Figure S2. (A) Flowchart showing processing steps for intra-host deep-sequence data. (B) Target site depth based on number of reads overlapping the target site in an alignment for 4 patients with deep-sequence data. Black dots indicate outlier target sites (outside 1.5 × IQR), and target sites are grouped and colored according to which consensus sequence they were identified from (the group- or subtype-level consensus from LANL alignments, or from the patient’s HIV consensus sequence). (EPS 246 kb
