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Thus, approximately 1175 out of these 1206 significant tests are expected to be truly alternative in the sense that a cis-acting or trans-acting QTL is linked to the marker in question.
With the list of positive BAC clones for the marker in question, the anchoring process is completed.
The map distance between the target marker in question and the most highly associated marker was used to evaluate the resolution of the panel.
Heterozygosity corresponds to a probability that two alleles taken at random from a population can be distinguished using the marker in question.
The single-step permuted p-value for any given marker was then calculated as the fraction of maximal beta values that were greater than or equal to the absolute value of the unshuffled test statistic for the marker in question.
If the target of the top hit (i.e., the alignment with the lowest e-value) for a given marker sequence agreed with the target reported for one or more other markers on the same linkage group that returned only a single robust hit, then the top hit for the marker in question was considered "supported" and retained.
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Two measures of LD were investigated; D' measures the degree to which recombination has occurred between the two markers in question, while r2 measures the statistical correlation between two loci.
Where one or the other map suggested a merging of linkage groups, or if groupings conflicted, the markers in question were re-tested with JoinMap v.3 [ 34] using a small data set that included only those markers.
Criteria are needed to a) identify markers that have the promise to be clinically useful; b) assess the best methodology for clinical evaluation of the markers in question and c) confirm or validate that using the marker adds useful information compared to using standard prognostic factors alone.
Each solution was subjected to the analysis of its computational complexity, expressing the cost in terms of the number of samples, markers, and traits in question.
SIM tests for the presence of a QTL at any location along the genome using the nearest fully informative genetic markers (flanking markers) that capture the position in question.
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