Table 1. Higher mismatch rate with Ex Taq DNA polymerase and a lower reverse transcription reaction temperature.

Library	RT reaction temperature	PCR polymerase	Mismatch rate per nucleotidea
Structure-seq2 (–DMS)	55°C	Q5	0.89%
Structure-seq2 biotin variation (–DMS)	55°C	Q5	0.83%
Ex Taq DNA polymerase	55°C	Ex Taq	1.15%
Lower RT reaction temperature	50°C	Q5	0.97%

^aReads with more than three mismatches are not included as they cannot be confidently mapped.