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In general, accuracies were greatest for QTL with a moderately low average MAF and smallest for QTL with an extremely low average MAF.
In each simulation, 100 or 1000 QTL were sampled assuming that they followed one of the three QTL MAF patterns i.e. moderately low average MAF, very low average MAF, or extremely low average MAF.
When genotypes for the imputed variants representing QTL were included in the dataset used to calculate G a and G w, genotypes of all imputed variants in the three classes were used i.e. 80 515 variants with a moderately low average MAF, 97 296 with a very low average MAF and 4064 with an extremely low average MAF.
All variants that segregated in the entire dataset, consisting of 3000 Holstein-Friesian and 3000 Jersey individuals, were considered as potential QTL, which resulted in 65 920 potential QTL with a moderately low average MAF, 67 097 with a very low average MAF, and 2142 with an extremely low average MAF.
For the multi-breed reference populations, the proportion of variance explained by the within-breed animal component was equal to ~27% and ~52% for the RANDOM and VAR scenarios, respectively, when QTL had a moderately low average MAF, ~33% and ~53% when QTL had a very low average MAF, and ~40% and ~63% when QTL had an extremely low average MAF.
In general, the absolute difference in accuracy was only ~0.01 between the averages after five and 10 replicates for all scenarios using the base model and QTL with a moderately low average MAF, very low average MAF or extremely low average MAF.
Similar(51)
(A) Variants with on average a moderately low minor allele frequency; (B) Variants with on average a very low minor allele frequency; (C) Variants with on average an extremely low minor allele frequency.
Genotypes of three classes of variants obtained from whole-genome sequence data, with moderately low, very low or extremely low average minor allele frequencies (MAF), were imputed in 3000 Holstein-Friesian and 3000 Jersey cows that had real high-density genotypes.
The study area was divided into five zones (low, moderately low moderate, moderately high and high) on the basis of relative groundwater vulnerability to pollution index.
Description: Figure S1 shows the distribution of allele frequencies of variants with on average a moderately low minor allele frequency (MAF), very low MAF or extremely low MAF in real data and imputed data for Holstein-Friesian animals.
Description: Figure S2 shows the distribution of allele frequencies of variants with on average a moderately low minor allele frequency (MAF), very low MAF or extremely low MAF in real data and imputed data for Jersey animals.
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pretty low average
comparatively low average
relatively low average
fairly low average
quite low average
reasonably low average
rather low average
moderately heritable average
moderately low nitrate
moderately differentiated average
moderately low dose
moderately low Vp
moderately low variability
moderately cold average
moderately low value
moderately overweight average
moderately low temperature
moderately low expression
moderately high average
moderately useful average
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