Table 2. Summary statistics from a sequencing run of an E. coli strain DH10B Illumina library prepared on the AMCC chip using carboxylated beads for DNA purification and on-chip size selection.

Library	Throughput (Mbp)	Number of reads	Alignment rate	Sequencing depth (mean / median)	Genome coverage	Unique reads in a sub-sample**
Manual*	316.6	12,663,406	99.27%	69.6× / 69×	100%	99.8%
AMCC chip, reaction module 13	254.1	10,165,992	99.24%	55.8× / 55×	100%	99.8%

* The library labeled "Manual" was prepared off-chip using the standard benchtop protocol recommended by Illumina. The libraries were run on the MiSeq using the 2x25 bp paired-end sequencing protocol.

** Subsampling for each sequencing run was performed by randomly selecting 10,000 reads for analysis. Similar results were obtained when subsampling was performed with sample sizes ranging from 10,000–100,000 reads (Table S2 in File S1).