Table 3. Intrapatient stop codon frequencies stemming from likely A3 and RT mutations.

	Plasma dataset 1 (2,908 sequences)*		Plasma dataset 2 (1,573 sequences)†		Proviral dataset (500 sequences)‡
	gp120 OA	Rest of env	gp120 OA	Rest of env	gp120 OA	Rest of env
Premature stop codons	12	41	5	24	162	1,322
Available targets (NSMTs)	379,586	753,733	200,679	406,084	68,550	124,500
Stop codon frequency	3.2 × 10−5	5.4 × 10−5	2.5 × 10−5	5.9 × 10−5	2.4 × 10−3	1.1 × 10−2

^*Subtype B sequences (www.hiv.lanl.gov/content/sequence/HIV/USER_ALIGNMENTS/keele.html), see Supplementary Data 7 for details.

^†Subtype C sequences (www.hiv.lanl.gov/content/sequence/HIV/SI_alignments/set5.html), see Supplementary Data 7 for details.

^‡Data from this study, see Supplementary Data 8 for details.