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Not all deviations from the genome project's reference sequences are harmful mutations.
As a threshold, we select those windows/genes having an R value two standard deviations from the genome average R value as exhibiting unusual compositional properties.
Nonsynonymous sites and RNA genes also exhibit large deviations from the genome average, suggesting that selective effects (both adaptive and constraining) are also acting to exacerbate or mitigate these mutational biases.
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The significance of deviation from the genome average for the unique, segmental duplicate and tandem duplicate groups was estimated via bootstrap analysis as described above.
The significance of deviation from the genome average for the unique, segmental duplicate and tandem duplicate groups was estimated via bootstrapping as described above.
For non-vertebrate genomes, simulations show that the deviations from the vertebrate genome can be explained by excessive intron loss.
A deviation from the genome-wide average of one parental population ancestry seen in cases but not in controls provided evidence of a disease locus.
Subsequently, we estimated the number of eQTLs within each set either up or down regulated in any accession and test for deviation from the genome-wide 1.6 1 Col Cvi eQTL ratio using a hypergeometric test [ 20].
Frazer et al. (41) recommended an empirical rule of thumb, which was to identify regions as strong candidates for selection only if >10% of SNPs within a 100 kb region have an LRH score [ln REHH) deviation from the genome-wide average] greater than 3.92.
These offer higher sensitivity over the RP-guided hybrid approaches because they can analyze the smallest deviations from the reference genome on a single nucleotide level.
Using a combination of wet lab and dry lab approaches, we demonstrated the feasibility in resolving regions that have marked deviations from the reference genome.
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