Table 1.

Parameters for the simulation scenarios

Simulation set	HOM	HET	Base error rate	Repetitive	SNP% in SV	Mix
HOM/HET	HOM	HET	HOM	HOM	HOM	HET
SNP% in SV	0	0	0	0	0.01–0.25	0.01
REP region	0	0	0	100%	0	50%
Number of SV	100 × 3	100 × 3	100 × 3	100 × 3	100 × 3	100 × 3
Insert size	500	500	500	500	500	500
SD of insert size	50	50	50	50	50	50
Base error rate	0.01	0.01	0.001–0.025	0.01	0.01	0.01
SNP rate	0.01	0.01	0.01	0.01	0.01	0.008
Indel rate	0.01	0.01	0.01	0.01	0.01	0.01

HOM/HET represents homozygous and heterozygous SV, respectively; SNP% in SV represents the percentage of SNPs that occur in a SV region; REP region represents the percentage of SV that fall in repetitive regions (LINE regions). One hundred each for deletions, inversions and tandem duplications were simulated under each simulation. Default insert size and standard deviation of insert size of 500 and 50, respectively, were used; SNP rate is the overall SNP percentage that exists across the whole cattle genome