Table 2.

Effective Sample Size for Association Test

Method	Percent of Samples Contaminated
5%	10%	25%	50%	75%	90%	100%
	Low-Pass
Adjusted	194	194	193	192	191	190	190
Ignored	193	193	190	186	182	179	177
Dropped	184	174	144	96	47	18	0
	High-Depth
Adjusted	195	195	195	194	194	193	193
Ignored	195	194	192	189	186	184	182
Dropped	186	176	146	98	48	18	0

Shown here are the effective sample size estimates when α = 10% and total sample size is 198 under three scenarios: all samples included and adjusted with our method (“adjusted”), all samples included but contamination ignored (“ignored”), and contaminated samples $\left(\hat{\alpha }>0.01\right)$ removed from analysis (“dropped”).