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 381 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	57.5%	16.8 / 47.8	40	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	1,478,324	0	T	G	54.7%	52.1 / 88.2	53	G33G (GGT→GGG)	ynbB	putative CDP‑diglyceride synthase
*	NC_000913	357,890	0	C	A	51.3%	6.4 / 40.4	37	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	1,413,735	0	A	T	50.6%	57.5 / 133.5	79	Y2* (TAT→TAA)	ydaC	DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein
*	NC_000913	357,875	0	A	T	48.8%	35.7 / 21.2	43	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	941,713	0	T	G	48.4%	81.8 / 25.1	63	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	1,506,038	0	A	C	46.8%	101.4 / 12.9	64	F15V (TTT→GTT)	ydcO	BenE family inner membrane putative transporter
*	NC_000913	3,206,435	0	C	T	44.9%	73.9 / 40.3	69	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	354,288	0	T	G	44.1%	91.5 / 19.2	59	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	1,376,505	0	A	C	43.9%	84.2 / 22.9	57	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
*	NC_000913	4,302,658	0	T	G	43.6%	87.0 / 13.4	56	T141P (ACC→CCC)	mdtO	membrane translocase (MDR) of MdtNOP efflux pump, PET family
*	NC_000913	4,538,109	0	A	C	41.9%	135.4 / 27.2	74	G219G (GGT→GGG)	nanM	N‑acetylneuraminic acid mutarotase
*	NC_000913	4,378,802	0	A	C	41.7%	102.9 / 17.2	60	V48G (GTA→GGA)	ampC	penicillin‑binding protein; beta‑lactamase, intrinsically weak
*	NC_000913	2,303,672	0	C	A	40.7%	92.8 / 29.2	55	intergenic (‑175/‑233)	napF/eco	ferredoxin‑type protein, role in electron transfer to periplasmic nitrate reductase NapA/ecotin, a serine protease inhibitor
*	NC_000913	1,222,596	0	G	A	40.7%	76.5 / 31.3	59	F13F (TTC→TTT)	ymgD	uncharacterized protein
*	NC_000913	1,413,751	0	A	C	40.5%	105.1 / 29.8	75	N59K (AAT→AAG)	ralR	Rac prophage; restriction alleviation protein
*	NC_000913	345,328	0	C	A	40.5%	124.7 / 43.3	84	intergenic (+337/‑76)	yahL/yahM	uncharacterized protein/uncharacterized protein
*	NC_000913	1,621,118	0	A	C	40.4%	88.1 / 10.3	52	V7G (GTG→GGG)	eamA	cysteine and O‑acetyl‑L‑serine efflux system
*	NC_000913	599,576	0	T	G	39.1%	131.5 / 14.5	65	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	1,097,581	0	A	G	38.9%	130.8 / 15.3	72	noncoding (72/88 nt)	serX	tRNA‑Ser

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 =	65 (0.900)	19 (0.260) +C	15/296	7.4	25.5%	noncoding (71/88 nt)	serW	tRNA‑Ser
	?	NC_000913	= 1097399	47 (0.650)					intergenic (+570/+166)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
*	?	NC_000913	1207790 =	81 (1.120)	10 (0.150)	10/266	8.6	13.2%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	59 (0.910)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	86 (1.190)	4 (0.060)	4/266	12.2	5.6%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	59 (0.910)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related