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Table 3 Error rates found by each method when using cut-offs for the probabilities provided by PHASE

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

GH1 – cutoff 70% (5 SNPs)

MD

Method

Abs IER

Rel IER

Res rate

0%

Global

2.18%

2.24%

97.31%

 

Local

2.56%

2.65%

96.54%

2%

Global

2.92%

2.99%

96.78%

 

Local

2.97%

3.05%

94.78%

5%

Global

3.33%

3.49%

95.38%

 

Local

3.17%

3.51%

90.42%

10%

Global

4.50%

4.92%

91.40%

 

Local

4.07%

5.00%

81.50%

15%

Global

5.83%

6.56%

88.88%

 

Local

4.85%

6.42%

75.54%

20%

Global

7.06%

8.14%

86.80%

 

Local

6.00%

8.81%

68.12%

GH1 – cutoff 50% (5 SNPs)

MD

Method

Abs IER

Rel IER

Res rate

0%

Global

2.99%

2.99%

99.82%

 

Local

3.50%

3.50%

99.83%

2%

Global

3.82%

3.98%

99.81%

 

Local

4.18%

4.26%

97.47%

5%

Global

5.03%

5.06%

99.42%

 

Local

5.08%

5.32%

95.45%

10%

Global

7.17%

7.28%

98.45%

 

Local

7.24%

8.04%

90.06%

15%

Global

9.41%

9.62%

97.84%

 

Local

9.50%

10.95%

86.83%

20%

Global

11.25%

11.58%

97.18%

 

Local

11.96%

14.45%

82.77%

  1. This table presents the summary of average error rates when using a cut-off on resolution probability given by PHASE instead of Rmax when choosing the resolution obtained by each method. The 2 cut-offs chosen were respectively 50% and 70%. The error rate is almost always lower than with Rmax, but the number of assigned haplotypes strongly decreased.
  2. IER: individual error rate, Abs IER: absolute IER, Rel IER: relative IER, Res Rate: resolution rate, MD: Missing Data.