Fig. 1

Overview of the Gaussian Mixture Model (GMM) based method used by nQuire to estimate ploidy. We illustrate the workflow using a diploid individual as an example. a After sequenced reads are mapped to a reference genome, base frequencies are calculated at variable sites where only two bases are segregating. b The base frequencies are modeled using a GMM and the likelihood is maximized using an Expectation-Maximization (EM) algorithm for both the free and the three fixed models (diploid, triploid and tetraploid). The maximized log-likelihoods (logL) are extracted for subsequent model comparison. The curves show a possible final state of the GMM under the assumptions of each of the four models. c The ΔlogL is calculated between the free model and each of the three fixed models (here represented as barplots). The fixed model with the smallest ΔlogL is chosen as the true ploidy level (diploid in this example)