Optimal sequencing depth design for whole genome re-sequencing in pigs

BMC Bioinformatics

Table 2 Summary statistics of variants discovered for three pig breeds, Duroc, Landrace and Yorkshire

Sample	Mean Depth	Total Variants	%variants in dbSNP	Ti/Tv Ratio	Exons	LoF
3DD-sample	22.76	10,260,949	84.50	2.24	68,313	28,193
3LL-sample	20.60	12,239,211	85.53	2.25	78,968	31,980
3YY-sample	21.88	12,887,321	86.99	2.34	85,372	33,538

Mean Depth the sequencing depth for each breed on average, TotalVariants the number of SNPs discovered for each breed by 3 sample multisample calling, %variants in dbSNP the number of SNPs in the dbSNP database, Ti/Tv Ratio the proportion of the SNPs observed as transitions (between purines or between pyrimidines) versus transversions (between purines and pyrimidines), Exons the number of SNPs in exons, LoF the number of loss-of-function variants

ISSN: 1471-2105