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Statistics on genomic relationships between reference and validation sets are in Table 2.
Furthermore, the accuracy of imputation has been shown to depend on the relationship between reference and validation animals [ 7].
Distributions of genomic relationships between reference and validation populations obtained with different scenarios of imputation are represented by density curves in Fig. 4.
As imputation accuracy depends (amongst others) on the relationship between reference individuals and individuals to be imputed, the trend of imputation accuracy when there was a different number of generations between reference and validation individuals was investigated.
The model tests the effect of reference population size, relationship between reference and validation populations, level of linkage disequilibrium at 70 kb, and number of effective ancestors on imputation error rate.
Differences in imputation accuracy between breeds were related to the high-density-genotyped sample size and to the genetic relationship between reference and validation populations, whereas differences in effective population size and level of linkage disequilibrium showed limited effects.
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The gene-based validation between the reference and validation studies was hampered by the use of different microarray platforms with different probes and probe content.
The proportion of shared haplotypes between the reference and validation populations gives an appropriate interpretation for the performance of imputation in both purebred and crossbred pigs.
To avoid use of overlapping information between the reference and validation animals [ 20], we based the validation on the own phenotype of genotyped validation animals, adjusted for fixed effects and non-genetic random effects.
If a haplotype in the validation population could exactly match at least one haplotype at the same position in the reference population, this haplotype was considered to be shared between the reference and validation populations.
Second, low genetic relatedness between reference animals and validation animals appears to favour mixture-distribution models [ 14], presumably because mixture-distribution models utilize linkage disequilibrium more efficiently than normal and thick tailed distribution models.
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