Population genetics
Draws the last population-genetics run: sites along the chromosome, the pairwise LD matrix, samples in principal-component space with the scree, or one ancestry bar per sample with the cross-entropy by K.
What it does
Opens beside the Population Genetics panel when a question runs, and redraws when another runs. Every mark is a value the run returned; hover one for its numbers.
What this computes
- Hardy–Weinberg along the chromosome: −log10 of each site's exact-test p-value at its position, with the Bonferroni bound for the run's number of tests drawn across
- heterozygosity along the chromosome: observed and expected heterozygosity at every site, so a deficit or excess stands out where it happens
- Fst along the chromosome: each site's Fst for every comparison, one colour and marker per pair of populations
- the LD matrix: every pair of sites, darker for stronger LD; r² or |D′| for haplotype LD; grey where the pair is undefined
- the PCA scatter: every sample at its coordinates on any two components you choose, coloured and shaped by its population, each population's name at its centre, with each axis labelled by the variance it explains. Color by regroups the samples by any column of the sample table (super-population, population, sex) without running again
- the scree: the share of variance of every reported component, the two drawn above marked; click a bar to draw that component on the vertical axis
- the ancestry bars: one bar per sample, split by its share of each ancestral population at the K you choose, groups ordered by the ancestral population that dominates them and samples within a group by their share of it; Group by regroups by any column of the sample table, and Then by splits each group by a second column (the populations within a continent), labelled beneath
- cross-entropy by K: the masked cross-entropy of every K fitted, the lowest marked
Amplification curves
Every reaction's fluorescence against cycle number with the fitted model and its quantification cycle, so a Cq is read from the curve it came off rather than trusted as a number.
RNA-seq
Draws the last RNA-seq run: the volcano, MA plot or dispersion fit of a differential-expression run, the strongest over-represented gene sets, or one gene set's running enrichment score along the ranking.