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The solvent cut off was set to 5 min.
The e-value cut off was set at 1e-5.
The E-value cut off was set to 10−6.
The minimal codon usage cut off was set at 2% and the ΔG optimization was set to -15 to -25 kcal/mol.
When the overlapping cut off was set to the 30% of the alignment length, virtually no hits were recovered for the unassembled reads (Additional file 4: Figure S3).
To be considered as a reliable recombination event, the highest multiple-comparison-corrected P-value cut off was set at 10−5 for at least three different methods.
The protein identification cut off was set at a confidence level of 95% (Mascot score > 33) with at least two peptides matching to a protein.
The cut off was set at Fold Change ≥ 2. The results of the analysis are presented as scatter plots,.
Cut-offs were set at log2 FC = 0.585 and FDR at 0.05 (Benjamin-Hochberg).
In the generation of MEPs, the cut-offs were set at 1.62 Å.
Values for estimated coverage and coverage cut-off were set to auto.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com