Fig. 5

Raw read alignment for several common deletions Examples of the raw reads (10 raw reads randomly chosen) for indels with strong homogeneity in one host and high heterogeneity in another host. The red line the reads below indicates where the insertion or deletion of interest is. A “-” indicates a gap in a read relative to the reference, or vice versa, whereas blank spaces simply indicate the ends of a read. (a) Examples of raw reads with a strong homogeneity at the indel, suggesting that the indel arose from an event in a previous host. (b) Examples of raw reads with intra-host heterogeneity at the indel, suggesting that these indels are de novo events