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A plot of pairwise linkage disequilibrium values log(p) against R showed that the most significant linkages between a reference SNP and its linked SNP occurred for R > 0.8 (Additional file 1: Figure S1).
A decreasing LOD (Log10 of the odd ratio) score approach (from 6 to 3, step = 1) was used to reveal the most significant linkages (LOD = 6) to the weakest linkages (LOD = 3) and was used to group linked markers in LGs.
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Microsatellite INRA004 shows the most significant linkage with the rex phenotype among the 359 rabbits (LOD = 78; ⊖ = 0).
However, the most significant linkage was found for male normal weight gallstone carriers (p = 0.01410, OR = 6.85), indicating that the occurrence of the rs9514089 polymorphism is gender- and weight-specific.
The most significant linkage was recorded for each permutation round.
The most significant linkage was between marker FCA700 and Tabby (Z = 7.56, θ = 0.03).
The marker with most significant linkage was added to the mapping model as a cofactor.
Of the 671 SNPs analyzed, the most significant linkage to susceptibility to PIFS was observed with markers on chromosomes 12 and 17, as illustrated by log-likelihood plots.
For the subset analyses, the most significant linkage signal was on chromosome 15q13.3-q14 for IQ ≥ 70 (LOD score = 4.01, p =.00001, δ [the locus-specific effect size] =.25).
For the most significant linkage results from the subset analyses, the FLexible Ordered SubSet (FLOSS v1.4.1, http://www.stat.auckland.ac.nz/∼browning/floss/floss.htm osa) software was used to generate empirical p values (47).
For the most significant linkage result on chromosome 11 (LOD score = 3.40, p =.00004 for the ASD families with DelayedPhrase and LOD score = 1.75, p =.002 for all the ASD families), the probability that a subset of 412 families randomly selected from all the ASD families could reach a LOD score of 3.40 at this locus was.03 with a 95% confidence interval of.02 tof.02
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