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While the low genomic mutation rate found in thermophiles might be an adaption to extreme temperature conditions [33], the mutation rate of the mesophilic halophile, H. volcanii was also found to be extremely low with 4.5×10−4 mutations per genome per replication [5].
This is 15-fold higher than the average mutation rate found in conifer orthologues (see Table 1).
Our results show that the mutation rate varies around the chromosome, with the lowest mutation rate found near the origin of replication.
The mutation rate found in our study is much higher comparing to European countries yet lower than in regions where aflatoxin exposure is endemic.
The lower BRAF mutation rate found in our study compared to the literature might be due to a selection bias since we screened only patients with metastatic disease.
Given the higher mutation rate found in the control region relative to the cytochrome b gene, we used a range of estimated mutation rates for control region sequence that span values found previously in other large mammal species.
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Overall, ∼6% of tumors exhibited mutations in FBW7, with the highest mutation rates found in cholangiocarcinoma (35%) and T-cell acute lymphoblastic leukemia (31%).
The mutation frequencies for wheat reported here and by Slade et al. [ 18] are five to ten times higher than mutation rates found in diploids such as barley, pea and Arabidopsis [ 25, 37, 38].
For comparison, we also show the mutation rates found by Zhivotovsky et al. (2003), which are based on a subset of the CEPH-HGDP markers obtained by removing markers with extreme variances.
Specifically, we compare results obtained using different statistical approaches applied to di-, tri-, and tetra-nucleotides separately, as we would expect the effect of bias to depend on the different mutation rates found for markers with different motif lengths.
The combination of representation and crossover type along with mutation rate were found to be the most significant parameters in the algorithm design.
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