SCUEAL screening results on partial HIV-1 reverse transcriptase sequences from the Stanford Drug Resistance database.

Subtype lists the sequence subtype as annotated in the database. Sequences provides the number of sequences downloaded from the database. Agree gives the percentage of sequences for which SCUEAL returned the same subtype as that stored in the database. within-subtype–SCUEAL inferred within-subtype recombination within the same subtype as the one stored in the database; figures in parentheses show the proportion of within-subtype recombinants identified when DRAM positions were masked. Diff. pure subtype–the proportion of cases where SCUEAL inferred a pure subtype different from the annotated one. Diff. recombinant–the proportion of cases where SCUEAL inferred a recombinant mosaic with at least one fragment different from the annotated subtype; figures in parentheses show the proportion of within-subtype recombinants identified when DRAM positions were masked. Top 3 CRFs and URFs–three most frequent mosaics inferred by SCUEAL.