Table 1

Summary of the accuracies of IMPUTE using data from chromosome 21 in the NNC set

Accuracy


Missing

0.1%

1%

10%

40%

60%


Complete missing

Overall

97.42%

(0.20, 0.93, 0.99, 1)

97.42%

(0.01, 0.93, 0.99, 1)

97.05%

(0.01, 0.92, 0.99, 1)

95.20%

(0.01, 0.88, 0.99, 1)

91.88%

(0.01, 0.82, 0.97, 1)


0.95 P.P.

99.24%

(0.00, 0.98, 1.00, 1)

99.24%

(0.00, 0.98, 1.00, 1)

99.22%

(0.00, 0.98, 1.00, 1)

99.06%

(0.00, 0.98, 1.00, 1)

98.86%

(0.00, 0.97, 1.00, 1)


Percentage

82.30%

82.31%

80.38%

71.16%

59.39%


80% missing

Overall

97.24%

(0.28, 0.93, 0.99, 1)

97.70%

(0.01, 0.93, 0.99, 1)

97.24%

(0.01, 0.93, 0.99, 1)

95.39%

(0.01, 0.88, 0.99, 1)

91.71%

(0.00, 0.82, 0.97, 1)


0.95 P.P.

99.38%

(0.00, 0.98, 1.00, 1)

99.42%

(0.00, 0.98, 1.00, 1)

99.27%

(0.00, 0.98, 1.00, 1)

99.04%

(0.00, 0.98, 1.00, 1)

98.95%

(0.00, 0.97, 1.00, 1)


Percentage

81.92%

82.08%

80.53%

71.39%

59.12%


The columns report the accuracy of imputation when different proportions of SNPs ranging from 0.1% to 60% were imputed. The first three rows labelled as "Complete missing" summarize the accuracy when the genotype data were completely removed, while the last three rows labelled "80% missing" summarize the accuracy when 80% of the genotype data were randomly removed. The row labelled "Overall" reports the median accuracy and the minimum, 1st quartile, 3rd quartile, and maximum accuracy value within brackets. The row labelled "0.95.P.P" reports the median accuracy of the imputed genotypes when a minimum posterior probability of 0.95 was required for an imputed genotype to be acceptable. The row labelled "Percentage" reports the percentage of imputed genotype data that were acceptable by using the minimum posterior probability of 0.95 as a requirement.

Zhao et al. BMC Genetics 2008 9:85   doi:10.1186/1471-2156-9-85

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