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
*	CP009273	4,178,500	0	C	T	60.0%	20.4 / 42.5	35	R1075C (CGT→TGT)	rpoC	RNA polymerase, beta prime subunit
*	CP009273	2,654,126	0	G	A	24.4%	79.7 / 25.6	41	A255A (GCC→GCT)	iscS	cysteine desulfurase (tRNA sulfurtransferase), PLP‑dependent
*	CP009273	3,618,160	0	A	G	21.9%	87.1 / 22.0	41	G141G (GGA→GGG)	yhhI	putative transposase

Marginal new junction evidence (sorted from low to high skew)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 370556	66 (1.440)	10 (0.250)	6/232	2.0	17.2%	noncoding (171/436 nt)	REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences	REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences
	?	CP009273	= 372808	40 (1.020)					noncoding (18/187 nt)	REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences	REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences
*	?	CP009273	= 370385	55 (1.610)	4 (0.130)	3/184	2.4	7.4%	intergenic (+48/‑530)	mhpE/mhpT	4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter
	?	CP009273	= 372977	NA (NA)					noncoding (187/187 nt)	REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences	REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences
*	?	CP009273	1282164 =	58 (1.270)	6 (0.160)	4/228	2.5	8.3%	intergenic (+182/+358)	narI/rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
	?	CP009273	= 1282697	83 (2.150)					intergenic (‑5/+3)	rttR/tyrV	rtT sRNA, processed from tyrT transcript/tRNA‑Tyr
*	?	CP009273	= 1972861	44 (0.960)	8 (0.170)	4/270	2.9	15.4%	intergenic (‑407/‑373)	flhD/uspC	flagellar class II regulon transcriptional activator, with FlhC/universal stress protein
	?	CP009273	= 3577555	NA (NA)					intergenic (+15/‑1)	insB1/yrhA	IS1 transposase B/pseudogene, interrupted by IS1E
*	?	CP009273	= 370657	66 (1.440)	7 (0.180)	3/232	3.0	12.7%	noncoding (272/436 nt)	REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences	REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences
	?	CP009273	= 372808	40 (1.020)					noncoding (18/187 nt)	REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences	REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences
*	?	CP009273	= 233496	15 (0.330)	4 (0.090) +TATTAAGAAG	3/250	3.1	7.4%	intergenic (+2/‑326)	aspV/yafT	tRNA‑Asp/lipoprotein
	?	CP009273	= 400969	93 (2.030)					coding (132/810 nt)	proC	pyrroline‑5‑carboxylate reductase, NAD(P)‑binding
*	?	CP009273	2508779 =	NA (NA)	3 (0.070)	3/266	3.3	3.5%	coding (970/1113 nt)	insL1	IS186 transposase
	?	CP009273	3543417 =	85 (1.860)					coding (13/2085 nt)	malQ	4‑alpha‑glucanotransferase (amylomaltase)
*	?	CP009273	= 1380912	25 (0.550)	3 (0.070)	3/268	3.3	6.9%	intergenic (+83/‑65)	ycjF/tyrR	UPF0283 family inner membrane protein/aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase
	?	CP009273	= 3837577	56 (1.230)					coding (254/1767 nt)	ade	cryptic adenine deaminase
*	?	CP009273	49892 =	19 (0.420)	3 (0.070)	3/266	3.3	11.2%	coding (70/480 nt)	folA	dihydrofolate reductase
	?	CP009273	= 4471099	29 (0.640)					coding (2556/2856 nt)	valS	valyl‑tRNA synthetase