Table 2 SNVs in tumor samples.

Sample	Gene	Chr.	Pos.*	Ref.†	Var.‡	Discovery		Validation		dbSNP	Type∥
						Freq.§	P value	Freq.§	P value
T1	VHL	chr3	10188193	G	A	0.0004	2e-03				Intronic
			10191572	G	T	0.3500	<2e-300				p.E189*
			10191635	C	T	0.0002	9e-03				p.R210W
	TP53	chr17	7572600	G	A	0.0008	2e-05				3′ UTR
			7577407	A	C	0.0010	9e-14	0.0007	1e-07	Yes	Intronic
			7577427	G	A	0.0008	1e-09	0.0007	3e-03	Yes	Intronic
			7577653	G	A	0.0004	7e-05	0.0001	6e-01		Intronic
			7578183	C	T	0.0007	2e-06			Yes	p.P222P
T2	VHL	chr3	10183359	T	C	0.0005	1e-04				5′ UTR
			10188161	G	A	0.0003	8e-05			Yes	Intronic
			10188329	G	A	0.0003	4e-08	0.0002	2e-02		Intronic
			10188427	G	A	0.0004	2e-05	0.0004	3e-02		Intronic
			10188549	G	A	0.0003	9e-06	0.0002	3e-01		Intronic
			10191572	G	—	0.1686	5e-297				c.565delG
			10191620	C	T	0.0005	2e-03				p.R205C
			10192372	G	A	0.0004	5e-06				3′ UTR
	TP53	chr17	7573512	G	A	0.0006	4e-03				Intronic
			7573681	C	T	0.0006	3e-04			Yes	Intronic
			7577368	G	A	0.0007	4e-03				Intronic
			7577999	T	C	0.0003	9e-03				3′ UTR (variable)
			7578257	C	A	0.0113	7e-89	0.0177	2e-21		p.E198*
T3	TP53	chr17	7573682	G	A	0.0003	9e-03				Intronic
P1	VHL	chr3	10188206	T	—	0.2396	2e-278				c.349delT
P2	VHL	chr3	10188206	T	—	0.2412	3e-288				c.349delT
M	VHL	chr3	10188206	T	—	0.2440	1e-303				c.349delT
	VHL		10192220	C	G	0.0046	1e-29	0.0051	1e-38		3′ UTR

Abbreviations: Chr., chromosome; Freq., frequency; Pos., position; Ref., reference; SNP, single-nucleotide polymorphism; SNVs, single-nucleotide variants; UTR, untranslated region; Var. variant;
* UCSC hg19 coordinates.
† Major allele in control sample.
‡ Variant detected by deepSNV.
§ Average frequency of both strands in tumour−average frequency in control.
|| Coordinates refer to the Ensembl transcripts ENST00000256474 (VHL) and ENST00000269305 (TP53).

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