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 376 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,221,754	0	T	C	42.9%	44.2 / 14.8	49	pseudogene (484/1436 nt)	mdtQ	multidrug resistance outer membrane protein MdtQ
*	NZ_CP009273	1,170,061	0	T	C	41.6%	111.4 / 28.9	77	G187G (GGA→GGG)	ycfT	acyltransferase family protein
*	NZ_CP009273	4,277,638	0	G	A	40.0%	130.6 / 45.5	95	intergenic (‑339/‑54)	acs/nrfA	acetate‑‑CoA ligase/ammonia‑forming nitrite reductase cytochrome c552 subunit
*	NZ_CP009273	3,199,805	0	C	A	39.3%	93.8 / 31.6	90	intergenic (‑190/‑17)	ttdR/ttdA	DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha
*	NZ_CP009273	2,319,929	0	T	G	39.3%	159.4 / 21.3	84	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NZ_CP009273	2,089,571	0	A	G	38.4%	167.5 / 29.0	99	I83V (ATT→GTT)	hisF	imidazole glycerol phosphate synthase subunit HisF
*	NZ_CP009273	4,277,647	0	T	A	37.1%	132.9 / 47.1	89	intergenic (‑348/‑45)	acs/nrfA	acetate‑‑CoA ligase/ammonia‑forming nitrite reductase cytochrome c552 subunit
*	NZ_CP009273	3,524,799	0	A	C	37.0%	274.7 / 24.0	135	Y334D (TAT→GAT)	yhgE	DUF4153 domain‑containing protein
*	NZ_CP009273	3,151,752	0	G	A	36.0%	141.7 / 34.7	86	E248E (GAG→GAA)	yqhG	YbjP/YqhG family protein
*	NZ_CP009273	714,125	0	C	T	35.9%	106.4 / 23.7	64	E598K (GAA→AAA)	speF	ornithine decarboxylase SpeF
*	NZ_CP009273	3,806,632	0	C	T	35.1%	89.5 / 33.0	74	S181L (TCG→TTG)	coaBC	bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate‑‑cysteine ligase CoaBC
*	NZ_CP009273	1,155,293	0	A	G	35.1%	170.4 / 28.0	94	I572T (ATC→ACC)	fhuE	ferric‑rhodotorulic acid/ferric‑coprogen receptor FhuE
*	NZ_CP009273	2,033,556	0	C	G	35.1%	78.0 / 26.7	61	L200V (CTG→GTG)	msrP	protein‑methionine‑sulfoxide reductase catalytic subunit MsrP
*	NZ_CP009273	4,526,014	0	A	T	34.7%	150.3 / 63.8	98	intergenic (+166/+102)	yjhR/BW25113_RS26295	helicase YjhR/HNH endonuclease
*	NZ_CP009273	1,995,399	0	A	C	34.6%	229.7 / 15.9	104	intergenic (‑129/+192)	fliA/fliC	RNA polymerase sigma factor FliA/H48 family flagellin FliC
*	NZ_CP009273	29,496	0	T	A	34.4%	181.4 / 37.4	90	intergenic (+301/‑155)	dapB/carA	4‑hydroxy‑tetrahydrodipicolinate reductase/glutamine‑hydrolyzing carbamoyl‑phosphate synthase small subunit
*	NZ_CP009273	3,101,758	0	T	A	34.2%	153.0 / 33.4	79	N253Y (AAT→TAT)	speC	ornithine decarboxylase
*	NZ_CP009273	2,476,733	0	G	A	34.2%	157.4 / 24.4	82	S29L (TCA→TTA)	emrK	multidrug efflux MFS transporter periplasmic adaptor subunit EmrK
*	NZ_CP009273	1,170,082	0	G	A	34.1%	142.7 / 21.0	85	F180F (TTC→TTT)	ycfT	acyltransferase family protein
*	NZ_CP009273	3,199,794	0	C	T	34.1%	97.1 / 57.7	89	intergenic (‑179/‑28)	ttdR/ttdA	DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha

Marginal new junction evidence (sorted from low to high skew)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 4532507	144 (1.270)	7 (0.060)	7/478	17.2	4.8%	intergenic (+57/‑425)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	= 4532803	139 (1.270)					intergenic (+353/‑129)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
*	?	NZ_CP009273	4532499 =	142 (1.250)	7 (0.060)	7/478	17.2	4.8%	intergenic (+49/‑433)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	4532813 =	141 (1.290)					intergenic (+363/‑119)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA