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However, most sequence variants were common and extensively shared among worldwide parasite populations, demonstrating long term persistence of those polymorphisms, probably maintained through balancing selection.
If mutations occur randomly (i.e. none is favored by selection), most sequence variants (haplotypes) will each appear in only a few individual plants.
We currently lack the capability to evaluate the impact of most sequence variants found and what their functional consequences are.
In most sequence variants, histone H2A contains a lysine or arginine residue at position 99, however variants 1-A, 2-B, and H2Ax do not contain K/R99.
With an average of >5 amplicons per exon there is enough redundancy for most sequence variants that might alter primer bindings in other amplicons to be detected.
We found that 50-fold coverage is sufficient for genome assembly and for the detection of most sequence variants, although some additional variants are detected at higher coverage depths.
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Identification of the most conserved sequence variants and consensus monomer reconstruction of satellite repeat PaB6 were conducted using k-mer frequency analysis as described previously (Macas et al., 2010), using 25 bp long k-mers for final sequence reconstruction.
In addition to the lognormal OR coefficient and modeled OR at the most severe sequence variant grade, Table 6 also reports the OR point estimate at the most severe sequence variant grade.
For example, using MEME, we identified 872 (79%) that matched the single most common sequence variant (TAnnnT).
Nevertheless, promoter sequences were identified that also matched the single most common sequence variant of the −35 box consensus (GnTTnG).
MEME analysis of sequences immediately upstream of TSSs associated with pervasive transcription revealed that a high proportion (61%) matched the single most common sequence variant (TAnnnT) of the −10 box of P. acnes vegetative promoters (data not shown).
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