Table 2 Type I error rates stratified by variant-specific AAC, MAF, and average genotype quality
Response variable | Regression model | Median AAC | # P values | # Nonmissing p values | % Nonmissing p values | % Nonmissing p values under 0.05 |
AAC | ZI-NB | [0,60] | 4728 | 3598 | 76.1 | 0.050 |
(60,254) | 4089 | 2917 | 71.3 | 0.080 | ||
254 | 105 | 84 | 80.0 | 0.083 | ||
(254,426] | 35 | 9 | 25.7 | 0.000 | ||
Hu-NB | [0,60] | 4728 | 3580 | 75.7 | 0.029 | |
(60,254) | 4089 | 2912 | 71.2 | 0.043 | ||
254 | 105 | 84 | 80.0 | 0.036 | ||
(254,426] | 35 | 9 | 25.7 | 0.111 | ||
AAC/total read depth | Standard linear (SL) | [0,60] | 4728 | 4719 | 99.8 | 0.062 |
(60,254) | 4089 | 4088 | 100.0 | 0.062 | ||
254 | 105 | 105 | 100.0 | 0.029 | ||
(254,426] | 35 | 35 | 100.0 | 0.114 | ||
Robust linear (RL) | [0,60] | 4728 | 767 | 16.2 | 0.068 | |
(60,254) | 4089 | 708 | 17.3 | 0.068 | ||
254 | 105 | 10 | 9.5 | 0.100 | ||
(254,426] | 35 | 24 | 68.6 | 0.083 | ||
Response variable | Regression model | MAF | # P values | # Nonmissing p values | % Nonmissing p values | % Nonmissing p values under 0.05 |
AAC | ZI-NB | [0.003,0.01] | 3707 | 3694 | 99.6 | 0.036 |
(0.01,0.05] | 1927 | 1895 | 98.3 | 0.144 | ||
>0.05 | 3323 | 1019 | 30.7 | 0.016 | ||
Hu-NB | [0.003,0.01] | 3707 | 3695 | 99.7 | 0.044 | |
(0.01,0.05] | 1927 | 1886 | 97.9 | 0.031 | ||
>0.05 | 3323 | 1004 | 30.2 | 0.011 | ||
AAC/total read depth | SL | [0.003,0.01] | 3707 | 3698 | 99.8 | 0.058 |
(0.01,0.05] | 1927 | 1927 | 100.0 | 0.053 | ||
>0.05 | 3323 | 3322 | 100.0 | 0.072 | ||
RL | [0.003,0.01] | 3707 | 2 | 0.1 | 0.000 | |
(0.01,0.05] | 1927 | 0 | 0.0 | 0.000 | ||
>0.05 | 3323 | 1507 | 45.4 | 0.068 | ||
Response variable | Regression model | Average genotype quality | # P values | # Nonmissing p values | % Nonmissing p values | % Nonmissing p values under 0.05 |
AAC | ZI-NB | Low | 2985 | 2973 | 99.6 | 0.067 |
Medium | 2986 | 2810 | 94.1 | 0.060 | ||
High | 2986 | 825 | 27.6 | 0.058 | ||
Hu-NB | Low | 2985 | 2974 | 99.6 | 0.044 | |
Medium | 2986 | 2812 | 94.1 | 0.031 | ||
High | 2986 | 799 | 26.7 | 0.016 | ||
AAC/total read depth | SL | Low | 2985 | 2975 | 99.7 | 0.056 |
Medium | 2986 | 2986 | 100.0 | 0.062 | ||
High | 2986 | 2986 | 100.0 | 0.068 | ||
RL | Low | 2985 | 9 | 0.3 | 0.000 | |
Medium | 2986 | 96 | 3.2 | 0.031 | ||
High | 2986 | 1404 | 47.0 | 0.071 |