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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.