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

Marginal read alignment evidence
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,206,435	0	C	T	40.7%	19.7 / 20.3	27	intergenic (‑179/‑28)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
*	NC_000913	4,568,504	0	T	G	40.3%	106.6 / 17.6	72	T6P (ACC→CCC)	mdtM	multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter
*	NC_000913	4,111,747	0	G	T	36.4%	62.7 / 21.3	33	N156K (AAC→AAA)	yiiQ	DUF1454 domain‑containing protein YiiQ
*	NC_000913	4,604,344	0	C	T	34.9%	53.9 / 22.5	43	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional regulator BglJ
*	NC_000913	3,206,444	0	T	A	31.0%	45.5 / 10.7	29	intergenic (‑188/‑19)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
*	NC_000913	4,429,984	0	T	G	30.9%	77.2 / 14.7	42	L41V (TTG→GTG)	cycA	serine/alanine/glycine/cycloserine:H(+)symporter
*	NC_000913	4,101,514	0	G	T	30.6%	83.5 / 16.0	36	intergenic (+84/‑176)	sodA/kdgT	superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter
*	NC_000913	1,019,046	0	A	G	29.0%	38.4 / 18.5	31	G336G (GGT→GGC)	ompA	outer membrane porin A
*	NC_000913	646,747	0	T	G	27.5%	75.9 / 16.2	40	T255P (ACC→CCC)	citG	triphosphoribosyl‑dephospho‑CoA synthase
*	NC_000913	4,296,060	0	C	T	26.6%	136.6 / 51.1	79	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
*	NC_000913	753,125	0	T	A	26.2%	93.3 / 10.4	42	intergenic (‑330/+60)	ybgD/gltA	putative fimbrial protein YbgD/citrate synthase
*	NC_000913	753,105	0	A	T	25.9%	131.0 / 13.1	54	intergenic (‑310/+80)	ybgD/gltA	putative fimbrial protein YbgD/citrate synthase
*	NC_000913	1,315,936	0	T	A	24.5%	110.4 / 11.0	49	K34* (AAA→TAA)	yciG	protein YciG
*	NC_000913	2,664,896	0	T	G	24.0%	111.9 / 13.5	50	G169G (GGT→GGG)	yfhR	putative peptidase
*	NC_000913	2,782,509	0	A	C	21.8%	216.2 / 10.3	87	V73G (GTA→GGA)	ypjA	adhesin‑like autotransporter YpjA
*	NC_000913	3,740,909	0	T	G	21.7%	137.4 / 10.3	60	V402G (GTG→GGG)	avtA	valine‑‑pyruvate aminotransferase
*	NC_000913	4,287,719	0	T	A	20.8%	120.7 / 10.0	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	57 (0.900)	8 (0.140)	8/244	3.6	15.0%	coding (305/630 nt)	ycfK	e14 prophage; protein StfP
	?	NC_000913	= 1209602	40 (0.710)					pseudogene (54/537 nt)	stfE	e14 prophage; putative side tail fiber protein fragment
*	?	NC_000913	1396044 =	NA (NA)	6 (0.100) +CTAA	5/268	4.9	100%	noncoding (1/1195 nt)	IS5	repeat region
	?	NC_000913	1979271 =	0 (0.000)					intergenic (‑56/‑482)	insA‑5/uspC	IS1 protein InsA/universal stress protein C
*	?	NC_000913	4373295 =	NA (NA)	4 (0.070)	3/256	5.6	NA	noncoding (2/34 nt)	other	REP328b
	?	NC_000913	4374499 =	NA (NA)					noncoding (1/34 nt)	other	REP329a
*	?	NC_000913	1979271 =	0 (0.000)	4 (0.060) +T	3/274	5.9	100%	intergenic (‑56/‑482)	insA‑5/uspC	IS1 protein InsA/universal stress protein C
	?	NC_000913	= 2067356	NA (NA)					intergenic (‑35/‑1279)	insH‑6/yoeA	CP4‑44 prophage; IS5 transposase and trans‑activator/CP4‑44 prophage; TonB‑dependent receptor plug domain‑containing protein YoeA