Fig. 1.

Tree showing mutations that occurred in patient 1 isolates during chronic airways infection. Isolates are numbered 1–35 in black type. Isolates 1 and 35, both circled, are the respective 6- and 96-month isolates whose genomes were sequenced. Mutations are shown in red italic type; mutations present in the 96-month isolate are numbered m1–m68, and mutations present only in intermediate isolates are numbered s1–s17. Mutations s9 and m52 are both in the same highly mutable repeat and appear to have occurred consecutively during the infection. Refer to Tables 4 and 5 for more information on individual mutations.