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There were many haplotypes in the Exp2 region, of which the most favorable was Hap_6.
Many haplotypes in hwc2-2 candiers and only two haplotypes in Hwc2-2 carriers led us to the following inferences: (1) the hwc2-2 alleles have been differentiated at sequence level, some similar to Hwc2-1, others not.
Even when there are many haplotypes in the population, the sharing of one or zero haplotypes provides very little information on whether a potential mate is likely to be a full sib or a nonrelative, whereas the sharing of both haplotypes considerably increases the likelihood that animals are full sibs.
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It may be because of less number of accessions grouping in many haplotypes resulting in low minor allele frequencies (<2 %), and synonymous or noncoding nature of the SNPs.
The gene-content, and allele-content motifs contained in the centromeric and telomeric regions of these 27 haplotypes are likely to account for many common haplotypes in many human populations, and should provide a strong base from which to investigate the rarer and more population-specific haplotypes.
Many haplotypes are found in more than one geographic population.
Within the major gene pool SC, the parapatric SCn and SCs shared many haplotypes from the second clade, but with higher haplotype diversity in SCs (12 haplotypes) than in SCn (6 haplotypes), despite a larger sample size in the later.
In contrast, Rh. nivata had four times as many haplotypes as genotypes.
Many haplotypes were defined common haplotypes because they were shared by at least two animal species in the study.
In haplotype populations this is an important issue for haplotypes of a few SNP in length, as there are usually many rare haplotypes in a sample.
Data sets revealed a shallow genetic structure in S. japonica, with many shared haplotypes in four genetic clusters (Fig. 2; Additional file 2: Figure S1).
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