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 936 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	50.9%	31.7 / 80.9	55	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	599,576	0	T	G	44.7%	177.8 / 70.9	123	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	3,585,086	0	A	C	44.4%	206.3 / 25.5	111	Y580D (TAC→GAC)	ggt	gamma‑glutamyltranspeptidase
*	NC_000913	2,326,450	0	T	G	44.2%	180.7 / 20.7	95	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	366,526	0	T	G	43.3%	170.5 / 41.5	104	T329P (ACC→CCC)	lacI	lactose‑inducible lac operon transcriptional repressor
*	NC_000913	2,434,882	0	T	G	42.9%	200.3 / 23.6	112	Y252S (TAC→TCC)	truA	tRNA pseudouridine(38‑40) synthase
*	NC_000913	29,496	0	T	A	42.0%	148.9 / 54.6	100	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	2,001,911	0	G	A	41.2%	152.6 / 60.4	114	intergenic (‑122/+199)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
*	NC_000913	1,159,837	0	A	G	41.1%	102.5 / 21.5	73	I572T (ATC→ACC)	fhuE	ferric‑rhodotorulic acid outer membrane transporter
*	NC_000913	1,413,735	0	A	T	40.9%	173.4 / 64.5	110	Y2* (TAT→TAA)	ydaC	DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein
*	NC_000913	3,261,055	0	A	C	40.9%	209.7 / 20.9	116	V455G (GTG→GGG)	tdcE	pyruvate formate‑lyase 4/2‑ketobutyrate formate‑lyase
*	NC_000913	2,001,918	0	A	C	40.5%	226.0 / 22.5	111	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
*	NC_000913	1,097,581	0	A	G	40.4%	195.3 / 32.6	109	noncoding (72/88 nt)	serX	tRNA‑Ser
*	NC_000913	357,880	0	T	C	40.4%	84.6 / 13.8	57	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	2,984,441	0	A	C	40.2%	187.7 / 21.8	92	G384G (GGT→GGG)	yqeF	short chain acyltransferase
*	NC_000913	4,112,578	0	T	G	40.2%	227.2 / 28.8	114	G88G (GGT→GGG)	yiiR	DUF805 family putative inner membrane protein
*	NC_000913	1,825,056	0	G	A	40.0%	146.6 / 44.3	95	intergenic (‑119/+84)	ves/spy	cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced
*	NC_000913	599,579	0	T	G	39.8%	240.2 / 19.7	123	V289G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	1,222,596	0	G	A	39.8%	138.5 / 57.9	103	F13F (TTC→TTT)	ymgD	uncharacterized protein
*	NC_000913	1,764,785	0	T	A	39.8%	142.4 / 58.6	103	intergenic (‑399/+149)	sufA/ydiH	Fe‑S cluster assembly protein/uncharacterized 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	925901 =	102 (0.830)	27 (0.220) +C	20/296	13.1	23.5%	noncoding (71/88 nt)	serW	tRNA‑Ser
	?	NC_000913	= 1097399	75 (0.610)					intergenic (+570/+166)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
*	?	NC_000913	4542682 =	163 (1.320)	7 (0.060)	7/280	19.8	4.5%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	141 (1.210)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	1411899 =	111 (0.900)	4 (0.040)	4/246	20.4	4.2%	coding (50/936 nt)	ttcA	tRNA s(2)C32 thioltransferase, iron sulfur cluster protein
	?	NC_000913	= 1434958	90 (0.880)					pseudogene (51/51 nt)	ttcC	pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related