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. 2017 Jan 25;49:13. doi: 10.1186/s12711-017-0286-5

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