Table 2

Imputation on RPO SNPs

IGCT 50%

IGCT 70%

IGCT 90%


discordance

No-call

N. of SSNPs

discordance

No-call

N. of SSNPs

discordance

No-call

N. of SSNPs


MAF

#SNP


0

107

3,38%

0,00%

97

2,90%

1,13%

92

2,49%

2,47%

89

0-0.05

124

3,29%

0,02%

103

2,75%

1,55%

95

2,23%

4,07%

79

0.05-0.10

77

4,46%

0,13%

59

2,93%

3,06%

55

1,83%

8,09%

45

0.1-0.2

98

4,47%

0,31%

75

3,27%

3,43%

68

2,20%

9,37%

56

0.2-0.3

97

7,27%

1,11%

66

4,39%

7,43%

61

2,17%

15,25%

42

0.3-0.4

72

6,77%

1,07%

53

3,88%

7,26%

46

2,21%

14,10%

37

0.4-0.5

79

4,41%

0,26%

63

2,92%

3,60%

59

1,95%

9,22%

47


MAF: Minor Allele Frequency

#SNP: Number of SNPs

IGCT: imputed genotype calling threshold

Discordance: the proportion of genotype calls for which the imputed genotype did not match the experimental genotype call, averaged over all SNPs.

No-call: proportion of genotypes whose posterior probability did not reach a pre-specified IGCT

For instance, the first row reports the results of 107 SNPs having a MAF = 0 in the study sample for IGCT = 50%: the discordance is 3.38% and the no-call rate is 0.00%. For the IGCT = 90%, the discordance and no-call are 2.49% and 2.47%, respectively.

Mijatovic et al. BMC Bioinformatics 2012 13(Suppl 14):S7   doi:10.1186/1471-2105-13-S14-S7

Open Data