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We removed the HBV site and one duplicate site of COL18A1 gene from this list.
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Duplicate sites were merged with the MergeDuplicateSNPsPlugin (options: -callHets, -misMat 0.05), and duplicated taxa were merged with the MergeIdenticalTaxaPlugin (options: -hetFreq 0.8).
Duplicate sites will clearly not have the ability to get the same level of attention.
Our assumption of independence between duplicate sites may not hold if they are tandem and in linkage disequilibrium.
Duplicate sites located too close to one another (within 10 nt) were removed manually.
However, duplicate sites of one sample were not in agreement with each other, requiring repetition, upon which, discrepancies were resolved.
Following the automated search in TESS, we manually searched the lists for duplicate sites at each position, and removed them prior to further analysis.
Complete non-LTR transposons were identified by the structural characteristics of each superfamily, including the number of ORFs, duplicate sites and the presence of repetitive regions at the 3' end.
By comparing mapped mRNA-seq reads to the S. noctiflora reference mitochondrial genome, we identified a total of 290 RNA editing sites (Additional file 1: Tables S4 and S5) with a minimum read depth of 100× and a minimum of 20%% edited reads (not counting duplicate sites in large repeat regions).
Peaks in A-genome coverage relative to D5-53 reputativeputative duplicated sites that were sampled at a higher frequency during sequencing.
Sites of duplications have been shown to lead to an increase in coverage of the respective sites [ 48]; however, we found that the mean coverage at the ASHM sites in this study was is in fact lower than the mean coverage across the whole genome (see Additional file 8), suggesting that as a group they are not enriched with duplicated sites.
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