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 491 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,105,499	0	A	C	48.3%	86.7 / 10.1	60	Y356S (TAC→TCC)	mltC	membrane‑bound lytic murein transglycosylase C
*	NC_000913	3,350,853	0	A	C	48.3%	76.6 / 14.0	60	S725A (TCA→GCA)	arcB	aerobic respiration control sensor histidine protein kinase, cognate to two‑component response regulators ArcA and RssB
*	NC_000913	3,350,844	0	A	C	47.5%	80.4 / 17.7	60	L728V (TTA→GTA)	arcB	aerobic respiration control sensor histidine protein kinase, cognate to two‑component response regulators ArcA and RssB
*	NC_000913	1,174,605	0	T	C	47.3%	95.7 / 24.5	75	G187G (GGA→GGG)	ycfT	inner membrane protein
*	NC_000913	2,483,254	0	G	A	47.3%	46.6 / 35.1	58	S29L (TCA→TTA)	emrK	multidrug resistance efflux pump membrane fusion protein
*	NC_000913	2,483,268	0	T	A	47.3%	47.5 / 34.1	56	L24F (TTA→TTT)	emrK	multidrug resistance efflux pump membrane fusion protein
*	NC_000913	786,855	0	A	C	45.7%	120.8 / 19.2	82	G247G (GGT→GGG)	gpmA	phosphoglyceromutase 1
*	NC_000913	802,118	0	A	C	44.8%	91.6 / 13.0	69	T78P (ACC→CCC)	ybhI	putative DASS family tricarboxylate or dicarboxylate transporter
*	NC_000913	2,434,861	0	G	T	44.6%	67.4 / 37.3	66	P259Q (CCA→CAA)	truA	tRNA pseudouridine(38‑40) synthase
*	NC_000913	599,576	0	T	G	44.1%	96.5 / 31.0	69	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	29,496	0	T	A	43.4%	95.9 / 60.2	83	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	2,001,918	0	A	C	41.9%	123.9 / 12.5	74	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
*	NC_000913	4,101,507	0	T	G	41.8%	127.2 / 12.7	80	intergenic (+77/‑183)	sodA/kdgT	superoxide dismutase, Mn/2‑keto‑3‑deoxy‑D‑gluconate transporter
*	NC_000913	3,585,086	0	A	C	41.7%	117.2 / 22.2	72	Y580D (TAC→GAC)	ggt	gamma‑glutamyltranspeptidase
*	NC_000913	2,984,441	0	A	C	41.4%	85.2 / 22.2	58	G384G (GGT→GGG)	yqeF	short chain acyltransferase
*	NC_000913	1,174,626	0	G	A	41.1%	83.2 / 32.7	74	F180F (TTC→TTT)	ycfT	inner membrane protein
*	NC_000913	2,001,911	0	G	A	40.3%	93.1 / 37.7	77	intergenic (‑122/+199)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
*	NC_000913	941,713	0	T	G	40.0%	91.7 / 28.2	65	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	2,676,106	0	C	A	40.0%	74.8 / 21.7	50	L240F (TTG→TTT)	yphD	putative sugar ABC transporter permease
*	NC_000913	357,875	0	A	T	39.3%	39.3 / 11.7	28	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor

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	1207790 =	58 (0.750)	11 (0.160)	10/266	9.1	17.8%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	50 (0.730)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	58 (0.750)	10 (0.150)	8/266	10.1	17.0%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	46 (0.670)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related