Journal of Probability and Statistics

Research Article

Design and Statistical Analysis of Pooled Next Generation Sequencing for Rare Variants

Table 1

Estimated bias and standard error (SE) of the sequencing error rate and the allele frequency for the unbalanced and balanced designs under different sequencing depths of coverage, numbers of pools, allele frequencies, and sequencing error rates.
Depths of coveragePool number θeUnbalanced designBalanced design
 Bias (e)SE (e)Bias (θ)SE (θ)Bias (e)SE (e)Bias (θ)
5×  0.01 0.005 0.0000 0.0015 0.0002 0.0029 −0.0011 0.0007 0.0011 0.0019
2 0.01 −0.0001 0.0020 0.0001 0.0034 −0.0063 0.0014 0.0062 0.0025
  0.05 0.005 −0.0002 0.0014 0.0002 0.0046 −0.0011 0.0056 0.0010 0.0062
  0.01 −0.0002 0.0019 0.0002 0.0051 −0.0066 0.0054 0.0061 0.0060
  0.01 0.005 −0.0001 0.0014 0.0003 0.0028 −0.0009 0.0024 0.0011 0.0029
10 0.01 0.0000 0.0021 0.0003 0.0034 −0.0074 0.0027 0.0078 0.0033
  0.05 0.005 0.0002 0.0014 −0.0004 0.0047 0.0084 0.0116 −0.0076 0.0108
  0.01 0.0000 0.0020 −0.0001 0.0051 0.0031 0.0127 −0.0032 0.0119
  0.01 0.005 0.0002 0.0014 −0.0001 0.0027 0.0007 0.0017 −0.0003 0.0017
40 0.01 0.0001 0.0020 0.0001 0.0034 −0.0005 0.0033 0.0010 0.0038
  0.05 0.005 0.0019 0.0015 −0.0018 0.0046 0.0098 0.0063 −0.0078 0.0058
  0.01 0.0009 0.0020 −0.0005 0.0048 0.0090 0.0079 −0.0073 0.0072
10×  0.01 0.005 −0.0001 0.0010 0.0002 0.0020 −0.0006 0.0002 0.0006 0.0012
2 0.01 −0.0001 0.0014 0.0001 0.0025 −0.0056 0.0001 0.0055 0.0014
  0.05 0.005 −0.0001 0.0010 0.0000 0.0033 0.0002 0.0035 −0.0002 0.0038
  0.01 −0.0001 0.0014 0.0004 0.0035 −0.0049 0.0033 0.0045 0.0039
  0.01 0.005 0.0000 0.0010 0.0000 0.0020 −0.0003 0.0017 0.0004 0.0019
10 0.01 0.0000 0.0014 0.0000 0.0024 −0.0074 0.0023 0.0076 0.0029
  0.05 0.005 0.0000 0.0010 0.0001 0.0032 0.0041 0.0093 −0.0037 0.0087
  0.01 −0.0001 0.0014 0.0001 0.0037 −0.0010 0.0101 0.0009 0.0093
  0.01 0.005 0.0000 0.0009 0.0001 0.0017 0.0006 0.0010 −0.0001 0.0008
40 0.01 0.0000 0.0014 0.0002 0.0023 0.0002 0.0015 0.0001 0.0011
  0.05 0.005 0.0006 0.0011 −0.0004 0.0032 0.0035 0.0021 −0.0021 0.0024
  0.01 0.0003 0.0016 0.0000 0.0035 0.0025 0.0032 −0.0015 0.0032
20×  0.01 0.005 −0.0001 0.0006 0.0001 0.0014 −0.0003 0.0001 0.0003 0.0009
2 0.01 −0.0001 0.0010 0.0001 0.0017 −0.0053 0.0000 0.0052 0.0010
  0.05 0.005 0.0000 0.0007 0.0001 0.0024 0.0000 0.0023 0.0000 0.0027
  0.01 −0.0001 0.0010 0.0001 0.0025 −0.0051 0.0014 0.0047 0.0021
  0.01 0.005 −0.0001 0.0007 0.0001 0.0014 −0.0002 0.0011 0.0003 0.0011
10 0.01 0.0000 0.0010 0.0000 0.0017 −0.0074 0.0026 0.0076 0.0032
  0.05 0.005 0.0000 0.0007 0.0000 0.0023 0.0003 0.0034 −0.0002 0.0035
  0.01 0.0000 0.0010 0.0001 0.0026 −0.0047 0.0042 0.0043 0.0042
  0.01 0.005 0.0001 0.0006 0.0000 0.0010 0.0004 0.0007 0.0000 0.0004
40 0.01 0.0000 0.0009 0.0001 0.0013 0.0002 0.0009 0.0000 0.0005
  0.05 0.005 0.0002 0.0008 −0.0002 0.0022 0.0019 0.0013 −0.0006 0.0014
  0.01 0.0002 0.0011 −0.0001 0.0024 0.0009 0.0019 −0.0003 0.0017