Table 3

Accuracy of computational inferences of haplotype structure of the GH1 gene promoter.

15 Promoter SNPs

Error Rate Based on # of Heterozygous Sites (N)



Error Rate


Algorithm

MSE

IH # correct/# wrong

IF

Overall

Ambiguous Individuals

2 (13)

3 (32)

4 (24)

5 (28)

6 (11)


Phase v2, no LD

3.6 × 10-5

0.81 27/4

0.91

0.11

0.15

0.08

0.09

0.25

0.11

0.27

Phase v2, with LD

2.2 × 10-5

0.81 28/5

0.93

0.10

0.13

0

0.09

0.17

0.14

0.27

Haplotyper 1.0

2.0 × 10-5

0.81 28/5

0.93

0.09

0.13

0

0.06

0.13

0.18

0.27

PL-EM 1.0

2.5 × 10-5

0.82 31/9

0.92

0.11

0.15

0

0.09

0.13

0.21

0.36

SNPHAP 1.0

2.0 × 10-5

0.82 30/7

0.93

0.09

0.13

0

0.09

0.13

0.14

0.27

8 SNPs with Minor Allele Frequency ≥ 5%


Phase v2, no LD

4.8 × 10-5

0.79 19/3

0.92

0.11

0.15

Phase v2, with LD

4.1 × 10-5

0.80 20/4

0.92

0.11

0.15

Haplotyper 1.0

3.8 × 10-5

0.81 19/2

0.93

0.10

0.14

PL-EM 1.0

2.3 × 10-5

0.85 22/4

0.94

0.08

0.11

SNPHAP 1.0

3.3 × 10-5

0.85 22/4

0.93

0.08

0.11


Adkins BMC Genetics 2004 5:22   doi:10.1186/1471-2156-5-22

Open Data