HPM baseline: influence of A/missing data
distance = 1cM

A\missing      0%    5%   10%   15%   20%
10.0%        0.42  0.43  0.31  0.36  0.33
7.5%         0.39  0.35  0.33  0.27  0.18
5.0%         0.11  0.07  0.07  0.08  0.06
2.5%         0.04  0.03  0.02  0.04  0.02


distance = 2cM

A\missing      0%    5%   10%   15%   20%
10.0%        0.62  0.63  0.57  0.62  0.51
7.5%         0.66  0.55  0.54  0.46  0.35
5.0%         0.25  0.18  0.16  0.15  0.08
2.5%         0.06  0.05  0.03  0.08  0.02


distance = 5cM

A\missing      0%    5%   10%   15%   20%
10.0%        0.93  0.93  0.87  0.87  0.80
7.5%         0.84  0.78  0.81  0.65  0.58
5.0%         0.58  0.37  0.25  0.26  0.21
2.5%         0.10  0.11  0.08  0.11  0.11


distance = 10cM

A\missing      0%    5%   10%   15%   20%
10.0%        0.98  0.97  0.93  0.95  0.85
7.5%         0.94  0.86  0.87  0.79  0.70
5.0%         0.64  0.50  0.39  0.41  0.33
2.5%         0.17  0.22  0.17  0.24  0.21


HPM baseline: influence of A/corrupted data
distance = 1cM

A\corrupted      0%    1%    2%    5%   10%
10.0%          0.42  0.44  0.45  0.35  0.29
7.5%           0.39  0.40  0.33  0.37  0.26
5.0%           0.11  0.13  0.12  0.12  0.06
2.5%           0.04  0.04  0.04  0.02  0.01


distance = 2cM

A\corrupted      0%    1%    2%    5%   10%
10.0%          0.62  0.63  0.62  0.62  0.56
7.5%           0.66  0.68  0.59  0.58  0.49
5.0%           0.25  0.24  0.23  0.23  0.18
2.5%           0.06  0.06  0.05  0.04  0.05


distance = 5cM

A\corrupted      0%    1%    2%    5%   10%
10.0%          0.93  0.92  0.93  0.97  0.81
7.5%           0.84  0.87  0.86  0.78  0.73
5.0%           0.58  0.49  0.54  0.45  0.27
2.5%           0.10  0.08  0.09  0.12  0.10


distance = 10cM

A\corrupted      0%    1%    2%    5%   10%
10.0%          0.98  0.98  0.98  1.00  0.94
7.5%           0.94  0.94  0.93  0.87  0.79
5.0%           0.64  0.61  0.60  0.54  0.34
2.5%           0.17  0.12  0.19  0.24  0.17


Long haplotypes: influence of A/missing data
distance = 1cM

A\missing      0%    5%   10%   15%   20%
10.0%        0.30  0.36  0.32  0.22  0.27
7.5%         0.37  0.34  0.34  0.27  0.18
5.0%         0.11  0.07  0.07  0.08  0.06
2.5%         0.04  0.03  0.02  0.04  0.02


distance = 2cM

A\missing      0%    5%   10%   15%   20%
10.0%        0.56  0.59  0.52  0.51  0.53
7.5%         0.62  0.57  0.56  0.46  0.35
5.0%         0.24  0.18  0.16  0.15  0.08
2.5%         0.06  0.05  0.03  0.08  0.04


distance = 5cM

A\missing      0%    5%   10%   15%   20%
10.0%        0.91  0.90  0.88  0.85  0.88
7.5%         0.83  0.79  0.82  0.65  0.58
5.0%         0.57  0.37  0.25  0.26  0.21
2.5%         0.10  0.11  0.09  0.11  0.10


distance = 10cM

A\missing      0%    5%   10%   15%   20%
10.0%        0.98  0.97  0.93  0.89  0.92
7.5%         0.93  0.86  0.88  0.79  0.70
5.0%         0.64  0.50  0.39  0.41  0.33
2.5%         0.17  0.23  0.21  0.24  0.20


Long haplotypes: influence of A/corrupted data
distance = 1cM

A\corrupted      0%    1%    2%    5%   10%
10.0%          0.44  0.42  0.45  0.41  0.26
7.5%           0.42  0.45  0.29  0.28  0.19
5.0%           0.14  0.13  0.09  0.14  0.08
2.5%           0.02  0.04  0.03  0.02  0.00


distance = 2cM

A\corrupted      0%    1%    2%    5%   10%
10.0%          0.66  0.66  0.68  0.65  0.51
7.5%           0.68  0.70  0.57  0.60  0.40
5.0%           0.30  0.29  0.21  0.29  0.13
2.5%           0.05  0.07  0.04  0.05  0.02


distance = 5cM

A\corrupted      0%    1%    2%    5%   10%
10.0%          0.91  0.94  0.92  0.93  0.84
7.5%           0.88  0.92  0.84  0.86  0.64
5.0%           0.48  0.45  0.40  0.46  0.24
2.5%           0.10  0.12  0.12  0.11  0.11


distance = 10cM

A\corrupted      0%    1%    2%    5%   10%
10.0%          0.98  1.00  0.98  0.96  0.92
7.5%           0.92  0.95  0.87  0.89  0.76
5.0%           0.58  0.58  0.51  0.54  0.36
2.5%           0.20  0.22  0.26  0.26  0.18


Long gaps: influence of A/missing data
distance = 1cM

A\missing      0%    5%   10%   15%   20%
10.0%        0.40  0.39  0.36  0.22  0.25
7.5%         0.39  0.33  0.33  0.26  0.17
5.0%         0.11  0.07  0.06  0.08  0.06
2.5%         0.04  0.03  0.02  0.04  0.02


distance = 2cM

A\missing      0%    5%   10%   15%   20%
10.0%        0.62  0.58  0.54  0.51  0.52
7.5%         0.65  0.54  0.55  0.45  0.34
5.0%         0.25  0.19  0.16  0.15  0.08
2.5%         0.06  0.05  0.03  0.08  0.05


distance = 5cM

A\missing      0%    5%   10%   15%   20%
10.0%        0.93  0.91  0.89  0.86  0.87
7.5%         0.85  0.78  0.81  0.65  0.57
5.0%         0.57  0.38  0.25  0.26  0.22
2.5%         0.10  0.11  0.09  0.11  0.11


distance = 10cM

A\missing      0%    5%   10%   15%   20%
10.0%        0.98  0.96  0.94  0.89  0.92
7.5%         0.94  0.86  0.87  0.80  0.70
5.0%         0.64  0.51  0.39  0.41  0.34
2.5%         0.16  0.22  0.21  0.24  0.21


Long gaps: influence of A/corrupted data
distance = 1cM

A\corrupted      0%    1%    2%    5%   10%
10.0%          0.40  0.37  0.41  0.36  0.29
7.5%           0.39  0.40  0.31  0.35  0.24
5.0%           0.11  0.12  0.10  0.12  0.05
2.5%           0.04  0.04  0.04  0.02  0.00


distance = 2cM

A\corrupted      0%    1%    2%    5%   10%
10.0%          0.62  0.59  0.61  0.64  0.56
7.5%           0.65  0.65  0.59  0.58  0.49
5.0%           0.25  0.24  0.23  0.24  0.17
2.5%           0.06  0.07  0.05  0.04  0.04


distance = 5cM

A\corrupted      0%    1%    2%    5%   10%
10.0%          0.93  0.91  0.94  0.97  0.82
7.5%           0.85  0.89  0.85  0.79  0.73
5.0%           0.57  0.48  0.53  0.47  0.28
2.5%           0.10  0.10  0.09  0.12  0.09


distance = 10cM

A\corrupted      0%    1%    2%    5%   10%
10.0%          0.98  0.99  0.98  1.00  0.93
7.5%           0.94  0.95  0.93  0.87  0.79
5.0%           0.64  0.60  0.61  0.54  0.34
2.5%           0.16  0.15  0.22  0.23  0.16


No gaps: influence of A/missing data
distance = 1cM

A\missing      0%    5%   10%   15%   20%
10.0%        0.44  0.38  0.35  0.35  0.27
7.5%         0.42  0.28  0.28  0.16  0.17
5.0%         0.14  0.09  0.08  0.07  0.02
2.5%         0.02  0.01  0.00  0.01  0.02


distance = 2cM

A\missing      0%    5%   10%   15%   20%
10.0%        0.66  0.63  0.59  0.56  0.45
7.5%         0.68  0.52  0.58  0.42  0.32
5.0%         0.30  0.16  0.16  0.12  0.07
2.5%         0.05  0.03  0.01  0.04  0.04


distance = 5cM

A\missing      0%    5%   10%   15%   20%
10.0%        0.91  0.92  0.83  0.76  0.72
7.5%         0.88  0.76  0.75  0.55  0.46
5.0%         0.48  0.36  0.22  0.20  0.17
2.5%         0.10  0.11  0.13  0.12  0.11


distance = 10cM

A\missing      0%    5%   10%   15%   20%
10.0%        0.98  0.97  0.90  0.80  0.80
7.5%         0.92  0.80  0.82  0.66  0.59
5.0%         0.58  0.46  0.36  0.34  0.34
2.5%         0.20  0.15  0.20  0.20  0.17


No gaps: influence of A/corrupted data
distance = 1cM

A\corrupted      0%    1%    2%    5%   10%
10.0%          0.44  0.42  0.45  0.41  0.26
7.5%           0.42  0.45  0.29  0.28  0.19
5.0%           0.14  0.13  0.09  0.14  0.08
2.5%           0.02  0.04  0.03  0.02  0.00


distance = 2cM

A\corrupted      0%    1%    2%    5%   10%
10.0%          0.66  0.66  0.68  0.65  0.51
7.5%           0.68  0.70  0.57  0.60  0.40
5.0%           0.30  0.29  0.21  0.29  0.13
2.5%           0.05  0.07  0.04  0.05  0.02


distance = 5cM

A\corrupted      0%    1%    2%    5%   10%
10.0%          0.91  0.94  0.92  0.93  0.84
7.5%           0.88  0.92  0.84  0.86  0.64
5.0%           0.48  0.45  0.40  0.46  0.24
2.5%           0.10  0.12  0.12  0.11  0.11


distance = 10cM

A\corrupted      0%    1%    2%    5%   10%
10.0%          0.98  1.00  0.98  0.96  0.92
7.5%           0.92  0.95  0.87  0.89  0.76
5.0%           0.58  0.58  0.51  0.54  0.36
2.5%           0.20  0.22  0.26  0.26  0.18


SNP data: missing = 12.5%

A\distance     1cM   2cM   5cM  10cM
10.0%         0.37  0.63  0.90  0.94
7.5%          0.18  0.37  0.49  0.63
5.0%          0.07  0.12  0.27  0.35
2.5%          0.04  0.05  0.16  0.24