breseq  version 0.32.1  revision aa8f2595a244 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 29 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,171,557	0	C	A	55.6%	4.4 / 49.6	27	intergenic (+13/‑80)	rrlB/rrfB	23S ribosomal RNA of rrnB operon/5S ribosomal RNA of rrnB operon
*	NC_000913	3,667,400	0	C	T	54.4%	11.0 / 152.6	114	A61T (GCC→ACC)	gadA	glutamate decarboxylase A, PLP‑dependent
*	NC_000913	2,857,141	1	.	G	53.1%	89.2 / 80.1	49	coding (49/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,147	0	A	.	53.1%	76.2 / 111.6	49	coding (55/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,148	0	G	.	53.1%	70.9 / 102.1	49	coding (56/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,144	0	C	G	52.1%	29.7 / 75.0	49	L18V (CTC→GTC) ‡	mutS	methyl‑directed mismatch repair protein
*	NC_000913	3,761,969	0	T	C	51.5%	20.7 / 123.6	97	intergenic (‑14/‑214)	yibF/rhsA	glutathione S‑transferase homolog/Rhs protein with putative toxin 55 domain, putative polysaccharide synthesis/export protein, putative neighboring cell growth inhibitor
*	NC_000913	3,736,591	0	T	C	51.4%	31.9 / 181.6	140	Y196C (TAC→TGC)	bax	putative glucosaminidase
*	NC_000913	2,857,143	1	.	A	51.0%	83.5 / 80.2	49	coding (51/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	1,286,965	0	A	G	50.9%	7.4 / 223.9	173	intergenic (+439/+101)	narI/rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
*	NC_000913	566,173	0	C	G	48.6%	15.6 / 273.0	140	pseudogene (204/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	2,857,142	0	A	G	46.9%	‑1.2 / 63.8	49	Y17C (TAT→TGT)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,143	0	T	A	46.9%	12.4 / 74.6	49	Y17* (TAT→TAA)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,145	0	T	A	46.9%	11.3 / 75.0	49	L18H (CTC→CAC) ‡	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,146	0	C	G	46.9%	13.7 / 85.4	49	L18L (CTC→CTG) ‡	mutS	methyl‑directed mismatch repair protein
*	NC_000913	3,709,555	2	.	C	41.0%	33.3 / 183.0	100	coding (921/1692 nt)	eptB	KDO phosphoethanolamine transferase, Ca(2+)‑inducible
*	NC_000913	566,245	0	G	A	40.4%	78.8 / 108.1	104	pseudogene (132/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	566,205	0	T	C	38.8%	72.4 / 144.6	129	pseudogene (172/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	566,277	0	C	T	38.4%	110.1 / 105.6	113	pseudogene (100/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	4,296,060	0	C	T	33.3%	84.2 / 51.0	66	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein

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	1390544 =	41 (0.600)	4 (0.060)	4/202	6.7	8.5%	coding (55/729 nt)	mpaA	murein peptide amidase A
	?	NC_000913	1390553 =	45 (0.670)					coding (46/729 nt)	mpaA	murein peptide amidase A
*	?	NC_000913	= 2460503	52 (0.760)	4 (0.060)	3/196	7.1	8.4%	intergenic (‑34/+147)	fadI/yfcZ	beta‑ketoacyl‑CoA thiolase, anaerobic, subunit/UPF0381 family protein
	?	NC_000913	= 2460504	37 (0.570)					intergenic (‑35/+146)	fadI/yfcZ	beta‑ketoacyl‑CoA thiolase, anaerobic, subunit/UPF0381 family protein
*	?	NC_000913	= 3277865	NA (NA)	5 (0.070)	3/202	7.3	5.9%	coding (801/810 nt)	agaR	transcriptional repressor of the aga regulon
	?	NC_000913	3277872 =	81 (1.190)					coding (794/810 nt)	agaR	transcriptional repressor of the aga regulon