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Perfect linkage was nevertheless found between a kanamycin resistance marker and the mutant phenotype (0 EMB/EMB plants among 204 resistant transplants screened), consistent with T-DNA tagging [4].
The opposite extreme is perfect linkage.
If the values used in the linkage have not been masked, then we can expect perfect linkage accuracy.
These SNPs, although not functional, are in perfect linkage disequilibrium (LD) with the causal polymorphism in this material, and therefore can be utilized to identify varieties carrying the favorable allele.
These estimates also assume that the SNP genotyped is in perfect linkage disequilibrium (Δ2 = 1) with the causal polymorphism.
Variant 3 (v3) is in near perfect linkage disequilibrium with v311 but it occurs less frequently that v311.
Also this polymorphism is in perfect linkage disequilibrium (r2 = 1) with a missense mutation Thr504Ala (SNP-110) and two polymorphisms in the 5'-UTR region (UCSNP134 and UCSNP135) [38].
This score provides an estimate of disease association by using the linkage disequilibrium score (range 0 to 1, where 1 is perfect linkage disequilibrium) as a weighting for the p-value for a given SNP.
Polymorphisms T1088A and C1095A were in perfect linkage disequilibrium.
† trans eSNPs were grouped within blocks of perfect linkage disequilibrium (r = 1).
Protective haplotypes were in perfect linkage (r = 1.0) with a nonsynonymous coding variant (rs8103142).
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