Table 2. Effect of copy number amplifications on germline alleles.

			Normal		Metastatic		Transcriptome
ChromPos	AA mutation	Gene	Depth	Freq. Nref	Depth	Freq. Nref	Ref.	Ref. Count	Nref.	Nref. Count	Chi sq. q-value
1:144932587	F218C	AL139152.7	17928	0.3169	18017	0.2164	T	55	G	3	1.27E-102
1:149999951	I213V	MRPL9	5387	0.2046	8770	0.0409	T	154	C	28	4.29E-211
1:150543396	R3530S	FLG	61790	0.6191	78410	0.3981	N	0	N	0	0
8:146033676	A76V	ZNF7	92012	0.4499	147007	0.2683	C	2	N	0	0
9:33375641	CF	AQP7	24722	0.2781	22104	0.1985	N	0	N	0	1.12E-89
10:29823914	M1259T	SVIL	128591	0.3867	110884	0.4808	A	6	N	0	0
11:390124	N477K	PKP3	37172	0.4601	57560	0.2907	C	11	N	0	0
11:17499485	R357Q	USH1C	101208	0.5595	58749	0.1548	N	0	N	0	0
11:65860057	A79T	RIN1	75400	0.4044	97848	0.1738	N	0	N	0	0
11:116569101	R710C	SIDT2	260320	0.5342	237372	0.1390	C	51	T	19	0
11:124827464	E358Q	FEZ1	249388	0.5259	171924	0.1372	C	0	G	2	0
12:122455439	R279P	STED8	208542	0.3071	175257	0.4182	G	17	N	0	0
17:36549887	SP	KRTAP4-15	1774	0.3207	4409	0.1851	N	0	N	0	1.51E-30
19:40691038	RQ	DMKN	209119	0.5478	247223	0.1696	C	5	T	2	0
19:42074256	H426R	ZNF829	6402	0.4531	10867	0.1214	T	1	C	1	0
19:50869860	R190Q	GIPR	70793	0.4878	90262	0.1843	G	26	A	5	0
19:59415177	RK	LILRB3	34753	0.1592	46500	0.0642	N	0	N	0	0

These variants exhibit an amplification of the reference allele and show allelic skew, and as a result suggest an unbalanced allelic amplification over the tumor evolution.Impact refers to functional impact as determined by MutationAssessor.