Table 1. Polymorphisms in cDNA sequences from pro amplicons in 13 cancer cell lines and reference to 22 full-length or near full-length proviruses.

				Nucleotide a
Viral genome positionb				3018	3171	3189	3219	3262	3297	3316	3412	3519	3641	3642	3657
Plurality c				A	T	A	G	A	G	A	C	G	C	T	C
Cell lines	LNCaP			.G	.C	C	.	.	A	.G	.	.	T	.G	.
	DU145			.	.	.	.	.	.	.	.	.	.	.	.
	PC3			.	.	.	.	.	.	.	.	.	.	.	.
	C33A			n	n	n	n	n	n	n	n	n	n	n	n
	SiHa			.	.	.	.	.	.	.	.	.	.	.	.
	CaSki			.	.	.	.	.	.	.	.	.	.	.	.
	HeLa			.	.	.	.	.	.	.	.	.	.	.	.
	UPCISCC-90			.	.	.C	.	.	.	.	.	.	.	.	.
	UMSCC-47			.	.	.	.	.	.	.	.	.	.	.	.
	FaDu			.	.	.	.	.	.	.	.	.	.	.	.
	MDA-MB-468			.	.	.C	.	.	.	.	.	.	.	.	.
	MDA-MB-231			.	.	.	.	.	.	.	.	.	.	.	.
	MCF7			.G	.C	C	.	.	.A	.G	.	.	.T	.G	.
	Virus	Type	Position
Homo sapiens specific	K101	I	chr22∶18,926,187–18,935,361	G	C	C	A	.	.	.	.	.	.	G	.
	K102	I	chr1∶155,596,457–155,605,636	.	.	.	.	.	.	.	.	.	.	.	.
	K103	I	chr10∶27,182,399–27,183,366	G	C	C	.	.	.	.	.	.	.	.	.
	K104	II	chr5∶30,486,760–30,496,205	G	C	.	.	.	A	G	T	.	.	.	.
	K106	I	chr3∶112,743,124–112,752,282	G	C	C	.	.	A	G	.	.	T	G	.
	K107	I	chr5∶156,084,717–156,093,896	G	.	.	.	.	.	.	.	.	.	.	G
	K108	II	chr7∶4,622,057–4,640,031	G	C	C	.	.	A	.	.	.	.	G	.
	K109	II	chr6∶78,426,662–78,436,083	G	.	C	.	.	.	G	.	.	T	G	.
	K113	II	chr19∶21,841,536–21,841,541	G	.	C	.	.	A	.	.	.	.	G	.
	K114	II	chr11∶101,565,794–101,575,259	G	C	C	.	.	A	.	.	.	.	.	.
	K115	II	chr8∶7,355,397–7,364,859	–	.	.	.	.	A	.	.	.	T	G	.
	K116	I	chr3∶85,280,336–185,289,515	G	C	C	.	G	.	.	T	A	.	G	.
	K117	II	chr12∶58,721,242–58,730,698	G	C	C	.	.	A	.	.	.	.	.	.
	K(I)	II	chr3∶125,609,302–125,618,439	G	C	.	A	.	A	.	T	A	.	.	.
	K4	I	chr1∶75,842,771–75,849,143	G	C	C	.	.	A	.	.	–	–	–	–
	K60	I	chr21∶19,935,621–19,940,996	G	C	.	A	G	.	.	.	A	.	.	.
Shared with Pan and Gorilla	K105	I	chrUn:gl000219∶175210–176178	G	C	.	.	G	A	.	T	A	.	.	T
	K110	I	chr1∶160,660,575–160,669,806	G	C	G	.	G	A	.	T	.	.	.	.
	K111	I	chr11∶118,591,724–118,600,883	G	C	.	.	G	A	.	T	.	.	.	.
	K112	II	chr10∶6,866,141–6,875,603	G	C	G	.	T	A	.	T	.	.	.	T
	K118	I	chr3∶101,410,737–101,419,859	G	.	G	A	G	.	G	T	A	.	C	T
	K5	I	chr4∶165,916,840–165,924,068	G	C	.	A	G	A	.	T	A	.	.	T
	K51	I	chr19∶22,757,824–22,764,561	G	C	G	.	G	A	.	T	A	.	.	T
	K50F	II	chr19∶37,597,549–37,607,066	G	C	.	A	G	A	G	T	.	.	.	.

^aNotations: “.” = same as in consensus, “n” = non detectable, “.G” = primary and secondary peaks of approximately equal detection, “–” = absent in alignment.

^bPosition in the reference HERV-K genome (K108).

^cPlurality sequence indicates the most common nucleotide at that position among amplicons from the 13 cell lines.