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 24 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	380,013	0	G	.	62.3%	43.4 / 115.5	69	intergenic (‑132/+56)	frmR/yaiO	regulator protein that represses frmRAB operon/outer membrane protein
*	NC_000913	1,286,965	0	A	G	61.6%	52.8 / 80.6	86	intergenic (+439/+101)	narI/rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
*	NC_000913	2,857,144	0	C	T	55.6%	‑3.7 / 33.0	22	L18F (CTC→TTC) ‡	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,141	1	.	G	54.5%	36.7 / 32.3	22	coding (49/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,147	0	A	.	54.5%	28.1 / 45.1	22	coding (55/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,148	0	G	.	54.5%	‑6.0 / 41.1	22	coding (56/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	566,205	0	T	C	52.1%	24.5 / 116.0	96	pseudogene (172/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	1,769,471	1	.	G	51.7%	43.2 / 48.0	29	coding (398/1113 nt)	ydiK	UPF0118 family inner membrane protein
*	NC_000913	4,171,557	0	C	A	48.1%	14.7 / 41.7	27	intergenic (+13/‑80)	rrlB/rrfB	23S ribosomal RNA of rrnB operon/5S ribosomal RNA of rrnB operon
*	NC_000913	566,277	0	C	T	46.7%	34.0 / 107.6	92	pseudogene (100/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	2,857,142	0	A	G	45.5%	‑2.2 / 24.4	22	Y17C (TAT→TGT)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,143	0	T	A	45.5%	5.4 / 27.5	22	Y17* (TAT→TAA)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,145	0	T	A	45.5%	5.1 / 28.2	22	L18H (CTC→CAC) ‡	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,146	0	C	G	45.5%	8.7 / 30.7	22	L18L (CTC→CTG) ‡	mutS	methyl‑directed mismatch repair protein
*	NC_000913	566,245	0	G	A	45.3%	43.2 / 111.1	96	pseudogene (132/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	566,173	0	C	G	43.0%	58.4 / 184.0	114	pseudogene (204/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	2,857,143	1	.	A	36.4%	6.1 / 35.2	22	coding (51/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	566,323	0	C	T	34.7%	114.1 / 77.2	95	pseudogene (54/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	566,326	0	T	C	34.7%	84.5 / 85.7	95	pseudogene (51/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	566,332	0	T	G	31.9%	141.1 / 106.6	95	pseudogene (45/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related

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	= 1323147	46 (0.720)	24 (0.380)	10/208	3.8	50.5%	intergenic (‑65/‑73)	trpL/yciV	trp operon leader peptide/PHP domain protein
	?	NC_000913	= 3742633	1 (0.020)					intergenic (‑101/‑100)	yiaJ/yiaK	transcriptional repressor for the yiaKLMNO‑lyxK‑sgbHUE operon/2,3‑diketo‑L‑gulonate reductase, NADH‑dependent
*	?	NC_000913	4542682 =	15 (0.240)	11 (0.190)	8/190	4.1	24.5%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	54 (0.930)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	3071743 =	88 (1.390)	3 (0.050)	3/202	6.4	3.7%	coding (880/1164 nt)	pgk	phosphoglycerate kinase
	?	NC_000913	3245211 =	70 (1.140)					intergenic (‑470/‑13)	uxaC/exuT	uronate isomerase/hexuronate transporter