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 37 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,286,965	0	A	G	64.1%	51.1 / 78.7	92	intergenic (+439/+101)	narI/rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
*	NC_000913	1,287,202	0	A	G	60.0%	‑2.9 / 21.1	25	noncoding (35/171 nt)	rttR	rtT sRNA, processed from tyrT transcript
*	NC_000913	566,205	0	T	C	58.6%	45.7 / 71.6	70	pseudogene (172/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	1,287,220	0	A	G	55.6%	‑4.3 / 27.1	30	noncoding (17/171 nt)	rttR	rtT sRNA, processed from tyrT transcript
*	NC_000913	566,173	0	C	G	55.4%	50.0 / 148.5	92	pseudogene (204/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	2,857,144	0	C	T	53.1%	‑1.2 / 64.8	35	L18F (CTC→TTC) ‡	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,141	1	.	G	51.4%	57.5 / 60.2	35	coding (49/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,147	0	A	.	51.4%	53.3 / 82.3	35	coding (55/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,148	0	G	.	51.4%	52.4 / 77.0	35	coding (56/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	1,287,215	0	T	C	50.0%	1.6 / 39.1	30	noncoding (22/171 nt)	rttR	rtT sRNA, processed from tyrT transcript
*	NC_000913	1,287,217	0	G	T	50.0%	16.2 / 47.6	30	noncoding (20/171 nt)	rttR	rtT sRNA, processed from tyrT transcript
*	NC_000913	1,287,219	0	G	A	50.0%	6.2 / 34.3	30	noncoding (18/171 nt)	rttR	rtT sRNA, processed from tyrT transcript
*	NC_000913	3,728,110	2	.	C	48.6%	55.8 / 81.7	37	coding (1262/1455 nt)	xylB	xylulokinase
*	NC_000913	2,857,142	0	A	G	48.6%	‑5.8 / 44.3	35	Y17C (TAT→TGT)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,143	0	T	A	48.6%	1.8 / 53.7	35	Y17* (TAT→TAA)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,145	0	T	A	48.6%	1.7 / 53.9	35	L18H (CTC→CAC) ‡	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,146	0	C	G	48.6%	0.7 / 62.7	35	L18L (CTC→CTG) ‡	mutS	methyl‑directed mismatch repair protein
*	NC_000913	566,245	0	G	A	48.2%	15.8 / 103.5	85	pseudogene (132/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	566,277	0	C	T	46.9%	34.9 / 116.8	98	pseudogene (100/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	2,857,143	1	.	A	42.9%	47.8 / 71.8	35	coding (51/2562 nt)	mutS	methyl‑directed mismatch repair 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	= 1323147	43 (0.720)	17 (0.290)	10/206	3.6	44.2%	intergenic (‑65/‑73)	trpL/yciV	trp operon leader peptide/PHP domain protein
	?	NC_000913	= 3742633	0 (0.000)					intergenic (‑101/‑100)	yiaJ/yiaK	transcriptional repressor for the yiaKLMNO‑lyxK‑sgbHUE operon/2,3‑diketo‑L‑gulonate reductase, NADH‑dependent
*	?	NC_000913	4542682 =	24 (0.400)	6 (0.110)	6/188	4.5	13.1%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	58 (1.070)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)