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Table 8 Estimates of index hopping incidence through concordance between low- and high-coverage sequence data in the real and simulated datasets, expressed as percentages and as isometric log-ratios

From: Impact of index hopping and bias towards the reference allele on accuracy of genotype calls from low-coverage sequencing

 

Concordance by genotype (%)

Isometric log-ratios

True = 0

True = 1

True = 2

3 partsa

2 partsb

0|0

1|0

2|0

0|1

1|1

2|1

0|2

1|2

2|2

0|0 vs. 1|0, 2|0

1|1 vs. 0|1, 2|1

2|2 vs. 0|2, 1|2

0|0 vs. 1|0

2|2 vs. 1|2

Observed

98.45

1.42

0.13

24.15

52.62

23.23

0.18

1.71

98.10

4.44

0.65

4.22

3.00

2.86

Simulated

 0%

99.62

0.35

0.03

23.57

52.98

23.45

0.04

0.47

99.48

5.61

0.66

5.35

4.00

3.78

 0.1%

99.53

0.44

0.03

23.59

53.52

22.89

0.08

0.52

99.40

5.47

0.68

5.06

3.83

3.72

 0.5%

99.28

0.66

0.06

23.91

53.22

22.87

0.10

0.92

98.98

5.07

0.67

4.72

3.55

3.31

 1%

98.99

0.90

0.10

23.70

53.23

23.07

0.14

1.33

98.53

4.72

0.67

4.43

3.32

3.04

 2%

98.20

1.64

0.16

23.73

52.90

23.37

0.23

2.16

97.62

4.29

0.66

4.04

2.89

2.70

 5%

96.34

3.29

0.37

23.56

53.37

23.07

0.59

4.75

94.66

3.65

0.68

3.29

2.39

2.12

Regression

 R2

0.999

0.998

0.999

0.014

0.044

0.014

0.989

1.000

0.999

0.993

0.213

0.981

0.995

0.989

 Estimate

1.74

1.77

1.47

–

–

–

1.28

1.45

1.43

1.58

–

1.48

1.67

1.46

  1. aThe 3-part isometric log-ratios take the form \(\sqrt {\frac{2}{3}} \ln \frac{(0|0)}{{\sqrt {\left( {1|0} \right)\cdot\left( {2|0} \right)} }}\)
  2. bThe 2-part isometric log-ratios take the form \(\frac{1}{\sqrt 2 }\ln \frac{(0|0)}{{\left( {1|0} \right)}}\)
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Genetics Selection Evolution

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