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Table 3 Summary statistics of variants discovered for each individual

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

Breed

Sample

Total Variants

%variants in dbSNP

Ti/Tv Ratio

Exons

LoF

DD

SAMN05791661

4,361,699

83.84

2.18

28,321

11,783

DD

SAMN05791665

4,720,118

84.00

2.20

31,091

13,272

DD

SAMN05791663

4,761,804

85.38

2.26

29,916

11,992

LL

SAMN05791650

4,664,664

84.42

2.16

29,287

12,430

LL

SAMN05791651

5,255,293

85.29

2.21

33,575

13,768

LL

SAMN05791660

5,433,413

86.27

2.25

35,521

14,111

YY

S494203

5,730,270

86.99

2.31

39,094

15,304

YY

S409308

5,528,070

86.74

2.30

38,986

15,630

YY

S474607

6,047,346

86.81

2.28

38,828

15,482

  1. TotalVariants the number of SNPs discovered for each individual by single-sample calling, %variants in the dbSNP databbase the number of SNPs in the dbSNP database, Ti/Tv Ratio the proportion of the SNPs observed as transitions (between purines, or between pyrimidines) to transversions (between purines and pyrimidines), Exons the number of SNPs on exons, LoF the number of loss-of-function variants