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The frequencies of insertions extracted from the retroposon matrix were used to calculate their activity probabilities (Additional file 2).
The lowest frequencies of insertions and deletions were linked to proteins involved in genetic information processing, whereas the highest frequencies were associated with cellular processes (Table 3), with a difference of ~50% between them.
We independently verified these observations with an estimation of CR1 activity in the TinT model that considers relative frequencies of insertions of different RE subtypes nested within each other (Kriegs et al. 2007; Churakov et al. 2010).
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This suggests genotype frequencies of insertion homozygotes could be changed quickly under selection for rapid genetic progress.
In addition, we compared the frequencies of insertion, substitution and deletion mismatches, with respect to the consensus repeated motifs, between hotspot-associated microsatellites and those in other regions.
This study was, however, performed in a major teaching hospital which is in the top 15% of UK Hospital Trusts by number of beds, and it is questionable whether practitioners are reaching higher frequencies of insertion at other centres.
This novel methodology was used to confirm the relative frequencies of insertion of dATP versus insertion of dCTP via the lesion loop-out mechanism predicted from the kinetic efficiencies of each pathway and to provide information about more rare mutation events both opposite and downstream from the lesion.
These observations stand in stark contrast to the low frequency of insertions into the Hsp83 gene.
The frequency of insertions and deletions across the 20 soybean chromosomes is shown in Figure 1A.
It is of note that the same gene classes show a high frequency of insertions and deletions.
We then tried to assess how many integrations hit these two groups of genes in PBL-GT or in HSC-GT (Fig 3B column graph), considering that the calculated random frequency of insertions is 0.5% in each group.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com