breseq  version 0.33.1  revision 8505477f25b3 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	3,728,183	0	C	G	66.7%	13.1 / 12.7	18	A397P (GCG→CCG)	xylB	xylulokinase
*	NC_000913	3,770,229	0	C	G	61.5%	‑3.0 / 13.0	13	intergenic (+83/+14)	yibU/yibH	pseudogene, H repeat‑associated protein/putative membrane fusion protein (MFP) component of efflux pump
*	NC_000913	3,770,232	0	C	G	61.5%	‑5.6 / 12.9	13	intergenic (+86/+11)	yibU/yibH	pseudogene, H repeat‑associated protein/putative membrane fusion protein (MFP) component of efflux pump
*	NC_000913	3,770,233	0	C	G	61.5%	‑3.0 / 12.9	13	intergenic (+87/+10)	yibU/yibH	pseudogene, H repeat‑associated protein/putative membrane fusion protein (MFP) component of efflux pump
*	NC_000913	3,770,231	0	C	G	58.3%	‑6.6 / 14.9	13	intergenic (+85/+12)	yibU/yibH	pseudogene, H repeat‑associated protein/putative membrane fusion protein (MFP) component of efflux pump
*	NC_000913	4,296,060	0	C	T	49.0%	5.5 / 74.3	50	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
*	NC_000913	2,253,023	0	C	G	47.6%	10.2 / 23.8	21	A375P (GCG→CCG)	nupX	nucleoside permease
*	NC_000913	890,115	0	G	C	41.7%	30.6 / 11.1	26	G9G (GGG→GGC)	ybjM	inner membrane protein
*	NC_000913	1,135,975	0	G	C	40.6%	35.3 / 25.4	32	A138P (GCC→CCC)	flgH	flagellar protein of basal‑body outer‑membrane L ring
*	NC_000913	1,563,398	0	G	C	38.5%	30.1 / 11.5	28	S779C (TCC→TGC)	dosP	oxygen sensor, c‑di‑GMP phosphodiesterase, heme‑regulated; cold‑ and stationary phase‑induced bioflim regulator
*	NC_000913	2,253,024	0	C	G	38.1%	22.7 / 11.2	21	G374G (GGG→GGC)	nupX	nucleoside permease
*	NC_000913	34,508	0	G	C	35.7%	63.6 / 32.7	42	G70A (GGA→GCA)	caiF	cai operon transcriptional activator
*	NC_000913	2,778,212	0	C	G	35.1%	54.7 / 21.3	37	G1505G (GGG→GGC)	ypjA	adhesin‑like autotransporter
*	NC_000913	391,701	0	G	C	32.6%	72.7 / 18.8	46	pseudogene (1451/1458 nt)	yaiT	pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein
*	NC_000913	1,041,386	0	G	C	32.0%	44.2 / 11.3	25	G257A (GGA→GCA)	appA	phosphoanhydride phosphorylase
*	NC_000913	823,451	0	G	C	30.8%	34.7 / 11.0	26	P97A (CCC→GCC)	clsB	cardiolipin synthase 2
*	NC_000913	1,527,602	0	G	C	28.1%	67.2 / 16.7	32	intergenic (+450/‑300)	yncH/rhsE	IPR020099 family protein/pseudogene, Rhs family
*	NC_000913	669,840	0	G	C	25.8%	62.4 / 10.5	32	A23G (GCG→GGG)	cobC	putative alpha‑ribazole‑5'‑P phosphatase
*	NC_000913	2,367,979	0	C	G	25.0%	53.1 / 10.2	32	R303R (CGC→CGG)	arnC	undecaprenyl phosphate‑L‑Ara4FN transferase

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	= 3579387	39 (1.220)	3 (0.110)	3/112	2.5	9.2%	coding (259/696 nt)	yhhW	quercetinase activity in vitro
	?	NC_000913	= 3579470	26 (0.960)					coding (176/696 nt)	yhhW	quercetinase activity in vitro
*	?	NC_000913	= 2532662	28 (0.880)	3 (0.100)	3/124	2.8	9.2%	coding (254/972 nt)	cysK	cysteine synthase A, O‑acetylserine sulfhydrolase A subunit
	?	NC_000913	= 2532707	33 (1.100)					coding (299/972 nt)	cysK	cysteine synthase A, O‑acetylserine sulfhydrolase A subunit