Table 1. Overview of study design for the MethylMiner versus MethylCap comparison and number of reads in each condition.

Captured DNA (ng) indicates the amount of DNA that was captured in the MBD enrichment; % Mapped Reads are percent of the Total Reads that successfully aligned and % Used Reads are percent of the Total Reads that successfully aligned and remained after rigorous quality control.

Individual	Technical Duplicate	MBD-capture Kit	Captured DNA (ng)	Total Reads	% Mapped Reads	% Used Reads
A	1	MethylMiner	284	32,786,373	71.9	28.2
A	2	MethylMiner	273	43,543,509	71.9	25.1
A	1	MethylCap	77	32,213,938	72.9	29.9
A	2	MethylCap	85	23,883,650	74.0	30.3
B	1	MethylMiner	317	48,397,266	72.2	32.2
B	2	MethylMiner	312	42,712,240	70.5	34.0
B	1	MethylCap	115	31,148,759	74.0	34.9
B	2	MethylCap	106	29,959,582	72.9	31.5