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Table 2 Summary of enzyme combinations that achieve the best genomic coverage in human, rat, and mouse genomes

From: In silico analysis identifies novel restriction enzyme combinations that expand reduced representation bisulfite sequencing CpG coverage

Enzyme combinations

CpGs covered

Fragments generated

Genomic CpG coverage (%)

CpG/fragment ratio

Read coverage

I. Homo sapiens

HaeIII

6,755,710

4,521,945

25.0

1.49

33.2×

MspI HaeIII

8,703,801

5,613,529

32.2

1.55

26.7×

MspI AluI

10,642,461

9,505,806

39.4

1.12

15.8×

MspI HpyCH4V

11,443,197

10,567,403

42.3

1.08

14.2×

MspI BfaI HaeIII

12,111,370

11,319,689

44.8

1.07

13.3×

MspI AluI HaeIII

13,769,398

14,064,014

50.9

0.98

10.7×

AluI HaeIII

13,957,636

13,633,940

51.6

1.02

11.0×

HaeIII HpyCH4V

14,395,279

14,532,544

53.2

0.99

10.3×

II. Rattus novergicus

HaeIII

4,292,555

3,206,578

17.9

1.34

46.8×

MspI HaeIII

5,859,114

4,154,939

24.5

1.41

36.1×

MspI AluI

9,423,433

8,934,858

39.4

1.05

16.8×

MspI BfaI HaeIII

9,643,490

9,579,581

40.3

1.01

15.7×

HaeIII HpyCH4V

10,937,751

11,405,956

45.7

0.96

13.2×

MspI AluI BfaI

11,837,958

13,122,827

49.5

0.90

11.4×

MspI BfaI HpyCH4V

12,246,891

13,543,165

51.2

0.90

11.1×

AluI HpyCH4V

12,674,196

14,657,325

53.0

0.86

10.2×

III. Mus musculus

MspI HaeIII

5,708,849

4,591,528

26.1

1.24

32.7×

MspI AluI

8,524,374

9,393,465

39.0

0.91

16.0×

MspI BfaI HaeIII

9,221,025

10,607,497

42.2

0.87

14.1×

HaeIII HpyCH4V

10,164,473

12,447,516

46.5

0.82

12.1×

AluI HaeIII

10,229,379

12,588,763

46.8

0.81

11.9×

MspI AluI HaeIII

10,706,690

13,170,774

49.0

0.81

11.4×

MspI HaeIII HpyCH4V

10,759,254

13,095,284

49.2

0.82

11.5×

MspI BfaI HpyCH4V

11,347,760

14,601,495

51.9

0.78

10.3×

  1. Calculations assumed a fragment size inclusion of 40–400 bp, a sequencing depth of 50 nt, and a 150 M read NGS throughput.