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 384 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,578,143	0	A	C	52.6%	37.9 / 85.8	57	L79V (TTA→GTA)	maeB	malic enzyme: putative oxidoreductase/phosphotransacetylase
*	NC_000913	3,443,277	0	A	C	50.7%	74.3 / 120.1	67	V274G (GTA→GGA)	secY	preprotein translocase membrane subunit
*	NC_000913	357,880	0	T	C	50.0%	45.0 / 15.3	48	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	357,890	0	C	A	49.0%	32.6 / 32.3	51	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	4,056,115	0	A	C	49.0%	50.5 / 15.9	49	G75G (GGT→GGG)	glnL	sensory histidine kinase in two‑component regulatory system with GlnG
*	NC_000913	4,536,197	0	A	T	48.9%	32.2 / 47.1	47	intergenic (+166/+417)	yjhR/nanS	pseudogene, helicase family; putative frameshift suppressor/9‑O‑acetyl N‑acetylneuraminic acid esterase
*	NC_000913	5,159	0	G	A	47.5%	54.5 / 36.9	59	intergenic (+139/‑75)	thrC/yaaX	L‑threonine synthase/DUF2502 family putative periplasmic protein
*	NC_000913	4,580,634	0	C	T	47.1%	45.4 / 29.3	51	E277K (GAA→AAA)	hsdS	specificity determinant for hsdM and hsdR
*	NC_000913	15,410	0	T	G	46.7%	57.8 / 12.7	45	intergenic (+112/‑35)	dnaJ/insL1	chaperone Hsp40, DnaK co‑chaperone/IS186 transposase
*	NC_000913	4,378,802	0	A	C	46.6%	85.8 / 17.5	58	V48G (GTA→GGA)	ampC	penicillin‑binding protein; beta‑lactamase, intrinsically weak
*	NC_000913	1,376,505	0	A	C	46.3%	115.6 / 34.2	82	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
*	NC_000913	15,395	0	G	A	45.8%	46.1 / 25.3	48	intergenic (+97/‑50)	dnaJ/insL1	chaperone Hsp40, DnaK co‑chaperone/IS186 transposase
*	NC_000913	1,487,163	0	C	T	45.8%	49.0 / 27.7	48	intergenic (+200/‑72)	hrpA/ydcF	putative ATP‑dependent helicase/DUF218 superfamily protein, SAM‑binding
*	NC_000913	15,436	0	A	T	44.7%	39.4 / 19.9	38	intergenic (+138/‑9)	dnaJ/insL1	chaperone Hsp40, DnaK co‑chaperone/IS186 transposase
*	NC_000913	4,536,212	0	T	A	44.2%	73.0 / 33.8	52	intergenic (+181/+402)	yjhR/nanS	pseudogene, helicase family; putative frameshift suppressor/9‑O‑acetyl N‑acetylneuraminic acid esterase
*	NC_000913	4,536,190	0	T	G	44.0%	80.1 / 12.6	50	intergenic (+159/+424)	yjhR/nanS	pseudogene, helicase family; putative frameshift suppressor/9‑O‑acetyl N‑acetylneuraminic acid esterase
*	NC_000913	2,434,882	0	T	G	43.9%	107.2 / 18.5	66	Y252S (TAC→TCC)	truA	tRNA pseudouridine(38‑40) synthase
*	NC_000913	298,960	0	A	C	42.9%	91.3 / 15.1	56	Y659D (TAT→GAT)	paoC	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
*	NC_000913	1,079,468	0	A	G	42.6%	78.0 / 16.9	54	D55G (GAT→GGT)	putP	proline:sodium symporter
*	NC_000913	2,096,090	0	A	G	42.4%	94.3 / 19.3	67	I83V (ATT→GTT)	hisF	imidazole glycerol phosphate synthase, catalytic subunit with HisH

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	43 (0.630)	12 (0.200)	12/266	7.3	19.4%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	61 (0.990)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	43 (0.630)	8 (0.130)	8/266	9.3	13.5%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	64 (1.040)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related