Fregene: Simulation of realistic sequence-level data in populations and ascertained samples

BMC Bioinformatics

Table 1 Simulation parameters.

General parameters (only applies to populations A and B)
Chromosome Length	20 Mb
# Generations	200, 000
# Sequences	21, 000
Per-site mutation rate	2.3 × 10^-8
Recombination model
Per site crossover rate:	1.1 × 10^-8
Per site Gene conversion rate:	4.5 × 10^-9
Proportion of recombination events occurring in hotspots	80%
Hotspot length:	2.0 kb
Gene conversion length:	0.5 kb
Mean distance between hotspots:	8.5 kb
Selection parameters (if applicable)
Prop. of sites under selection:	5 × 10^-4
Proportion of selected sites locally under selection:	0.5
Mean # generations before selected sites are switched off	50, 000
selection coefficient:	s ~ 0.1 × $N$ (0.005, 0.05²) + 0.9 × $N$ (-0.01, 0.005²)
dominance coefficient:	h ~ 0.8 × $N$ (0.5, 0.2) + 0.3 × $N$ (1.2, 0.2²)

The first section only applies to populations A and B; the corresponding values for population C are detailed in the main the text and some are also illustrated in Figure 2.

ISSN: 1471-2105