Table 2.

Summary of SNPs identified from Hanwoo and Yanbian cattle in this study.

	Fields	Hanwoo	Yanbian cattle	Total
Sample counts		10	10	20
SNP counta		13,544,560	15,857,687	17,926,093
dbSNP		11,477,894	12,892,393	13,936,399
Ti/Tv ratio		2.26	2.26	2.26
SNP categories
Exon	Synonymous variant	49,684	59,232	70,079
	Non-synonymous variant	36,457	42,595	50,827
	Initiator codon variant	4	4	5
	Start lost	34	43	48
	Stop gained	399	491	580
	Stop lost	16	25	27
	Stop retained variant	39	43	52
	Non coding exon variant	5,393	6,180	7,322
Splice site	Splice region variant	8,499	10,098	11,961
	Splice acceptor variant	224	269	318
	Splice donor variant	230	268	331
Intron	Intron variant	3,347,348	4,047,275	4,703,213
	Intragenic variant	40,614	49,950	56,469
UTR	5 prime UTR variant	4,094	4,917	5,855
	5prime UTR premature - startcodon gain variant	674	818	956
	3prime UTR variant	26,280	31,680	37,323
Intergenic	Upstreamd gene variant	531,123	637,361	742,563
	Downstreamd gene variant	545,133	656,190	764,392
	Intergenic region	9,502,323	11,284,480	13,090,691
Functional classes
	Missense	36,511	42,667	50,907
	Nonsense	399	491	580
	Silent	49,723	59,275	70,131

^aSNP count; the overlapped SNP loci between samples were counted as one.

^bBecause the analysis to categorize the SNPs was done non-exclusively, some SNPs were counted at multiple categories.

^cSNP categories were clustered by six genomic regions: Exon, Splice site, Intron, UTR, Flanking region and Intergenic

^dUpstream/downstream: 5 Kbp regions that are adjacent to the both ends of a gene were defined as upstream and downstream regions respectively.