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 22 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	61.9%	85.9 / 111.8	118	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	57.6%	‑3.6 / 64.0	42	L18F (CTC→TTC) ‡	mutS	methyl‑directed mismatch repair protein
*	NC_000913	4,171,557	0	C	A	55.6%	3.0 / 47.5	27	intergenic (+13/‑80)	rrlB/rrfB	23S ribosomal RNA of rrnB operon/5S ribosomal RNA of rrnB operon
*	NC_000913	2,857,141	1	.	G	54.8%	77.7 / 67.8	42	coding (49/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,147	0	A	.	52.4%	64.3 / 96.2	42	coding (55/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,148	0	G	.	52.4%	60.6 / 90.8	42	coding (56/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	566,205	0	T	C	49.4%	5.8 / 131.8	89	pseudogene (172/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	566,173	0	C	G	49.1%	‑0.3 / 215.5	110	pseudogene (204/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	2,857,145	0	T	A	47.6%	4.8 / 66.4	42	L18H (CTC→CAC) ‡	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,146	0	C	G	47.6%	10.6 / 72.4	42	L18L (CTC→CTG) ‡	mutS	methyl‑directed mismatch repair protein
*	NC_000913	566,277	0	C	T	45.3%	50.6 / 124.1	106	pseudogene (100/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	2,857,142	0	A	G	45.2%	3.0 / 50.4	42	Y17C (TAT→TGT)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,143	0	T	A	45.2%	14.8 / 59.8	42	Y17* (TAT→TAA)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	566,245	0	G	A	44.2%	54.5 / 103.5	95	pseudogene (132/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	4,296,060	0	C	T	39.1%	61.2 / 60.6	64	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
*	NC_000913	4,037,803	0	G	A	35.3%	91.0 / 56.0	68	noncoding (285/2905 nt)	rrlA	23S ribosomal RNA of rrnA operon
*	NC_000913	2,857,143	1	.	A	33.3%	33.4 / 64.0	42	coding (51/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	4,518,992	0	C	.	32.1%	262.6 / 118.6	106	pseudogene (272/504 nt)	insB1	IS1 transposase B,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related
*	NC_000913	566,323	0	C	T	23.8%	153.8 / 39.8	80	pseudogene (54/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	1,287,048	0	A	C	23.5%	35.8 / 10.8	17	intergenic (+522/+18)	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	4542682 =	17 (0.290)	10 (0.180)	10/192	3.1	19.3%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	68 (1.250)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	= 1207805	64 (1.070)	9 (0.180)	9/178	3.1	17.6%	coding (305/630 nt)	stfP	e14 prophage, uncharacterized protein
	?	NC_000913	= 1209602	30 (0.600)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related
*	?	NC_000913	= 4542690	22 (0.370)	4 (0.070)	3/192	5.5	8.3%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	68 (1.250)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)