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Replication, detailed genotyping, and functional studies subsequently determine which of the variations in a given locus are most likely to be directly associated with disease and which are inherited along with other variants in the population (linkage disequilibrium).
There can be several prioritized genes in a given locus.
This test compares whether the level of intra-specific polymorphism parallels the level of nucleotide divergence between two species in a given locus relative to neutrally evolving loci.
Finally, from a set of overlapping transcripts in a given locus, a single representative transcript that had the longest CDS was selected.
If multiple SNPs in a given locus were described in the GWAS, only the SNP with the lowest P value was selected for inclusion.
In a given locus, 0 denotes the absence of a C4 trait, 1 denotes the presence of a C4 trait, and 2 denotes missing data.
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In addition, an SNP at a given locus in one individual may be part of a haplotype that has an effect on protein expression or function, whereas exactly the same SNP in another individual may not form part of the functional haplotype and no functional effect is seen.
We also estimated, the squared differences in repeat units between two alleles in an individual at a given locus averaged over all loci (Coulson et al. 1998).
Furthermore, we show that resequenced lanes from the same library correlate very well, and that additional lanes of data have a small impact on saturation (data reproducibility) and a large impact on 5X CpG coverage (confidence in methylation calls at a given locus).
In fact, across permutations at a given locus this is enforced in the locus-specific P-value computation by ranking of values at each locus between permutations, which results in an even distribution of values at each position.
Therefore, the presence of an element at a given locus in a lineage and its absence in the genome of another one indicates that the insertion is posterior to the radiation.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com