breseq  version 0.35.4  revision f352f80f4bc9 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 22 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	753,125	0	T	A	33.3%	79.8 / 19.9	45	intergenic (‑330/+60)	ybgD/gltA	putative fimbrial protein YbgD/citrate synthase
*	NC_000913	650,809	0	T	G	32.6%	81.6 / 13.7	46	T350P (ACC→CCC)	citC	citrate lyase synthetase
*	NC_000913	4,604,344	0	C	T	31.9%	70.3 / 19.1	47	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional regulator BglJ
*	NC_000913	2,001,918	0	A	C	31.1%	81.5 / 14.8	45	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein
*	NC_000913	729,659	0	T	G	28.0%	98.9 / 12.6	50	V26G (GTA→GGA)	rhsC	rhs element protein RhsC
*	NC_000913	2,007,619	0	G	A	28.0%	35.8 / 14.3	25	V488V (GTG→GTA)	amyA	alpha‑amylase
*	NC_000913	3,401,459	0	T	C	27.5%	127.2 / 17.9	69	D625G (GAT→GGT)	csrD	regulator of CsrB and CsrC decay
*	NC_000913	1,644,297	0	A	G	27.3%	57.1 / 29.1	44	V3A (GTA→GCA)	ydfU	Qin prophage; protein YdfU
*	NC_000913	29,496	0	T	A	27.0%	85.5 / 10.8	38	intergenic (+301/‑155)	dapB/carA	4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha
*	NC_000913	4,111,747	0	G	T	25.6%	96.9 / 12.1	39	N156K (AAC→AAA)	yiiQ	DUF1454 domain‑containing protein YiiQ
*	NC_000913	4,098,155	0	A	C	24.7%	181.4 / 13.7	81	L140F (TTA→TTC)	rhaS	DNA‑binding transcriptional activator RhaS
*	NC_000913	2,406,530	0	T	C	24.7%	117.9 / 48.4	77	T38A (ACT→GCT)	lrhA	DNA‑binding transcriptional dual regulator LrhA
*	NC_000913	2,326,450	0	T	G	24.4%	90.3 / 12.1	41	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	3,634,086	0	T	C	23.5%	152.6 / 51.5	85	pseudogene (373/1607 nt)	yhiL	putative uncharacterized protein YhiL
*	NC_000913	2,585,975	0	T	C	23.5%	172.0 / 59.0	98	V82A (GTA→GCA)	narQ	sensory histidine kinase NarQ
*	NC_000913	1,068,173	0	T	G	23.1%	118.6 / 12.3	52	G31G (GGT→GGG)	ymdF	conserved protein YmdF
*	NC_000913	3,844,219	0	T	G	21.9%	195.1 / 18.4	82	F86V (TTT→GTT)	adeD	adenine deaminase
*	NC_000913	4,442,146	0	A	G	21.2%	176.4 / 12.2	80	S11P (TCC→CCC)	msrA	methionine sulfoxide reductase A
*	NC_000913	4,568,512	0	C	A	21.1%	162.4 / 13.7	57	R3L (CGT→CTT)	mdtM	multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter
*	NC_000913	4,287,719	0	T	A	20.8%	111.5 / 14.0	48	intergenic (‑348/‑45)	acs/nrfA	acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase

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	= 1207805	81 (1.190)	7 (0.120)	6/244	4.7	11.1%	coding (305/630 nt)	ycfK	e14 prophage; protein StfP
	?	NC_000913	= 1209602	41 (0.680)					pseudogene (54/537 nt)	stfE	e14 prophage; putative side tail fiber protein fragment
*	?	NC_000913	4001531 =	97 (1.430)	3 (0.050)	3/260	6.2	3.2%	coding (106/951 nt)	corA	Ni(2(+))/Co(2(+))/Mg(2(+)) transporter
	?	NC_000913	= 4001527	89 (1.390)					coding (102/951 nt)	corA	Ni(2(+))/Co(2(+))/Mg(2(+)) transporter
*	?	NC_000913	= 3621784	NA (NA)	3 (0.040)	3/272	6.4	100%	coding (2593/4236 nt)	rhsB	rhs element protein RhsB
	?	NC_000913	3621788 =	0 (0.000)					coding (2597/4236 nt)	rhsB	rhs element protein RhsB