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Table 1 Dataset summary

From: Fast accurate missing SNP genotype local imputation

Dataset:

human

mouse

hd cattle

ld cattle

Physical length

79 mbp

95 mbp

76 mbp

76 mbp

#samples

83

15

64

469

#SNPs

40,755

288,229

22,266

1,508

Missing genotype rate

0.268%

11.1%

2.224%

0.078%

#complete SNPs

34,071

144,820

5,487

1,271

  1. The summary of the four datasets we used in the simulation studies. These four datasets are all on chromosome 17, for human, mouse and cattle. The “physical length” refers to the chromosome length, in million basepairs (mbp). “#samples” is the number of individuals genotyped in the dataset, “#SNPs” is the number of SNP markers in the original dataset, and “missing genotype rate” refers to the percentage of missing genotype values in the original dataset. “#complete SNPs” is the number of SNP markers at which all samples have genotype values. All the other SNP markers were removed, leaving a complete sub-dataset to be used in the simulation studies.