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Table 3 Features of different haplotype block partitioning methods on haplotype samples in ENCODE regions.

From: Global haplotype partitioning for maximal associated SNP pairs

 

HOT

MB

HB

MDL

GAM

GAB

GPG

GPF

Average block length (kbp)

68.9

46.8

36.2

17.1

13.3

23.3

35.7

39.7

Average block length (SNP)

52

36

27

13

10

18

27

30

Total run time (sec.)

N/A

22

743

3295

112

143

5

5

Common haplotype coverage

0.67

0.89

0.91

0.96

0.96

0.93

0.88

0.87

Hole freq.

0.50

0.23

0.14

0.06

0.04

0.04

0.15

0.18

Island freq.

0.08

0.10

0.09

0.17

0.19

0.11

0.06

0.07

Robustness

N/A

92.0

69.2

99.4

99.7

100

100

97.6

  1. Result summary of haplotype blocks obtained by different methods on HapMap haplotypes of CEU in ENCODE regions. Common haplotype coverage denotes the fraction of all chromosomes that are covered by common haplotype variations in blocks. Hole freq. and Island freq. show the probability of a hole in blocks and the probability of an island out of any block. Robustness shows the probability that any block boundary is placed at the same location during resampling. See Table 1 for method abbreviations.