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 302 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,743,669	0	G	A	51.1%	30.0 / 66.7	47	E313K (GAA→AAA)	yiaK	2,3‑diketo‑L‑gulonate reductase, NADH‑dependent
*	NC_000913	599,576	0	T	G	50.0%	71.6 / 20.5	58	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	2,421,443	0	A	C	49.1%	79.0 / 21.4	59	Y40S (TAC→TCC)	folX	D‑erythro‑7,8‑dihydroneopterin triphosphate 2'‑epimerase and dihydroneopterin aldolase
*	NC_000913	2,434,882	0	T	G	49.1%	72.7 / 16.0	57	Y252S (TAC→TCC)	truA	tRNA pseudouridine(38‑40) synthase
*	NC_000913	3,206,435	0	C	T	47.6%	54.9 / 40.3	64	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	4,536,197	0	A	T	47.2%	33.1 / 58.6	53	intergenic (+166/+417)	yjhR/nanS	pseudogene, helicase family; putative frameshift suppressor/9‑O‑acetyl N‑acetylneuraminic acid esterase
*	NC_000913	354,288	0	T	G	46.9%	76.2 / 11.4	49	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	3,105,499	0	A	C	46.8%	87.3 / 10.3	62	Y356S (TAC→TCC)	mltC	membrane‑bound lytic murein transglycosylase C
*	NC_000913	2,386,862	0	G	A	46.2%	40.5 / 44.0	52	intergenic (+31/‑72)	yfbL/yfbM	putative M28A family peptidase/DUF1877 family protein
*	NC_000913	4,332,791	0	A	C	44.6%	80.2 / 25.7	56	V161G (GTG→GGG)	basS	sensory histidine kinase in two‑component regulatory system with BasR
*	NC_000913	3,705,661	0	T	C	44.3%	123.3 / 23.1	79	I44V (ATC→GTC)	dppB	dipeptide/heme ABC transporter permease
*	NC_000913	2,248,431	0	A	C	44.2%	76.4 / 16.3	52	G34G (GGT→GGG)	lysP	lysine transporter
*	NC_000913	5,159	0	G	A	44.1%	59.0 / 31.2	59	intergenic (+139/‑75)	thrC/yaaX	L‑threonine synthase/DUF2502 family putative periplasmic protein
*	NC_000913	3,743,657	0	A	C	44.0%	77.5 / 15.2	50	T309P (ACC→CCC)	yiaK	2,3‑diketo‑L‑gulonate reductase, NADH‑dependent
*	NC_000913	659,940	0	T	A	43.9%	88.8 / 34.4	66	I93F (ATT→TTT)	lipA	lipoate synthase
*	NC_000913	503,820	0	T	C	43.5%	93.0 / 24.2	69	K293E (AAA→GAA)	fsr	putative fosmidomycin efflux system protein
*	NC_000913	2,865,867	0	T	G	42.9%	74.7 / 13.5	49	V256G (GTT→GGT)	ygbN	putative transporter
*	NC_000913	3,285,853	0	G	T	42.9%	71.9 / 29.1	56	A126S (GCC→TCC)	agaD	N‑acetylgalactosamine‑specific enzyme IID component of PTS
*	NC_000913	3,556,207	0	T	C	42.9%	92.9 / 18.9	63	S215G (AGT→GGT)	rtcA	RNA 3'‑terminal phosphate cyclase
*	NC_000913	1,776,263	0	T	G	42.6%	81.4 / 13.0	55	V226G (GTG→GGG)	ydiF	putative acetyl‑CoA:acetoacetyl‑CoA transferase: alpha subunit/beta subunit

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	925901 =	62 (0.970)	17 (0.270) +C	12/296	7.5	24.8%	noncoding (71/88 nt)	serW	tRNA‑Ser
	?	NC_000913	= 1097399	42 (0.650)					intergenic (+570/+166)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
*	?	NC_000913	= 4542690	67 (1.040)	6 (0.100)	6/280	10.0	8.3%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	70 (1.160)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	4542682 =	65 (1.010)	4 (0.070)	4/280	11.4	5.7%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	71 (1.180)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)