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Table 1 Error rates obtained according to the level of missing information in the GH1 dataset

From: Computation of haplotypes on SNPs subsets: advantage of the "global method"

GH1

MD

Method

IER

SimER

IF

Res rate

0%

Global_3snp

1.12%

0.37%

0.994

100%

 

Local_3snp

1.56%

0.52%

0.9904

100%

 

Global_5snp

3.16%

0.65%

0.9834

100%

 

Local_5snp

3.57%

0.72%

0.9784

100%

 

Global_7snp

4.87%

0.74%

0.9714

100%

 

Local_7snp

5.57%

0.83%

0.9704

100%

2%

Global_3snp

1.63%

0.38%

0.9937

100%

 

Local_3snp

2.57%

0.68%

0.9898

100%

 

Global_5snp

4.34%

0.88%

0.9826

100%

 

Local_5snp

5.26%

1.20%

0.9792

100%

 

Global_7snp

6.83%

0.82%

0.9693

100%

 

Local_7snp

8.70%

1.03%

0.961

100%

5%

Global_3snp

2.03%

0.46%

0.9934

100%

 

Local_3snp

3.65%

0.79%

0.9894

100%

 

Global_5snp

5.40%

0.88%

0.98

100%

 

Local_5snp

7.68%

1.20%

0.972

100%

 

Global_7snp

8.43%

1.07%

0.967

100%

 

Local_7snp

11.00%

1.37%

0.959

100%

10%

Global_3snp

3.57%

0.73%

0.989

100%

 

Local_3snp

6.60%

1.33%

0.983

99.87%

 

Global_5snp

8.06%

1.19%

0.973

100%

 

Local_5snp

12.91%

1.86%

0.962

100%

 

Global_7snp

11.84%

1.35%

0.959

100%

 

Local_7snp

16.41%

1.88%

0.946

100%

15%

Global_3snp

5.21%

1.01%

0.987

100%

 

Local_3snp

9.49%

1.84%

0.977

99.45%

 

Global_5snp

10.67%

1.47%

0.97

100%

 

Local_5snp

17.00%

2.33%

0.953

100%

 

Global_7snp

15.70%

1.67%

0.953

100%

 

Local_7snp

21.87%

2.35%

0.931

100%

20%

Global_3snp

6.65%

1.26%

0.984

98.44%

 

Local_3snp

12.45%

2.41%

0.97

97.02%

 

Global_5snp

12.83%

1.72%

0.964

100%

 

Local_5snp

22.15%

3.02%

0.936

99.60%

 

Global_7snp

18.47%

1.92%

0.946

99.72%

 

Local_7snp

26.44%

2.81%

0.916

100%

  1. Summary of the mean error rates obtained by each subhaplotyping method when they used the Rmax resolution produced by PHASE. The average individual error rate (IER) and similarity error rate (SimER) were computed according to the level of missing data (MD) introduced in the population (0%, 2%, 5%, 10%, 15%, 20%). Tests were performed on randomly selected SNP subsets of size 3, 5, and 7 taken out of the 14 SNPs present in the GH1 genomic dataset (see text and Material and Methods). This table presents the average of the IF coefficients which compares the accuracy of the subhaplotypes frequencies found by each subhaplotyping method. The global method fares always better.
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BMC Genomic Data

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