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The lowest false SNP discovery rate (~10%) in the technical replicates was detected at a stringent coverage parameter (20×).
The other set was based on a stringent coverage criterion, requiring that the alignment cover 80% of the coding sequence.
Calculations with lower coverage thresholds revealed higher NCO GC rates compared to calculations with more stringent coverage thresholds.
We next addressed the question if the differences detected can be overcome using more stringent coverage cutoffs.
For this analysis only, we relaxed our stringent coverage threshold from ≥32 rM to ≥16 rM for inclusion of antisense transcripts.
Note that the numbers are lower than for each individual parent because only ~7 Mb met the stringent coverage and quality thresholds.
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With less stringent 10× coverage, 2 Kb was still below the threshold.
A more stringent 95% coverage was used to be considered FL for terpenoid biosynthetic genes.
Two of the helAs, named helitron_mc1 (AC186621.4, 1615 bp) and helitron_mc2 (AC188746.2683683 bp), possessed 50 and 54 copies with a high stringent criteria (coverage >95% and identities >95%), respectively.
Comparisons with the predicted proteome of M. anisopliae E6 and the PHI-database were conducted employing Blastp analysis and the results were filtered according a stringent criteria (coverage ≥ 50% and e-value ≤ 10-5).
In the absence of additional data or models, more stringent thresholding of coverage is needed.
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