Table 2.

CellCoal simulation parameters

Scenario	Constant rate			Variable rates
	No SNV errors	Varying FN errors	Varying FP errors	No SNV errors	Varying FN errors
Number of cells	30	30	30	100	100
Genome length	10,000	10,000	10,000	10,000	10,000
Mutation rate	1 × 10−6	1 × 10−6	1 × 10−6	8 × 10−7, 5 × 10−7, 3 × 10−7	8 × 10−7, 5 × 10−7, 3 × 10−7
Rate change factor	–	–	–	2×, 5×, 10×	2×, 5×, 10×
Number of cells subsampled	–	–	–	10, 30, 50, 70, 90	10, 30, 50, 70, 90
Sequencing depth mean (×)	20	20	20	20	20
Sequencing depth dispersion (×)	0	5	5	0	5
Sequencing error (%)	0	1	1	0	1
ADO per cell (mean) (%)	0	5, 10, 20, 40, 60	20	0	5, 10, 20, 40, 60
ADO per cell (variance) (%)	0	10	10	0	10
Amplification error (%)	0	1	0.1, 1, 2	0	1
Number of replicates	1,000	1,000	1,000	3,000	3,000

SNV, single-nucleotide variant; FN, false negative; FP, false positive; ADO, allelic dropout.