Fig. 4

A phylogeny and associated heatmap showing the placement of read subsamples for 100 iterations of three E. coli isolates. The maximum likelihood phylogeny was inferred by RAxML [20] from a concatenation of approximately 225,000 single nucleotide polymorphisms called against the reference genome, K-12 W3110 [30]. Raw reads were randomly sampled from three genomes at four different depths and reference positions were identified. Each genome, at each level, was then inserted into the phylogeny with the evolutionary placement algorithm (EPA) in RAxML [26]. Duplicate placements were removed from the tree and redundancies were represented as a heatmap