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Table 2 Proportion of p values < 0.05 in 1000 times for different levels of linkage using summary statistics (only “Bias = Both” is shown, more details in Additional file 14: Table S7)

From: mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes

X.1 Panel size Number of linked markers Linkage Bias Total number of heterozygous loci (K) Total number of shared alleles (X)
1 10 0 Unlinked Both 0.047 0.039
2 20 0 Unlinked Both 0.05 0.036
3 30 0 Unlinked Both 0.051 0.048
4 40 0 Unlinked Both 0.055 0.038
5 50 0 Unlinked Both 0.045 0.053
6 100 0 Unlinked Both 0.047 0.051
31 16 2 HalfQuarter-Linked Both 0.045 0.044
32 32 4 HalfQuarter-Linked Both 0.069 0.041
33 48 6 HalfQuarter-Linked Both 0.072 0.063
34 64 8 HalfQuarter-Linked Both 0.082 0.065
35 80 10 HalfQuarter-Linked Both 0.094 0.068
36 96 12 HalfQuarter-Linked Both 0.109 0.069
53 8 2 Quarter-Linked Both 0.015 0.047
54 16 4 Quarter-Linked Both 0.03 0.058
55 24 6 Quarter-Linked Both 0.057 0.074
56 32 8 Quarter-Linked Both 0.052 0.094
57 40 10 Quarter-Linked Both 0.186 0.09
58 64 16 Quarter-Linked Both 0.303 0.137
59 80 20 Quarter-Linked Both 0.382 0.154
60 96 24 Quarter-Linked Both 0.421 0.209
81 8 4 Half-Linked Both 0.011 0.116
82 12 6 Half-Linked Both 0.29 0.15
83 16 8 Half-Linked Both 0.326 0.171
84 20 10 Half-Linked Both 0.388 0.221
85 24 12 Half-Linked Both 0.419 0.242
86 32 16 Half-Linked Both 0.513 0.297
87 40 20 Half-Linked Both 0.638 0.374
88 60 30 Half-Linked Both 0.83 0.516
89 80 40 Half-Linked Both 0.934 0.687
90 100 50 Half-Linked Both 0.982 0.819
105 16 12 ThreeQuarter-Linked Both 0.582 0.372
106 24 18 ThreeQuarter-Linked Both 0.738 0.499
107 32 24 ThreeQuarter-Linked Both 0.845 0.635
108 40 30 ThreeQuarter-Linked Both 0.914 0.719
109 64 48 ThreeQuarter-Linked Both 0.986 0.943
110 80 60 ThreeQuarter-Linked Both 0.997 0.974
111 96 72 ThreeQuarter-Linked Both 0.999 0.995
124 10 10 Fully-Linked Both 0.604 0.404
125 20 20 Fully-Linked Both 0.835 0.691
126 30 30 Fully-Linked Both 0.957 0.849
127 40 40 Fully-Linked Both 0.989 0.936
128 50 50 Fully-Linked Both 0.997 0.973
129 100 100 Fully-Linked Both 1 1
  1. For both number of heterozygous loci and number of shared alleles, the proportions of detecting dependency in unlinked dataset are approximately less than 5%; in fully linked dataset, is over 70% when the number of markers is larger than 10. When the percentage of linked markers increases, the power of test increases