TABLE 3.

Summary of the measured error rates determined for the sequencing of the 8E5 HIV-1 RNA controls

Control variablea	Error rateb
	env (set 1)		env (set 2)		env (set 3)		Protease (set 1)
	V1/V2	C2/V3	V1/V2	C2/V3	V1/V2	C2/V3	R1	R2	combined
Consensus sequences (no.)	23,385	23,385	18,408	18,408	15,205	15,205	14,778	14,778	14,741
Mispriming (no.)	6	41	8	40	4	5	8	15	7
In-frame deletions (no.)	5	12	0	8	1	2	0	0	0
Frameshift (no.)	138	134	151	87	184	25	43	42	55
Consensus sequences (no. without in/del)	23,236	23,198	18,249	18,273	15,016	15,173	14,727	14,721	14,679
Length (no. of nucleotides)	265	256	265	256	265	256	265	256	340
Substitutions (no.)	206	748	73	412	158	311	426	488	565
Substitution rate (%)	0.003	0.013	0.002	0.009	0.004	0.008	0.011	0.013	0.011
Substitutions (%; excluding first and last two positions)		0.009		0.005		0.008

^aFor the number of consensus sequences, the template consensus sequences were pooled from two repeats of library construction and sequencing for each enzyme/region. Mispriming was defined as sequence reads at regions other than the targeted regions. An in-frame deletion was defined as a deletion that could be evenly divided by 3. A frameshift was defined as a deletion that could not be evenly divided by 3. Length was defined as the nucleotide size of the sequenced regions. in/del, insertions and/or deletions.

^bSet 1, Superscript III as the reverse transcriptase and KAPA2G robust as the first-round PCR polymerase; set 2, Supperscript III as the reverse transcriptase and Phusion as the first-round PCR polymerase; set 3, AccuScript as the reverse transcriptase and KAPA2G robust as the first-round PCR polymerase.