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All polymorphisms that are only in linkage disequilibrium with functional ones should be excluded from both lists.
In many cases, the causal variant is unknown, and the associated marker is only in linkage disequilibrium with the actual site.
Clearly, many of these SNPs are not only in linkage disequilibrium but also the genes studied are part of interacting pathways.
A 'high- FST peak' approximately in the same genomic location was observed only in linkage groups 13 and 18, but the peaks were detected in only two of the three comparisons.
The additional difficulty is due in part to the study of polymorphisms that are not causal of the interaction, but only in linkage disequilibrium (LD) with the nongenotyped causal polymorphisms (markers or tags) [ 44].
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Here, 33-ϕ-OEG-lipid and 33-OEG-lipid possess the same trisaccharide and differ only in the linkage: the bulkier click-linkage to OEG in the former or the peptide linkage to OEG in the latter.
Pairwise Fst was calculated in Microsatellite Analyser 4.2 [17] between all 12 BC populations, NC and SC, and between BC populations pooled with NC and SC, with 10 000 permutations on alleles using only loci in linkage and HW equilibrium.
However, the loci identified may only be in linkage disequilibrium with the functional site(s).
By setting a significance threshold, only variants in linkage disequilibrium (LD) with undiscovered mutations of moderate effect size are effectively considered in the enrichment or depletion analysis.
The only primers in linkage disequilibrium were found in C. angusta (Camas29/56, Camas33/49, Camas29/49, and Camas62/90) and C. leichtlinii (Camas13/51, Camas20/51, Camas33/90, and Camas51/56).
H3 is likely only in partial linkage (i.e., D'<1.0) with the causal variants, and the underlying functional alleles are probably both common and rare [52], [56].
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