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Table 1 Summary of Roche 454 data

From: GAP-Seq: a method for identification of DNA palindromes

 

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

  1. 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].
  2. bAnalysis of repeat masked elements are based on RepeatMasker.
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BMC Genomics

ISSN: 1471-2164

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