Table 4

Comparison of chromosomal coverage. Sequence coverage per 100 base bin is shown for both repeat and unique regions from unamplified control or whole genome amplified samples.

Halobacterium species NRC-1 main (NRC1) and minichromomes (pNRC100 and pNRC200)


Chromosome

Sample

Reads per unique bin

Reads per repeat bin

Percent chromosomal reads/genome

Percent unique chromosomal reads/genome

Percent repeat chromosomal reads/genome

Percent unique reads/chromosomal reads

Percent repeat reads/chromosomal reads


NRC1

2.01 Mb

68% GC

1.4% repeats

Control

1.91

22.38

44%

38%

6%

86%

14%

Average Unamplified Replicates

1.92

22.18

44%

38%

6%

86%

14%

GenomiPhi

0.83

30.92

25%

16%

9%

66%

35%

Repli-G

0.55

36.23

21%

11%

10%

52%

48%

PEP-PCR

0.69

28.67

22%

14%

8%

63%

37%

DOP-PCR

0.38

28.07

15%

8%

8%

49%

51%

pNRC100

191Kb

57.9% GC

79.4% repeats

Control

6.42

13.84

24%

3%

21%

11%

89%

Average Unamplified Replicates

6.51

13.77

23%

3%

21%

11%

89%

GenomiPhi

9.47

18.64

32%

4%

28%

12%

88%

Repli-G

9.81

19.68

34%

4%

30%

12%

88%

PEP-PCR

11.09

20.51

35%

4%

31%

13%

88%

DOP-PCR

2.59

20.19

32%

1%

31%

3%

97%

pNRC200

365 Kb

59.2% GC

45.0% repeats

Control

3.78

14.97

32%

8%

25%

24%

76%

Average Unamplified Replicates

3.85

14.89

32%

8%

24%

24%

76%

GenomiPhi

4.86

20.19

43%

10%

33%

23%

77%

Repli-G

4.54

21.92

45%

9%

36%

20%

80%

PEP-PCR

3.76

21.40

43%

8%

35%

18%

82%

DOP-PCR

7.65

22.92

53%

15%

38%

29%

71%


Campylobacter jejuni single chromosome


Chromosome

Sample

Reads per unique bin

Reads per repeat bin

Percent chromosomal reads/genome

Percent unique chromosomal reads/genome

Percent repeat chromosomal reads/genome

Percent unique reads/chromosomal reads

Percent repeat reads/chromosomal reads


C. jejuni

1.64 Mb

31% GC

2.71% repeat

Control

5.90

12.94

N/A

94%

6%

N/A

N/A

Average Unamplified Replicates

5.90

12.97

94%

6%

GenomiPhi

5.96

10.81

95%

5%

Repli-G

5.87

13.85

94%

6%

PEP-PCR

5.35

32.42

86%

15%

DOP-PCR

6.12

4.91

98%

2%


Pinard et al. BMC Genomics 2006 7:216   doi:10.1186/1471-2164-7-216

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