breseq  version 0.33.1  revision 8505477f25b3 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,728,183	0	C	G	65.2%	9.6 / 21.0	23	A397P (GCG→CCG)	xylB	xylulokinase
*	NC_000913	1,984,188	0	C	G	50.0%	9.3 / 39.0	30	G294G (GGG→GGC)	araG	L‑arabinose ABC transporter ATPase
*	NC_000913	1,308,750	0	G	C	43.8%	9.4 / 10.2	16	intergenic (‑105/‑38)	clsA/yciY	cardiolipin synthase 1/uncharacterized protein
*	NC_000913	4,296,060	0	C	T	40.9%	42.4 / 87.6	66	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
*	NC_000913	2,375,835	0	C	G	40.7%	33.9 / 19.7	28	G43A (GGG→GCG)	menC	O‑succinylbenzoyl‑CoA synthase
*	NC_000913	516,893	0	G	C	37.5%	46.3 / 20.6	35	G104A (GGA→GCA)	fetB	iron export ABC transporter permease; peroxide resistance protein
*	NC_000913	1,081,353	0	G	C	37.0%	38.2 / 14.3	28	intergenic (+540/‑3)	putP/efeU	proline:sodium symporter/ferrous iron permease (pseudogene)
*	NC_000913	1,667,883	0	C	G	34.4%	38.1 / 23.8	32	V228L (GTC→CTC)	mlc	glucosamine anaerobic growth regulon transcriptional repressor; autorepressor
*	NC_000913	1,135,975	0	G	C	33.3%	57.8 / 19.0	33	A138P (GCC→CCC)	flgH	flagellar protein of basal‑body outer‑membrane L ring
*	NC_000913	2,879,536	0	C	G	33.3%	82.5 / 17.8	45	G79G (GGG→GGC)	ygbT	multifunctional endonuclease Cas1, CRISPR adaptation protein; DNA repair enzyme
*	NC_000913	2,367,979	0	C	G	30.8%	42.7 / 10.1	26	R303R (CGC→CGG)	arnC	undecaprenyl phosphate‑L‑Ara4FN transferase
*	NC_000913	1,041,386	0	G	C	27.7%	96.0 / 24.1	47	G257A (GGA→GCA)	appA	phosphoanhydride phosphorylase
*	NC_000913	34,508	0	G	C	27.5%	89.4 / 20.5	40	G70A (GGA→GCA)	caiF	cai operon transcriptional activator
*	NC_000913	4,164,132	0	G	C	27.3%	59.8 / 11.8	34	G165A (GGA→GCA)	btuB	vitamin B12/cobalamin outer membrane transporter
*	NC_000913	3,641,407	0	G	C	22.9%	77.1 / 11.8	36	G182G (GGG→GGC)	dtpB	dipeptide and tripeptide permease B
*	NC_000913	2,778,212	0	C	G	22.7%	109.3 / 20.5	45	G1505G (GGG→GGC)	ypjA	adhesin‑like autotransporter
*	NC_000913	2,035,587	0	C	G	22.2%	94.6 / 15.9	47	intergenic (+344/‑248)	yedS/hchA	pseudogene, outer membrane protein homology; putative outer membrane protein/glyoxalase III and Hsp31 molecular chaperone
*	NC_000913	669,840	0	G	C	20.4%	123.4 / 10.7	52	A23G (GCG→GGG)	cobC	putative alpha‑ribazole‑5'‑P phosphatase
*	NC_000913	890,115	0	G	C	20.0%	87.2 / 11.8	36	G9G (GGG→GGC)	ybjM	inner membrane protein

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	4102317 =	33 (0.930)	3 (0.100)	3/112	2.6	9.6%	coding (628/984 nt)	kdgT	2‑keto‑3‑deoxy‑D‑gluconate transporter
	?	NC_000913	4102353 =	28 (0.910)					coding (664/984 nt)	kdgT	2‑keto‑3‑deoxy‑D‑gluconate transporter
*	?	NC_000913	1964259 =	34 (0.960)	4 (0.130)	3/114	2.7	11.3%	coding (792/2079 nt)	flhA	putative flagellar export pore protein
	?	NC_000913	1964341 =	33 (1.060)					coding (710/2079 nt)	flhA	putative flagellar export pore protein
*	?	NC_000913	= 2698122	40 (1.130)	6 (0.190)	3/118	2.8	15.1%	coding (429/636 nt)	pgpC	phosphatidylglycerophosphatase C, membrane bound
	?	NC_000913	= 2698142	31 (0.960)					coding (409/636 nt)	pgpC	phosphatidylglycerophosphatase C, membrane bound