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In cases where a functional annotation was available, there was no similarity between a marker pair suggesting that these SNPs belonged to different genes rather than to different contigs of the same gene.
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Mean values of LD for adjacent SNP pairs suggest that a higher density of markers will be required for powerful genome-wide association studies.
The nominal distanced between each marker pair was 100 mm.
For each marker pair, the population frequencies of the 4 possible two-marker haplotypes were computed.
Among the shared markers, we detected only one marker pair with significant recombination heterogeneities at α≤0.01 and another three marker pairs at α≤0.05.
LD was also high for marker pair rs737865 – Val/Met.
A marker could only appear in one affected marker pair in the data generation process.
Update the remaining marker set ẞ by removing the marker pair selected.
For each marker pair, the physical distance between markers was computed on a chromosome basis.
Correlation coefficients and respective P values of each DA matrix test with the full-loci dataset are shown in Table 2. Most coefficients of marker pairs are above 0.20 and respective P values are all less than 0.05, suggesting distance measurements by different markers are overall positively correlated.
Inversion of marker positions observed between Pop-DG and T × E in three locations (linkage groups G2, G3, and G5) were among marker pairs that were close together on the T × E map (< 10 cM), suggesting that they are more probably caused by errors in the assignment of marker order than to inversion of chromosome fragments [ 8].
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