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In the majority of cases, the 3' end (for forward primers of left locus fragments) and the 5' end (for reverse primers of right locus fragments) were the last nucleotides before/after the comparison fragment for each locus on the C. jejuni MLST database website.
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The mean NAA/Ch values for left loci #5 (1.03) and #6 (1.10) were somewhat higher than the group mean and closer to the values in controls.
All 11 genes and all individuals (in total 255 SNPs) were used in one analysis whereas a more stringent approach, excluding 15 individuals for which only a few genes were successfully sequenced and filtering loci with more than 15% missing data, left loci from seven genes represented by 112 SNPs to be analyzed.
This resulted in the removal of 59,960 loci, leaving 80,168 loci with counts above this threshold for further consideration.
The F2 population size was determined by examining the micro scale phenotypes measured in [ 16] and determining the number of samples required such that the baseline for variation, as determined through the permutation test, left multiple loci for the traits which were statistically determined to have multiple loci.
This left seven loci that were selected for further analysis.
Our strategy may have left some loci undetected, but should have a low false positive rate.
A) The complete data, non-supervised analysis; B) at a 5 % FDR that left six loci on the list.
Primers that worked on both photobionts and provided clear electropherograms were selected, which left 24 loci worth further testing, comprising 13 di-, four tri-, and seven tetranucleotide repeats.
These two loci were removed leaving 60 loci.
These filters were not independent and resulted in 9360 of the 54 442 loci being removed, leaving 45 082 loci for analysis.
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