Over 99% of all qPCR samples were classified with a posterior probability of copy number group membership greater than 99%.
Bdelloid alpha tubulin copies are monophyletic with respect to monogonont copies (posterior probability, pp = 1.0, Figure 3).
As a result of this, the method generates inferences of the number of clones detected in the sample, their population frequencies across time and/or space, and subclone-specific posterior probabilities of copy-number profiles and somatic variant genotypes.
Proposed estimates of f and M lead to a posterior distribution over total copy-number states per subclone along the genome, e.g., showing strong evidence for a deletion of one particular chromosome copy in subclone 1: c i 1 = 1.
Inspection of the copy-number posterior for the green subclone, which is visible only in time points (a), (c), and (e), suggests that it represents a fitting of noise: these three time points possibly have a slightly different technical bias so that the bias field, derived from the matched normal sample, cannot fully correct for it.
A posterior probability of the integer copy number call being correct was given for each sample.
192 (16.9%) samples gave an integer copy number call posterior probability of less than 0.8.
The data are collected in both the anterior-posterior (CoPx) and medio-lateral (CoPy) axes at a sampling rate of 1000 Hz.
In general, these consistency constraints are probabilistic, with the copy-number profile posterior distribution γ i (c i ) informing the BAF and SNV genotype prior distributions at each locus (see Supplemental Experimental Procedures).
A posterior inversion event repositioned the functional copy of serX to a location distant from SPI-19 in the genome of serotypes Dublin, Weltevreden, Agona, Gallinarum and Enteritidis.
