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