Comprehensive evaluation of SNP identification with the Restriction Enzyme-based Reduced Representation Library (RRL) method

Table 1 Summary of in silico digestion results

Restriction Enzyme			Fragments (200 -700 bp)				Distance between two adjacent reads		#Putative SNPs^b
	#Total selected fragments	#Total length of target regions^a	% Percent of coverage	#Length of repetitive on target regions	%percent of repetitive contents	Mean (Mb)	Median (Mb)	S.D.(Mb)
Sac I	65,734	11,832,120	0.38%	4,642,275	39.24%	22,732	442	131.63	48,250
Ava I	69,204	12,456,720	0.40%	5,388,814	43.26%	21,582	368	140.26	59,204
Hin d III	114,374	20,587,320	0.67%	8,376,468	40.69%	13,027	425	95.84	79,308
Pvu II	194,918	35,085,240	1.14%	12,510,491	35.66%	7,607	379	73.01	137,942
Sfc I	442,338	79,620,840	2.59%	33,483,887	42.05%	3,303	348	47.28	319,623
Dra I	1,131,481	203,666,580	6.61%	74,549,862	36.60%	1,237	235	29.41	774,892
Tsp 45I	1,479,019	266,223,420	8.64%	104,133,241	39.12%	926	224	25.64	1,074,049
Bcc I	2,419,310	435,475,800	14.14%	216,911,945	49.81%	531	170	19.95	1,750,903
Mbo II	3,308,660	595,558,800	19.33%	251,315,078	42.20%	365	148	17.04	2,298,087

The in silico digestion results of nine restriction enzymes using hg18 genome as reference were shown. ^a regions sequenced in the final corresponding library and calculated according to pair-end sequencing with average read length of 90 bp. ^b The number of putative SNPs are calculated based on dbSNP v129 data.

ISSN: 1471-2164