Table 2. Read mapping statistics.

Sample	Sequence read type	hrpL-FLAG	ΔhrpL
ChIP-Seq	Total reads	45,479,930	22,170,715
	Reads that align uniquely to the chromosome	35,185,956	9,513,703
	Reads that align uniquely to plasmid B	2,699,119	571,096
	Reads that align uniquely to plasmid A	3,308,504	573,047
RNA-Seq	Total reads	36,272,771	44,500,185
	Reads containing 18-mer	356,915	3,351,960
	Untagged reads that alignuniquely to the chromosome	29,349,347	32,953,858
	Untagged reads that align uniquely to plasmid B	1,426,734	515,184
	Untagged reads that align uniquely to plasmid A	878,164	426,741
	Tagged reads that align uniquely to thechromosome	237,794	2,069,913
	Tagged reads that align uniquely to plasmid B	20,570	30,903
	Tagged reads that align uniquely to plasmid A	7,452	30,501