	X	3090477	X	3154453	-	-	somatic_tumour	-	64	X:3090477-3154453	Homozygous deletion	0.72	-0.82	-	-	-	-	-	kirre, intron	N, intron	kirre, N	NA	snp_su:0; snp_op:0	0
D197R05	2	novobreak	BND	2L	17782723	2L	17782826	19	0	somatic_tumour	3	0.1	2L:17782723-17782826	3to3	0.7	0	-	-	CATTTCATTATTTTATAAGAGTTTATATTATAAGCTAATATAAACTATTCTAGCTCAAGTCAAAAAATCAGCATGATAACATACGTAGGTTACTTAATAACATAAAACATAATAGGTTATTAACCTTAACCTTAAGATAGAATTCTAAAGGTGATAATAGTAAGATAGATTAGGTAGCACTTTAACTATTTAATTTTGTTAATAAAAAATACCTGAATTCATGAAGACTTAGGATGCAGCTTCCTTCTCCTTTCAGC	-	-	intergenic	intergenic	-	NA		0
D197R05	6	novobreak	TRA	2R	11730762	X	3353629	12	0	somatic_tumour	8	8377.1	2R:11730762 X:3353629	3to3	0.32	0	-	-	TTAATTTATTATATTTATCTTTTAGGTTTTATATGAAAAAAAAAAAAAAAAAAAAAAATTAAAAACAAAAATGTTAATTAATTTCTGTATAGAAATTTCTGTGCATAGAAACTCCGGCCGATAATCTTGCTTTGGTTTACTCTCGGAGAAATCCAATC	-	-	intergenic	intergenic	-	NA		0
D197R05	7	lumpy	BND	2R	12768397	2R	12768492	2	2	somatic_normal	2058_1	0.1	2R:12768397-12768492	[2R:12768492[N	0.083	0	-	-	-	-	-	intergenic	intergenic	-	NA		0
D197R05	11	Control-Freec	DUP	3L	14292214	3L	14297176	-	-	somatic_tumour	-	5	3L:14292214-14297176	Heterozygous duplication	0.41	0.52	-	-	-	-	-	fz, intron	fz, intron	fz	NA	snp_su:1; snp_op:4; snp_ratio:0.25	2.27
D197R05	14	novobreak	DEL	3L	18257813	3L	18258031	10	0	germline_private	16	0.2	3L:18257813-18258031	3to5	-	0	-	-	AGCAAGCTAAATTTTTAATTTAGTATGCAGATCTAGATCAATAAAAGTAAAAATTATTAATAAAGCTAAAATTGTTCTGTATAACATGTTTATAATATAATTATTACATTATTTTAATATATTTTAACTATTTATTTAATATTAATAATAATGGGTTCTATTTTGCTTTAACACTTTTGCTTTTGTGTGCATGTAATTATTAATGTATGGCAGGCAAATTCTTTTATTTTTAGGTTTCGCATTATGCAATTTATTTCAGGTCTACTGCTTGGAAAGCTTTCTGCACATTTTATGCCCCGATGGACAAGCCTTTTTTGATTAATTACGAGCTTAAAATGTGACATAATTGAGGAGGGGCTCAAAAAGGCGTCTTTAATTATTAATTGCCCTTAGAAGTGAAACGATTAAAGTTTAATACGTCTCGGTAAACTTGTAGTATATATAAACTTCAAGTAAATGACAATGCTAATTTCACAATTTTAC	-	-	intergenic	intergenic	-	NA		0
D197R05	16	Control-Freec	DUP	3L	19588322	3L	19590803	-	-	somatic_tumour	-	2.5	3L:19588322-19590803	Heterozygous duplication	0.39	0.51	-	-	-	-	-	CG9330, exon_6	ash1, 3UTR	CG9330, CG14100, ash1	NA	snp_su:2; snp_op:2	5.9
D197R05	17	novobreak	TRA	3L	28110227	2.11E+14	196	52	16	germline_private	18	28110	3L:28110227 211000022278951:196	3to5	-	0	-	-	ATTCTATGTTACTCTATGTTATTCCATGTTATTCTATGTTGTTCTATGTTATTATATGTTATTCTATGTTTTTCTATGTTATCCAATGTTATTCAATGTAATTCAATGTTATTCTATGTTATTCTTTGTTATTCTATGTTTTTCTATGTTATGCTATGTTATTCAATGTTATTCTATGTTAGTCTATGCCATTCTATGTTA	-	-	intergenic	intergenic	-	NA		0
D197R05	18	novobreak	DUP	3R	4634949	3R	4636707	36	34	germline_private	20	1.8	3R:4634949-4636707	3to5	-	0	-	-	TCCAGAAACATTAAAGCTTTATAACGACAAAGATTTCAAGAGCATGCAGACTAATTATTATTCTGGTCACGTCTATACCGAAAAATCCAAACTAAATGCAATCAATTCTATTTAAATTCCCAATATATTGAGACTAGATATTTCATTTGCGAATTTACTTAAATAAATAAATAAATATTAAATAGGACAGGACAGAGTAAAAACTAACCAATGCAAACAGCCTTTGCGAACCCACTACCCTTAATTTCCCCACAATCTAAACCGAAAGTAATTTGGATCAAACTAAGAAAACTGGGTGGCCTCCACAAGAC	-	-	intergenic	intergenic	-	NA		0
D197R05	19	novobreak	DEL	3R	14095060	3R	14095577	10	2	somatic_tumour	21	0.5	3R:14095060-14095577	5to3	0.29	0	-	-	CTTTAATTGCTTAATAGTGAGCTGATAATTATAAATTTGTCATGACATTCTGAGATATCAACAAAATTTATGCTAGAGAGAAAAGGCATATATATAAATTAAATATAAACTTTATAAACTTTATAAACTATTTTTCTTATATATTCAAACTTTTAGCTAAAGTAGGGAATTTGTAAAAATCTTTTAAACTTTAACCATTAAGATCTTGCTAAATATTTTTTATCCGTGTGATGGTCTTTGGCACGCAGTTGGGATTAATTTACGATGGCAATCGAAAGCGTTAAAAGCGTGTTGGCAGGGCAGTGTGTCGGTTCCGATGGTGAAATCGAGAGCCCCTGATCTCTCCAATCCGCAGTGGAAAGCCCTATTTCCCCCGATCCCCGGATTC	-	-	CCHa1, intron	CCHa1, intron	CCHa1	NA		0
D197R05	20	Control-Freec	DUP	4	176978	4	181113	-	-	somatic_tumour	-	4.1	4:176978-181113	Heterozygous duplication	0.41	0.56	-	-	-	-	-	intergenic	intergenic	Arl4	NA	snp_su:0; snp_op:3; snp_ratio:0.0	0
D197R05	22	Control-Freec	DUP	4	625212	4	632655	-	-	somatic_tumour	-	7.4	4:625212-632655	Heterozygous duplication	0.37	0.42	-	-	-	-	-	mav, exon_1	Gat, exon_5	mav, mir-954, Gat	NA	snp_su:1; snp_op:3; snp_ratio:0.34	2.6
D197R07	5	lumpy	DEL	2R	14517488	2R	14518749	8	1	somatic_tumour	2461	1.3	2R:14517488-14518749	5to3	0.16	-0.67	-	-	-	-	-	intergenic	intergenic	-	NA	snp_su:1; snp_op:0	24.72
D197R07	9	Control-Freec	DUP	3R	15596258	3R	15598916	-	-	somatic_tumour	-	2.7	3R:15596258-15598916	Heterozygous duplication	0.41	0.33	-	-	-	-	-	intergenic	intergenic	-	TRUE	t_contamination: 178 n_contamination: 14; low FC; snp_su:11; snp_op:4; snp_ratio:2.75	13.53
D197R07	12	Control-Freec	DEL	X	3158590	X	3162134	-	-	somatic_tumour	-	3.5	X:3158590-3162134	Homozygous deletion	0.98	-2.83	-	-	-	-	-	N, intron	N, intron	N	NA	snp_su:0; snp_op:0	0
D197R07	12	lumpy	DEL	X	3158734	X	3161854	10	1	somatic_tumour	6892	3.1	X:3158734-3161854	5to3	0.59	-2.96	-	-	-	-	-	N, intron	N, intron	N	NA	snp_su:0; snp_op:0	0
D197R09	4	delly	BND	2L	18881522	2L	18882130	5	0	somatic_tumour	INV00000010	0.6	2L:18881522-18882130	5to5	0.09	0	12	-	GTGTGGCACTGGTGCAGCTGCAACCGGTTCCGAGCCAGTTCTGCGTGTACTTCTCGGATAGCCGATAACGGATAGCCGACTCTACGGACTGACGGTCTGCAGGGGGGGGGGGGGTGGAGATTGGAGCGCTCCCCAAAAGACCAGAAGACGAAATCAAAAGATCAATAATTATTATGATGTTGCAGCACACCCGAAACGAGACGC	-	-	intergenic	intergenic	-	NA		0
D197R09	19	Control-Freec	DUP	2R	22638096	2R	22640202	-	-	somatic_tumour	-	2.1	2R:22638096-22640202	Heterozygous duplication	0.43	0.63	-	-	-	-	-	bonsai, intron	intergenic	bonsai, CG3732	NA	snp_su:0; snp_op:1	0
D197R09	23	novobreak	TRA	3L	8450769	3R	18640787	3	0	somatic_tumour	4	10190	3L:8450769 3R:18640787	5to5	0.04	0	-	-	CAAACAAACATTGCAAAAGGTCGAGGCATAAATCAAACACACGTAGTGGGAGTCGAAAAAAAAAAGGAAAAAGGAATCGCAAGCGCAGCAGCAGCAACAACAAAGCAAAAATCCAAGCGTCAGCAGCACGGGCAGCAACTAAAACAACAAAAACAGGCCAAGCAACAACAGCAGCAACCCACCAC	-	-	Gug, intron	CG14301, 5UTR	Gug, qin, CG14301	NA		0
D197R09	28	Control-Freec	DUP	3L	22574916	3L	22577022	-	-	somatic_tumour	-	2.1	3L:22574916-22577022	Heterozygous duplication	0.4	0.63	-	-	-	-	-	CG14459, 3UTR	CG14459, 3UTR	CG14459	NA	snp_su:5; snp_op:3; snp_ratio:1.66	14.63
D197R09	29	lumpy	BND	3L	22892904	3L	22893109	5	5	somatic_normal	5786_1	0.2	3L:22892904-22893109	[3L:22893109[N	0.089	0	-	-	-	-	-	slif, exon	slif, exon	slif	NA		0
D197R09	31	novobreak	DEL	3L	25231705	3L	25231949	12	0	germline_private	5	0.2	3L:25231705-25231949	5to3	-	0	-	-	TAAACATAATTGAAAGTTCAAGAAGTTTCTAAAGAAACTTATTATTAATTATTTTAAACATAATTGAAAGTTCAAGAAGTTTCTAAAGAAAAGCTTGTGGCCGAGGTTGATTGGATTAGGATTAAGAATTATAAGATCGGTCTGATAAAGTCGTCCACATACTGATTGGGTGGAAAATAAAATATTCCAGAGTAGGAGTGTCTGTGGACAATTTTAT	-	-	intergenic	intergenic	-	NA		0
D197R09	39	Control-Freec	DEL	X	0	X	8900658	-	-	somatic_tumour	-	8900.7	X:0-8900658	39:39_43	0.25	-0.39	-	-	-	-	-	intergenic	intergenic	CR40469, CG17636, RhoGAP1A, mir-4915, CR45473, tyn, CG17707, CR43863, CG3038, G9a, CG42376, cin, CG13377, CR43906, CG13376, ewg, CG3777, mir-980, CG13375, CG12470, Or1a, CG32816, CG43181, CG43182, y, yar, ac, CR44751, CR44752, CR44753, sc, l(1)sc, pcl, ase, Cyp4g1, ebo, CR18275, CG13373, CG32817, CR18166, CG3176, CG18273, CG3156, CR45797, CG17896, CG17778, svr, CR44891, CR44892, elav, arg, CG4293, Appl, mir-4960, vnd, CG13366, CR45474, CG13365, Vsp37A, CG13369, CG13364, CR45475, CG17829, RpL36, l(1)1Bi, Dredd, mir-9372, su(sable), CR44839, CG13367, Roc1a, Hmt4-20, SkpA, sdk, CG13362, CG5254, CG13361, CG5273, CR44965, RpL22, CR42491, snoRNA:Psi18S-531, snoRNA:Psi28S-2179, CR44966, fz3, tw, CG13360, CR44469, CG16989, Rbf, CG13359, CG13358, Sec22, CG43867, CG14635, CG3713, CG14634, CG11664, CG11663, CG3711, MED22, CG3708, CG3706, CG32815, TRAM, CG3704, mus81, CG3703, CG3699, CG3690, CR45476, CG18823, TfIIA-S-2, CG14631, su(w[a]), CG11638, CG32814, CG3021, CDC45L, CG33082, CG14630, CG42259, CR44779, CG14629, CG3655, CG14628, eIF4E-7, CR34320, CG11378, CG11384, CG11379, CG14627, CG14626, CG11380, CG14625, CG11381, CG14624, CG11382, CG11398, CG3638, CG11403, Atf3, CG32812, DAAM, CG32811, CR46248, fs(1)N, CG11409, CG11412, CG11418, Tsp2A, CG12773, CG11417, png, CG14770, ssx, mir-4961, AMPKalpha, CG3719, CG32813, CG11448, futsch, Gr2a, CG14785, Lrpprc2, CG14787, Ns3, O-fut2, CG14777, CG14778, CG32808, pck, CG14780, Rab27, mei-38, rush, sta, snoRNA:M, snoRNA:Me28S-G980, inc, Nmdar2, CG14795, Mur2B, snmRNA:400, br, dor, CG3740, hfw, CG32809, CG14797, b6, CG14798, a6, CG3795, Scgdelta, CG42666, Adar, mir-981, CG32806, CG14810, CG14811, CG14812, deltaCOP, CG14814, MED18, Pex5, CG14803, Pgam5, Vps26, CG14817, CG14805, CG14818, CG14806, trr, mRpL16, arm, CG32803, CR45929, CR43864, CG32801, Edem1, mip130, Rbcn-3B, eIF2B-epsilon, Ocrl, CG11596, CG3857, CG3587, Hr4, CG4406, CR45478, mir-2496, east, Actn, mir-4954, usp, CG4313, CG4325, moody, Sik2, CR44896, CG4281, CG14054, CR44381, CG4199, CG4194, CR44382, Rtca, CG4045, CG4025, CG16903, Unc-76, csw, snoRNA:Me18S-C1024, ph-d, ph-p, D2hgdh, Pgd, bcn92, wapl, Cyp4d1, CG3630, mir-3641, ND-B14.5A, Cyp4d14, CR45479, CR44690, Cyp4d2, Cyp4ae1, pn, Nmd3, CG17776, CG17777, CG3457, Mct1, CG14053, CR43637, CG18031, SmydA-8, Vinc, CG14052, pcx, kz, fs(1)K10, Or2a, crn, CG3191, CG3091, CG3078, temp, CG3071, CG2924, CR45480, CG2918, Vml, CG2865, Raf, CR34052, CG14050, CG2854, CR33218, Ilp6, mRpL14, CG2841, PsGEF, CG12496, CG32797, gt, tko, boi, z, trol, mir-4955, Pdfr, Vha36-3, CG13759, CG13760, wds, egh, Klp3A, Zw10, Smyd3, eIF3ga, Tsp3A, Seipin, brv3, PI4KIIIalpha, sgg, CR45197, HLH3B, CG2652, CR44470, per, CG2650, CG2658, CG2662, Csat, eIF2B-beta, CG2680, CG2681, CG2685, CG2694, CG2701, fs(1)Yb, fs(1)Ya, vilya, dwg, ttm50, CG2712, crm, Syx4, kirre, CR43494, CG32795, w, CG12498, CG14416, CG14417, CG14418, CG14419, CG3526, CG3588, CG14424, CG32793, CG3592, CG3598, CG14420, CG14421, CG14422, CG14423, CG17959, CG3603, rst, CG4116, N, CG18508, Fcp3C, CG3939, dnc, CG14265, ng2, ng3, ng1, ng4, Pig1, Sgs4, CR44886, CG10793, CR46243, CR44999, Myc, CG12535, tRNA:Gln-TTG-2-1, CG14269, CG16782, CG10801, CG16781, CG12206, CG10804, CG10802, CG14270, CG10803, Gas8, DIP-alpha, CG13021, MRE16, ppk8, CG2875, AstA-R1, Ilp7, Parg, Mnt, CR45102, Rala, Tlk, mir-4962, HIP-R, CR44117, Crg-1, CR42499, CR33221, HIP, CR44118, fd3F, ec, tRNA:Gln-CTG-2-1, tRNA:Pro-CGG-3-1, CG2901, roX1, yin, CG2930, VhaAC39-1, CG15239, CG42541, CG2938, CG2941, CG32786, CG32783, Vap33, lva, CG6428, CG6414, CR45481, CR43298, CR45482, CR46247, CG43689, CG6379, CG15375, Xpac, brn, cib, Nsun2, dgt4, Tip60, tyf, GlcAT-I, Fas2, CG43288, CG15571, CG15570, Femcoat, Muc4B, CG43134, CG43135, CG15576, CG12691, CG15572, CR45483, CG15577, CG15578, CG12692, CG15579, CR44957, CR46156, mei-9, CG2982, mRpL33, norpA, CG12693, mir-982, mir-303, CG3626, mir-983-1, mir-983-2, mir-984, CR43614, CR45484, CG12688, CR32773, bi, CG3556, rb, CHOp24, CG3568, Usf, CG15912, CG11436, CG3527, CG11444, CG3546, CG12684, peb, CG12184, CG12179, pon, CG3081, CG3062, HLH4C, mRpL30, Torsin, Cbp80, CG15473, CG3009, rap, Pp2C1, ctp, l(1)G0334, CG7024, Proc-R, CG15472, Klf15, CR45515, CG2871, CG15471, CG6978, CG2861, CR45516, CG12682, CG42594, CR43495, CG12681, CG6927, CG32772, CG4041, CG6903, CG44774, Ptp4E, CR44833, CG15468, CR45792, CG12680, ovo, CG32767, rg, CG15465, Rpn13R, CG5062, CR44834, CG42749, CG3323, CG17764, Cdk7, snf, TrxT, dhd, CG4198, CG15930, Sas10, Rnp4F, Mcm3, CG3309, XRCC1, CanB, SK, NAAT1, spoon, Usp16-45, CG16756, CR45517, CG15784, CR44471, SPR, frma, CG32762, CG4151, CR45519, CG12730, CR45518, snoRNA:Psi28S-3342, Vsx2, Vsx1, CG34435, CG34434, RhoGAP5A, Mlc-c, mir-3645, l(1)G0045, CG42492, CG42265, CR45520, Sirt4, CG4119, Rab18, RpL35, Tre1, Gr5a, CR44958, CG42449, CG3160, CR45525, cv, CG3149, CR42794, CG4096, CG33080, CG32758, CG15773, IntS6, CG4078, CG15772, lin-52, CR45528, CG15771, MAPk-Ak2, CG42699, CG3097, CG42264, CG3108, CG15767, mir-4963, CR44832, CG12239, Cpr5C, Prosbeta2R1, CR45529, CG44329, CG15766, CG15765, CR43264, tRNA:Glu-CTC-6-1Psi, CG12729, CG43136, CG43137, CG15764, GAA1, mof, Usp30, CG16721, CR45668, Act5C, CG4020, CG12236, CG3011, CR44108, CG3726, CG12728, CG32756, CG6041, CG32755, CG6048, CG6067, fs(1)M3, Grip, CG5966, CG4766, CR44498, mab-21, CR44499, rux, MCTS1, CG5937, CG5921, CG43115, CG5928, Tsp5D, CG4666, CG4660, raptor, Mipp2, CR44959, Nep1, Ca-alpha1T, CG32750, CG32751, CG43090, vanin-like, Btnd, Efr, sqh, CG14446, CG14445, Rbcn-3A, Spx, schlank, CG3781, Spt6, CG3566, Ubi-p5E, CR45530, CR32745, CG11700, Top3beta, wuho, Rpt4, CG15896, CG15892, CG15891, CG3815, CG12219, CG3823, CG15894, CG42240, CG3842, CG3847, ND-B16.6, kdn, swaPsi, swa, Marf, CR44816, PpV, CG33664, CG33669, CG33668, CG42340, CG33667, CG33666, CG33665, tRNA:Phe-GAA-1-1, CG3918, CG3342, Spat, RpL7A, snoRNA:Or-CD10, dx, CG34417, CG17717, Pat1, CR43832, APC7, pigs, CG14443, CR44817, CG3226, Cdc7, CG3224, Ctr1A, CG3198, Mcm6, ND-ASHI, l(1)G0255, CG4095, Pink1, CG44303, CG3184, CG14442, CG14440, CG14441, CG3168, CR43461, RpL17, snoRNA:Psi28S-3436b, snoRNA:Psi28S-3436a, snoRNA:Psi28S-1060, snoRNA:Psi28S-1232, tRNA:Phe-GAA-1-2, CR44895, CR44964, CG14439, CG14438, CR43496, COQ7, shf, C3G, pod1, iav, Nf-YC, xit, Atx-1, nonC, CG12796, CG14435, CG4557, Cht11, CG4558, CG14434, CR45531, CG43736, CG14431, CR4575, CR32733, CG32732, CG4586, CG3040, ogre, CR44084, bou, Inx7, CR43837, Inx2, cm, CG42308, CG32736, CG3032, CG4593, CG12541, CG14427, nullo, CG4607, Sxl, mir-4956, CG4615, CG4617, CG8300, fz4, CR45532, CR46245, CG9650, CR32730, CR44357, CG1958, CG1677, CG2059, unc-119, brk, Atg5, Dok, CG18155, CG42780, CBP, CG15034, CG1999, CheA7a, CG42781, CG15035, CG32727, CG42246, CG42704, CG42705, CG34337, CG9657, CG15036, CG32726, CR45533, CR43199, CG11368, CG43198, CR44500, CR45534, CR43278, CR43279, CR43835, CG32719, CG43138, CG32720, CR44501, CR44502, CG11369, CG12689, ct, CR45667, CR45666, CR45665, CHES-1-like, CR43287, CG15478, Hira, NELF-B, CG12155, Pdp, Rab39, Tom40, Ir7a, CG34338, CG32718, CG1402, CG10920, CG1409, Ir7b, dec-1, CR43615, Ir7c, Ir7d, Ir7e, Ir7f, Ir7g, CG10932, Nek2, ND-MNLL, CG45089, p115, CR11386, CR33222, RpS6, snoRNA:Or-aca2, bys, dpr14, CG1444, snz, hdm, Ykt6, mahe, CG10778, RpS14a, RpS14b, Ubr3, l(1)G0193, CG15332, CG15330, sws, CR45620, sn, Tbh, CG15333, CG2233, fs(1)h, mys, Upf2, CG1571, CG2254, CG2256, CR45535, UbcE2H, CG2258, Gclc, CG1575, CG2260, cyr, CG2116, CG10958, CG2120, Smox, CG17982, alpha-PheRS, CG2129, CG15336, CG10959, Gbeta5, CG18262, Traf6, GIIIspla2, CG15337, CG10761, CR45536, Or7a, CG2278, slpr, sdt, CG2147, sni, Trxr-1, ND-75, CG1632, Corp, CG15343, CG1636, nAChRalpha3, CR43695, CG1387, CR15345, CG10555, CG11190, lawc, Trf2, CG32712, Miga, CG1440, CG12123, org-1, CG32713, CG15347, Es2, Sptr, CG33223, CG12116, Cp7Fa, Cp7Fb, Cp7Fc, Cp36, Cp38, CR43834, otu, CG33181, Nrg, PIP82, IntS4, CG12112, Trf4-1, CR46195, CG12111, spirit, CG12065, CG12081, CG12659, Crag, Caf1-180, oc, CG12772, CG11284, Ppt1, Ogg1, CG11294, CR44507, CR44508, Hexo2, CG2004, CG1785, l(1)G0020, CG1789, CR43297, Lim1, CR45537, CG12075, Moe, CG1885	TRUE	low FC; snp_su:12043; snp_op:3284; snp_ratio:3.67	18.97
D197R09	39	Control-Freec	DEL	X	8901360	X	14259726	-	-	somatic_tumour	-	5358.4	X:8901360-14259726	43:39_43	0.25	-0.41	-	-	-	-	-	intergenic	intergenic	Rbm13, e(r), rdgA, CR44111, CG12661, CG43255, mir-4964, CG10962, CR43836, CG12662, mir-31b, Nost, CG15365, CG10970, CR45538, CG44325, CG7246, HP1b, APC4, CG32708, CG32706, CG6999, CG7033, mir-13b-2, CG7766, Bx42, Arfrp1, AP-1gamma, CR45539, fend, CR44517, CG7065, fh, Bap111, His3.3B, Ost48, Dlip1, CG9034, Zpr1, CG44532, mei-P26, CG12115, CG12057, CG12056, CG12106, CG12118, su(r), SmydA-9, Obp8a, CG15368, CG15369, t, CG15370, Gr8a, CG12121, Ir8a, mir-4916, mxc, Larp7, amx, Dsor1, CG17754, ric8a, CR17438, ric8b, Erk7, CG17440, Cfp1, CG16892, snoRNA:CG16892-a, c11.1, lz, CR44534, c12.1, c12.2, CG34449, CG34450, BCL7-like, mgl, CG44815, CG32700, CG34028, CG34026, l(1)G0320, RpS28b, CG15317, CR42767, Cubn, LPCAT, CG42395, CR45540, CR45541, Hex-A, CR45542, CR45543, Gga, Lst8, LysRS, CG42797, Ptpmeg2, CG3106, nej, CR42657, CR44016, btd, CR43498, Sp1, CG1354, CG32698, Ser7, CG45060, CG45061, CG32695, CG15247, CG1468, CG9686, CG9689, CG9691, CG15249, CG1986, Idgf4, snoRNA:Me28S-U1688, CG1791, CG1889, CG43386, CG15252, CG32694, CG33557, CG2990, Cht6, CR45185, Yp2, Yp1, CR45601, CG15312, Gr9a, CR45602, ZAP3, CG2972, CG2974, RhoU, CR44894, snoRNA:Me18S-A627, CG12645, CG43902, CR32690, CG15309, CR43899, ATPsyndelta, CG2962, CR45629, CG15308, CG34408, Ipod, Hk, CR43959, CG12643, alpha-Man-Ia, CG2909, Gip, CG15306, CG43740, snoRNA:U3:9B, l(1)G0289, CG32679, CG17841, CG32686, CG2898, CG32681, Psf3, flw, CG32683, RabX2, CG12640, snoRNA:Me28S-A1705, Or9a, Neb-cGP, nocte, CG2889, CG2887, PPP4R2r, CG32687, spri, CG15296, Rab9D, Hmr, CG2124, CG1628, CG43347, Rab9Db, CG9806, X11Lbeta, CG2111, Rab9E, CG12637, CG32676, ras, CR44766, Rph, Tango5, Atg8a, BTBD9, CG15211, Ant2, sesB, Imp, CR45204, CR45624, sbr, CG15210, CG15209, CG32669, CG17333, CG2202, feo, sofe, CG2186, CG2157, CG1637, Ork1, CR45616, CR45617, CR44524, CG1582, CG15208, CG43901, v, CG2145, Myo10A, Rab9Fa, Rab9Fb, C901, CG42339, SmydA-4, CG1552, CG1545, CG1537, CR45614, CG15203, sev, CR44358, CR45604, Vago, CG2076, CG2061, CG42249, Hsp60A, CG11122, Rpt3, Gtp-bp, Klp10A, CG44385, CDK2AP1, CR44054, ssp7, CG15199, CG15202, CG15201, Ran, Lint-1, rtv, Dlic, CG32668, antdh, CG1394, CG15200, CR44765, CG11106, CG44422, CG15198, Ir10a, sisA, l(1)10Bb, CG1657, Kap3, CG34348, GCS1, CG11756, CG1738, CG11752, CG1737, dsh, Pa1, hop, Tim8, dlg1, CG15196, Gr10b, Or10a, Gr10a, Gs2, Evi5, Sk1, HP5, CG43155, Cyp4g15, CG1749, Spase25, CG33235, CR44556, Drak, mir-2492, CG1572, PGRP-SA, RpII215, CR44266, CG11699, Kmn1, CG11697, CG11696, e(y)2, CG11695, roX2, nod, CG1561, CR43217, CR43216, CR43215, CR43214, CR43213, CR43212, CR43211, rho-4, CG2533, CG2247, CG1703, RPA3, Met, Ptp10D, CG2371, bif, PhKgamma, CG2444, FucT6, Amun, mir-9370, CR45618, prtp, Tango10, CG15221, inaF-B, inaF-D, inaF-A, inaF-C, CR43385, m, CG9360, dy, Karl, CR44962, CkIIbeta, Hsc70-3, CG1578, rudhira, CG15741, CR43908, Cyp28c1, CG15740, CR45619, p24-1, CG10347, ATP7, CG2025, CG1847, CG11802, CG15739, CG10352, CG10353, SelG, CG1840, sicily, wisp, Upf1, CG43156, pot, CR32661, CR43157, Sclp, CR32660, CG10362, cac, gd, tsg, CG18130, fw, CG1806, CG1492, regucalcin, Chrac-16, CG15735, Tango4, Usp7, Cyp311a1, Cyp318a1, Ten-a, CR43960, Uch-L5R, Muc11A, CR43961, CG34323, CG12721, CG15734, CR32657, CR32658, CG11356, CG2750, CG1924, CG32655, CG45603, CG2577, Ir11a, CG32651, CG2574, CR32652, Pkcdelta, CG15927, CR45615, CG15731, Rab40, CG42258, Cpr11A, Lsp1alpha, Mks1, CG2556, snoRNA:Me18S-G894, CG43921, Cpr11B, CG11138, LIMK1, CG1824, Sec16, CG1463, CG2543, CR45621, CG11085, CR44568, CG15728, Aven, CG2540, Tomosyn, mir-970, CkIalpha, Tis11, CR33963, mir-9377, Smr, CG15725, CR43963, CR45623, CG4004, CR44619, ade5, CG12717, CG3812, CG32647, Pde9, CG3775, CG4661, CG32650, CG32649, CG4407, CG4404, mRpL49, Brms1, CG4645, CR45625, CR45626, fne, hec, CG32642, Mur11Da, CR43636, CG15721, CR43152, CG12716, CG32643, rad, CG15719, CG2209, CG12715, CR44840, mir-971, hep, lic, CG2200, CG43313, Fer3HCH, CG42237, CG32638, snmRNA:204, CG15717, MFS10, CG32645, CG4318, CG4332, Bap60, CG12096, Lgr4, CG32640, CG32641, CG12723, CG2453, sno, CG44437, REG, mew, CG32639, CG15742, comt, HDAC4, CG15743, CG15744, CG1764, CG1622, IP3K2, CR45018, Jafrac1, CR32636, RpS15Aa, CG15747, CR45708, CR45709, Syt12, dmrt11E, CG1640, Rbp1-like, Tim9a, Yippee, CG1662, CR44620, CR44621, CG1673, CG12725, GstT4, CG1998, Set2, Neto, CG34324, CG15754, CR44427, CG44428, CG15756, Cpr12A, CG11816, CG32631, CG32633, Tango13, up, CR44654, CG11178, Ndc80, BthD, tth, Tango2, CG2691, NFAT, Lig4, CG11164, CG15760, CG11162, CG12177, CG11158, CG9940, Nna1, CG9941, mus101, g, Grip91, CG11134, CG11151, CR42861, Pdcd4, CR43833, CG32625, Rtc1, Yp3, rdgB, CtsB1, CG11103, inaE, CG10993, CG10996, CG11095, Clic, Nup93-1, jub, AMPdeam, mamo, CG11068, CR44655, ben, Ste12DOR, tRNA:Arg-TCG-2-1, tRNA:Ser-CGA-1-1, tRNA:Ser-CGA-1-2, tRNA:Arg-TCG-3-1, tRNA:Arg-TCG-3-2, tRNA:Arg-TCG-3-3, tRNA:Arg-TCG-3-4, tRNA:Ser-AGA-3-1, tRNA:Ser-AGA-2-1, Ste:CG33247, Ste:CG33246, Ste:CG33245, Ste:CG33244, Ste:CG33243, Ste:CG33242, Ste:CG33241, Ste:CG33240, Ste:CG33239, Ste:CG33238, Ste:CG33237, Ste:CG33236, tRNA:Ser-AGA-1-1, CR46242, tRNA:Ser-CGA-1-3, tRNA:Arg-TCG-1-1, tRNA:Ser-AGA-3-2, CR44657, tRNA:Ser-AGA-2-2, CR44658, CG12479, CG12480, betaNACtes1, CG1368, CG11581, CG11584, CR45995, CG32603, CG12481, CG11585, CG13403, yl, mir-4917, CG11590, l(1)G0007, l(1)G0469, CG11674, mRpL38, CG42271, Fbxl4, CG1434, mRNA-cap, CG32599, mud	NA	snp_su:8487; snp_op:2160; snp_ratio:3.93	19.57
D197R09	40	lumpy	DEL	X	3134963	X	3138096	15	9	somatic_tumour	8345	3.1	X:3134963-3138096	5to3	0.44	-1.4	-	-	-	-	-	N, 5UTR	N, intron	N	NA	snp_su:0; snp_op:0	0
D197R09	40	delly	DEL	X	3134963	X	3138096	10	16	germline_private	DEL00000023	3.1	X:3134963-3138096	3to5	0.440007467	0	1	-	CGGTCACACTGCCGTTTTGAAACAGATCGCTTTTTTCCAGTGGACGAAACGGTTGTGAAAGCGGACGAGCGTTAGGCAGACGAACCTGGAAAGCGCAGAGCACAGTTCTCAACATCGAGAAGGGAAATGAGCGGGCATAGAGTAGAGATACTTTTGTATCTGCGCGCTCTCTCGGCTATTTCCTGTATATCCTGTGCGCACCCCAAAAACCAAAGAAG	-	-	N, 5UTR	N, intron	N	NA		0
D197R09	41	novobreak	DEL	X	3134963	X	3138096	15	9	somatic_tumour	12	3.1	X:3134963-3138096	5to3	0.44	-1.4	-	-	GCCAAAATGGCTCCCCGCCATACGGTATCTTTTTCTTGCACCGACGCGGTCACACTGCCGTTTTGAAACAGATCGCTTTTTTCCAGTGGACGAAACGGTTGTGAAAGCGGACGAGCGTTAGGCAGACGAACCTGGAAAGCGCAGAGCACAGTTCTCAACATCGAGAAGGGAAATGAGCGGGCATAGAGTAGAGATACTTTTGTATCTGCGCGCTCTCTCGGCTATTTCCTGTATATCCTGTGCGCACCCCAAAAACCAAAGAAGTAAAAACTGAAAACACATTTCTTGACTTTCGTAAGTCACGCAC	-	-	N, 5UTR	N, intron	N	NA	snp_su:0; snp_op:0	0
D197R09	42	lumpy	DEL	X	5159772	X	5159821	7	0	somatic_normal	8469	0	X:5159772-5159821	-	0.11	0	-	-	-	-	-	CG15465, intron	CG15465, intron	rg, CG15465	NA		0
D197R09	44	Control-Freec	DEL	X	14332734	X	19298682	-	-	somatic_tumour	-	4965.9	X:14332734-19298682	Heterozygous deletion	0.25	-0.39	-	-	-	-	-	dpr8, intron	intergenic	dpr8, betaNACtes3, betaNACtes4, CG9411, CG12540, CR44110, CR45521, CG14414, mRpS25, nmdyn-D6, CG9413, NetA, CG5321, NetB, CG43088, hog, CG15890, CG5334, CG5347, Ag5r2, Ag5r, CR45522, rut, CG14408, CG14411, CG14410, CG14407, CG32590, Flo2, CG12539, CG9522, CG9521, CG9519, CG9518, CG45064, CG45065, CG9514, CG9512, CG9509, CG14406, CG12398, Eo, CG9503, CG32591, pdgy, CR44831, CG9030, eag, hiw, be, CG5541, ND-B18, opm, dob, Lsd-2, CR44662, CR44661, CG33177, CR44960, CG33178, CG9065, CG15027, CG5599, Rab3-GEF, CG9072, Cyp4s3, drd, RpL37a, CG9095, CG43737, CG32588, CG5662, CG43075, CG43076, CR44430, CG9101, PPYR1, CG9106, CR44663, CR44664, CG5877, CR44429, gce, CR44961, Top1, mir-4957, dah, CG9114, HDAC6, CR44998, CG9123, CG12608, CG6227, acj6, Pp1-13C, CG9164, Cngl, Scamp, Ahcy13, CG11655, shtd, CG6299, CG6294, CG15642, CG15641, Grip128, CG6308, mh, CG6324, CG6340, Gmap, CR44888, mir-283, mir-304, mir-12, Ac13E, CR44353, CR44354, CG42300, CG7860, CG15643, CG9213, CG42299, betaNACtes5, cerv, CG7872, CG9215, CG8097, CG9220, CG8105, sog, CR44423, CR44893, CG8117, CR43299, CG8119, CG15646, CG12708, CG15599, CR43132, CR45523, CR45524, CR45526, CG8128, CG9240, Pis, CG8134, CG9281, CG15601, CG8184, CG8191, CG12379, MagR, Arp6, CG11679, CG8206, CG8944, Tcp-1zeta, CG8239, Graf, CG8260, mRpL3, CG17209, CG8952, CG33172, CG43672, CG43673, Efhc1.1, Paf-AHalpha, mRpS30, Rhp, CG8974, CR44383, CG32581, CG15602, PGRP-LE, sd, CR44384, CG8509, Chc, CR32582, CG8565, ArgRS, CG8578, sun, UBL3, CG15914, Myb, AlkB, Gbeta13F, Gapdh2, CG16952, tay, MSBP, CG15916, shi, CycD, CG8909, CG8916, Lcch3, CR45000, Ranbp16, Stim, CG8924, Rrp47, mmd, mir-927, CR45527, Or13a, CG42766, CG9170, CG8931, ND-20, eIF5, exd, CG8939, vap, CG12698, Muc14A, CG12395, dpr18, Nipsnap, Tob, mir-4958, CG8958, CG42354, CG42353, disco-r, CR46211, mir-985, disco, snRNA:U5:14B, snRNA:U2:14B, CG12507, kat80, Mfe2, Prosalpha4, eas, CG32576, UQCR-14, caz, CG9911, CG3632, CG3679, CG9914, CR45485, CG9915, SWIP, Cyp1, CG9917, CG32579, CalpC, CG9919, CG9921, Dsp1, sl, U2af50, Gpi1, nonA, Fur2, CG9992, CG4239, TH1, mei-41, CG9981, CG4301, Traf-like, AnxB11, hang, CG9947, rngo, eIF-2alpha, CG34015, Rbp2, para, Cnx14D, CG9903, CG9902, Arp2, Pp2B-14D, CanA-14F, CG13014, SMC3, Ubc7, CG9784, Nup153, mir-4965, mbt, CG9782, Rok, CG9777, CR45001, RpS19a, SNRPG, mthl1, CR46147, CG42512, CG32573, CG9723, r, CG15865, CG13012, CG13010, sing, Axs, Sep4, CG4678, CG9676, spheroide, CG9673, CG4653, CG9672, CG13008, CG34325, CG32572, goe, TwdlX, TwdlY, TwdlZ, CG32568, Twdlalpha, if, mRpL22, CG9609, Sap30, Rrp45, CG4768, CG9132, CG4789, CG9125, CG13005, CR44053, ppk28, CG4829, CR44129, CG13004, RSG7, CG13003, CG4872, Nprl2, Rcp, DENR, CG4880, CR43768, CG13002, CG33252, CR44754, CG4928, wus, CG13001, RhoGAP15B, CG13000, Ubr1, CG45002, CG43996, CG43997, CG43077, wcy, CG4949, CG8945, CG4955, CG4991, CG16700, Arpc3B, CG5004, mei-218, mei-217, RpS5a, snoRNA:Psi28S-1192d, snoRNA:Psi28S-1192c, snoRNA:Psi28S-1192b, snoRNA:Psi28S-1192a, snoRNA:Psi28S-2876, snoRNA:Psi18S-1854c, snoRNA:Psi28S-1135f, snoRNA:Psi18S-1854b, snoRNA:Psi28S-1135e, snoRNA:Psi18S-1854a, snoRNA:Psi28S-1135d, snoRNA:Psi28S-1135c, snoRNA:Psi28S-1135b, snoRNA:Psi28S-1135a, CG5010, xmas-1, xmas-2, baz, CR44026, CG8918, CG5070, CG32564, CG32563, CG12995, CG18258, CG5162, CG12998, CG5172, CG34327, CG10598, CG10597, f, CG8915, CG42854, CG8675, CG8664, CG5445, CG8661, Fim, B-H2, CR43491, B-H1, CG8611, CG12994, CG5613, p-cup, CG8568, CG43658, CR44692, ppk23, Ankle2, CR44124, CG12991, CG12992, X11L, stas, CG8326, corolla, ND-24, CG8289, CG5800, RhoGAPp190, IntS2, beta-Spec, CG12990, chas, CG8188, par-6, CG8173, CG42684, unc-4, OdsH, CG12986, Socs16D, CR44691, CG6398, e(y)1, CG8142, Ucp4A, CG15814, Spt7, CG32554, CG32557, CG6762, CR43981, Arp8, CG6769, mnb, CG12985, CG6788, GSS, CR32496, CG32495, CG7772, Vps4, CG6847, Sh, CG12672, CG6867, CG15373, Dhc16F, CG7536, Ada3, CG7206, scu, RhoGAP16F, Mvb12, Taf8, CG7135, wupA, CR45605, CR45606, mir-969, CR32553, mir-210, CG43133, ari-1, CG43229, Frq1, Frq2, Andorra, Hesr, Him, CG33639, CR45622, upd2, CR45607, CR45613, CG15059, upd3, CR15061, upd1, CR45608, CR45609, CG6023, CG6123, CG6106, CrebB, CR43686, por, CG6179, betaCOP, Tsf1, CG32549, CG34328, CG15056, CG42323, CG32548, CG6290, CG32551, CG43841, CG32547, CG43843, CR43842, Hayan, CR45714, psh, CG15046, CG15044, CG15043, CR45627, GalNAc-T2, Xrcc2, Wnt5, Ggt-1, CG6470, HisRS, Bx, CG6481, CG15042, CG15047, tRNA:Pro-CGG-2-1, CR43492, CG15040, CR43289, CR44705, wgn, Rip11, CG6540, CG6617, Ing3, CG6659, fu, CG6696, CR45514, CR45710, CR44707, phm, Cyp18a1, CCKLR-17D1, Cyp308a1, CG42302, CR45512, CR45513, CG6873, CG12609, CCKLR-17D3, CG6891, CG18259, CR6900, CG6961, S6KL, Atg101, bnb, CR44841, CG7058, CG42450, CG7101, Pvf1, htk, CG7280, CG7322, Usp39, CG32544, CG7326, CG34401, CG7332, CG7358, SdhBL, CG7378, CR44708, CG43759, Diedel3, CG14190, CG34330, CG7406, CG14191, CG7423, CR45503, CG15882, tgy, CR45711, Obp18a, RhoGAP18B, Inx5, mir-4959, CG33939, CG7556, CG7453, CG33253, Mec2, HP1D3csd, CG7914, CG14194, CG7990, Ulp1, CG14195, Mur18B, Muc18B, CG7884, CG14196, CG7889, CG7992, Hs3st-B, rictor, Vav, CG8010, CG32537, CG32536, CG8028, CG8034	TRUE	low FC; snp_su:8572; snp_op:2297; snp_ratio:3.73	19.33
D197R11	1	novobreak	DEL	2L	7031883	2L	7035395	11	1	somatic_tumour	1	3.5	2L:7031883-7035395	5to3	0.21	-0.34	-	-	CGTCTTGTTACCCACCAGGATTTTGAGTACCTTGGAGTTGGCATACTCCTGGATCTCGCGCAGCCAGTCCGGCAGGCAGTCAAATGTGGGCTGGCAGCTGATGTCGTACACCAGGATCAAGGCGTGAGCCGATCGATAGTAGCTCTATCTGTGTAGAATGTCAGTGCGGGCAGCGGTGGACGTGGTGGACGCAAGCGCAGCGGCAGCAGTCCAGGCGGCGGCGGTGGACACGATGACGACTACGCCGAGAATGGTCCGCGGAACGGCAGCGGCGGCGGAAGCTCACACAAAAAGCAAAGCAAACGATCCCGGTAAGATTAATCAATAA	-	-	Rab30, exon	Caper, exon_3	Rab30, Caper	NA	snp_su:1; snp_op:0	23.93
D197R11	2	Control-Freec	DUP	2L	7891081	2L	7893490	-	-	somatic_tumour	-	2.4	2L:7891081-7893490	Heterozygous duplication	0.46	0.61	-	-	-	-	-	intergenic	Snoo, 3UTR	Snoo	NA	snp_su:0; snp_op:0	0
D197R11	3	lumpy	DEL	2L	9831533	2L	9831544	4	0	somatic_normal	624	0	2L:9831533-9831544	-	0.12	0	-	-	-	-	-	nAChRalpha6, intron	nAChRalpha6, intron	nAChRalpha6	NA		0
D197R11	12	novobreak	TRA	2R	10024018	X	3453221	46	29	germline_private	4	6570.8	2R:10024018 X:3453221	5to5	-	0	-	-	TTCCATTCCAGTCCATTCGGTTTGATTCCATTCCATTCCATTCCTTTCCATTCCTTTCCATTCCTTTCCATTCCATTCCATTTCATTCCATTCGGGTTGATTCCATTCCAAACCGTTCCATTCCATTCCATTCCATTCCACTCCATTCCATTGCACTCGGGTTGATTCCATTCCATTCCATTCCATTCCATTCCATTCAATTCCATTCCATTCCGGAAGATTCCATTCCATTTCATTCCATTCCATTCCATTCCCCTGCACTCGCGTTGAT	-	-	Pka-R2, intron	CR44999, ncRNA	Pka-R2, CR44999	NA		0
D197R11	20	Control-Freec	DUP	3L	20755141	3L	20759959	-	-	somatic_tumour	-	4.8	3L:20755141-20759959	Heterozygous duplication	0.39	0.59	-	-	-	-	-	CG33912, intron	intergenic	CG33912, CG43251	NA	snp_su:2; snp_op:1	9.83
D197R11	23	Control-Freec	DUP	3R	19312953	3R	19351497	-	-	somatic_tumour	-	38.5	3R:19312953-19351497	23:23_24	0.34	0.44	-	-	-	-	-	Dl, intron	intergenic	Dl, CR44175, mir-997-1, CR43258	NA	snp_su:107; snp_op:90; snp_ratio:1.19	10.02
D197R11	23	novobreak	TANDUP	3R	19313455	3R	19351709	5	2	somatic_tumour	9	38.3	3R:19313455-19351709	24:23_24	0.09	0.44	-	-	AATTATATGCATTCAAAGAGAGCGTGGCGAAACATTTTTTTAAGGAGCAGCTTAAGTTTTACTGCTTAAATTTATCGTGTGGAATGTTTGCGGCATGTTGTCGCTCGTTGATGCCACACACGAAAAACTACAAGAAATTAAAGTTTTAAAGTTGGTTTTATTTACATTTGCAACACCGACACACACGTTAGCTTCGGCAGTGCGATAAAGCGCATGGATTTGTGGCATGACAGGTTATTAGACAAGCCGGCAAGAGACGCACAATTTCTGGCCAGTTTGGCCAGTTTGCAAAAAACGTGCAATAAAATAT	-	-	Dl, intron	intergenic	Dl, CR44175, mir-997-1, CR43258	NA	snp_su:106; snp_op:92; snp_ratio:1.15	9.9
D197R11	30	Control-Freec	DUP	X	2470028	X	2472437	-	-	somatic_tumour	-	2.4	X:2470028-2472437	Heterozygous duplication	0.46	0.81	-	-	-	-	-	boi, exon_1	trol, intron	boi, trol	NA	snp_su:0; snp_op:0	0
D197R11	31	Control-Freec	DUP	X	3786948	X	3789357	-	-	somatic_tumour	-	2.4	X:3786948-3789357	Heterozygous duplication	0.43	0.79	-	-	-	-	-	Tlk, 3UTR	Tlk, 3UTR	Tlk	NA	snp_su:0; snp_op:0	0
D197R11	34	Control-Freec	DUP	X	11218713	X	11223531	-	-	somatic_tumour	-	4.8	X:11218713-11223531	Heterozygous duplication	0.4	0.65	-	-	-	-	-	intergenic	CG44422, 3UTR	CG44422	NA	snp_su:0; snp_op:1	0
D197R13	1	Control-Freec	DEL	2L	17732736	2L	17853024	-	-	somatic_tumour	-	120.3	2L:17732736-17853024	Heterozygous deletion	0.43	-0.46	-	-	-	-	-	CadN, intron	CadN2, intron	CadN, CR43419, CG42830, CadN2	NA	snp_su:229; snp_op:196; snp_ratio:1.17	10
D197R15	1	Control-Freec	DUP	2L	167291	2L	179862	-	-	somatic_tumour	-	12.6	2L:167291-179862	Heterozygous duplication	0.39	0.52	-	-	-	-	-	spen, intron	spen, intron	spen	NA	snp_su:14; snp_op:5; snp_ratio:2.8	17.72
D197R15	2	novobreak	COMPLEX_BND	2L	549264	2L	549415	2	2	somatic_tumour	1	0.2	2L:549264-549415	3:2_3	0.09	0	-	-	GCCCAACTGGCGGGGCCGGCTGCATCCGGAGGCCAAAGCGCCGGTTGAAGTCCTCCGAGAGGCGCCACATGACGCCCACGTCCACGCTGACGCTCATGGTCGCAAAAGTCTTTTTCAGAAATTGCAAGTGCAAGTCACTAAACTATAATAGCTAACCAAATAGAAAGAAATTGCTTACAAGCTTACAATTTCTAACTGCAAAGTGTAAAATGC	-	-	Ets21C, 5UTR	Ets21C, 5UTR	Ets21C	NA		0
D197R15	7	novobreak	BND	2L	1413914	2L	1414397	4	2	somatic_tumour	2	0.5	2L:1413914-1414397	3to3	0.15	0	-	-	GCCAGTTTTCCCCACACTCCCCCCCAGAGATCATGGATCCTAAATTCCAGATTGCAGATCGCGGATCGCTGGACGTTGATGCCTATTGACAGCTCACAGCGGTTTATTAATGATCATGCTGCGGCTGCCCAGAGATCGAGATATAGTCTCCGTGGATCTGGGTTCGTTTCGAGTTACAGAACTCTCCGACATTTGTTGGTGGAATTGTTTACGGTTTGG	-	-	robo2, intron	robo2, intron	robo2	NA		0
D197R15	8	novobreak	INV	2L	2013726	2L	2014948	22	96	germline_private	3	1.2	2L:2013726-2014948	3to3	-	0	-	-	TCTGTCTCCTGGCACTTGTGTCACTTTTAACTGCTTGCGAGCATCCGCAGGCTCTCGGTTGGGGTATAAAACCTTTTAATTTGCTCAGCCGCATTTTCCCCATATCCCTAGTCGTGCTCCATCTGCGACTTTCCCGGCCTCCAGTTGGTTCTGGCCCCGAAGTCCTCGCCTCTTTTTCATCCTGCACTTTGTATTAGCATAAAGTACGCATTTCGACCC	-	-	CG4238, intron	CG4238, intron	CG4238	NA		0
D197R15	9	lumpy	BND	2L	2024251	2L	2024519	3	2	somatic_tumour	196_1	0.3	2L:2024251-2024519	3to3	0.13	0	-	-	-	-	-	CG4238, exon_1	CG4238, intron	CG4238	NA		0
D197R15	9	novobreak	BND	2L	2024251	2L	2024519	3	2	somatic_tumour	4	0.3	2L:2024251-2024519	3to3	0.13	0	-	-	CATGCTTCAAATTAAATTATTCCACCCCATAAACTTAATTAATTATAGATGGCTATCAGCAGGCAGAACGACATGAAAACATCAAGCATACGCCTCGTTGCTCGTTTGGCATAAGTAATTGATTCGGCAAAGCACAATTTCACTTTGAGCGTGGGAAAAGTCTTGCCACCCGTGGCCGCATGCATGACGCCACCTACGTTGATGTGGCTAACTAGCATGGATATATCGAAGCG	-	-	CG4238, exon_1	CG4238, intron	CG4238	NA		0
D197R15	10	novobreak	BND	2L	2256800	2L	2257556	3	1	somatic_tumour	5	0.8	2L:2256800-2257556	3to3	0.08	-0.13	-	-	GGATATACGCAGCCATTTCCGGCGCCATAGCTGCCAGCTTCCGCTTTACCTTTTACCACCACAGCACCACCCCCTTTGGCACTTTGACGGTGGCGCCCAGAGCTGTCGGGAAATCCACCGTCTGGCCCCACTTCCCACTCAGCTTATCCCCACTCAATCGTCTGGCAAATGGAGGCTTGACTTTAAGCGATGGAAATTTTAATGCGCCAATGCGCAATTTATGATTATTTCATGCTCATTTTAATTTGCCCATTCAGCAGACACGCAGTCGTTTGGTCGCTCGTTCGCCAATTTAGTTTTAACGGTGCAGCTGCTGCTTGTGTTATCATTCAATTGCCGCCTGCACTGAAATTTTGCATACCAGGTAC	-	-	intergenic	intergenic	-	NA		0
D197R15	12	Control-Freec	DEL	2L	2477454	2L	2503563	-	-	somatic_tumour	-	26.1	2L:2477454-2503563	Heterozygous deletion	0.32	-0.45	-	-	-	-	-	intergenic	intergenic	Slh, oaf	NA	snp_su:0; snp_op:0	0
D197R15	13	novobreak	BND	2L	2571711	2L	2572030	4	0	somatic_tumour	7	0.3	2L:2571711-2572030	3to3	0.1	0	-	-	ACCCACTAGATCGTCGTGGGTGGCCTGCTTCTGATCCCGAAGCTTCAGCAGATGCGAAAGATAGTCCGTGCGAGTGGAATCGCCAGCCTTCAGTCGCAGCTCAATGGACTCCTTGGTCAGGTTGGAGAAGAGTCTCGACTTTGAGAAGCTCTCCTCCTTACAATATTTAGAGCAAGTGATCTATGGTAAGCATATATATCGGCTTTGCCAATTTCACCATATTATA	-	-	Cyp309a2, exon_4	Cyp309a2, exon_3	Cyp309a2	NA		0
D197R15	14	lumpy	BND	2L	3218942	2L	3219693	1	2	somatic_tumour	292_1	0.7	2L:3218942-3219693	3to3	0.07	-0.09	-	-	-	-	-	intergenic	intergenic	-	NA		0
D197R15	15	novobreak	BND	2L	3336000	2L	3336392	3	1	somatic_tumour	8	0.4	2L:3336000-3336392	5to5	0.09	0	-	-	CACCCAGCTGTTCGGCGGATATCTGTCTTCGCGCATTCCGGAGGGGACTGTAAAGAACAAAGATCAATAAAGGACAATGATTTCCGTTCGCAATCCCATCCAGACTCACATGAATTAAGGGCCCCGAAGAGGGCGAAGAGCATCCAGTAGGTCTGCGAGAAGAACATCCATCCCTGGAGGTCGTGCAGGAACTCCTCGGTTCTGGGCAGCTGGAACCAAATGGCACCGGC	-	-	E23, exon_8	E23, exon_7	E23	NA		0
D197R15	16	Control-Freec	COMPLEX_DUP	2L	3698775	2L	3704577	-	-	somatic_tumour	-	5.8	2L:3698775-3704577	17:16_17	0.41	0.59	-	-	-	-	-	CG10031, intron	CG31778, exon	CG10031, CG42464, CG42465, Sfp24C1, CG42467, CG43145, CR44311, CG2816, CG31778	NA	snp_su:19; snp_op:15; snp_ratio:1.27	10.8
D197R15	18	lumpy	BND	2L	4248314	2L	4249542	2	1	somatic_tumour	407	1.2	2L:4248314-4249542	5to5	0.06	-0.18	-	-	-	-	-	CR44059, ncRNA	CR44059, exon_1	CR44059	NA		0
D197R15	19	lumpy	BND	2L	4315223	2L	4316182	1	2	somatic_tumour	413	1	2L:4315223-4316182	3to3	0.13	-0.12	-	-	-	-	-	tutl, 3UTR	tutl, intron	tutl	NA		0
D197R15	21	lumpy	BND	2L	6047302	2L	6047713	2	4	somatic_tumour	562_1	0.4	2L:6047302-6047713	3to3	0.24	0	-	-	-	-	-	CG34179, 3UTR	CG34179, 3UTR	slmo, CG34179	NA	bp1_accord_Gypsy=2	0
D197R15	24	novobreak	BND	2L	7579881	2L	7581096	3	2	somatic_tumour	10	1.2	2L:7579881-7581096	3to3	0.14	-0.05	-	-	ATATTTCTATACAATCGTATAGCTTAGGATCAAGAATAAGCTTAATATTTCTTTGTTAAACTTTATATTTATTTATTAAACATAATTTTTTCCTGTCTATAGGAAGGGGTAAGAATCAGATAAGAGAAAATCTTGATGGATTGTTTAATTAATTAACCAAAGTCTAAATGGTGATTGATTGGAGCATTGA	-	-	intergenic	intergenic	-	NA		0
D197R15	25	lumpy	BND	2L	7699435	2L	7699525	4	2	somatic_tumour	699_1	0.1	2L:7699435-7699525	5to5	0.22	0	-	-	-	-	-	Tep2, exon_2	Tep2, exon_2	Tep2	NA		0
D197R15	28	novobreak	COMPLEX_BND	2L	8214816	2L	8214944	3	0	somatic_tumour	12	0.1	2L:8214816-8214944	29:28_29	0.08	0	-	-	ACTCCTTACACTCATTGACAAGATCTAAGTTTAATTCTTGAGCGTGGCGTGCATTGTTTCGACTTCCAGATCCGTCTGTTCAAGAACTTCTGACAGCTGCTTTTCAAGTGCGCCAGCTGGCATACGTTCCATATAGTGGCTTCAAAGTTGGGGCTGCTTTTCGGGCCAAGGTCGATGGAAAGATCTTCACTGGCTGCAATGTGGAAAACGCCGCAAGGAGTGGTGAATACATTAGGTTCGTAGGCCAAAACAGCACCTGCCAAAAATTCGGTGGCTCCTTCGCTTACGGCCTTAGCAATGGCCGTTCTCTCGGCACAAGAGCCCGGCGTAAAGG	-	-	CG8353, exon	CG8353, exon	CG8353	NA		0
D197R15	30	novobreak	BND	2L	8863980	2L	8864256	3	1	somatic_tumour	13	0.3	2L:8863980-8864256	3to3	0.12	0	-	-	GCATTGTATCCCGAGAATATCCTACTACTCTCCCTGTAAGTGGTTCATGACAGGTCTGGTGGTTGTGTGTACCACCTTGTTTGGCTGCCATTTCATCCACGACTTGAGCCCGCTCATTATCAGTTTCGTGATGATCGGCGTGGCCCTGATCATTATGTTACTCAACTTCTCTGGGGCCATGCGCCCACCGTAATTCCGATAAGGATCAGGCCAATGTTATAGATGC	-	-	CG32987, exon	CG32987, exon	CR45260, CG32987	NA		0
D197R15	33	lumpy	BND	2L	9410259	2L	9410751	2	2	somatic_tumour	881	0.5	2L:9410259-9410751	3to3	0.13	0	-	-	-	-	-	Shawl, intron	Shawl, intron	Shawl	NA		0
D197R15	34	lumpy	BND	2L	10391382	2L	10392143	2	1	somatic_tumour	979	0.8	2L:10391382-10392143	5to5	0.09	-0.18	-	-	-	-	-	da, exon	da, exon	da	NA		0
D197R15	36	novobreak	BND	2L	10831472	2L	10831749	4	0	somatic_tumour	15	0.3	2L:10831472-10831749	3to3	0.07	0	-	-	GTGGTGTGCTCCACATATCTGTGATAAATGCAATCCTTACCTGCCGGCACGCGACCGATAATCCTGTGACATCTTTCTGGGCTGCTGTTGGTTTTTCGGCGACGGCGATAGTTCCCGCGAACTTTTTCCGGACGCAGTGCAGCTGCCCGAGGGAGGACAACCCGCACCCTGACCAACGCCAACGTTGAATGGCAATGGGCTCTTGAGCGGCAATCCAAATGGCGAAGGCGGTGACTCCTCGCCCAGCCATGAAGTGGACCATCCGGGTGG	-	-	Nos, exon_2	Nos, exon_2	Nos	NA		0
D197R15	39	novobreak	BND	2L	11965766	2L	11965906	3	0	somatic_tumour	16	0.1	2L:11965766-11965906	5to5	0.11	0	-	-	GGGCTAAGCTGCTGTGCCTTTCGGCCAATATCCCTGCCAGATGGGCAAACCAGTTTTTTGGCTGCCCATTCGAATCGAGCGATGCAGCGCAACCGCAAAAGCCAAAAAAAAAAAATGAATAACAAAACCGAAAAAACTGACATCCCAACTTTGAGCCGGGCCAAGGAAAAAGTGAAATCTGCTAGAATTGATCTTGTGGGGAGTCGAAGTCATCGTCTTGGTCTTCT	-	-	CR43314, ncRNA	CR43314, ncRNA	CR43314	NA		0
D197R15	40	lumpy	BND	2L	12628272	2L	12628372	3	0	somatic_tumour	1149_1	0.1	2L:12628272-12628372	3to3	0.17	0	-	-	-	-	-	Ref2, intron	Ref2, intron	Ref2	NA		0
D197R15	41	novobreak	INV	2L	13964532	2L	13968821	29	76	germline_private	17	4.3	2L:13964532-13968821	3to3	-	0	-	-	GCTGGTGGTGTTCACGTCGTAGCGATATCCTTCGCGGCAGTGACACTTGTACCGCGACTCACAGAGCCCATTCTCGCAGTTCCTGAAAGAAATGTATTAAATTATTAAATGTAAAAGGAGAGGCGTCTAGTCCTAACACTCACATATAGCAATCGCCTTCGCAGGCGATGCCGTTCTTGCGTTTTTGGAATCCGGGGAAGCACTCGCATTCGT	-	-	NimB1, intron	NimB4, exon	NimB1, NimB4	NA		0
D197R15	43	novobreak	INV	2L	16638281	2L	16639537	10	70	germline_private	18	1.3	2L:16638281-16639537	3to3	-	0	-	-	CGTAATTTTTGCATGCTGCTGGCTCTGCGATAAGCGAACTCGAACAAATATGCCGTGTGTGTGTGTGTGTGTGGGTTAATTTGAAAGTTTCAACTGTCACAAATGTTAGAATTGACGGCAGCCACTTTAGCAGGTCTTTGAACTTGAATTTAATTATGAAACTTAAGTTGG	-	-	CG42389, intron	CG42389, intron	CG42389	NA		0
D197R15	45	novobreak	BND	2L	16944336	2L	16944648	3	0	somatic_tumour	19	0.3	2L:16944336-16944648	5to5	0.09	0	-	-	CTTTTCTTTTCGTGGGCCCTGTTTTTTTCATATTGTGGTTACCTTTGCTACTTTATGTTTAAGTGCAGCTGCACAAAATATACCAAAAAGGACATCACAGGGCGGCGAAAGAAGAAGAGCCCAACCTTAACAAGCAAACAAGCGATGACAAGCTTTTCCTTGCCATTTGATTGAGCTGTTTATAGACTTGAAGTGGCAAACGCGGTGTACACAAACAATGCAACAAATATGTTTGAATAAAAGTAATACTTTACACCAAAGTAAAATTGTTGAATTTGAGAAATATAAATTCCTTTATCGAATCTGTTGTTCTTGAGAGGCTGTGAGATTATTTCCCGTGCACGTCAGATAATGTGTATATACGTAGGCACACCAGGTGCACTTTTGTGTCTGTGTGGGTGTGTCCTTGTCCGCTTGTCAGTGTGTCTGTG	-	-	intergenic	intergenic	-	NA	bp2_roo_BEL=2	0
D197R15	47	Control-Freec	DUP	2L	17356683	2L	17379891	-	-	somatic_tumour	-	23.2	2L:17356683-17379891	Heterozygous duplication	0.36	0.42	-	-	-	-	-	intergenic	Lrch, intron	CR44346, CG31804, Lrch	NA	snp_su:52; snp_op:40; snp_ratio:1.3	10.4
D197R15	48	Control-Freec	DEL	2L	17606169	2L	17866292	-	-	somatic_tumour	-	260.1	2L:17606169-17866292	Heterozygous deletion	0.33	-0.51	-	-	-	-	-	intergenic	CadN2, intron	CR44412, CR44413, CG15147, CG43054, CR45699, CadN, CG43231, CR43419, CG42830, CadN2	NA	snp_su:300; snp_op:218; snp_ratio:1.38	12.12
D197R15	51	Control-Freec	DUP	2L	21388106	2L	21394875	-	-	somatic_tumour	-	6.8	2L:21388106-21394875	52:51_52	0.45	0.67	-	-	-	-	-	nrv3, intron	intergenic	nrv3	NA	snp_su:0; snp_op:2	0
D197R15	54	Control-Freec	DUP	2L	21734292	2L	21745896	-	-	somatic_tumour	-	11.6	2L:21734292-21745896	Heterozygous duplication	0.41	0.6	-	-	-	-	-	intergenic	step, intron	step	NA	snp_su:8; snp_op:10; snp_ratio:0.8	10.33
D197R15	60	novobreak	BND	2R	1488346	2R	1488763	3	1	somatic_tumour	27	0.4	2R:1488346-1488763	3to3	0.14	0	-	-	GGATATGTGACACTACCGATAGGTACACCATGTTTATGCAATTTAGAGAGCAGTTGGTTGTGGTTTCAAAGATTGTTCAAAAGTGTGGGTGTGGCCGATTTGTATGAGTTAGAGTGGATGTGGCAACATGGGTCAACAAACTTGCGCAGTGTCTATGTCTCTAGAATCTGTGTGCCGAATCTCAACCTTCTAGCTTTTATAGTTCTGAAGATCTCGACGTTCATACGGACAGACGGACGTGCAC	-	-	intergenic	intergenic	-	NA	bp1_INE-1_Helitron=3; bp2_INE-1_Helitron=2	0
D197R15	61	novobreak	BND	2R	1600672	2R	1600805	5	0	somatic_tumour	28	0.1	2R:1600672-1600805	5to5	0.15	0	-	-	CCTTTTATTCAATGTTTTATGTGCATCTTTTGGCAATTTTTTGGCACACTAGCAGCTTTTCTACTTCTGACGTCAGGAGGAGCAATCTTGACCGACACCACTGCTGTTCGTAGAAGAGACTGGCACCAATCAGGAAATCAATGAGAACGATAAAACTCTCTGTCCAGCTACAAATGTCAATATTGAAGGGCGGCGGAATTTCAATTATATTGAAGGCATTAAC	-	-	intergenic	intergenic	-	NA	bp1_diver2_BEL=2	0
D197R15	62	Control-Freec	DUP	2R	2961921	2R	2968690	-	-	somatic_tumour	-	6.8	2R:2961921-2968690	Heterozygous duplication	0.44	0.75	-	-	-	-	-	Scp1, intron	intergenic	Scp1	NA	snp_su:0; snp_op:1	0
D197R15	63	novobreak	BND	2R	4271241	2R	4271346	3	0	somatic_tumour	29	0.1	2R:4271241-4271346	5to5	0.08	0	-	-	ATGAGCTGTGTTTTCCAGCGCACTTTACTCAAGTAGGGTCTTTGGTGCAGTAATTTTTTGTATGACCTTTGCATTTGTCCCATTGTCAGTTTGGTTTTCGTCTTCATCATCCTGTACTATTAACACAAGATCGGATAGAACAAGCATTAAATGTGCACTATGCAGTGAAAACCACACTGCAAAATATAAAGGTTGTATGGTGTACAAAGCACTGCCAATTCAAAAATAC	-	-	intergenic	intergenic	-	NA		0
D197R15	64	lumpy	BND	2R	5274310	2R	5275353	3	3	somatic_tumour	2106	1	2R:5274310-5275353	3to3	0.15	0.11	-	-	-	-	-	d4, intron	d4, intron	d4	NA	bp2_R1-2_R1=3	0
D197R15	65	novobreak	COMPLEX_BND	2R	5490535	2R	5492604	3	2	somatic_tumour	31	2.1	2R:5490535-5492604	3to3	0.16	0.09	-	-	AGTTTTTTGGGAAGTCGATAGACATTTTCAAAACTAACAAAATTATGAAAACATATCCAAAACTTTTTTCAAAAGCGAGGGCGTGGCAGTTTTAGGACGTTAGAGTAGGCGTGCCAAAATGTTTTTTTTGCAAATCAATATAAATTTAAAGACTAATAAAATTATGAAAAAAATATCCAAC	-	-	CG30440, intron	CG30440, intron	CG30440	NA	bp1_INE-1_Helitron=3; bp2_INE-1_Helitron=3	0
D197R15	65	novobreak	COMPLEX_BND	2R	5490778	2R	5492331	3	2	somatic_tumour	32	1.6	2R:5490778-5492331	3to3	0.15	0.08	-	-	GAAAGCTATTTTCGGCAAGCCGAAGTTTAAAATCCAGTAACTATAGTCGAGTTCCCCGGCAAACGCCAAATATGCTAAATCTTAACCTTTTAGCTTTAATAGTTCTGAAATCTCGAAGTTATATACCCTTTTACTCTACGAGTAACGGGTTAACAAGAAAAATTCGACTAACAGATAGCCGTTACTCGGCTTGTGTGACCGCGAATGCGAAAGTTCATAACTTTTCTGGGATATCGATAGATATTGTTCC	-	-	CG30440, intron	CG30440, intron	CG30440	NA	bp1_INE-1_Helitron=2; bp2_INE-1_Helitron=2	0
D197R15	66	lumpy	BND	2R	6193843	2R	6194872	1	2	somatic_tumour	2329	1	2R:6193843-6194872	5to5	0.07	-0.1	-	-	-	-	-	Ptr, intron	Ptr, intron	Ptr	NA		0
D197R15	67	novobreak	BND	2R	6243325	2R	6243889	3	0	somatic_tumour	33	0.6	2R:6243325-6243889	5to5	0.08	0	-	-	GTCGAATATAGCATTTTTGTTGTACCCGTTACTCGTAGAGTAAAAGGGTATACTAGATTCGTTAAAAAGTATGTAACAGACAAAACGTTTTCGACCATATAAAGTATATTATTTATTTATTATTATAAAGTATATATATTCTTGATCAAGATTATTAATTGAGTCGATTATGTCCGTTCGTATATCCATTTGAACTTCGGGATCTCTGTACCTATAAAGGATTCAGCATACAGATCCTAAAGACTTTCCACACGTATGCTTATTTCCAAACGTAGCCACACCCAATGTAACGTCGACACACTGCAAAC	-	-	Pld, intron	Pld, intron	Pld	NA	bp1_INE-1_Helitron=3; bp2_INE-1_Helitron=2	0
D197R15	72	novobreak	BND	2R	8915347	2R	8916970	2	1	somatic_tumour	37	1.6	2R:8915347-8916970	3to3	0.07	-0.16	-	-	CTGGAGTCGTTGCCGCGGCGACAGCCGGACAACATGGTCAGTCTGATCGGCTACAATGGCAAGCCGATGGTGTACGCCAATGGAACAATTACCCTGGCACATGCCGCGCAATCAGGGGACAGCGAAGAGGACGAGGAGAGCGAGGAGCACAGGTGGCTGTTGCTGTTGGCGTCCAGGTCCAGTATATCCGGCGGATGGGGCGGCTGGGG	-	-	lin, exon	lin, exon	lin	NA		0
D197R15	74	lumpy	BND	2R	9550136	2R	9550359	8	2	somatic_tumour	2601_1	0.2	2R:9550136-9550359	3to3	0.24	0	-	-	-	-	-	intergenic	intergenic	-	NA		0
D197R15	76	Control-Freec	DUP	2R	10598320	2R	10603155	-	-	somatic_tumour	-	4.8	2R:10598320-10603155	Heterozygous duplication	0.43	0.7	-	-	-	-	-	psq, intron	psq, intron	psq	NA	snp_su:9; snp_op:10; snp_ratio:0.9	12.19
D197R15	77	lumpy	BND	2R	10852474	2R	10853698	1	3	somatic_tumour	2726	1.2	2R:10852474-10853698	5to5	0.1	0.12	-	-	-	-	-	CG30015, intron	CR45136, exon_2	CG30015, CR45136	NA		0
D197R15	80	Control-Freec	DUP	2R	11630109	2R	11639779	-	-	somatic_tumour	-	9.7	2R:11630109-11639779	Heterozygous duplication	0.4	0.55	-	-	-	-	-	CG9005, intron	CG9005, intron	CG9005	NA	snp_su:24; snp_op:14; snp_ratio:1.71	11.65
D197R15	81	novobreak	BND	2R	12187449	2R	12189388	2	2	somatic_tumour	38	1.9	2R:12187449-12189388	5to5	0.1	-0.05	-	-	GCCATCTCGTACAGGGCAAAAGACATGGTCGAGGAGGAGGACTCAAAGCCGGCGGTGAAGAAGAGTACCGCCTGGGCGACCAGGATGTCGCCCTCGAACACAAATTGATCCTTGATACCCGATGCCTTCGCCAGCTGCGTGCTCCTACGGAACTCAATG	-	-	Cyp6g1, exon_3	Cyp6g2, exon_1	Cyp6g1, Cyp6g2	NA		0
D197R15	82	novobreak	INV	2R	12634231	2R	12635506	15	80	germline_private	39	1.3	2R:12634231-12635506	3to3	-	0	-	-	GGCGAGGGATTGCGCGTTAGTTCGCTGGATGACTGATGCGGTTTCGTTTTGTATTGCTAATGCCTTTCGAGTGGACGACCTGCGACAAGTAGTTAAACTTTTATGGCTGTATTTCTTTATGTAACTTATGCATTTAGTGGATCATTTGCGTCTGTCT	-	-	CG33671, 3UTR	CG33671, 5UTR	CG33672, CG33671	NA		0
D197R15	83	novobreak	BND	2R	12660274	2R	12660461	2	3	somatic_tumour	40	0.2	2R:12660274-12660461	5to5	0.14	0	-	-	GCCCATCCACGCCAGCTTGGGACTGGCCAACTTCTGGCTGGCCATTGCCACATCCGTCACGGGACTGATCGAGAAGGAGCGCGAAACCGTCAACGAGGCGGGCGCATTGGAACGCCGCACCGCGAAGGTGACGATGATGCCGATGAAGATCAGTGTTACGCCGATGGCACTGGTGATGTAGTGCTCCACCAGCTTATTCTCACTGCTGTAAAGATATTACGAACGAATTAACCACTGATATCAATGCTTAAAAGTAGTACTTAATAC	-	-	nemy, exon	nemy, exon_5	nemy	NA		0
D197R15	84	novobreak	BND	2R	12907895	2R	12908027	3	0	somatic_tumour	41	0.1	2R:12907895-12908027	3to3	0.09	0	-	-	CCATGCGACACTATATTTTTTTGCATGTTCAACAAGGTCAAATGCCCGGCCAGCCGAAGTGCTTGACAAACTTTCGATTGCACATCCGTGCAAATTGAATGCACAAAAAGTGGTGAAAGGAGCCGGCGGCAAGCGACGGGCCGGGATGGGTATCGGATGGGTTCAGTCAAT	-	-	intergenic	intergenic	-	NA		0
D197R15	85	lumpy	BND	2R	14463708	2R	14464434	3	1	somatic_tumour	3031	0.7	2R:14463708-14464434	5to5	0.08	0.14	-	-	-	-	-	Oaz, exon	Oaz, exon	Oaz	NA		0
D197R15	86	lumpy	BND	2R	15092784	2R	15093140	3	1	somatic_tumour	3097_1	0.4	2R:15092784-15093140	3to3	0.13	0	-	-	-	-	-	intergenic	intergenic	-	NA		0
D197R15	88	lumpy	BND	2R	15965634	2R	15966362	1	3	somatic_tumour	3164_1	0.7	2R:15965634-15966362	3to3	0.1	-0.19	-	-	-	-	-	Strn-Mlck, intron	Strn-Mlck, exon_2	Strn-Mlck	NA		0
D197R15	89	novobreak	DEL	2R	17553011	2R	17553847	2	1	somatic_tumour	43	0.8	2R:17553011-17553847	90:89_90	0.06	-0.13	-	-	GGTATCGCCTATCGCAACAAGCAGGATATTTCAAAGCATCTATTCTGGAAGCACGGAACGGAGAGTGCAGGATGCAAGCAATGCCTACAAAAGCGCTGGCGCCATGTCTACCACTTTTGCGTGCCGCCCGCAAAGCTGCACGTTGCCTGGTCTGATCACGATTATTGCAAGTTGTACCGCAC	-	-	MESR4, exon	MESR4, exon	MESR4	NA		0
D197R15	92	novobreak	BND	2R	18328041	2R	18328238	4	2	somatic_tumour	44	0.2	2R:18328041-18328238	3to3	0.24	0	-	-	CTCTAATGCCAAACAAAACCAGAGGCGAAATAACCGAAGGATTCCACTTAATGATACCCCAAGCTAATGAAACAGCTAATTTGATTTTGAACTGGTGATATGTGCTGATGATTTTGTCTGGCATGCTCTTCATTAAATGAATTCAAGGGGTACGTATGTATAGTATGTAAAGTTGCTGTGTCAAAAGGGTCGAAAGCAAACCGACGAAGCCACACCATCTGTGTATCTAGATGAATATAGAGAATTTTCCCTCCATCAGTCAAAAACATAAAACTTTCCAAACCGCAACACACACACACACACAAGTATAACTTGGTTGGGC	-	-	sbb, intron	sbb, intron	sbb	NA		0
D197R15	95	lumpy	BND	2R	20228882	2R	20229088	1	5	somatic_tumour	3534_1	0.2	2R:20228882-20229088	3to3	0.17	0	-	-	-	-	-	intergenic	intergenic	-	NA		0
D197R15	96	lumpy	BND	2R	20873278	2R	20875550	3	1	somatic_tumour	3595	2.3	2R:20873278-20875550	3to3	0.13	-0.21	-	-	-	-	-	Ipk1, intron	Ipk1, intron	Ipk1	NA		0
D197R15	98	lumpy	BND	2R	21560352	2R	21560442	3	1	somatic_tumour	3670_1	0.1	2R:21560352-21560442	3to3	0.15	0	-	-	-	-	-	twz, 3UTR	twz, 3UTR	twz	NA		0
D197R15	100	novobreak	BND	2R	23483159	2R	23484070	3	1	somatic_tumour	46	0.9	2R:23483159-23484070	5to5	0.07	0.07	-	-	CCTACTTACGCCCACTTCTGGCGGCAGGAAGCAGCAGGATGTGGGCGTTCCCGGCTGTGCGAATGTTTGCACTTCCGCTTATGCGCGACCATATCCGCTGTCCTGTTGGCCTGTTGCCGCCTGTCCGGCTTTGTTGCGGGTCATCGCCTTGGGAGCATTCTTCATCTACTGCACGGTAAGTAATGGATGGCGTTTTCCATTAGTCAATCGACTGCATACACAATAACTAAGCAATTCAGTTTCAATTGAGTGGCATAATCAATAGCAAACGCCTGCTTTCACTGCAATCCGAATTAATTAAGAGTCATCGAATGCATCTGAAACATTTTCCGGGGGGCTTACAAAC	-	-	CG43795, intron	CG43795, exon_8	CG43795	NA		0
D197R15	102	novobreak	BND	2R	23854825	2R	23855110	3	0	somatic_tumour	47	0.3	2R:23854825-23855110	5to5	0.06	0	-	-	TACAAGGAGTGGCAAAACCGAATGCACAACAGGACGCCGCCGCTATACCTTAAGGATGAGTATGAATTCATGCTGAATGGCCTGATGGAGCAACTCACCTCCATTCGTTCCGAGATCGTGAGTATTGGATCCAGGCAGCGCAGCAGGATGCCGAAGATCAGCATGCGACCGAGTTGACAGGAGACCGGGATGTCCATCAGGCGGCAGCCCAGCCAGGTCACATCCTCGGCGTCATCGAGCACATCTATTTTCTTGAGGAAC	-	-	bgcn, exon_3	bgcn, exon_3	bgcn	NA		0
D197R15	105	novobreak	INV	3L	1403970	3L	1408093	21	18	germline_private	48	4.1	3L:1403970-1408093	3to3	-	0	-	-	ACTACCTGATTTGGTGCCCTTCATTGTGGTATTTGTGGTCACTAATGCCACCTTTTTTTTTGTTACAACAATTAATTGGAAGATTTTAAGACTAGACTATTAAAATCTAAAAATCCAATCCAAGTCCAAGGCGAAGGTGATCGAGAAGGCCGGCGTCTTGGCCGCTGGGTGTGGCCATGTGTGGGTCTCTCTCTCTTTTCTTCTCCAAGTGCCTTCCTTGTGTGGGGGCATCAATCAAAGC	-	-	Ptp61F, intron	Ptp61F, intron	Ptp61F	NA		0
D197R15	106	novobreak	BND	3L	1736654	3L	1736845	3	2	somatic_tumour	49	0.2	3L:1736654-1736845	5to5	0.12	0	-	-	CTTCGTTCTAAACAGTTTCGCTTGCAGGTTTGTTGGTGATCCACCAGTTTGGCCTGAGTGTCCTGGGCATCTCCGACTATGTGATGAACGAGGTCCACAGGATAAGCACCAGATAGAACAGACGCCTCAGCTTCCTGACAAACTCGGAGTAGGTGAGCAGACTTTTCGCCACCATCCAACGGTTGACGTAAATGGACAGCAGAAACAGGCCAACGAATCCTGGCAAGGAGACTAGACCTTCACGATTTGCATTAAGGAAGCTGGAGCGCTCCACATC	-	-	CG18173, exon	CG18173, exon	CG18173	NA		0
D197R15	107	novobreak	BND	3L	3208457	3L	3208583	8	1	somatic_tumour	50	0.1	3L:3208457-3208583	5to5	0.2	0	-	-	CCTTCAGCTCAAGCAACCACTTCAAGCCTCCATTGCGAAACCCATCTCCTTGGCCGTGCGATCTCCGCGACCTGGATCTTTTGTCCGGGTTTCCGGCTGGGGATTAACCGACTCGAGCGCCACGTCGTGGTCCAATGTGGTGCGACTGTAGGCCGATGGCATCAGTATTTTCCTCACATATCGCGAATTACGCATATCACTCAGATAGGTCACCCCGCCACGAACCACAAAATCCGATGGATTGCCATCTTTAAGGCAGTGGGCTGCAGTCAAGACGCAGCGTGGAGTGACCAGGGAACCGCCGCACTCAAAGTTCCCACGTCGCCGGATATTAACCATG	-	-	CG32270, exon	CG32270, exon	gry, CG32269, CG32270	NA		0
D197R15	110	novobreak	BND	3L	3904259	3L	3904537	3	4	somatic_tumour	52	0.3	3L:3904259-3904537	3to3	0.16	0	-	-	TTGTCAAAATTGGTCAAGCAATTTGTTATGTTATATGTGGTTTATATTTGGGACCCATTAATCATATATGCAGACCCACAAACTAAGCCGCACACTTTTCACTTTCAGCTCTGCGAACTAGGAAACTTTTCGGTGCACATGCAGGGCGAGGTGAACTGCGGATGGTTCACGTGGTAGGACACATAGGCCGTGAATCCCCAGTAGTATGTGC	-	-	Sc2, exon_2	Sc2, exon_3	Sc2	NA		0
D197R15	111	novobreak	BND	3L	4155466	3L	4155647	3	1	somatic_tumour	53	0.2	3L:4155466-4155647	3to3	0.11	0	-	-	GCCTCATTGACGCACACCTCGTGCAAGGTCAGCGGCTTCTCCGGCCGCCTTTTGCAATCGAAACGGCCGTAGATGGCCGAGTACTTACGGATCTCGTCCATGCGCCGCGGATCCTGTTCCCCCTGGCACGGCAGATTGTCAAGGATGCCGGGTTCGGCCACTCGGCCAGCATTGCCCGGTACGGTGGTCTGCTCACCCAGCTGCCGTCGCAGGGAGCGGGATTGGGC	-	-	nab, exon_3	nab, exon_3	nab	NA		0
D197R15	112	lumpy	BND	3L	4190574	3L	4191076	1	3	somatic_tumour	4408	0.5	3L:4190574-4191076	5to5	0.1	0	-	-	-	-	-	tipE, 5UTR	tipE, exon_2	CG18675, tipE	NA		0
D197R15	114	novobreak	BND	3L	5593455	3L	5596622	3	0	somatic_tumour	54	3.2	3L:5593455-5596622	3to3	0.06	-0.08	-	-	CAATCAGCGTGTCCTCCTCGTCGGTCATTTTCCTAGCCAGTTCCACGGCTGCCGCGAATTCTTCGGTGTCCTCCAGAGCCTTCATCGCCTTGGTGGCGTGATGGGCCATATCAATGCGTCCACTCTCCACGAAGAGGAAGTATCCCTGCTCTTCGGTTTCCAGCACTTCAATGGCCTTCTGTGTCATCTCCTCCAAGGTGGGCTCATTGTTGTCCGGATCGGCCAGTTGCTCCAGATGATAGTGCATGTGGCTCTTGCTGAAC	-	-	CG10592, exon_2	CG5150, exon	CG10592, CG5150	NA		0
D197R15	115	novobreak	BND	3L	5665471	3L	5665679	5	2	somatic_tumour	55	0.2	3L:5665471-5665679	3to3	0.19	0	-	-	GCCGCCTTCAACGGCCACAGCATCCCTCTCTCTCTCTCTCTCTCTCAGCAAACACAAAAAACAAAAAGGAAAACGAGAGAGCGAGTCCTTTGCTTGCGCCAGTGTGTGAGTGCGTGCGTGTGTGTGTGTGATATATCCTGCTGGTATGTCCTGGCCTATATGGCGTATACGTATGTCGAGTGTATTATTTATGC	-	-	sif, exon_2	sif, exon_2	sif	NA		0
D197R15	121	novobreak	BND	3L	7568560	3L	7568797	3	2	somatic_tumour	56	0.2	3L:7568560-7568797	3to3	0.13	0	-	-	GCTTCTAGTGAAAACACACGGGTGGATTTGGGTTCGGATACCTCCAACTATTGTCCTCCATCCACTGAAGTATATCTGAAGGAGAATCAGAATCTGCGTTCAGTGGTGTGGGATGAGCCACGATTCGAGGGAAAACTTGGAATTTGGTAAAGGAAACTGGTTTTGGAGTTGCATCCAGGGCTTTGAATGCAGGAAATGAGAATGAACTACCAGTGGACAAAGTCGCAAATGGAGCCGGTCTGGGAAGTGATGA	-	-	frac, exon_6	frac, exon_6	frac	NA		0
D197R15	122	novobreak	BND	3L	8224734	3L	8225051	4	2	somatic_tumour	57	0.3	3L:8224734-8225051	3to3	0.16	0	-	-	ATTAAATAATGTACTAAAATGTACCAAAGCTCTTTTAAGTGCTGATACCACAAACAAACTTTCGACCCACATGTACCACTTCAAAATTGAGCTTAAACAAGTCAAACTATGGGTTCACAGGTCTAGAAATTTGGTTACTATATCCCAAAATGGACCTTTCAAAAATGACCATTAAATTTTCTGATTGAAATTGAATCACATTCGAATAAAGCACTTTACTTTTCTTAATCTACTAACCAGCAAAGTTTTTTTTTTCAGTGCTCCTGCTTACATTTCGTTGCGCTTGCCGTACAAAAGCAACCGCAAGAAGTTTCTTACGGGCTGT	-	-	intergenic	intergenic	-	NA		0
D197R15	124	novobreak	BND	3L	9104999	3L	9106706	1	2	somatic_tumour	58	1.7	3L:9104999-9106706	3to3	0.09	0.05	-	-	GTTTTGATGCCATCATCATAACAATAGATACAACAGAATCTTAAGTGAGTGTAGAAAAACAGAAATTACAAAATCAACATTTACGCAGAGCTTGTTTTGCTTGTACATTAGTTTATTAACTTATTATTTTATTTTCGGTTTTGCTTGCTGTAAATAGCAGAGAATGAATGTAAATAGTAGTAGTTGGCACAATCACTTTGCTTATATATATATATATA	-	-	bol, intron	bol, 3UTR	bol	NA	bp1_Rt1a_R1=14	0
D197R15	126	Control-Freec	DUP	3L	12028513	3L	12039150	-	-	somatic_tumour	-	10.6	3L:12028513-12039150	Heterozygous duplication	0.41	0.58	-	-	-	-	-	rols, intron	rols, intron	rols, CG43993	NA	snp_su:65; snp_op:46; snp_ratio:1.41	10.36
D197R15	127	lumpy	BND	3L	12804993	3L	12806057	1	0	somatic_tumour	5254	1.1	3L:12804993-12806057	5to5	0.03	0.4	-	-	-	-	-	Atg1, 5UTR	Sap130, intron	Atg1, Sap130	TRUE	low read support=1; snp_su:6; snp_op:0; snp_ratio:601.0	26.97
D197R15	128	lumpy	BND	3L	12897319	3L	12897910	1	2	somatic_tumour	5266	0.6	3L:12897319-12897910	5to5	0.08	0	-	-	-	-	-	intergenic	intergenic	-	NA		0
D197R15	129	novobreak	INV	3L	13065926	3L	13066069	21	0	germline_private	59	0.1	3L:13065926-13066069	3to3	-	0	-	-	ATCAGTTTCAGTTGGTTTCGGGCGCAATAAACCAAATCAAACCGTGGGATGGAGCCCTTTGGCTACCCACCGCCACCATGACGTATGCACATTGTCATCATAACTCTGGCCATTGTCTCTGATTTCGACTCCCAGATAGATACAGATACAGATACAACTCAATCAGTGGGCACTTTGGATGGGAGGAAGC	-	-	intergenic	intergenic	-	NA		0
D197R15	131	delly	COMPLEX_BND	3L	13378183	3L	13379055	4	1	somatic_tumour	INV00002588	0.9	3L:13378183-13379055	3to3	0.11	0.06	18	-	GTGAAAACAGATCCAAAGGCAGCTCTTGCCTTCAGGAAAACCAGGCGTTAACAAGAAATTTCTAGGGGGACAGGGTCGTCTTCTTGCCGTTGAGGATCATCTCGGTGAGTCCCAGTTGCCGGA	-	-	CG14111, intron	SNCF, exon	CG14111, SNCF	NA		0
D197R15	131	novobreak	COMPLEX_BND	3L	13378197	3L	13379055	4	1	somatic_tumour	60	0.9	3L:13378197-13379055	3to3	0.11	0.06	-	-	GCGTGGACGAGCTTAAGGAACTCAGCCGCGAGGTGCAGTTCCAGAAACGCCTCTGCCATCAAGTGGAGCGCCTGCAGCAATTCCGGCAACTGGGACTCACCGAGATGATCCTCAACGGCAAGAAGACGACCCTGTCCCCCTAGAAATTTCTTGTTAACGCCTGGTTTTCCTGAAGGCAAGAGCTGCCTTTGGATCTGTTTTCACTTCACTAAGTTACATTCACATTTCTAGCTGTTACCAAAAAATCC	-	-	CG14111, intron	SNCF, exon	CG14111, SNCF	NA		0
D197R15	135	lumpy	BND	3L	15645363	3L	15646112	2	3	somatic_tumour	5537_1	0.7	3L:15645363-15646112	3to3	0.13	-0.11	-	-	-	-	-	comm3, intron	comm3, intron	comm3	NA		0
D197R15	137	novobreak	BND	3L	17556560	3L	17556814	4	2	somatic_tumour	61	0.3	3L:17556560-17556814	5to5	0.14	0	-	-	GGCCAATTCGCCAAGCAGAAGATGCGGCATCAAGGGCGACGATGAGCTGCAGTACCGCCAGATGACCGCCTATCTGATACAGGAAATGGGTCAGCGTCTGCAGGAGCACGTTCTCGTTGAACACAAGCTCCTGGGCGAGTTCGGCGTAATTCTGCTCGGTGGTCGGCGGCAGGCACTTGTTGGCGGCCCGAATAACATGCTCCAGCTTCCGCGGTTGCTCTTCTACCTTGGCGGCCAAGAAGAGGCTCGCCGACGCCATGGAGTTGCGATGAAAGTGGGTGAAGGAGTGAAAGGCGTAGAACCGATGCATGTACACAATGGCCGTGTTGATGCACAGTTGGGACAC	-	-	CycT, exon_1	CycT, exon_1	CycT	NA		0
D197R15	138	Control-Freec	DUP	3L	18749163	3L	18769470	-	-	somatic_tumour	-	20.3	3L:18749163-18769470	Heterozygous duplication	0.38	0.51	-	-	-	-	-	Atg3, intron	ftz-f1, intron	Atg3, CR45938, ftz-f1	NA	snp_su:18; snp_op:11; snp_ratio:1.64	11.52
D197R15	139	novobreak	COMPLEX_BND	3L	18918580	3L	18921195	2	1	somatic_tumour	63	2.6	3L:18918580-18921195	5to5	0.06	0	-	-	GGTCTCGTAGTAGTTGCTTCCGGGCTCCAACTTGTGGCGAGTGTATCGGGTCACTTACTATGCCACCGGAGTGGATCGCATTACATTTGGAGCCGGCGGCTATTTCGCGGGTAAGAATGTGGACAAATTGTACACCCAAGCCACCCAGCTGGAGACCATCAACAATGAACTGGGCGGAGATGCGGAAAAGTACTTCGATAGTAGCAGCAATGTCTACCTGGCACGTGGTCACATGGGTGCCAAGGCTGACTTCGTATTTGCCCCGGAGCAGAGGGCCACCTTCCTGTTCATCAACGCTGCTCCTCAGTGGCAGACTTTCAATGCCGGAAAC	-	-	CG6839, exon	CG3819, exon	CG6839, CG3819	NA		0
D197R15	139	novobreak	COMPLEX_BND	3L	18918618	3L	18921161	2	1	somatic_tumour	64	2.5	3L:18918618-18921161	5to5	0.07	0	-	-	CAAGCTATACACGCAGGCTGTTCAGAAGGAGACCATCAACAATGAACTGGGCGGAGATGCGGAAAAGTACTTCGATAGTAGCAGCAATGTCTACCTGGCACGTGGTCACCTGGGTGCCAAGGCTGATTTCGACTACGCTCCCGAGCAGAGGGCAACCTTCCTGTTTATTAAC	-	-	CG6839, exon	CG3819, exon	CG6839, CG3819	NA		0
D197R15	139	novobreak	COMPLEX_BND	3L	18919055	3L	18920718	2	1	somatic_tumour	65	1.7	3L:18919055-18920718	5to5	0.07	0.07	-	-	GCCTTGATGTCTGTAGTCTTCCAGTTGATGTAGGTCACCTGATCGCTGACATCGTCACAGATGACATAGTCGCGCTTGATCTCCTCCAAACTCAAATGGGGATTGTTGACGCCGATCAGAACGATGCCCTTCTTGGTGGATGGTTCGATTACCACTCGGAAGTATAGCTTGGGAACTGGAATCAGACCGTTGC	-	-	CG6839, exon	CG3819, exon	CG6839, CG3819	NA		0
D197R15	141	Control-Freec	DUP	3L	19628166	3L	19638803	-	-	somatic_tumour	-	10.6	3L:19628166-19638803	Heterozygous duplication	0.4	0.59	-	-	-	-	-	wnd, exon_4	CG8786, 3UTR	wnd, CG8786	NA	snp_su:22; snp_op:16; snp_ratio:1.37	10.74
D197R15	142	novobreak	INV	3L	19697113	3L	19698302	2	36	germline_private	66	1.2	3L:19697113-19698302	3to3	-	0	-	-	GAGCTGGATTGATTTTTCTAACCAATCTGCTTTTTATCGGTGATTTTTCACGACCAAAGATGCATTTAATGCGGTACTTATCACATTTTGAATAATTACTTTAAAAAATGGGTGGTTAGCATAAAAGAATTTTACACCCAAATAACTATGCAATGTGCTGGAAATACTCGAATAAATTGCATTAACACGCCACCACCAGTCGATTCCTTCTAGATCGAACACGAATGAAAC	-	-	intergenic	intergenic	-	NA		0
D197R15	145	lumpy	BND	3L	21069061	3L	21069158	3	0	somatic_tumour	6035_1	0.1	3L:21069061-21069158	5to5	0.1	0	-	-	-	-	-	siz, exon_2	siz, exon_2	siz	NA		0
D197R15	147	novobreak	INV	3L	22937021	3L	22938259	4	74	germline_private	68	1.2	3L:22937021-22938259	5to5	-	0	-	-	GCTTCTAAAGTTCAGAATCTAAATACAACTGGAACTATATTAGTATGATAGTCCGCGGTGGCAGCGGAACAGGCTGCTTTTTCTCTAAGAAGCTTTCCCCAATTTAAAAGTACGAAAGAAGTACGAAGAAGTACGTCGACACATGCTGCCACCCAGTTCCTGTTCAACATGCTCGGCCTTCCTTCTGTTTTTGCC	-	-	intergenic	intergenic	-	NA		0
D197R15	148	novobreak	BND	3R	3752688	3R	3753111	3	1	somatic_tumour	69	0.4	3R:3752688-3753111	3to3	0.1	0	-	-	GTTAAGGGGGTGGACGCCACAAATTAACAGAAAGTTACTAGTTGCGCTTGATCCTCGTCCGAATCCATCACGTTCACCTAAATAAGCCATGTAGCTCGTTTGTCGCAAAGCTCTCACTCTGACATCTTTCGAGCGATTCCACTTAAAAATGCATGCAGTGGTTTATCGCTCGTTTTCGCGCAATATTATCGCTTCTCGAACAC	-	-	intergenic	intergenic	-	NA	bp1_Cr1a_CR1=2	0
D197R15	149	novobreak	BND	3R	5242854	3R	5244165	2	2	somatic_tumour	70	1.3	3R:5242854-5244165	5to5	0.07	-0.03	-	-	CCTGTCTATATGTCTTGGCTGTGAACTGGGGTTGGGTTGGCCCCAAGTGCCGGTATGTATGAGAGGTTAAGTGGGTGGAGGCTCAGGATTCCCCTCCCGCTCGCCGGGATTCAGAACGTGGACCAGCGTGATCGGGGGCTCACTCACCGCCTGGTCCGTTGTTGTTTCTGAAGATTCCGTGCTCTATTTGTACGGGTTTTGAGGATTTGAACGGATTGGGG	-	-	CG12163, intron	CG12163, exon_2	CG12163	NA		0
D197R15	150	delly	BND	3R	5779407	3R	5779962	2	1	somatic_tumour	INV00003094	0.6	3R:5779407-5779962	5to5	0.09	0	8	-	CGACCATTGGTCCGCCGCGCGTTGCCATTTCGTTGCCTTCGTTCGTGGGCCGCGTCGTTGCTCACCTCCTTCCTGGGCCTTTCGGCCGCCAGGGGCAACAAGGTGCGCGAAATGCAGAAGTATATGG	-	-	jagn, 5UTR	jagn, exon_2	CG2082, jagn	NA		0
D197R15	152	lumpy	BND	3R	7141666	3R	7142462	1	4	somatic_tumour	6667	0.8	3R:7141666-7142462	3to3	0.13	0.16	-	-	-	-	-	Fer1, exon	intergenic	Fer1	NA		0
D197R15	153	novobreak	INV	3R	8970939	3R	8972010	11	72	germline_private	71	1.1	3R:8970939-8972010	3to3	-	0	-	-	GGCCTACATACGAGGCACTCAGACACTCAAGGCATTCTTTACACACACATTCTCCGCTTCTTTCTTTTTTCTTTTTGATACCTCTTTTTTTTTTGCGTCGTTCGCTTGCCAAGTGGGTCACTTGCGATTTCATGACCGAGTTTTTGTTGTTGGCTCTTCTCTGCGCACATTTTTCGTTTC	-	-	intergenic	intergenic	-	NA		0
D197R15	154	lumpy	BND	3R	10395831	3R	10396591	1	3	somatic_tumour	6900	0.8	3R:10395831-10396591	5to5	0.09	0.02	-	-	-	-	-	cwo, intron	cwo, exon_2	cwo	NA		0
D197R15	155	novobreak	BND	3R	10432246	3R	10434075	3	1	somatic_tumour	72	1.8	3R:10432246-10434075	3to3	0.09	-0.1	-	-	TTAGGCTGCAAAAGTCGATTTTTGTTGGTTTAGGTCAGTTTAGTTAGCTGGCTTTGACAGCTCAAAGTCGAGGTCAACTTTTGTATGCCCATCATCAGCTGTCTCTGTGTGAGTGTGAGTGTGAGCGAGCGTGTGTGTGCGTGCGTTGAGCCAAAGTAGCAATTCATCATAGAAAATGGCGGAAGTAAGCTTCCCTTTGTGTGGGTGCCCTGTGTGTGAGTGTGTCTGTGAGTGCGGATGACACGCAC	-	-	intergenic	intergenic	-	NA		0
D197R15	156	novobreak	INV	3R	10533694	3R	10535200	11	13	germline_private	73	1.5	3R:10533694-10535200	3to3	-	0	-	-	AGTAATTTACAACATCCATTTTTTGTGCTTTTTTTTCTGCCAAGCCCCTCGTTTCCTCGTGCTGGTTTTTTTTTTTTTTTTTTTAACTTAAATGGAATATTAAATTGCCAGCGAAACTGCACCTGCCCAATTAAAATGTAACGTAATAGGGCCAAAAATAAAATCGGCAAAAATAACAAACAGTGGAAAAATATCTAT	-	-	hth, intron	hth, intron	hth	NA		0
D197R15	157	novobreak	BND	3R	11333110	3R	11333421	3	0	somatic_tumour	74	0.3	3R:11333110-11333421	3to3	0.07	0	-	-	GGTGCAATCCGACCGATACTGCAAGGCACTGCAACCGTTCGAAAAGCCGCCAGATTTTCATAGCGATCCTCTGGAGCGGCTGTCTCAGCTTTTCCGGCTGGACTTGTCGCACCGTTACGCGTTCCCGGCGACGGCGACGCAGACGAGTGGACGCCGTTGACTGGACTGTTTCAATCGAGGCTGGATCTTTGGGTTCAAGATGTCAGCAAAACGTTTTGGTTTAATGGAGCGTTTTAAATTTTGGTCTTTATGGGGGC	-	-	pros, exon_1	pros, exon_1	pros	NA		0
D197R15	158	lumpy	BND	3R	11449890	3R	11449986	3	0	somatic_tumour	6995_1	0.1	3R:11449890-11449986	3to3	0.17	0	-	-	-	-	-	CG17230, intron	CG17230, intron	sals, CG17230	NA		0
D197R15	159	novobreak	BND	3R	11782801	3R	11783222	2	1	somatic_tumour	75	0.4	3R:11782801-11783222	3to3	0.08	0	-	-	GTTAAAACAAATCTTCTAATATTAATTGTCTACTTACGCCACTGGCTGATTGCAAAAGAGCCTGGAGCCACTCGGAGGCTACATACTCGTCGGGCGCAGCCATTTGCAGGACTTCGCCCTTTAGCGTAATCTCGAAGCAGTGGGGGCGCTCTGCCTGCAGTTGGTCAGCTGACTCTAGAACATTTGGCTCCACTGCAGGCTTTTGTGCGTGCCAACAGCTGTGTTGGCGTAGCAGAACATTGGATGCTCTATGCAGTGGTTAATGTGCCAGCTGGAGGGTCAATG	-	-	CG17360, exon_7	CG17360, exon_6	CG17360	NA		0
D197R15	163	novobreak	BND	3R	15160080	3R	15160254	3	0	somatic_tumour	77	0.2	3R:15160080-15160254	5to5	0.09	0	-	-	ATGAAACTGTCAGCTGAAAGAGCTCTGGGCGACCTTGGCAACCATCGCCATTTGACTCCTTGACTTGTCGAACAAAAAACTTTTGTCGCCGCCTCCGCCAGTCAGGCCCACGAATTTCGCCTGGAAAAAAAAGGGCATTTGATAGCATTTCAAAAAGTTATCGCTCGGCATCGTTATGTGGCTGCGTGTGTTTGGCATGTTTAATCAGACAGAAACCATAAGCAAATAGGCAAATTGTTTGCAAATAAACAAGTCAAAAAAGTTTACGAGAACGGGGTTGAAATGACGACGTGCAAAAGGGGGAAAACTTTGACGGCTT	-	-	Gyc88E, intron	Gyc88E, intron	Gyc88E	NA		0
D197R15	164	novobreak	BND	3R	15426015	3R	15427459	2	2	somatic_tumour	78	1.4	3R:15426015-15427459	3to3	0.08	0.14	-	-	GTATATACTCATATATCGCGGGGCCAAGGGGCAGAAGACTGCGAACTGAAGACTGAAGACAGCTCTGGCTCATACAAAAGTTTCACTTTCTTCGCAACAAGTTTAATGCGTGTGGGTCTTGAGTGTGTGTGTGTGTACCATGTAACCGGGCAGAGGCAGCCATTCCTGCATTTCAGCGATCAC	-	-	CG6118, intron	CG6118, intron	CG6118	NA		0
D197R15	165	novobreak	TRA	3R	16113646	X	6129146	12	5	germline_private	79	9984.5	3R:16113646 X:6129146	5to3	-	0	-	-	GTTGAGTAGAGCAAACGAAGTTTTAAACTTTAGCTTTAAGTTATCATCAGGAATAAAGGTAACTTTTACCATGCTTAATGGCAAGTACTTAAGGCGGGATTTGCACTGTATTAAGGATAATATTGATGGGTGGGGTTGATTCAAAGCTGAAATCAAACGAAATGGCTTACATTAAATGGTGGGCTATTAAAAGCCAAGACTGTGTTAGGTTC	-	-	intergenic	Ca-alpha1T, intron	Ca-alpha1T	NA		0
D197R15	166	lumpy	BND	3R	16433166	3R	16433758	3	1	somatic_tumour	7425_1	0.6	3R:16433166-16433758	5to5	0.11	0.03	-	-	-	-	-	CG17565, exon_1	CG17565, exon_3	CG17565	NA		0
D197R15	166	delly	BND	3R	16433166	3R	16433758	3	1	somatic_tumour	INV00003562	0.6	3R:16433166-16433758	5to5	0.11	0.03	12	-	CTGGAAGTATTCATCGGCTCTTATCTTTTCCTGGGCGACATTCGGGGATTACTCACCTGCTCGCGGGATGTGCGTGGCGCCTACTGCGCAATCTCCTGCGCAAAGCTGCTAAATCTTCCCGAGCGAGTGATCAAGGAGCTATTTGCCGGCA	-	-	CG17565, exon_1	CG17565, exon_3	CG17565	NA		0
D197R15	167	delly	BND	3R	16703794	3R	16704163	2	2	somatic_tumour	INV00003573	0.4	3R:16703794-16704163	5to5	0.16	0	12	-	TCATTCTATTGATTTGTTCCCCATTTGTATTTGTTTGTTTACCTCTTAATGAGTGTTTTTCCACCCACGCGTTGCGGCATGCAATGCATTTTAATTCGAAATCCAGAGGATGTGCCCGCGGAACTCGA	-	-	Ubx, intron	Ubx, intron	Ubx	NA		0
D197R15	168	novobreak	BND	3R	17019938	3R	17020060	4	0	somatic_tumour	80	0.1	3R:17019938-17020060	5to5	0.17	0	-	-	GCCCTTCGAGAGCACTCAGATTGGCTCCTCGGCCATGCCGTACAAGAGGAACCCTATGCGCTCGGAGCGTTGTTGCGCCCTGGCCCGTCACCTCATCACCTTGTTCAGCAGAGTAAGCAGGGCGGCATCTGCAGCCAGGAAGGCCTCGGATAGGGTCAACCTCCTGTTGGCAGAGTCATCCAGAGTGCGTTCCAGCCACTGAGTGGCATGTGTATTAGCAGCAC	-	-	AdSL, exon	AdSL, exon	Pxd, AdSL	NA		0
D197R15	169	novobreak	BND	3R	17342540	3R	17342647	3	1	somatic_tumour	81	0.1	3R:17342540-17342647	3to3	0.14	0	-	-	TAATTACAAATTGCATTAATAATAAACAAATACAGACGCGGGTCTAAGCCTGATTTGCGAATTCGATTTACCTTTTGGCAATTTTTGCGTGACTAGCATAATTTGTTTCGGTGGCGTGACTGCCAGCATGTGAGCCCACAATGCATGTTCGCACACCCATTCCC	-	-	beat-IIa, intron	beat-IIa, intron	beat-IIa	NA		0
D197R15	170	lumpy	BND	3R	17408724	3R	17409853	1	2	somatic_tumour	7489	1.1	3R:17408724-17409853	5to5	0.06	0.14	-	-	-	-	-	CG17283, exon	CG5860, exon	CG17283, CG5860	NA		0
D197R15	171	lumpy	BND	3R	18941781	3R	18942643	1	4	somatic_tumour	7640_1	0.9	3R:18941781-18942643	5to5	0.12	-0.06	-	-	-	-	-	CG42613, intron	CG42613, intron	CG42613	NA		0
D197R15	172	novobreak	DEL	3R	19311916	3R	19322712	3	1	somatic_tumour	82	10.8	3R:19311916-19322712	5to3	0.12	-0.78	-	-	CTCCCACGCAGAGTATTGCGTATTTAAAAACCATTTTCTACTTACGTATGTGACAGTAATCGCCCTGCCATCCGGTCAAACAGATAATTTCGCCCGTCTCCGAGCAAGTCGAGTGTCCAAATGAATCGTCGCGGGGCCGGCAGAACCCCATTTGACACCAATTTTGGTTATAGTTTCTCACACTGTTTTAAAGTCCCTCCAAGTATGCGGTTAGTATTAGCAAGCTCTTAAA	-	-	Dl, exon_4	Dl, intron	Dl	NA	snp_su:21; snp_op:12; snp_ratio:1.75	13.16
D197R15	174	lumpy	BND	3R	20030169	3R	20032526	1	5	somatic_tumour	7740_1	2.4	3R:20030169-20032526	5to5	0.11	0.08	-	-	-	-	-	trem, exon_3	CG4936, exon_2	trem, CG4936	NA		0
D197R15	175	lumpy	BND	3R	20138588	3R	20139419	1	3	somatic_tumour	7751	0.8	3R:20138588-20139419	5to5	0.08	0	-	-	-	-	-	intergenic	CR42836, exon_3	CR42836	NA		0
D197R15	176	Control-Freec	DUP	3R	21311713	3R	21316548	-	-	somatic_tumour	-	4.8	3R:21311713-21316548	Heterozygous duplication	0.47	0.87	-	-	-	-	-	Hsromega, ncRNA	Hsromega, ncRNA	Hsromega	NA	snp_su:0; snp_op:0	0
D197R15	177	lumpy	BND	3R	21723955	3R	21724876	10	1	somatic_tumour	7888	0.9	3R:21723955-21724876	5to5	0.25	-0.49	-	-	-	-	-	intergenic	intergenic	-	NA	snp_su:0; snp_op:0	0
D197R15	178	lumpy	BND	3R	21917544	3R	21918395	2	1	somatic_tumour	7913	0.8	3R:21917544-21918395	5to5	0.24	-0.14	-	-	-	-	-	intergenic	intergenic	-	NA		0
D197R15	179	lumpy	BND	3R	21963974	3R	21964230	4	1	somatic_tumour	7921_1	0.3	3R:21963974-21964230	3to3	0.19	0	-	-	-	-	-	Eip93F, intron	Eip93F, intron	Eip93F	NA		0
D197R15	180	lumpy	BND	3R	22552067	3R	22552211	2	1	somatic_tumour	7968_1	0.1	3R:22552067-22552211	3to3	0.14	0	-	-	-	-	-	bond, intron	bond, intron	CR44062, bond	NA		0
D197R15	181	lumpy	BND	3R	23049700	3R	23049827	4	0	somatic_tumour	8022_1	0.1	3R:23049700-23049827	3to3	0.14	0	-	-	-	-	-	p53, 3UTR	p53, 3UTR	p53	NA		0
D197R15	182	lumpy	BND	3R	23546919	3R	23547214	2	1	somatic_tumour	8059_1	0.3	3R:23546919-23547214	3to3	0.09	0	-	-	-	-	-	intergenic	intergenic	-	NA		0
D197R15	183	novobreak	BND	3R	24323369	3R	24323499	4	0	somatic_tumour	83	0.1	3R:24323369-24323499	5to5	0.11	0	-	-	CCTCTGGATCTGCCCGCTCGCTCATCATCGCTGCTGTCATCACTACTCCGGGGTCGCCGTGAGAGTGGCTTACGCTTGGATCGTTTTGGTGGTTCCAGATTCGGGCCAGGAGTATCCGCCACCCGAGGAAGAGGAGGAAGATGTGTCCAGCAACTCGTCCGGCGACACGAGCTACTCGAATGTGGAAGAAAACCTAGAGGACAGCAGCGATGAGTCGGAAACGGACAGTTCCGATTACTCTGACTG	-	-	BRWD3, exon_9	BRWD3, exon_9	BRWD3	NA		0
D197R15	184	novobreak	TRA	3R	24557215	2L	7872822	598	0	germline_private	85	16684.4	3R:24557215 2L:7872822	3to5	-	0	-	-	AAGCAGAGAGGGCGCCAGTGCTCACTACTTTTTATAATTCTCAACTTCTTTTTCCAGACTCAGTTCGTATATATAGACCTATTTTCAATTTAACGTCGGGGCTTTGAGTGTGTGTAGACATCAAGCATCGGTGGTTCAGTGGTAGAATGCTCGCCTGCCACGCGGGCGGCC	-	-	snRNA:U6:96Ac, snRNA	intergenic	snRNA:U6:96Ac	NA		0
D197R15	185	novobreak	BND	3R	25766042	3R	25771670	2	2	somatic_tumour	87	5.6	3R:25766042-25771670	3to3	0.07	-0.16	-	-	CCATTGCCAATATTAAGCCCTATGCCATTTATATATACTCATCGCCTTTGGCAGACGAACAAAAGCAATCGAGTGGAGCGGCTTTTCTTGATATTCTTCGCTGAGACGCTGACTGCGACGTTGCTGCTCTGCCACGGATCTGATTTCTCTCTGCTCTTCCGCTGCTTTTTCTCTGCTCTTCCGCTGCTTTTCCCCTGCTTTTCCTTTTGC	-	-	intergenic	intergenic	-	NA		0
D197R15	186	novobreak	BND	3R	26017622	3R	26017758	4	0	somatic_tumour	88	0.1	3R:26017622-26017758	3to3	0.14	0	-	-	GAACACTGAACCACAGCCAGGCCGGGGTGAGAGGTGAGCCCGCTGGAGGAGGCGGGGGAGGAGTTAAGGCCTTTTTATGTGCGCGTATTTCCCAAATAAATTCCAACAGGAATCCACAAGCTCCAGTCTTCTGTGTGTGAGAGTGCACTCAAATTTCGTACGGTGCTTGGGTTATAGCCGCTCGTG	-	-	intergenic	intergenic	-	NA		0
D197R15	188	novobreak	BND	3R	27660144	3R	27660254	7	0	somatic_tumour	89	0.1	3R:27660144-27660254	3to3	0.18	0	-	-	GCATATATTTATGTACATCTATATCACTGGATATTGGTGGAAGATGTGTGAAGACTCCTTGGCCGACTGGGCACTCACCATTTTGTCTGTTTGATGCGAAAATCAACTGTATCTGTGTCTGAGTGCTCGGCGATCGGCTGGTTGGCTTTCACCTCAGAATTACCTTGCCGTACTGCCACTGACGAATAACGTTCAGTCGAGAC	-	-	Mlc1, 5UTR	intergenic	Mlc1	NA		0
D197R15	189	novobreak	BND	3R	27895835	3R	27896045	3	0	somatic_tumour	90	0.2	3R:27895835-27896045	5to5	0.08	0	-	-	GAGTAATATCAAATTACAATGACTACCCATGTGAATCATGTGCCAGTGTGCGTGTGTCGATGTCTGCATGTGAACTATTCAATTCGCTCATTTCATTAAGTTTCTTGTCGCACTCAGGCACTTGACGTTGACAACGTGCCGTATGCGCAATATGTGTGTGCGAGG	-	-	CG34353, intron	CG34353, intron	CG34353	NA		0
D197R15	190	novobreak	BND	3R	28082140	3R	28082378	4	0	somatic_tumour	91	0.2	3R:28082140-28082378	5to5	0.14	0	-	-	GTATTTTGTGGATATACATTTTTCGTATGCCGTTTTATTGTCGCCATGCTTTTTGCACTCACTGTACGCCCTGCACAAAAGAATGCGTGTAAATCCCAGCGAAAAACTAAACAAAGACATAAACACGCAAGGCAGGCATTATTTTTAAAAGTGCAAATTTAGTTTTAACCTCAAAGGAAGTAATTAGTGTAGCTTTGCATACAAATACGTGCATTCATGGCGTATACGGAACAACAATCAGGGCAACGACAACGACAATGTGGGGT	-	-	CG34362, intron	CG34362, intron	CG34362	NA		0
D197R15	191	novobreak	BND	3R	28456119	3R	28456316	8	0	somatic_tumour	92	0.2	3R:28456119-28456316	5to5	0.22	0	-	-	GCACTATTCTAGCTTCCTCCAGACGGAGTTTTGCATAATTAAATGCCCCGCGGGATCGTCGAGCTTTCGGTGCCCCAGGCCTCCGAAAAACAAATATGCTCAAAATAACAGGTCAAAAAAATGGGTGCCTTGTATGGATTTAACCCAAGCTTGGTAAATTAACATGTCTACGGCAGGCAAAATCG	-	-	beat-VI, intron	beat-VI, intron	beat-VI	NA		0
D197R15	194	novobreak	INV	3R	29651785	3R	29653036	10	54	germline_private	93	1.3	3R:29651785-29653036	5to5	-	0	-	-	GTGTAAGCTAAAAATCGTAGAGCTTGTAATGAGTTACACCTTAATATCATCTTGTCGGCCATAATTTTTCGCTGTGTTTTTGCCACCCTGACTTGGCCGCCTTTGTGTGTATTTAGGCTCTTGTTCAACTGTTTGCTTTAAGTATTGTCTTGAATTGCACTCCGTGTGCTGGTGTGCGTGCGGTG	-	-	Dop1R2, intron	Dop1R2, intron	Dop1R2	NA		0
D197R15	195	lumpy	BND	3R	29779478	3R	29779766	4	0	somatic_tumour	8568_1	0.3	3R:29779478-29779766	3to3	0.12	0	-	-	-	-	-	fig, exon	fig, exon	kay, fig	NA		0
D197R15	195	novobreak	BND	3R	29779478	3R	29779766	4	0	somatic_tumour	94	0.3	3R:29779478-29779766	3to3	0.12	0	-	-	ACAGTTCCCTGGCCTTTTCCACCACCCGGCTGGCGCCCACAAGTAGATCGTGCTCTCCACGCTCCTTTAGGCCATTCAATATACTGAGCAACATGCTCTCGGGCATGTTATCGAACAAGCCATCGGTGGCCAGGAGCACCAGGTCGCCGGGTAGTAGAGAGTGCCTCGTGGACACGGCCATTTCCGGTTTGTCGCAGTAGTAGCTCTCCTTCCGATCCTCCGGCGGCGGAAAACCCGATGACATCACCCTAATCCTGTCCAGCGTCGAGGTGCCAAATGC	-	-	fig, exon	fig, exon	kay, fig	NA		0
D197R15	203	Control-Freec	COMPLEX_DUP	4	58020	4	60921	-	-	somatic_tumour	-	2.9	4:58020-60921	203:203_204_206_207	0.49	1.07	-	-	-	-	-	CR43957, ncRNA	CR43957, exon_4	CR43957	NA	snp_su:0; snp_op:0	0
D197R15	203	lumpy	COMPLEX_BND	4	312867	4	313465	2	2	somatic_tumour	8791	0.6	4:312867-313465	206:203_204_206_207	0.07	0	-	-	-	-	-	Zip102B, exon	Zip102B, 5UTR	Zip102B	NA		0
D197R15	205	lumpy	BND	4	148890	4	149022	3	0	somatic_tumour	8782_1	0.1	4:148890-149022	3to3	0.17	0	-	-	-	-	-	intergenic	intergenic	-	NA		0
D197R15	209	novobreak	BND	4	417838	4	418140	2	1	somatic_tumour	97	0.3	4:417838-418140	3to3	0.09	0	-	-	GCTATCTGATTGCCGCGGAACTCAACAGCGTTCTTTCTAGTTGTTTTATACAATATATACATTTTCTGAAAGGTTATGTAAGCTTTTGCTGCAGAAGCCTCCTGTCTTATTTTCAATTAATACATTTCCAAAAACGTTTTAGCCATGTCCGTCTGTTCGTATGAGCGTCGAGATCTCATGAACTATAAAAGATAGAAGGTTGAGATTTAGCATGTTGCTATGCCCACTCT	-	-	intergenic	intergenic	-	NA	bp2_INE-1_Helitron=4	0
D197R15	210	novobreak	INV	4	627592	4	627737	9	0	germline_private	98	0.1	4:627592-627737	3to3	-	0	-	-	GCATCCCGGAAAGGCTTCAGGGTGTTTTCCGAAATTAATATTTCTAGGATATTTACATATATTTATTACAAAGCTTTCGTGAACGTCACTCAGTAATGTTTCTTAAATACGTTTAGAAATCGACCACACGGATGCGTTTTGAATTGGGAGGTTTACAAAGTGATTGTAAAAAACTTGTCTCAATGTGATTAACGTAAGTGCGATATTTTGTAGAGCAAAATGATGACCACTTCGTCAATCTTAATCTAATTTTCCACATCGCTATGACC	-	-	intergenic	intergenic	-	NA		0
D197R15	211	Control-Freec	DUP	4	959264	4	1198113	-	-	somatic_tumour	-	238.8	4:959264-1198113	212:211_212	0.34	0.41	-	-	-	-	-	CR45201, ncRNA	intergenic	CR45201, CR44030, fuss, sphinx, toy, PlexA, CR44031, CG11077, CG11076, ATPsynbeta, CaMKII, Zyx, apolpp, Actbeta, sv, Cals, Arf102F, CG11155, CG32017, Kif3C, pho, CG33521, PIP4K	NA	snp_su:176; snp_op:111; snp_ratio:1.59	11.85
D197R15	213	novobreak	BND	4	1272513	4	1272786	5	3	somatic_tumour	99	0.3	4:1272513-1272786	3to3	0.13	0	-	-	GTTTTTGGTTAGGAGCGTAGGCGGGCTATTAGTCTTCGATAATTCACGGCTGGTAATCGATATGCTAGTAATTTTCTCGCCAGCTTATTATCGATATGTCGCGCGTTTTTGGGAGAGGTTAATCGATAGGCGTAGTCAGTATTTCCTGATAGTGATAGGATTTGGTGGATAAATGTGTGCGGGCACAATAATGGCCGCCATCGTAAGC	-	-	intergenic	intergenic	-	NA	bp1_ninja-Dsim-like_BEL/PAO=6; bp2_TART-A_Jockey=6	0
D197R15	214	novobreak	BND	X	149992	X	151573	3	1	somatic_tumour	113	1.6	X:149992-151573	3to3	0.08	0.19	-	-	CTACAAAAAAAAATTTGTATAATATCGAGTAAGCATTTGATTAACATTCATTAGTTCAAAACATAATGTTAGGGACTTTAAGTAGGTCAAAATATTTAAACGATTTAAAAAGTAATCATACCCGTTACTCGTAGAGTAACAGGGTATACTAGATTCGTTTTAATG	-	-	tyn, intron	tyn, intron	tyn	NA		0
D197R15	217	lumpy	BND	X	1981653	X	1981826	1	2	somatic_tumour	9015	0.2	X:1981653-1981826	5to5	0.09	0	-	-	-	-	-	Hr4, intron	Hr4, intron	Hr4	NA		0
D197R15	218	lumpy	BND	X	2008974	X	2009152	3	3	somatic_tumour	9022_1	0.2	X:2008974-2009152	3to3	0.15	0	-	-	-	-	-	CG4406, exon_1	CG4406, exon_1	CG4406	NA		0
D197R15	220	novobreak	BND	X	2248058	X	2248189	3	1	somatic_tumour	115	0.1	X:2248058-2248189	3to3	0.12	0	-	-	CGATCTTTTGCCGCTTCTTGATGCGCCGCGGCATCTTGTCCATTACCTTTTGCATCTCCTGCGAATCGGAGGCGTCGCGTTCAAAGTCGCGCCATGCCTCTAGCAACAGAACACGCGACTCCTTGTCTCCCAGCTGACGCAGCATGTGAAAGTGTGGATGTCGTTTGCCAAGTTCGAGATGGGCCTCAGCCACGGCGACAGCGGGCCAGATGCGGAGCTGAACGTGCAGCTGGCAAGGAGAATCTATGAGCGAGCCAACGAGATGT	-	-	crn, exon	crn, exon	crn	NA		0
D197R15	222	Control-Freec	DUP	X	2674722	X	2679557	-	-	somatic_tumour	-	4.8	X:2674722-2679557	Heterozygous duplication	0.46	0.73	-	-	-	-	-	sgg, exon_12	intergenic	sgg, CR45197	NA	snp_su:0; snp_op:0	0
D197R15	225	novobreak	BND	X	2861532	X	2861697	7	0	somatic_tumour	116	0.2	X:2861532-2861697	3to3	0.32	0	-	-	CCAAAAAAAATGGAAAAGGAAAACAAGGAACACCCACTCCGCCCGGCCAGTCCAAAAAAAAAAAGAAATAAAAAAAG	-	-	kirre, intron	kirre, intron	kirre	NA		0
D197R15	226	novobreak	BND	X	3044909	X	3045114	5	0	somatic_tumour	117	0.2	X:3044909-3045114	5to5	0.12	0	-	-	TTTCGTAATATGAAAAGAAGTTGAAAGAAGTACATAATTACCTCAAGAGAACTAGAGGAACATTTTTGGGCTAATTATGCTGCCTAACAATTGTATTTTCCAGTGTAGGCCTAGACTGAACCGGGTCCAGGAGCAGGTTGGAAGTGCCCGCGTTTCCACACATTGGCCATTGGCCATTGGCTACCACTTGGGCAAAGACCAAAGACCAAAGACCAGGCCCCAAACGCACATTTTCCCATC	-	-	kirre, intron	kirre, intron	kirre	NA		0
D197R15	227	Control-Freec	DUP	X	3386434	X	3401906	-	-	somatic_tumour	-	15.5	X:3386434-3401906	Heterozygous duplication	0.38	0.52	-	-	-	-	-	CR44999, ncRNA	CG12535, intron	Myc, CR44999, CG12535	NA	snp_su:0; snp_op:0	0
D197R15	228	lumpy	BND	X	3567478	X	3567532	6	0	somatic_tumour	9107_1	0.1	X:3567478-3567532	5to5	0.2	0	-	-	-	-	-	ppk8, intron	ppk8, intron	DIP-alpha, ppk8	NA		0
D197R15	229	lumpy	BND	X	3716906	X	3718104	1	2	somatic_tumour	9119_1	1.2	X:3716906-3718104	5to5	0.07	0.02	-	-	-	-	-	Rala, intron	Rala, intron	Rala	NA		0
D197R15	231	novobreak	BND	X	4529319	X	4530699	2	2	somatic_tumour	120	1.4	X:4529319-4530699	3to3	0.12	-0.25	-	-	GTTGTTATTGTATTATTATGTAAGCTTTTTGGAGTGTGTTGTGCTGTTGTTGTTGTCGCAATGAACTCTTTATTGTCAAAGGCAATTGAACGTTCGCAGCTGCCGCACACCACGCCCAAAAGGAAATGTTCGAACTTTGAAGTGAGCTAATTTCGTGCAGCTCCGGATGAGTCACTTTCAAAGGAGCCAAAGGATATTACAGCTCAGCTACAGGAAG	-	-	CR32773, ncRNA	CG3556, intron	CR32773, CG3556	NA		0
D197R15	233	lumpy	BND	X	4978698	X	4979222	2	2	somatic_tumour	9244	0.5	X:4978698-4979222	3to3	0.09	0	-	-	-	-	-	CR44833, ncRNA	CR44833, ncRNA	CR44833	NA		0
D197R15	235	novobreak	BND	X	5753053	X	5754490	2	1	somatic_tumour	122	1.4	X:5753053-5754490	3to3	0.08	-0.15	-	-	GCCAGGTGGCATCCAACACCGGAACTCCAGCCCCATCCGCCGGCGGCATTCACCAGCAGCATCAGCAGCAGCAACACCAGCAGCACCAGCAGCAGCAACACCAGCAGCAGCAGCACCAGCAACACCAGCAATCTGACCGATGATGATATGGTTAAGATTAATGGTAAG	-	-	CG15772, exon	lin-52, exon_3	CG15772, lin-52	NA		0
D197R15	239	lumpy	BND	X	7107165	X	7107253	3	0	somatic_tumour	9463_1	0.1	X:7107165-7107253	3to3	0.13	0	-	-	-	-	-	fz4, 3UTR	fz4, 3UTR	fz4	NA		0
D197R15	240	lumpy	BND	X	7517397	X	7518052	1	2	somatic_tumour	9495	0.7	X:7517397-7518052	3to3	0.11	-0.08	-	-	-	-	-	CG32719, intron	CG32719, intron	CG32719	NA		0
D197R15	242	lumpy	BND	X	7829534	X	7829672	2	1	somatic_tumour	9514_1	0.1	X:7829534-7829672	3to3	0.14	0	-	-	-	-	-	CG1402, intron	CG1402, intron	CG1402	NA		0
D197R15	245	novobreak	INV	X	8421252	X	8422590	23	43	germline_private	125	1.3	X:8421252-8422590	5to5	-	0	-	-	CAGTCCTTTTTATTAGGATCGCCTAAGTGCGCTGACCTTAACATAGATTTTCGCATGCCTGCTAAGAGTATGCACGAAGAAAGAGCGGTAATTGGCAGATGAAGAGAGAGAGAGAGAGAGAGCGGAGAGAGCGAAGAGCGCGCGAAATGTCAAACAAAGCAAAACAAACTGTCAAATGTCGACGTCATGTGAG	-	-	Trf2, intron	Trf2, intron	Trf2	NA		0
D197R15	246	novobreak	BND	X	8959998	X	8960895	2	4	somatic_tumour	126	0.9	X:8959998-8960895	5to5	0.13	0.05	-	-	ACAATGTGCAGCAGTGGGTGGCTTCCACTCCGACCACACCACACATGTAATTGTTGCTGAAAGCATATTTAATTGAAACTTATTTCGTGTGGCCAACACTTTTCGAACGCAACATAAGTTCACTAAGTACAGTTTGGCTAATAAAAATTAAAACCGATTGCAACATTATTGATTTTTAACGCATTTTAAGCCAAAACCTAATTGGCAATACAGTTTGTTAACCAAAAAATTAAGCTATAAGCAGAGAATGAGAACACGAACCAATAAATTAATCAAAAAAGTTCCGTGGTCAGCGGTGGCCAAAAGGCGTAAACCGAAACGCAAACACGAAACATTCGACCAAACAATTTTCGACCACGATTACATGGCGATCGTTGTTAAAACGGTAGCCAATCGATTGTCAAAGTGGGTAATTAATTTCAACGCCTTGTAATAATATAAATACGCTGACGTGCACCAATAATTAATGATGGGCACCGTCAGAAGCCACACG	-	-	rdgA, intron	rdgA, intron	rdgA	NA		0
D197R15	249	lumpy	BND	X	9859111	X	9859244	2	1	somatic_tumour	9720	0.1	X:9859111-9859244	3to3	0.15	0	-	-	-	-	-	intergenic	intergenic	-	NA		0
D197R15	250	Control-Freec	DUP	X	10923232	X	10926133	-	-	somatic_tumour	-	2.9	X:10923232-10926133	Heterozygous triplication	0.42	3.15	-	-	-	-	-	CG43901, 3UTR	intergenic	CG43901, v	NA	snp_su:12; snp_op:0; snp_ratio:1201.0; somatic_snvs:10	94.9
D197R15	251	Control-Freec	DUP	X	11398996	X	11410600	-	-	somatic_tumour	-	11.6	X:11398996-11410600	Heterozygous duplication	0.47	0.83	-	-	-	-	-	dlg1, intron	CG15196, exon	dlg1, CG15196	NA	snp_su:14; snp_op:9; snp_ratio:1.55	10.25
D197R15	257	lumpy	BND	X	12358674	X	12359176	1	4	somatic_tumour	9886_1	0.5	X:12358674-12359176	3to3	0.18	0	-	-	-	-	-	intergenic	intergenic	-	NA		0
D197R15	258	lumpy	BND	X	12462242	X	12464652	3	2	somatic_tumour	9899_1	2.4	X:12462242-12464652	3to3	0.16	0.04	-	-	-	-	-	Rab40, intron	CG42258, intron	Rab40, CG42258	NA		0
D197R15	260	lumpy	BND	X	12784003	X	12784203	2	1	somatic_tumour	9933	0.2	X:12784003-12784203	3to3	0.1	0	-	-	-	-	-	CG32647, intron	CG32647, intron	CG32647	NA		0
D197R15	262	delly	BND	X	13289080	X	13289347	2	1	somatic_tumour	INV00004970	0.3	X:13289080-13289347	5to5	0.07	0	11	-	TCCCACGCGCAGTTTCTTTAGCGGCATACCACCAAAGTCTTCGGCGATGTGAATCTAGAGACTCGCCATTCCACGGACTCGGGCA	-	-	CG15744, exon	CG15744, exon	CG15744	NA		0
D197R15	263	lumpy	BND	X	13743901	X	13744074	2	3	somatic_tumour	10010_1	0.2	X:13743901-13744074	3to3	0.22	0	-	-	-	-	-	Grip91, intron	Grip91, intron	Grip91	NA		0
D197R15	265	lumpy	BND	X	14322970	X	14324678	4	0	somatic_tumour	10062_1	1.7	X:14322970-14324678	3to3	0.12	-0.06	-	-	-	-	-	dpr8, intron	dpr8, intron	dpr8	NA		0
D197R15	266	novobreak	INV	X	14757967	X	14759104	18	57	germline_private	128	1.1	X:14757967-14759104	3to3	-	0	-	-	GGTCCTGGCCAGCGAGGCCAAGGGTCAGATGAACGGGATCATCGCCAATGTGATACACGAGTCCTTGGAGCACGCAGATCCTATATCGACACCACCCACAAACACCGCACAACAAATCGAACGGGGCATCGAGAACCATGGGTTCGTTCAGGAGGAGAAGGTCAAGGATCGGGATTGTTAGGCTAGATGAGAAGGGAATCAAAGTATTATCCCATCCTCATGTACATACTCACATTCCGCTGAGGAAATTGGAGATCGAGAATACGCCGTAGAATCCAATTTGCCTGTAAGTGAGATGATATTACAGATTTTACAAAAAAAATATACTATATATAAACCATATCTTATAATTTAACAATCATTTTCGGCAGTACACAAATAAAAACTCACTTGAGCAGCACTCCACTGAAGGCCATTCCGATCGGCACGCCCACCGAGAAGCAGACATTGAGAATGCCGATCCTCAGCGTGCGATCCTCCTCCGTGGTGATGTCCGCAATGTAGCTGAAGACGCCCATCAGCATGGTGAACCAGCCGCCGCTGAGAGAGGGGAAGATGGCTTCCGTGAGGGCGGCTGCCTCCATGGGCGCC	-	-	CG15890, 3UTR	CG15890, exon_4	CG15890	NA		0
D197R15	268	lumpy	BND	X	15095366	X	15095475	2	2	somatic_tumour	10124_1	0.1	X:15095366-15095475	3to3	0.19	0	-	-	-	-	-	Rab3-GEF, intron	CG9072, 3UTR	Rab3-GEF, CG9072	NA		0
D197R15	269	novobreak	BND	X	15437201	X	15437354	4	5	somatic_tumour	131	0.2	X:15437201-15437354	3to3	0.29	0	-	-	AGTCACATTCGAAATGTGTTCACAAAATAAACACTGAAGCAGAAGCGGCAAAAGTAAGACACACACACACACACTACCTACACACGCAAACATGTGAAGGCAGGGAGAGCGTCCTTTACACAGATACATTCGCACTTACTAGCAAAGATGTCGTCTGCTTGCCATTGTCCTTCTTCATAGTCGGCATCTTTGGCATTTTTCTTCTGCTGTTTTCTCGCTCTCACCGTGTCGCTTTCTCCGCGCTTTCTCTCCCTGCCTTCACATGTTTGCGTGTGTAGGTAGTGTGTGTGTGTGTGTGACAGCAATAATAATAAAACCCTAGAAGACCATGTGTGCGCGTCTCTTGGTCTCTCTTTATGCGAAATGCCAAAAGG	-	-	Cngl, intron	Cngl, intron	Cngl	NA		0
D197R15	270	lumpy	BND	X	15552822	X	15553632	2	3	somatic_tumour	10171_1	0.8	X:15552822-15553632	3to3	0.17	-0.17	-	-	-	-	-	Ac13E, intron	Ac13E, intron	Ac13E	NA		0
D197R15	273	delly	BND	X	16482295	X	16482707	2	2	somatic_tumour	INV00005131	0.4	X:16482295-16482707	3to3	0.12	0	12	-	AACAGAAAAATCAGATCAAATCGGTAAAGGTCTACGCTAAAACTATGCTATACTGTTTAGTTTCTGGGATCGAACTGAAAACTTTTCAATTAATTGAAAATAAATATTTTGAAACAG	-	-	para, intron	para, exon_23	para	NA		0
D197R15	277	lumpy	BND	X	17171666	X	17173314	2	3	somatic_tumour	10302_1	1.6	X:17171666-17173314	3to3	0.16	0.01	-	-	-	-	-	baz, intron	baz, intron	baz	NA		0
D197R15	278	Control-Freec	DUP	X	17280290	X	17299630	-	-	somatic_tumour	-	19.3	X:17280290-17299630	Heterozygous duplication	0.38	0.49	-	-	-	-	-	f, exon	Fim, intron	f, CG8664, CG8661, CG5445, Fim	NA	snp_su:46; snp_op:31; snp_ratio:1.48	11.95
D197R15	280	lumpy	BND	X	17349649	X	17349814	2	1	somatic_tumour	10325_1	0.2	X:17349649-17349814	5to5	0.12	0	-	-	-	-	-	intergenic	intergenic	-	NA		0
D197R15	281	novobreak	BND	X	17529362	X	17531178	3	3	somatic_tumour	132	1.8	X:17529362-17531178	5to5	0.15	0.78	-	-	TGCCTTAGACTCTCTCGCGTTATGATTGTGTCGGGATTTAGATGATGTTATTGTGAATTAGGCCTGGAATTGAGTGCGTGTAATGGCCTTTCAATTGATTAAATCCGCTTTGGATGGACCACCGCAGCAGCAGCAGCAGCAACAACGCAGCAGCATCAGCAGCAGCAGCAGCAGCAACATCAACAAACAAAAGTCAACAACAAGCGCGCACAATGAACGGGGAAATAAGCGACAACAAAAGTGCAATCATAATTCTCTCCGTTTTATTCGTCTTCAGATTTTTATGATGAATAATTGAATGGAATCTAGGAATAAGTTTGAAGGAGGGAGCACTATTTATTGCCATTTTCGCCATGCAAC	-	-	CG43658, intron	CG43658, exon_1	CG43658	NA	snp_su:0; snp_op:0	0
D197R15	282	lumpy	BND	X	17878490	X	17879341	2	1	somatic_tumour	10367_1	0.9	X:17878490-17879341	5to5	0.07	-0.26	-	-	-	-	-	mnb, 5UTR	mnb, intron	mnb	NA	snp_su:1; snp_op:0	12.52
D197R15	284	lumpy	BND	X	18677014	X	18677833	1	3	somatic_tumour	10209_1	0.8	X:18677014-18677833	5to5	0.15	0.01	-	-	-	-	-	intergenic	intergenic	-	NA		0
D197R15	285	lumpy	BND	X	19150554	X	19150669	3	0	somatic_tumour	10453_1	0.1	X:19150554-19150669	5to5	0.11	0	-	-	-	-	-	RhoGAP18B, intron	RhoGAP18B, intron	RhoGAP18B	NA		0
D197R15	286	lumpy	BND	X	19494272	X	19494759	2	1	somatic_tumour	10485	0.5	X:19494272-19494759	5to5	0.04	0	-	-	-	-	-	CG12204, exon	ksh, exon_2	CG12204, ksh	NA		0
D197R15	289	lumpy	BND	X	20287396	X	20287523	3	0	somatic_tumour	10559	0.1	X:20287396-20287523	3to3	0.14	0	-	-	-	-	-	intergenic	intergenic	-	NA		0
D197R15	292	novobreak	BND	X	22995038	X	22995394	4	1	somatic_tumour	134	0.4	X:22995038-22995394	5to5	0.15	0	-	-	ACGCCCAACAACAGTTATCGGATCAAAATCAGGGGGCTGCCGGCGGCGACGAGGAGTGGGCCAAATTTAAGGCACTAACATCAGGCGTCGATAGCATTCTACATAAAACCCAGGACGAGCTCGATCGGCACCAACAATAACCTTCTCCGCGTATGCGGTGTCAAAGGGATCGGGTCCGTCTTCGGCAAGGACGGGGGAATCTGGTACAACGGCTAGTTGGAGCTCGCCACTGGTGATAGCCTCAATGTAGTCGGTGGCAAAG	-	-	stnA, exon_2	stnA, exon_2	stnB, stnA	NA		0
HUM-1	18	lumpy	TRA	2L	16310775	4	1148246	3	0	somatic_tumour	4584_1	15162.5	2L:16310775 4:1148246	5to5	0.1	0	CGGTCAC	-	-	AATTTTTTATACTTTAATTAGTCTTGTAAATTTCTATCGATTTGCAAAAAAACCGGTCACATTGCAAATGAGGCTAATAAATAATCAGCTATCCATTATAAATCAAATATAATTTCATTTAAAGA	Alt-EJ	intergenic	Kif3C, intron	CG32017, Kif3C	NA	bp2_copia_Copia=2; mh:7; ins:0; tup:0; tdown:0	0
HUM-1	31	Control-Freec	DUP	2R	13941000	2R	13946000	-	-	somatic_tumour	-	5	2R:13941000-13946000	Heterozygous duplication	0.38	0.44	-	-	-	-	-	shot, intron	AGO1, 3UTR	shot, DJ-1alpha, AGO1	NA	snp_su:12; snp_op:12; snp_ratio:1.0	10.07
HUM-1	48	delly	DEL	3L	9892365	3L	9894889	4	2	somatic_tumour	DEL00000106	2.5	3L:9892365-9894889	5to3	0.35	-0.76	TA	-	CTCTTAAATTACTTGCAATTGCTACTATATTTCAAAAGTAAACCGTTCCTTTTAATCATATATATATATGCAATTTCGCAGTTTAGCAGTTGCTGTCTAAATTAATTTTCTTTATAT	ACAATTTACTCTTAAATTACTTGCAATTGCTACTATATTTCAAAAGTAAACCGTTCCTTTTAATCATATATATATATGCAATTTCGCAGTTTAGCAGTTGCTGTCTAAATTAATTTTCTTTATAT	Alt-EJ	CalpB, 3UTR	CG6707, 3UTR	CalpB, CG14164, CG6709, CG6707	NA	mh:2; ins:0; tup:0; tdown:0; snp_su:5; snp_op:0; snp_ratio:501.0	26.66
HUM-1	48	novobreak	DEL	3L	9892365	3L	9894889	4	2	somatic_tumour	43	2.5	3L:9892365-9894889	5to3	0.35	-0.76	TA	-	GTGTGCCATCAAGGTTAGAACATTCATCGAGATGTTCCGCGAACGGGACACGGACAATTCAGACACGGCCTTCTTCAACTTGGACGACTGGCTGGAGCGAACAATTTACTCTTAAATTACTTGCAATTGCTACTATATTTCAAAAGTAAACCGTTCCTTTTAATCATATATATATATGCAATTTCGCAGTTTAGCAGTTGCTGTCTAAATTAATTTTCTTTATATCTGCATGAGCGTTTGCTTGTTCTCTGTTGTTCAAGAAATGTTGCTTTGTTTATTTGC	ACAATTTACTCTTAAATTACTTGCAATTGCTACTATATTTCAAAAGTAAACCGTTCCTTTTAATCATATATATATATGCAATTTCGCAGTTTAGCAGTTGCTGTCTAAATTAATTTTCTTTATAT	Alt-EJ	CalpB, 3UTR	CG6707, 3UTR	CalpB, CG14164, CG6709, CG6707	NA	mh:2; ins:0; tup:0; tdown:0; snp_su:5; snp_op:0; snp_ratio:501.0	26.66
HUM-1	52	Control-Freec	DUP	3L	15393000	3L	15396000	-	-	somatic_tumour	-	3	3L:15393000-15396000	Heterozygous duplication	0.43	0.56	-	-	-	-	-	intergenic	intergenic	-	NA	snp_su:0; snp_op:0	0
HUM-1	74	CNV-Seq	DEL	X	2793253	X	3266169	-	-	somatic_tumour	-	472	X:2793253-3266169	74:74_75	0.9	-1.64	-	-	-	-	-	w, intron	dnc, intron	kirre, w, CG12498, CG14416, CG14417, CG14418, CG14419, CG3526, CG3588, CG14424, CG32793, CG3592, CG3598, CG14420, CG14421, CG14422, CG14423, CG17959, CG3603, rst, CG4116, N, CG18508, Fcp3C, CG3939, CG14265, ng2, ng3, ng1, ng4, Pig1, Sgs4, dnc	NA	snp_su:2; snp_op:0	17.62
HUM-1	74	Control-Freec	DEL	X	2794000	X	3266000	-	-	somatic_tumour	-	472	X:2794000-3266000	75:74_75	0.9	-1.64	-	-	-	-	-	w, intron	dnc, intron	kirre, w, CG12498, CG14416, CG14417, CG14418, CG14419, CG3526, CG3588, CG14424, CG32793, CG3592, CG3598, CG14420, CG14421, CG14422, CG14423, CG17959, CG3603, rst, CG4116, N, CG18508, Fcp3C, CG3939, CG14265, ng2, ng3, ng1, ng4, Pig1, Sgs4, dnc	NA	snp_su:2; snp_op:0	17.62
HUM-1	76	lumpy	DEL	X	4586393	X	4588701	3	1	somatic_tumour	3948	2.3	X:4586393-4588701	5to3	0.56	-1.19	-	-	-	CGGGGGAAAAGCAGCTAATGTAAATGAGCAGCTGAAAGTCAAAGGATACGTAGGAAGCATTTGGATGGTTGGATGGCTGGGCGTGATAGTTCGGAAGACTGTATCTATTGTCAGGGTATTGATTGCCTAACCGCCGC	NHEJ	CR32773, ncRNA	CR32773, ncRNA	CR32773	NA	mh:0; ins:0; tup:0; tdown:0; snp_su:0; snp_op:0	0
HUM-4	24	CNV-Seq	COMPLEX_DEL	X	3169736	X	3199425	-	-	somatic_tumour	-	30	X:3169736-3199425	24:24_25_26	0.95	-3.05	-	-	-	-	-	N, exon_7	dnc, intron	N, CG18508, Fcp3C, CG3939, dnc	NA	snp_su:0; snp_op:0	0
HUM-4	24	CNV-Seq	COMPLEX_DUP	X	3199425	X	3215747	-	-	somatic_tumour	-	30	X:3199425-3215747	25:24_25_26	0.89	0.81	-	-	-	-	-	dnc, intron	dnc, intron	dnc	NA	snp_su:0; snp_op:0	0
HUM-4	24	lumpy	COMPLEX_BND	X	3199427	X	3200763	6	1	somatic_tumour	5219_1	1.3	X:3199427-3200763	26:24_25_26	0.54	0.24	-	GTATACATGCAATATGATATGATAACACA	-	CGCCTTATATTTATGTTTCATTTACATTTTTCCAATAAATTTCGACGAACAGCAAACTTGGGTAGTGTGTTATCATATCATATTGCATGTATACCCACACTTTTATCATAGACTCAAGAACATTTTATTTCGCCAAGTGTT	FoSTeS	dnc, intron	dnc, intron	dnc	NA	mh:0; ins:29; tup:8; tdown:5	0
HUM-7	35	novobreak	TRA	3L	9960263	2R	13424638	3	0	somatic_tumour	44	3464.4	3L:9960263 2R:13424638	3to5	0.12	0	ATT	-	AACGATTTTGATATATTCAGTAAGTTAATTTGATTGATAATAGCTCAGCTAACACTGATTGACAAACGATTCATTCATTTATAAAAACAATTTACAAGACTAGTTCTAACAGTCGCTGATTAAGAA	AACGATTTTGATATATTCAGTAAGTTAATTTGATTGATAATAGCTCAGCTAACACTGATTGACAAACGATTCATTCATTTATAAAAACAATTTACAAGACTAGTTCTAACAGTCGCTGATTAAGAA	Alt-EJ	CG34356, intron	CG42321, 5UTR	CG34356, CG42321	NA	mh:3; ins:0; tup:0; tdown:0	0
HUM-7	54	novobreak	TRA	3R	27111074	2L	11937060	4	0	somatic_tumour	87	15174	3R:27111074 2L:11937060	3to3	0.15	0	-	-	CCCAGTCTAAAAATCAGATTCTGTAGGACTACTTCACTTCATTCAATCTACATATGTTATTTCGTTAAAAAAAAGGTAAAAGTGCAAAAAAAAATAACTAATATGATAATTGTTTACAAGGAAGTATTTAATATCATATGTAAATTAAGGAAAATGGGTTCCTTCTGGCGATAA	-	NHEJ	gb, intron	Or33b, intron	gb, Or33b	NA	mh:0; ins:0; tup:0; tdown:0	0
HUM-7	60	delly	COMPLEX_BND	X	3129531	X	3364620	3	1	somatic_tumour	INV00002662	235.1	X:3129531-3364620	60:60_61_62_63_64	0.28	-2.84	C	-	GCGGCAGCATCGTCAGCGAATGATGAAAGCAAACCGAAGGGCGGCGACAATGGTGGTCAGCACTTTGCGAATGTTGCGAATGTGGAGGGCAAAAGAAAGAATGCCAAATAAATTAAAATATTACA	GCTCCTCATCGGCGGCAGCATCGTCAGCGAATGATGAAAGCAAACCGAAGGGCGGCGACAATGGTGGTCAGCACTTTGCGAATGTTGCGAATGAGGAGGGCAAAAGAAAGAATGCCAAATAAATTAAAATATTACA	Alt-EJ	kirre, exon_9	intergenic	kirre, N, CG18508, Fcp3C, CG3939, dnc, CG14265, ng2, ng3, ng1, ng4, Pig1, Sgs4, CR44886, CG10793, CR46243	NA	mh:1; ins:0; tup:0; tdown:0; snp_su:0; snp_op:0	0
HUM-7	60	lumpy	COMPLEX_BND	X	3129531	X	3364620	3	1	somatic_tumour	6249_1	235.1	X:3129531-3364620	60:60_61_62_63_64	0.28	-2.84	C	-	-	GCTCCTCATCGGCGGCAGCATCGTCAGCGAATGATGAAAGCAAACCGAAGGGCGGCGACAATGGTGGTCAGCACTTTGCGAATGTTGCGAATGAGGAGGGCAAAAGAAAGAATGCCAAATAAATTAAAATATTACA	Alt-EJ	kirre, exon_9	intergenic	kirre, N, CG18508, Fcp3C, CG3939, dnc, CG14265, ng2, ng3, ng1, ng4, Pig1, Sgs4, CR44886, CG10793, CR46243	NA	mh:1; ins:0; tup:0; tdown:0; snp_su:0; snp_op:0	0
HUM-7	60	novobreak	COMPLEX_BND	X	3129531	X	3364620	3	1	somatic_tumour	96	235.1	X:3129531-3364620	60:60_61_62_63_64	0.28	-2.84	C	-	CTCCTCCTCATCCTCATCCTCGTCGAGTGGCTCCTCATCGGCGGCAGCATCGTCAGCGAATGATGAAAGCAAACCGAAGGGCGGCGACAATGGTGGTCAGCACTTTGCGAATGTTGCGAATGTGGAGGGCAAAAGAAAGAATGCCAAATAAATTAAAATATTACATCGCTGACCCTGAACCTCGTTTTTTTCGTATTGTTTTT	GCTCCTCATCGGCGGCAGCATCGTCAGCGAATGATGAAAGCAAACCGAAGGGCGGCGACAATGGTGGTCAGCACTTTGCGAATGTTGCGAATGAGGAGGGCAAAAGAAAGAATGCCAAATAAATTAAAATATTACA	Alt-EJ	kirre, exon_9	intergenic	kirre, N, CG18508, Fcp3C, CG3939, dnc, CG14265, ng2, ng3, ng1, ng4, Pig1, Sgs4, CR44886, CG10793, CR46243	NA	mh:1; ins:0; tup:0; tdown:0; snp_su:0; snp_op:0	0
HUM-7	60	CNV-Seq	COMPLEX_DEL	X	3129531	X	3364621	-	-	somatic_tumour	-	235.1	X:3129531-3364621	60:60_61_62_63_64	0.87	-2.84	-	-	-	-	-	kirre, exon_9	intergenic	kirre, N, CG18508, Fcp3C, CG3939, dnc, CG14265, ng2, ng3, ng1, ng4, Pig1, Sgs4, CR44886, CG10793, CR46243	NA	snp_su:0; snp_op:0	0
HUM-7	60	Control-Freec	COMPLEX_DEL	X	3129945	X	3164340	-	-	somatic_tumour	-	34.4	X:3129945-3164340	61:60_61_62_63_64	0.94	-3.07	-	-	-	-	-	kirre, exon_9	N, exon_6	kirre, N	NA	snp_su:0; snp_op:0	0
HUM-7	60	Control-Freec	COMPLEX_DEL	X	3171219	X	3352366	-	-	somatic_tumour	-	181.1	X:3171219-3352366	62:60_61_62_63_64	0.95	-3.18	-	-	-	-	-	N, 3UTR	intergenic	N, CG18508, Fcp3C, CG3939, dnc, CG14265, ng2, ng3, ng1, ng4, Pig1, Sgs4, CR44886, CG10793	NA	snp_su:0; snp_op:0	0
HUM-7	60	lumpy	COMPLEX_BND	X	3351890	X	3353248	10	0	somatic_tumour	6245_1	1.4	X:3351890-3353248	63:60_61_62_63_64	0.87	-0.32	-	CTTTG	-	TTGGGTCCCATGGGGATGTTTGATATGCTTAGCTGGAAGTGCGAAAAAAAAAGAAGAAAAATAGGGAGAATAATAAAGTGTAAACAAACAAAGACAAGGATGAGTCCAGGCGCAGATCGAAAATTGCAATA	FoSTeS	intergenic	intergenic	-	NA	mh:0; ins:5; tup:3; tdown:4; snp_su:0; snp_op:0	0
HUM-7	60	CNV-Seq	COMPLEX_DUP	X	3354465	X	3364533	-	-	somatic_tumour	-	10.1	X:3354465-3364533	64:60_61_62_63_64	0.92	0.89	-	-	-	-	-	intergenic	intergenic	CR46243	NA	snp_su:0; snp_op:0	0
