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Therefore, 0.030 and 0.012 recombination events per synonymous mutation are inferred, respectively.
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C-terminal deletion mutation was inferred by the occurrence of relative underexpression (undercounting) of the exon 28 probe versus the exon 19 probe.
Where flanking sequences were unavailable, the location of the mutation was inferred from either descriptions in the text, the corresponding R i value of the splice site, or relative coordinate numbering.
Then, genotypes of all F2 animals at the mutation were inferred for non recombinant haplotypes inherited from F1 individuals, using information from the pedigree and from the transmission of parental haplotypes for surrounding markers (SW2443 and SWC9).
For this, the millions of short reads produced by NGS are mapped to an a-priori sequenced reference genome of the wild-type (WT) [3] and mutations are inferred from the differences between the WT reference and the sequenced mutant [4].
The SNPs are grouped in the order in which the mutations are inferred to have occurred.
Mutations are inferred to have occurred along most of the branches, suggesting continuous refinement of the numit rps13 sequence.
The identities of the ancestral bases and the direction of mutations were inferred from human-chimpanzee genomic alignment.
In our work, the relative timing of mutations is inferred by longitudinal data with multiple time points.
Major comments: 1) Relative timing of mutations: It is not entirely clear in the Materials and methods or main text exactly how the temporal order of mutations is inferred.
Because the observed ratios of non-synonymous (missense) to synonymous (putatively silent) mutations are far smaller than the 3 1 ratio expected from random base substitutions in a genome with close to 25% of each base, strong purifying selection against missense mutations is inferred, rendering such mutations useless for rate estimations.
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