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Tag 462 that was detectable in all individuals may be located in a region that is conserved between the two populations and tags that were undetectable may be affected by sequences polymorphic between Japanese and Caucasian.
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pan-genome size might be affected by sequencing additional phylogenetic groups.
However this technique only applies to larger events and can be affected by sequencing biases.
In silico maps could also be affected by sequencing or assembly errors [ 10], but these are less likely to affect alignments because typically they are infrequent.
It was suggested by Lindsay et al. (2008) that codon models used to estimate ω might be affected by sequence composition.
There is a risk that the methylation differences detected by the MeDIP technique could be affected by sequence differences in the promoter regions used for the arrays.
The reason is that long open reading frames are likely to be affected by sequencing errors in form of in frame stop codons.
In addition, break points may be affected by sequence composition, with GC-rich regions appearing to be particularly susceptible to breakage [ 2].
Of conserved or shared putative ESEs, 61% (14/23) were predicted to be affected by sequence variants reported in the Breast Cancer Information Core database.
Multiple studies have shown that at some genomic loci DNA methylation levels could be affected by sequence polymorphisms in cis and subsequently be heritable [ 29, 33- 36].
Our results therefore suggest that in plants, both translation initiation and elongation are the most likely stages to be affected by sequence optimization of the ACHE gene.
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