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Significantly mutated genes (SMGs) were defined as the somatic mutations with higher mutated frequency than background mutation rate.
To distinguish beneficial SNPs in XI, we sequenced the metagenome of Xp to a depth equivalent to 140 sequence coverage of X514 genome, the pool of mutants that tolerated 2% ethanol, reasoning that non-synonymous mutations with higher mutation frequency (percentage of mutated reads to all reads at a single-base locus in the X514 mutant community) were more beneficial (Additional file 10B).
Genotypic analyses of subtype B- and C-infected patients undergoing HAART failure in Israel showed several drug resistance mutations with higher frequency in subtype B viruses [31].
Additionally, these results indicate that the sgRNAs customized with the 18-nt sequences following the first added GG can induce targeted mutations with higher efficiency.
The double mutation was not considered in the model, but its effect might be similar to those of single mutations with higher mutation rates.
A rank of zero indicates that the mutant has reached a fitness peak and that no 1-step mutations with higher fitness are available.
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Indeed, multiple neutral changes along the mutational landscape of a protein may precede mutations with high advantageous fitness effect [ 27].
We used Cas9 mRNA as opposed to CAS9 protein, as this approach has been shown to generate on-target mutations with high efficiency2.
The use of hrMCA in combination with SAG from genomic DNA enables rapid detection of COL3A1 mutations with high efficiency and specificity.
Recently, heavy-ion beams have been used widely to generate mutants of higher plants, because, in contrast to other mutagenic techniques, they induce mutations with high frequency at a relatively low dose, and various phenotypes may be obtained without other plant characteristics being affected9,10,11.
All five had mutations with high-level resistance to NNRTIs and three had mutations with high-level resistance to NRTIs.
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