breseq  version 0.29.0  revision 8f9c342918e4 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 411 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	50.0%	29.0 / 28.4	44	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	3,443,277	0	A	C	50.0%	75.8 / 42.8	68	V274G (GTA→GGA)	secY	preprotein translocase membrane subunit
*	NC_000913	4,332,791	0	A	C	48.5%	76.7 / 36.8	69	V161G (GTG→GGG)	basS	sensory histidine kinase in two‑component regulatory system with BasR
*	NC_000913	718,659	0	T	A	48.1%	67.7 / 26.1	52	D601V (GAT→GTT)	speF	ornithine decarboxylase isozyme, inducible
*	NC_000913	3,423,297	0	G	C	47.0%	98.9 / 40.0	66	intergenic (+103/+126)	yhdZ/rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
*	NC_000913	1,825,056	0	G	A	46.8%	48.7 / 26.2	47	intergenic (‑119/+84)	ves/spy	cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced
*	NC_000913	2,421,443	0	A	C	44.6%	101.5 / 10.0	56	Y40S (TAC→TCC)	folX	D‑erythro‑7,8‑dihydroneopterin triphosphate 2'‑epimerase and dihydroneopterin aldolase
*	NC_000913	1,825,061	0	G	A	44.0%	56.0 / 28.2	50	intergenic (‑124/+79)	ves/spy	cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced
*	NC_000913	1,079,468	0	A	G	43.6%	88.4 / 14.2	55	D55G (GAT→GGT)	putP	proline:sodium symporter
*	NC_000913	4,331,790	0	T	G	43.5%	79.4 / 11.3	46	V430G (GTT→GGT)	proP	proline/glycine betaine transporter
*	NC_000913	1,534,234	0	G	T	43.2%	51.8 / 17.1	37	E71* (GAG→TAG)	nhoA	N‑hydroxyarylamine O‑acetyltransferase
*	NC_000913	3,206,435	0	C	T	42.9%	69.2 / 29.2	56	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	15,410	0	T	G	42.5%	71.2 / 11.6	47	intergenic (+112/‑35)	dnaJ/insL1	chaperone Hsp40, DnaK co‑chaperone/IS186 transposase
*	NC_000913	1,576,077	0	C	A	42.4%	101.6 / 35.2	66	D515Y (GAT→TAT)	yddB	putative TonB‑dependent outer membrane receptor
*	NC_000913	3,556,207	0	T	C	42.1%	79.7 / 20.1	57	S215G (AGT→GGT)	rtcA	RNA 3'‑terminal phosphate cyclase
*	NC_000913	15,382	0	A	G	41.8%	82.3 / 18.0	55	intergenic (+84/‑63)	dnaJ/insL1	chaperone Hsp40, DnaK co‑chaperone/IS186 transposase
*	NC_000913	1,576,080	0	G	A	41.8%	104.7 / 24.6	67	L514F (CTT→TTT)	yddB	putative TonB‑dependent outer membrane receptor
*	NC_000913	1,574,051	0	G	T	41.7%	103.0 / 21.4	60	V384V (GTC→GTA)	pqqL	putative periplasmic M16 family zinc metalloendopeptidase
*	NC_000913	1,576,069	0	T	C	41.5%	88.9 / 32.1	65	G517G (GGA→GGG)	yddB	putative TonB‑dependent outer membrane receptor
*	NC_000913	354,288	0	T	G	41.5%	92.4 / 11.1	53	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase

Marginal new junction evidence (sorted from low to high skew)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 1207805	55 (0.830)	19 (0.320)	19/266	4.4	27.1%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	53 (0.900)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	59 (0.890)	12 (0.200)	12/266	6.8	18.1%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	56 (0.950)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1209618	57 (0.860)	16 (0.270)	4/268	11.4	21.7%	pseudogene (2/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
	?	NC_000913	2471897 =	64 (1.080)					pseudogene (226/579 nt)	yfdL	pseudogene, CPS‑53 (KpLE1) prophage;Phage or Prophage Related