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 29 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	65.9%	64.8 / 69.4	85	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	61.9%	9.4 / 69.8	49	L18F (CTC→TTC) ‡	mutS	methyl‑directed mismatch repair protein
*	NC_000913	566,245	0	G	A	56.1%	11.1 / 80.0	66	pseudogene (132/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	2,857,145	0	T	A	55.1%	3.7 / 76.5	49	L18H (CTC→CAC) ‡	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,147	0	A	T	55.1%	83.8 / 76.8	49	coding (55/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,148	0	G	C	55.1%	84.4 / 80.1	49	coding (56/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,143	0	T	A	53.1%	‑5.7 / 79.6	49	Y17* (TAT→TAA)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,146	0	C	G	53.1%	‑4.2 / 89.0	49	L18L (CTC→CTG) ‡	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,142	0	A	G	52.1%	1.0 / 59.2	49	Y17C (TAT→TGT)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	566,205	0	T	C	51.9%	17.7 / 98.4	79	pseudogene (172/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	566,277	0	C	T	51.2%	1.4 / 117.8	81	pseudogene (100/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	2,222,641	0	G	A	50.0%	2.0 / 59.5	46	G153S (GGC→AGC)	dld	D‑lactate dehydrogenase, FAD‑binding, NADH independent
*	NC_000913	566,173	0	C	G	49.3%	‑6.2 / 140.8	73	pseudogene (204/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	4,171,557	0	C	A	48.5%	18.7 / 55.6	33	intergenic (+13/‑80)	rrlB/rrfB	23S ribosomal RNA of rrnB operon/5S ribosomal RNA of rrnB operon
*	NC_000913	2,857,141	1	.	G	46.9%	77.6 / 104.4	49	coding (49/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	4,296,060	0	C	T	40.6%	26.0 / 27.8	32	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
*	NC_000913	4,518,992	0	C	.	34.2%	188.9 / 95.3	79	pseudogene (272/504 nt)	insB1	IS1 transposase B,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related
*	NC_000913	2,857,143	1	.	A	32.6%	44.2 / 73.2	49	coding (51/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	1,287,044	0	G	A	27.3%	67.7 / 23.7	45	intergenic (+518/+22)	narI/rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
*	NC_000913	566,323	0	C	T	27.2%	133.4 / 46.9	81	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	4542682 =	33 (0.640)	6 (0.130)	6/218	3.3	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 =	49 (1.030)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)