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Table 2 Estimating θ with Beta distributed sequencing error rate

From: Estimating DNA polymorphism from next generation sequencing data with high error rate by dual sequencing applications

Parameter α of Beta distribution

Sites used

θ = 0.1 / kb

θ = 1 / kb

Single-line

Pooled-lines

Single-line

Pooled-lines

   

single platform

dual applications

 

single platform

dual applications

 

S>0

19.917 (0.237)

38.335 (0.274)

2.534 (0.083)

20.759 (0.227)

39.095 (0.267)

3.444 (0.085)

0.1

S>1

4.709 (0.139)

17.500 (0.197)

0.336 (0.032)

5.605 (0.133)

18.347 (0.197))

1.248 (0.043)

 

S>2

1.172 (0.073)

9.541 (0.159)

0.130 (0.017)

2.073 (0.081)

10.425 (0.156)

1.041 (0.042)

 

S>0

23.170 (0.255)

51.539 (0.290)

3.499 (0.098)

23.964 (0.230)

52.237 (0.306)

4.393 (0.097)

0.2

S>1

3.343 (0.112)

18.415 (0.203)

0.250 (0.026)

4.243 (0.120)

19.249 (0.208)

1.160 (0.040)

 

S>2

0.534 (0.049)

7.555 (0.143)

0.109 (0.014)

1.443 (0.071)

8.444 (0.145)

1.015 (0.041)

 

S>0

25.398 (0.240)

64.217 (0.333)

4.243 (0.105)

26.210 (0.239)

64.855 (0.335)

5.134 (0.108)

0.4

S>1

2.259 (0.095)

17.193 (0.201)

0.181 (0.019)

3.164 (0.097)

18.017 (0.201)

1.090 (0.038)

 

S>2

0.267 (0.034)

4.916 (0.114)

0.103 (0.013)

1.175 (0.059)

5.808 (0.114)

1.010 (0.042)

 

S>0

26.772 (0.270)

74.504 (0.355)

4.717 (0.112)

27.578 (0.262)

75.097 (0.340)

5.609 (0.111)

0.8

S>1

1.591 (0.073)

14.860 (0.196)

0.143 (0.015)

2.492 (0.087)

15.706 (0.181)

1.054 (0.035)

 

S>2

0.171 (0.024)

2.870 (0.084)

0.101 (0.013)

1.076 (0.057)

3.773 (0.088)

1.010 (0.041)

  1. The average error rate is 0.005 per site. The average depth is 2X per individual in single line method, 2X per haploid genome in single platform method and 1X per haploid genome in each application in dual applications method. The means (and the standard deviations) of θ are estimated from 1000 replicates.