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 33 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	70.2%	45.9 / 35.4	57	intergenic (+439/+101)	narI/rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
*	NC_000913	2,857,141	1	.	G	52.9%	59.0 / 56.8	34	coding (49/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,147	0	A	.	52.9%	49.8 / 77.1	34	coding (55/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,148	0	G	.	52.9%	50.3 / 72.9	34	coding (56/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	566,205	0	T	C	51.6%	15.3 / 73.4	62	pseudogene (172/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	2,857,144	0	C	T	51.6%	7.1 / 66.7	34	L18F (CTC→TTC) ‡	mutS	methyl‑directed mismatch repair protein
*	NC_000913	4,171,557	0	C	A	50.0%	21.4 / 67.8	40	intergenic (+13/‑80)	rrlB/rrfB	23S ribosomal RNA of rrnB operon/5S ribosomal RNA of rrnB operon
*	NC_000913	1,287,143	0	G	A	47.1%	‑1.6 / 15.4	17	noncoding (94/171 nt) P12S (CCA→TCA)	rttR tpr	rtT sRNA, processed from tyrT transcript protamine‑like protein
*	NC_000913	2,857,142	0	A	G	47.1%	‑5.5 / 44.4	34	Y17C (TAT→TGT)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,143	0	T	A	47.1%	7.1 / 48.3	34	Y17* (TAT→TAA)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,145	0	T	A	47.1%	4.3 / 52.7	34	L18H (CTC→CAC) ‡	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,146	0	C	G	47.1%	7.8 / 58.0	34	L18L (CTC→CTG) ‡	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,143	1	.	A	44.1%	47.5 / 72.5	34	coding (51/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	566,173	0	C	G	43.4%	40.5 / 124.4	76	pseudogene (204/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	566,245	0	G	A	41.0%	57.6 / 79.3	78	pseudogene (132/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	1,287,041	0	A	G	38.7%	23.7 / 22.6	31	intergenic (+515/+25)	narI/rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
*	NC_000913	566,277	0	C	T	37.1%	109.8 / 94.4	105	pseudogene (100/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	1,287,044	0	G	A	32.3%	30.3 / 20.1	31	intergenic (+518/+22)	narI/rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
*	NC_000913	4,296,060	0	C	T	29.7%	113.0 / 46.7	74	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
*	NC_000913	566,323	0	C	T	29.1%	124.2 / 50.1	80	pseudogene (54/279 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	= 1207805	39 (0.720)	5 (0.110)	5/178	2.6	14.5%	coding (305/630 nt)	stfP	e14 prophage, uncharacterized protein
	?	NC_000913	= 1209602	26 (0.570)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related
*	?	NC_000913	4542682 =	22 (0.410)	4 (0.080)	4/192	3.0	9.3%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	58 (1.170)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)