Table S2 Non-significant correlations of the numbers of mutations per bin with various genomic features Feature


Gene Expression

No. of 



  Data obtained from http://bigg.ucsd.edu(Schellenbergeretal. 2010).The correlations were not improved by considering the direction of transcription of the genes relative to the replication fork movement.Data obtained from http://www.ncbi.nlm.nih.gov/geo/.The correlations were not improved by considering the direction of transcription of the genes relative to the replication fork movement.Bin 35 was eliminated for this calculation because the value of gene expression in it was more than two standard deviations greater than the mean. one point; eliminating bin 20 reduces the correlation to -0.024. Data obtained from http://www.ncbi.nlm.nih.gov/geo/. Values are the average per bin of the ratio of gene expression in a wildtype strain to that in a gyrA mutant. 


	genes			0.175	0.245	0.180	NCBI	b
	No. of expressed genes, microarray data	c	0.171	0.255	0.180	(Allen et al. 2006)
	" " minus ribosomal protein genes d		0.256	0.086	0.100	"
	Average gene expression, microarray data e	-0.247	0.100	0.106	(Jeong et al. 2004)
	" " minus ribosomal protein genes d		-0.254	0.089	0.100	"
	Average gene expression, RNA-Seq data		0.088	0.563	0.329	(Martincorena et al. 2012)
	" " minus outlier f			0.068	0.658	0.348	"
	Factor Binding Sites	g				
	Global transcription factor binding sites		0.004	0.977	0.435	Regulon DB
	FIS Binding Sites			0.046	0.763	0.380	"
	IHF Binding sites			0.009	0.950	0.435	"
	LRP Binding sites			0.219 h	0.145	0.136	"
	H-NS Binding sites			0.177	0.240	0.179	"
	Chi sites (forward in each replichore)		-0.158	0.295	0.200	This report b
	Genomic Structural Features				
	No. of H-NS sensitive genes (mid-log)		-0.020	0.896	0.433	(Blot et al. 2006)
	" " upregulated in H-NS -mutant		0.191	0.205	0.165	"
	" " downregulated in H-NS -mutant		-0.285	0.055	0.078	"
	H-NS response per gene (mid-log)		-0.208	0.166	0.148	"
	FIS response per gene (mid-log)		-0.073	0.632	0.345	"
	No. of supercoiling sensitive genes		0.225	0.132	0.131	(Peter et al. 2004)
	" " relaxation repressed		0.191	0.204	0.165	"
	" " relaxation induced		0.077	0.609	0.344	"
	Supercoiling response per gene		0.014	0.926	0.435	"
	Gyrase response per gene i		-0.153	0.310	0.202	(Jeong et al. 2004)
							The reference genome
	sequence was NC_000913.2 (MG1655).				
		d Twenty-eight highly expressed ribosomal protein genes in bin 42 were eliminated
	for this calculation.					

a ρ p is the correlation coefficient; p is a measure of the false positive rate; q is a measure of the false discovery rate appropriate for evaluating multiple comparisons (see Material and Methods). b c e f g FIS, IHF, LRP, H-NS, and HU are global transcriptional factors and nucleoid-associated proteins; Chi sites are recombination facilitating sites. h This correlation is due to i
Table S2 Non-significant correlations of the numbers of mutations per bin with various genomic features Feature