Table 1. SNV and indel variant-calling statistics of the prostate cancer cell lines PC3 and LNCaP.

	PC3 Private		LNCaP Private		Shared
Number and percentage of variants by type
SNVs	318,380	34.0%	404,282	72.1%	166,912	65.0%
Indels	618,149	66.0%	156,182	27.9%	89,919	35.0%
Number of events by type
3′-UTR	15,572		10,500		3938
5′-UTR premature start codon	211		289		49
5′-UTR	2613		1868		692
Conservative_inframe_deletion	39		22		7
Conservative_inframe_insertion	468		119		72
Disruptive_inframe_deletion	62		19		7
Disruptive_inframe_insertion	172		64		44
Downstream_gene	107,761		56,728		29,770
Frameshift	276		167		44
Intergenic_region	563,630		326,261		175,014
Intron	916,272		576,268		191,182
Missense	3520		5717		1667
Non_coding_transcript_exon	5848		3846		2091
Non_coding_transcript	18		10		1
Protein_protein_contact	120		17		5
Sequence_feature	7978		5930		1457
Splice_acceptor	80		131		21
Splice_donor	56		138		17
Splice_region	1313		1174		437
Start_lost	16		14		3
Stop_gained	58		378		29
Stop_lost	25		4		9
Structural_interaction	1160		808		1
Synonymous	2402		2727		81
Upstream_gene	107,281		57,447		1301

Common germline variants were excluded and variants were further filtered using SnpSift, with a total depth threshold at 30 (DP ≥ 30) and a minimum variance confidence of 200 (QUAL ≥ 200), and annotated by SnpEff. SNV, single nucleotide variant; UTR, untranslated region.