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The best probability threshold value for the resubstitution error rate and the best probability threshold value for the model performances were not the same except for the second model (the probability threshold values can be visualized on Additional File 3).
To confirm that chromatin-bound TopoIIα was used in these experiments, immunoprecipitated proteins were digested with proteinase K and the DNA was visualized on agarose gel (see Additional file 3D).
Full-length miRNA donor bands were visualized on ethidium bromide stained agarose/TBE gels (Additional File 2) to ensure primer extension.
To identify misassembled (hybrid or broken) scaffolds, uniquely mapped reads were visualized on the X. tropicalis 4.1 assembly (Additional file 4).
FST values based on Y chromosome haplogroup frequencies (Additional file 5: Table S5) were visualized on a multidimensional scaling (MDS) plot.
A total of 207 SNP outliers were visualized on the top 0.5% of the empirical distribution, corresponding to 122 genes (Additional file 6: Table S2).
Primer sequences are provided in Additional file 4. Equal volumes of each PCR reaction were visualized on 1% agarose gels.
The slides were visualized on a Nikon A1Rsi-TiE confocal microscope operated by NIS-Elements software (see also Additional file 1).
