Skip to main content

Table 1 Parameters for the simulation scenarios

From: Detection and validation of structural variations in bovine whole-genome sequence data

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

  1. 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