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In this situation, the level of linkage between regions would depend on the time elapsed between the hitchhiking events and the subsequent readjustment phenomena in the affected regions.
Only nine papers explicitly described some level of linkage between the study teams.
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Redevelopment, which retained a compact structure based upon spatial proximity, was found to encourage high levels of linkage between the component parts of the centre and generated favourable attitudes to the shopping environment.
To assess the level of linkage disequilibrium between SNPs, we calculated the pairwise r2 measure between consecutive pairs of markers throughout the genome using the expectation-maximization algorithm to estimate 2-locus haplotype frequencies which is implemented in the R package snpMatrix [48].
genepop software (v.3.1c, http://wbiomed.curtin.edu.au/genepop/; [34]) was used to calculate the level of linkage disequilibrium between all pairs of loci within regions.
There was a high level of linkage disequilibrium between certain allelic combinations of the two CD14 SNPs with a D′ statistics of 0.918.
Increasing marker density increases the level of linkage disequilibrium between quantitative trait loci (QTL) and SNPs and the accuracy of QTL localization and genomic selection.
The level of linkage disequilibrium between significant markers was determined by calculating r 2 statistics using the r2fast function implemented in GenABEL [ 29, 30, 37].
Due to a high level of linkage disequilibrium between the genes encoding TNF receptor associated factor 1 and complement component 5, it is currently not possible to assure which of these two genes at 9q33.2 encloses the causal variant.
For this breed, the Illumina® BovineHD chip (HD) is used as the "gold standard" for research purposes, since a low level of linkage disequilibrium between adjacent markers is observed in lower-density chips (e.g. 50 K) [ 6, 7].
Given the average size of cis-eQTL clusters (i.e., 248 to 456 kb), the average size of intervals between polymorphic SNPs in the RIS panel (2.59 ± 2.95 Mb) and the high level of linkage disequilibrium between adjacent informative SNPs (r = 0.8), the vast majority of neighboring and coexpressed cis-eQTLs within cis-eQTL clusters are likely to have the same allelic origin.
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