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Illumina short read sequencing used to generate the genomic data also poses a limitation of this study because of its propensity to generate uneven coverage profiles across the genome (e.g., high coverage at certain loci and little to no coverage at other loci) thus possibly influencing the probability of correctly detecting possible gene deletions.
During the initial SSR genotyping of the IR29/Pokkali QTL population, multiple Pokkali alleles were observed between RILs at certain loci.
Moreover, the genome wide analysis of DNA methylation at CpG sites in ESC and iPSC indicates that at certain loci iPSCs remain incompletely or aberrantly reprogrammed, and those are especially enriched at genes involved in developmental processes [71].
Analysis of the distribution and density of SNPs in the genomes suggest that recombination has generated allelic variation at certain loci in the BM407 chromosome, thereby increasing the apparent level of diversity.
In addition, our results have implications for endangered species such as the California gnatcatcher, where lack of differentiation at certain loci (e.g. mtDNA; [57]) may not reflect important genetic differentiation detectable with other markers such as microsatellites.
In practice, some sequencing errors systematically occur at certain loci on certain instruments [ 18].
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However, as it has been reported that transcriptional recruitment at certain locus may affect the expression of adjacent genes, we do not exclude the possibility that the acquirement of the transcription activity in the CCAT1-L locus during CRC pathogenesis may also contribute to the regulation of MYC transcription.
When this dropout occurs at a certain locus (locus i), no dropouts can occur at the other loci.
When two dropouts occur at a certain locus (locus i), no dropout can occur at the other analyzed loci.
The comprehension of the nucleotide sequences leading to genomic instability might ultimately lead to understand whether deleterious imbalances, both constitutional and acquired, occur at random in people sharing apparently identical genome sequences at a certain locus or are linked to specific haplotypes.
If humans tend to select mates that are similar to self at certain genetic loci, then we would expect those loci would show excessive homozygosity in the population over time (Additional file 10: Figure S3).
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