Figure 2

Hidden Markov Model architecture. (A) Diagram of the fully connected HMM structure. From left to right, the states represent read counts of increasing magnitude (essential, growth-defects, non-essential, and growth-advantage). (B) Diagram of the state transitions (from q_i-2 to q_i+13) and their corresponding emissions (i.e. read counts). A transition is made from the non-essential state to the essential state at time i+1, as the essential state is most likely to explain the consecutive observations of no insertions (from q_i+1 to q_i+12).