Table 1.

Summary of Roche 454 data

	aReference genome (hg18) (%)	MCF7 (%)	IMR90 (%)
Mapped to unique locus	40	28	22
bRepeat masked	46	48	43
SINEs	13	13	9
LINEs	20	18	15
LTRs	0.02	0.03	0.02
Simple repeats	0.85	0.91	0.98
Low complexity	0.55	0.37	0.34
Satellites	3	8	10.6
Other	8.58	4.7	7.1
Mitochondrial DNA	1.6	12	25
Low copy repeats	5.2	11	7
Human but not mapped	7.2	0.6	0.6
Non-human DNA		1	2
Total # reads		934,174	1,136,611

^aThe reference genome statistics were adapted from UCSC Genome Browser (NCBI Build 36.1, Mar. 2006 Assembly, hg18). Low copy repeats (segmental duplications) were adapted from [31, 33]. We used an average of 3000 copies of mtDNA in calculating the ratio in the human genome [32].

^bAnalysis of repeat masked elements are based on RepeatMasker.