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Although both the two- and five-factor models predict the general shape of the mutational pattern, both also fail to account for the high density of mutations in certain bins, particularly 7, 20, and 25.
It should be noted that due to the very large size of this dataset and the high rate of mutation in HIV, we detected a very high density of mutations, including mutations at the majority of individual nucleotide sites, most with large numbers of observations.
Strikingly, the CD0514 gene, encoding the cell wall protein cwpV [ 41, 42], contains an unusually high density of mutations.
Furthermore, the high density of mutations focussed to the small region between the TATA binding protein site (TBP) and the transcription start site (TSS), more precisely identify the pre-initiation complex (PIC) as the target for the deaminases.
The high density of mutations resulting from chemical mutagenesis means that, relative to insertional or deletional mutagenesis, far fewer plants are required for screening and much smaller genes can be effectively targeted.
We observe that in many cases the same DNA fragment is associated with high density of mutations (MELs) in both alleles of the same gene (frequently but not always at the same nucleotide position).
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We evaluated its technical performance using synthetic combinations of empirical data as well as simulation data of ongoing mutation in a genetic region with high density of mutation incorporating simulated Illumina HiSeq process errors.
Nonetheless we observe positive association of MELs with predicted R-loop potential genes although the paucity of these features across the genomes (between 59 78 sites) precludes any predictive dissociation between high density of mutation, R-loop potential and transcription rates.
Comparative analysis of modern domestic horses with a Przewalski horse suggested that regions of significant reduction of the genetic diversity in modern horses correspond to specifically selected loci while regions of high densities of mutations give evidence of continuous selection as it could be shown in immunity-related and olfactory genes in modern horses [ 8].
A small fraction of L1 elements are still active in the human genome [64] and on average L1 elements contain a higher density of mutations than other analyzed families (L2, MIR, DNA, LTR).
Deep phylogenetic nodes imply a higher density of mutations.
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