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Table 2 SNP prediction Coverage for HapMap population samples

From: TagSNP transferability and relative loss of variability prediction from HapMap to an admixed population

Population

Gene

Total SNPs

Density (SNP/Kb)

Common SNPs

n to 100% prediction

Prediction of selected SNPs (%)

Max. Prediction (%)

CHB+JPT

PTPN22

30

0.86

21 (70%)

14

87.15

99.59

CEU

 

28

0.80

21 (75%)

17

88.00

98.50

YRI

 

29

0.83

17 (59%)

12

93.91

99.17

CHB+JPT

HMGCR

23

0.81

20 (87%)

19

90.17

98.12

CEU

 

24

0.84

22 (92%)

21

93.56

97.50

YRI

 

23

0.81

17 (74%)

16

94.33

98.08

CHB+JPT

VDR

162

2.04

84 (52%)

73

92.91

98.00

CEU

 

161

2.02

94 (58%)

79

92.12

96.67

YRI

 

159

2.00

107 (67%)

101

88.20

93.17

CHB+JPT

CETP

102

3.33

55 (54%)

51

86.18

93.13

CEU

 

101

3.30

48 (48%)

40

82.74

93.07

YRI

 

102

3.33

69 (68%)

61

85.33

90.05

  1. Coverage is based on a total number of SNPs, region density measured by SNP/Kb, number of common SNPs (MAF <0.05), number of common SNPs to reach 100% of prediction, prediction of the selected SNPs and the maximum prediction using the same number of SNPs.