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 36 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	69.0%	42.1 / 40.3	59	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	56.7%	‑4.9 / 55.6	35	L18F (CTC→TTC) ‡	mutS	methyl‑directed mismatch repair protein
*	NC_000913	566,277	0	C	T	52.5%	‑1.2 / 87.6	61	pseudogene (100/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	2,857,141	1	.	G	51.4%	62.0 / 59.3	35	coding (49/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,147	0	A	.	51.4%	53.5 / 82.8	35	coding (55/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,148	0	G	.	51.4%	52.7 / 77.9	35	coding (56/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,142	0	A	G	48.6%	‑5.8 / 45.1	35	Y17C (TAT→TGT)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,143	0	T	A	48.6%	3.6 / 52.9	35	Y17* (TAT→TAA)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,145	0	T	A	48.6%	‑0.2 / 56.3	35	L18H (CTC→CAC) ‡	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,146	0	C	G	48.6%	2.3 / 63.1	35	L18L (CTC→CTG) ‡	mutS	methyl‑directed mismatch repair protein
*	NC_000913	1,287,143	0	G	A	45.0%	‑5.9 / 18.4	20	noncoding (94/171 nt) P12S (CCA→TCA)	rttR tpr	rtT sRNA, processed from tyrT transcript protamine‑like protein
*	NC_000913	566,245	0	G	A	44.6%	25.0 / 62.4	56	pseudogene (132/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	566,205	0	T	C	41.4%	20.6 / 84.6	70	pseudogene (172/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	4,171,557	0	C	A	41.4%	24.7 / 38.8	29	intergenic (+13/‑80)	rrlB/rrfB	23S ribosomal RNA of rrnB operon/5S ribosomal RNA of rrnB operon
*	NC_000913	2,857,143	1	.	A	37.1%	13.6 / 60.4	35	coding (51/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	1,287,202	0	A	G	36.8%	7.2 / 16.1	19	noncoding (35/171 nt)	rttR	rtT sRNA, processed from tyrT transcript
*	NC_000913	4,296,060	0	C	T	36.4%	32.0 / 26.3	33	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
*	NC_000913	566,173	0	C	G	36.1%	71.4 / 98.3	72	pseudogene (204/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	1,287,220	0	A	G	35.3%	5.2 / 13.0	19	noncoding (17/171 nt)	rttR	rtT sRNA, processed from tyrT transcript
*	NC_000913	1,287,041	0	A	G	34.4%	27.9 / 28.0	32	intergenic (+515/+25)	narI/rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/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	1207790 =	39 (0.980)	6 (0.180)	5/206	2.7	18.2%	coding (290/630 nt)	stfP	e14 prophage, uncharacterized protein
	?	NC_000913	1209619 =	20 (0.580)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related