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 967 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,378,802	0	A	C	46.9%	158.0 / 41.7	113	V48G (GTA→GGA)	ampC	penicillin‑binding protein; beta‑lactamase, intrinsically weak
*	NC_000913	3,206,435	0	C	T	46.4%	113.1 / 67.8	110	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	357,890	0	C	A	46.2%	58.5 / 52.3	78	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	2,984,441	0	A	C	46.0%	203.9 / 55.4	139	G384G (GGT→GGG)	yqeF	short chain acyltransferase
*	NC_000913	2,578,143	0	A	C	45.7%	160.9 / 39.7	105	L79V (TTA→GTA)	maeB	malic enzyme: putative oxidoreductase/phosphotransacetylase
*	NC_000913	3,556,207	0	T	C	44.1%	162.5 / 49.4	127	S215G (AGT→GGT)	rtcA	RNA 3'‑terminal phosphate cyclase
*	NC_000913	3,133,302	0	T	G	43.6%	168.2 / 16.6	102	H219P (CAC→CCC)	yghS	putative ATP‑binding protein
*	NC_000913	1,376,505	0	A	C	43.4%	175.8 / 34.6	106	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
*	NC_000913	3,001,164	0	A	C	43.1%	175.9 / 32.0	109	T274P (ACC→CCC)	xdhA	xanthine dehydrogenase, molybdenum binding subunit
*	NC_000913	3,508,662	0	T	A	43.0%	144.4 / 52.7	107	E384D (GAA→GAT)	yhfW	phosphopentomutase‑related metalloenzyme superfamily protein
*	NC_000913	925,900	0	A	G	42.6%	184.6 / 33.1	115	noncoding (72/88 nt)	serW	tRNA‑Ser
*	NC_000913	3,443,277	0	A	C	42.5%	199.2 / 48.7	121	V274G (GTA→GGA)	secY	preprotein translocase membrane subunit
*	NC_000913	501,575	0	A	C	42.0%	196.5 / 21.7	114	V555G (GTG→GGG)	ybaL	inner membrane putative NAD(P)‑binding transporter
*	NC_000913	357,880	0	T	C	41.6%	112.2 / 22.2	78	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	4,536,197	0	A	T	41.3%	170.9 / 101.1	128	intergenic (+166/+417)	yjhR/nanS	pseudogene, helicase family; putative frameshift suppressor/9‑O‑acetyl N‑acetylneuraminic acid esterase
*	NC_000913	1,356,201	0	T	G	41.1%	184.4 / 33.3	108	T304P (ACC→CCC)	sapA	antimicrobial peptide transport ABC transporter periplasmic binding protein
*	NC_000913	599,576	0	T	G	41.0%	197.9 / 32.7	117	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	2,421,443	0	A	C	40.9%	213.5 / 21.0	115	Y40S (TAC→TCC)	folX	D‑erythro‑7,8‑dihydroneopterin triphosphate 2'‑epimerase and dihydroneopterin aldolase
*	NC_000913	2,903,692	0	C	A	40.8%	275.9 / 88.0	157	intergenic (+318/+1055)	ygcE/queE	putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis
*	NC_000913	213,341	0	A	G	40.7%	211.3 / 45.5	135	G337G (GGA→GGG)	tilS	tRNA(Ile)‑lysidine synthetase

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	4542682 =	182 (1.300)	9 (0.070)	9/280	21.6	5.3%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	149 (1.130)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	= 4542690	185 (1.320)	4 (0.030)	4/280	26.0	2.4%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	149 (1.130)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)