breseq  version 0.29.0  revision 8f9c342918e4 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 489 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,423,294	0	T	C	48.6%	69.8 / 28.4	72	intergenic (+100/+129)	yhdZ/rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
*	NC_000913	29,496	0	T	A	46.5%	72.5 / 55.8	72	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	175,694	0	T	G	46.5%	103.6 / 13.3	72	G196G (GGT→GGG)	clcA	H(+)/Cl(‑) exchange transporter
*	NC_000913	599,576	0	T	G	45.8%	65.3 / 32.3	60	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	4,286,504	0	T	A	44.4%	71.9 / 30.0	54	K290* (AAA→TAA)	acs	acetyl‑CoA synthetase
*	NC_000913	3,423,290	0	A	C	43.8%	50.8 / 29.3	73	intergenic (+96/+133)	yhdZ/rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
*	NC_000913	2,678,039	0	T	G	42.9%	86.3 / 16.5	56	N108T (AAC→ACC)	yphE	putative sugar ABC transporter ATPase
*	NC_000913	4,604,344	0	C	T	42.5%	50.4 / 28.3	48	S62F (TCT→TTT)	bglJ	bgl operon transcriptional activator
*	NC_000913	3,862,668	0	A	G	41.7%	49.9 / 21.6	60	pseudogene (936/1617 nt)	glvC	pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component
*	NC_000913	2,434,882	0	T	G	41.6%	124.7 / 23.8	79	Y252S (TAC→TCC)	truA	tRNA pseudouridine(38‑40) synthase
*	NC_000913	3,423,297	0	G	C	41.4%	83.0 / 36.4	70	intergenic (+103/+126)	yhdZ/rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
*	NC_000913	2,001,918	0	A	C	41.2%	138.0 / 21.5	81	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
*	NC_000913	3,423,287	0	G	C	41.1%	76.9 / 34.9	73	intergenic (+93/+136)	yhdZ/rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
*	NC_000913	2,001,911	0	G	A	41.0%	89.6 / 53.5	83	intergenic (‑122/+199)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
*	NC_000913	4,346,675	0	T	G	40.9%	111.2 / 10.8	66	T218P (ACC→CCC)	fumB	anaerobic class I fumarate hydratase (fumarase B)
*	NC_000913	1,969,794	0	A	C	40.7%	88.6 / 20.2	59	G397G (GGT→GGG)	tap	methyl‑accepting protein IV
*	NC_000913	2,261,811	0	T	G	40.6%	84.7 / 28.3	66	K185N (AAA→AAC)	fruK	fructose‑1‑phosphate kinase
*	NC_000913	803,869	0	G	T	40.0%	67.1 / 31.8	55	V123L (GTG→TTG)	ybhJ	aconitase family protein
*	NC_000913	4,332,791	0	A	C	40.0%	103.9 / 15.9	60	V161G (GTG→GGG)	basS	sensory histidine kinase in two‑component regulatory system with BasR
*	NC_000913	1,489,174	0	G	T	39.6%	64.7 / 18.3	48	G315C (GGT→TGT)	aldA	aldehyde dehydrogenase A, NAD‑linked

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	58 (0.770)	24 (0.360)	23/266	4.3	30.6%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	57 (0.850)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 2817942	81 (1.080)	29 (0.450)	21/258	4.6	45.3%	intergenic (‑82/+117)	argQ/argZ	tRNA‑Arg/tRNA‑Arg
	?	NC_000913	2818492 =	0 (0.000)					noncoding (58/77 nt)	argV	tRNA‑Arg
*	?	NC_000913	1207790 =	52 (0.690)	17 (0.250)	16/266	6.4	23.4%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	65 (0.970)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 2818357	0 (0.000)	27 (0.420)	12/258	7.8	100%	intergenic (‑83/+116)	argY/argV	tRNA‑Arg/tRNA‑Arg
	?	NC_000913	2818492 =	0 (0.000)					noncoding (58/77 nt)	argV	tRNA‑Arg
*	?	NC_000913	4542682 =	94 (1.250)	13 (0.180)	12/280	8.5	12.7%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	90 (1.280)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	= 4542690	95 (1.270)	7 (0.100)	6/280	11.8	7.3%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	89 (1.260)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	= 1209618	68 (0.910)	24 (0.360)	4/268	12.8	25.8%	pseudogene (2/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
	?	NC_000913	2471897 =	77 (1.140)					pseudogene (226/579 nt)	yfdL	pseudogene, CPS‑53 (KpLE1) prophage;Phage or Prophage Related