Missing coverage evidence. a) The censored fit of read depth at sites with unique-only coverage across the reference genome to a negative binomial distribution is shown for one of the E. coli samples from the mutation accumulation evolution experiment. The threshold for extending putative deleted regions of the genome is determined by taking the coverage value that produces a left-tail probability from the fit distribution as described in the text (arrow). b) A missing coverage evidence item is shown for the same E. coli sample to illustrate how its boundaries are determined by extending outward from a seed region with zero coverage of uniquely aligned reads through regions with multiply-mapped reads that match genomic repeat sequences until the coverage of uniquely aligned reads exceeds the calculated propagation threshold. Note that the left and right boundaries both correspond to a range of positions because they fall within repeat regions. In some cases, this type of ambiguity in the extent of the deletion can be resolved by examining new junction evidence matching the endpoints.