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Table 1 Phasing performance for real data sets

From: A combined long-range phasing and long haplotype imputation method to impute phase for SNP genotypes

Dataset

1Nb individuals

2Nb SNP

3Core/CplusT length

4M/E%

5Time

6% phased

Sheep chr. 4

1019

2278

100/300

1.00

3 min 39 s

98.17

Sheep chr. 5

1016

1927

100/400

1.00

5 min 1 s

97.62

Pig chr. 1

2723

3999

100/500

0.00

364 min

96.87

Beef chr. 24

2171

874

100/300

0.00

17 min 8 s

98.42

Dairy chr. 1

5057

2296

100/400

0.00

456 min

97.99

Human chr. 1

879

4472

100/300

1.00

3 min 29 s

93.73

  1. 1Numbers of individuals in the dataset; 2Numbers of SNP to be phased; 3Optimal core and CplusT length parameter; 4Optimal missing genotype/genotype error % (M/E%) error threshold parameter; 5Computation time measured on a 64 bit desktop with an Intel i7 3.07 GHz quad core processor running Linux was used to measure computation time; computation time includes time required to parse and summarise the data and write out the results; 6Percentage of alleles phased