Additional file 5 of Notos - a galaxy tool to analyze CpN observed expected ratios for inferring DNA methylation types

CpG o/e ratios from dbEST analyzed by Notos: mode detection output - basic statistics. The density estimation step of Notos carried out for 603 species from dbEST provides the tab-separated file ‘modes_basic_stats.csv’. In the following we provide brief explanation on the content of the columns of this file. We are hereby using the following notation: σ – standard deviation, μ – mean, ν – median, Mo – mode, Q i – the i-th quartile, q s – the s % quantile. Future improvements of Notos may lead to changes, therefore consult the the readme section of the galaxy interface. • Name: name of the file analyzed • Number of modes: number of modes without applying any exclusion criterion • Number of modes (5% excluded): number of modes after exclusion of those with less then 5% probability mass • Number of modes (10% excluded): number of modes after exclusion of those with less then 10% probability mass • Skewness: Pearson’s moment coefficient of skewness E X − μ σ 3 $E\left [\left (\frac {X-\mu }{\sigma }\right)^{3}\right ]$ • Mode skewness: Pearson’s first skewness coefficient μ − Mo σ $\frac {\mu - Mo}{\sigma }$ • Nonparametric skew: μ − ν σ $\frac {\mu - \nu }{\sigma }$ • Q50 skewness: Bowley’s measure of skewness / Yule’s coefficient Q 3 + Q 1 − 2 Q 2 Q 3 − Q 1 $\frac {Q_{3} + Q_{1} - 2Q_{2}}{Q_{3} - Q_{1}}$ • Absolute Q50 mode skewness: (Q3+Q1)/2−Mo • Absolute Q80 mode skewness: (q90+q10)/2−Mo • Peak i, i=1,...,10: location of peak i • Probability Mass i, i=1,...,10: probability mass assigned to peak i • Warning close modes: flag indicating that modes lie too close. The default threshold is 0.2 • Number close modes: number of modes lying too close, given the threshold • Modes (close modes excluded): number of modes after exclusion of modes that are too close • SD: sample standard deviation σ • IQR 80: 80% distance between the 90% and 10% quantile • IQR 90: 90% distance between the 95% and 5% quantile • Total number of sequences: total number of sequences / CpG o/e ratios used for this analysis step (CSV 186 kb)