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 430 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	49.2%	61.6 / 29.6	65	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	357,890	0	C	A	49.2%	27.4 / 42.5	63	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	2,421,443	0	A	C	46.2%	144.3 / 19.6	91	Y40S (TAC→TCC)	folX	D‑erythro‑7,8‑dihydroneopterin triphosphate 2'‑epimerase and dihydroneopterin aldolase
*	NC_000913	29,496	0	T	A	45.5%	132.5 / 64.8	112	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	2,984,441	0	A	C	44.2%	131.0 / 23.6	86	G384G (GGT→GGG)	yqeF	short chain acyltransferase
*	NC_000913	2,511,772	0	A	C	43.8%	109.3 / 10.3	66	V312G (GTG→GGG)	mntH	manganese/divalent cation transporter
*	NC_000913	266,358	0	T	G	43.5%	97.9 / 20.6	71	T66P (ACC→CCC)	yafY	lipoprotein, inner membrane; degP regulator; CP4‑6 prophage
*	NC_000913	650,454	0	T	G	41.9%	98.7 / 11.4	63	T13P (ACC→CCC)	citE	citrate lyase, citryl‑ACP lyase (beta) subunit
*	NC_000913	3,105,499	0	A	C	41.8%	151.6 / 12.3	92	Y356S (TAC→TCC)	mltC	membrane‑bound lytic murein transglycosylase C
*	NC_000913	4,378,802	0	A	C	41.6%	160.7 / 16.3	90	V48G (GTA→GGA)	ampC	penicillin‑binding protein; beta‑lactamase, intrinsically weak
*	NC_000913	650,464	0	A	T	41.3%	81.6 / 24.9	63	R9R (CGT→CGA)	citE	citrate lyase, citryl‑ACP lyase (beta) subunit
*	NC_000913	436,516	0	C	A	41.1%	74.7 / 19.8	56	Q295K (CAA→AAA)	thiL	thiamine monophosphate kinase
*	NC_000913	2,248,431	0	A	C	41.0%	112.8 / 22.1	78	G34G (GGT→GGG)	lysP	lysine transporter
*	NC_000913	1,097,581	0	A	G	40.3%	98.3 / 13.3	63	noncoding (72/88 nt)	serX	tRNA‑Ser
*	NC_000913	4,536,197	0	A	T	40.0%	124.0 / 61.1	90	intergenic (+166/+417)	yjhR/nanS	pseudogene, helicase family; putative frameshift suppressor/9‑O‑acetyl N‑acetylneuraminic acid esterase
*	NC_000913	29,486	0	C	A	39.6%	188.7 / 56.1	111	intergenic (+291/‑165)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	2,151,686	0	G	T	39.6%	42.9 / 14.3	53	intergenic (+40/+25)	yegJ/yegK	uncharacterized protein/ser/thr phosphatase‑related protein
*	NC_000913	2,481,804	0	G	A	39.5%	135.8 / 29.7	81	P125S (CCA→TCA)	emrY	putative multidrug efflux system
*	NC_000913	2,895,032	0	T	C	38.9%	120.3 / 20.3	73	I250V (ATT→GTT)	ygcQ	putative flavoprotein
*	NC_000913	1,157,271	0	T	G	38.6%	148.7 / 13.3	88	G165G (GGT→GGG)	ycfH	putative DNase

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	1207790 =	39 (0.450)	29 (0.370)	24/266	3.8	48.4%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	27 (0.350)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	2473351 =	88 (1.020)	3 (0.040)	3/278	11.9	3.6%	pseudogene (235/708 nt)	oweS	pseudogene, CPS‑53 (KpLE1) prophage; bacteriophage replication protein O family;Phage or Prophage Related
	?	NC_000913	2473361 =	79 (0.980)					pseudogene (225/708 nt)	oweS	pseudogene, CPS‑53 (KpLE1) prophage; bacteriophage replication protein O family;Phage or Prophage Related