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	4,634,618	0	A	G	72.4%	581.0 / 278.0	313	G231G (GGT→GGC)	rob	DNA‑binding transcriptional dual regulator Rob
*	NC_000913	4,430,824	0	A	G	69.7%	396.9 / 253.2	251	M321V (ATG→GTG)	cycA	serine/alanine/glycine/cycloserine:H(+)symporter
*	NC_000913	523,735	1	.	G	65.8%	633.4 / inf	237	coding (475/4281 nt)	rhsD	protein RhsD
*	NC_000913	2,021,884	0	T	C	61.6%	274.1 / inf	310	S6P (TCT→CCT)	fliP	flagellar biosynthesis protein FliP
*	NC_000913	924,921	0	T	C	35.3%	379.5 / inf	289	V553A (GTC→GCC)	clpA	ATP‑dependent Clp protease ATP‑binding subunit ClpA
*	NC_000913	1,692,919	0	G	A	32.3%	515.6 / inf	356	Q449* (CAG→TAG)	uidB	glucuronide:H(+) symporter
*	NC_000913	4,469,089	0	C	T	31.9%	478.3 / inf	329	P489S (CCG→TCG)	mgtA	Mg(2(+)) importing P‑type ATPase
*	NC_000913	4,296,060	0	C	T	31.8%	899.9 / inf	534	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
*	NC_000913	4,093,134	0	T	G	23.6%	764.4 / 58.7	304	Y102S (TAC→TCC)	rhaM	L‑rhamnose mutarotase
*	NC_000913	4,568,504	0	T	G	21.0%	776.7 / 33.3	295	T6P (ACC→CCC)	mdtM	multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter
*	NC_000913	2,326,450	0	T	G	20.7%	693.4 / 43.4	237	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	3,452,723	0	G	A	20.0%	715.4 / 191.6	295	F68F (TTC→TTT)	rplC	50S ribosomal subunit protein L3

Marginal new junction evidence (lowest skew 10 of 13 shown)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1207790 =	195 (0.610)	126 (0.470)	85/162	5.1	46.0%	coding (290/630 nt)	ycfK	e14 prophage; protein StfP
	?	NC_000913	1209619 =	133 (0.490)					pseudogene (37/537 nt)	stfE	e14 prophage; putative side tail fiber protein fragment
*	?	NC_000913	= 1207805	188 (0.580)	115 (0.430)	75/162	7.2	45.1%	coding (305/630 nt)	ycfK	e14 prophage; protein StfP
	?	NC_000913	= 1209602	123 (0.460)					pseudogene (54/537 nt)	stfE	e14 prophage; putative side tail fiber protein fragment
*	?	NC_000913	= 3982676	0 (0.000)	123 (0.390) +CCC	70/172	9.6	100%	noncoding (71/87 nt)	leuT	tRNA‑Leu
	?	NC_000913	3982677 =	0 (0.000)					noncoding (72/87 nt)	leuT	tRNA‑Leu
*	?	NC_000913	3982677 =	22 (0.070)	130 (0.430)	66/184	12.0	47.0%	noncoding (72/87 nt)	leuT	tRNA‑Leu
	?	NC_000913	4606328 =	272 (0.890)					noncoding (74/87 nt)	leuQ	tRNA‑Leu
*	?	NC_000913	3982677 =	22 (0.070)	124 (0.410)	64/184	12.6	47.7%	noncoding (72/87 nt)	leuT	tRNA‑Leu
	?	NC_000913	4606092 =	251 (0.820)					noncoding (74/87 nt)	leuV	tRNA‑Leu
*	?	NC_000913	= 71350	352 (1.090)	121 (0.390)	61/188	13.9	41.5%	intergenic (+85/‑1)	araC/yabI	DNA‑binding transcriptional dual regulator AraC/DedA family protein YabI
	?	NC_000913	= 2857042	0 (0.000)					intergenic (‑236/‑51)	ygbA/mutS	protein YgbA/DNA mismatch repair protein MutS
*	?	NC_000913	3982677 =	70 (0.220)	61 (0.200)	39/184	20.8	28.0%	noncoding (72/87 nt)	leuT	tRNA‑Leu
	?	NC_000913	4606213 =	247 (0.810)					noncoding (74/87 nt)	leuP	tRNA‑Leu
*	?	NC_000913	4542682 =	397 (1.230)	21 (0.070)	19/176	29.4	5.6%	intergenic (+49/‑433)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	4542996 =	351 (1.200)					intergenic (+363/‑119)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	= 4542690	386 (1.200)	19 (0.070)	17/176	30.6	5.2%	intergenic (+57/‑425)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	= 4542986	348 (1.190)					intergenic (+353/‑129)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	= 1209618	188 (0.580)	17 (0.060)	11/164	33.2	6.8%	pseudogene (38/537 nt)	stfE	e14 prophage; putative side tail fiber protein fragment
	?	NC_000913	2471897 =	304 (1.120)					pseudogene (166/519 nt)	yfdL	CPS‑53 (KpLE1) prophage; putative uncharacterized protein YfdL