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Table 1 Characteristics of different classes of variants used to simulate QTL

From: Impact of QTL properties on the accuracy of multi-breed genomic prediction

Characteristic per class Holstein-Friesian Jersey Total
Moderately low average MAF 1,2
Segregating variants 63 119 55 363 65 920
Number of breed-specific variants 10 557 2801 13 358
Percentage of breed-specific variants 16.0 4.2 20.3
Average MAF1 of the 65 920 segregating variants (± standard deviation) 0.130 ± 0.169 0.115 ± 0.168 0.122 ± 0.146
Very low average MAF 1,3
Segregating variants 61 302 49 473 67 097
Number of breed-specific variants 17 624 5795 23 419
Percentage of breed-specific variants 26.3 8.6 34.9
Average MAF1 of the 67 097 segregating variants (± standard deviation) 0.082 ± 0.146 0.072 ± 0.142 0.077 ± 0.127
Extremely low average MAF 1,4
Segregating variants 1804 1245 2142
Number of breed-specific variants 897 338 1235
Percentage of breed-specific variants 41.9 15.8 57.7
Average MAF1 of the 2142 segregating variants (± standard deviation) 0.017 ± 0.067 0.015 ± 0.066 0.016 ± 0.059
  1. 1MAF = minor allele frequency; 2annotated as synonymous mutations; 3annotated as missense mutations; 4annotated as premature stop codon mutations.