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 27 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	62.8%	7.2 / 35.7	43	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	61.1%	‑3.9 / 26.4	19	L18F (CTC→TTC) ‡	mutS	methyl‑directed mismatch repair protein
*	NC_000913	1,287,044	0	G	A	60.0%	‑6.6 / 12.8	15	intergenic (+518/+22)	narI/rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
*	NC_000913	2,857,142	0	A	G	57.9%	3.0 / 16.3	19	Y17C (TAT→TGT)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,143	0	T	A	57.9%	‑4.7 / 24.1	19	Y17* (TAT→TAA)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,145	0	T	A	57.9%	0.1 / 24.0	19	L18H (CTC→CAC) ‡	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,147	0	A	T	57.9%	30.3 / 23.8	19	coding (55/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,148	0	G	C	57.9%	29.6 / 24.9	19	coding (56/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,146	0	C	G	55.6%	‑5.7 / 27.8	19	L18L (CTC→CTG) ‡	mutS	methyl‑directed mismatch repair protein
*	NC_000913	1,287,052	0	A	G	53.8%	‑3.5 / 10.4	13	intergenic (+526/+14)	narI/rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
*	NC_000913	1,287,048	0	A	C	53.3%	‑0.3 / 18.1	15	intergenic (+522/+18)	narI/rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
*	NC_000913	566,245	0	G	A	53.1%	‑5.2 / 65.0	49	pseudogene (132/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	566,205	0	T	C	50.0%	1.3 / 58.5	46	pseudogene (172/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	1,287,202	0	A	G	50.0%	5.1 / 25.9	20	noncoding (35/171 nt)	rttR	rtT sRNA, processed from tyrT transcript
*	NC_000913	566,277	0	C	T	48.4%	10.1 / 76.9	64	pseudogene (100/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	2,857,141	1	.	G	42.1%	‑2.1 / 33.5	19	coding (49/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	1,287,220	0	A	G	40.7%	21.3 / 26.8	28	noncoding (17/171 nt)	rttR	rtT sRNA, processed from tyrT transcript
*	NC_000913	1,287,215	0	T	C	39.3%	24.0 / 25.3	28	noncoding (22/171 nt)	rttR	rtT sRNA, processed from tyrT transcript
*	NC_000913	1,287,217	0	G	T	39.3%	45.4 / 31.5	28	noncoding (20/171 nt)	rttR	rtT sRNA, processed from tyrT transcript
*	NC_000913	1,287,219	0	G	A	39.3%	30.9 / 22.1	28	noncoding (18/171 nt)	rttR	rtT sRNA, processed from tyrT transcript

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	= 1207805	35 (0.960)	4 (0.130)	4/200	2.9	13.1%	coding (305/630 nt)	stfP	e14 prophage, uncharacterized protein
	?	NC_000913	= 1209602	23 (0.730)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related
*	?	NC_000913	= 3430739	28 (0.770)	4 (0.110)	4/226	3.2	14.0%	coding (100/819 nt)	aroE	dehydroshikimate reductase, NAD(P)‑binding
	?	NC_000913	= 3430742	22 (0.620)					coding (97/819 nt)	aroE	dehydroshikimate reductase, NAD(P)‑binding