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 428 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,859,432	0	C	T	79.7%	179.7 / ‑3.2	64	G780G (GGC→GGT)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	357,890	0	C	A	58.3%	‑1.1 / 35.4	36	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	357,880	0	T	C	55.3%	22.0 / 47.7	38	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	1,097,581	0	A	G	52.5%	69.6 / 88.0	60	noncoding (72/88 nt)	serX	tRNA‑Ser
*	NC_000913	357,875	0	A	T	52.5%	17.1 / 53.8	40	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	3,206,435	0	C	T	52.5%	31.9 / 85.6	61	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	436,516	0	C	A	50.0%	46.8 / 34.4	54	Q295K (CAA→AAA)	thiL	thiamine monophosphate kinase
*	NC_000913	2,903,692	0	C	A	47.1%	94.0 / 54.9	70	intergenic (+318/+1055)	ygcE/queE	putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis
*	NC_000913	2,252,646	0	T	G	46.4%	77.8 / 12.4	56	V316G (GTA→GGA)	yeiI	putative kinase
*	NC_000913	599,576	0	T	G	46.0%	106.2 / 30.1	74	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	3,812,792	0	C	A	45.7%	96.8 / 51.3	81	T21N (ACC→AAC)	dfp	fused 4'‑phosphopantothenoylcysteine decarboxylase/phosphopantothenoylcysteine synthetase, FMN‑binding
*	NC_000913	1,535,785	0	A	G	45.1%	97.4 / 22.1	71	F25S (TTC→TCC)	yddE	PhzC‑PhzF family protein
*	NC_000913	1,157,271	0	T	G	44.4%	88.8 / 11.0	54	G165G (GGT→GGG)	ycfH	putative DNase
*	NC_000913	2,001,918	0	A	C	44.4%	107.4 / 14.7	63	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
*	NC_000913	29,496	0	T	A	43.8%	92.4 / 30.6	64	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	1,097,593	0	G	C	43.5%	105.3 / 30.4	64	noncoding (60/88 nt)	serX	tRNA‑Ser
*	NC_000913	2,252,657	0	C	T	43.3%	76.4 / 30.3	60	L320F (CTT→TTT)	yeiI	putative kinase
*	NC_000913	3,206,444	0	T	A	43.1%	63.3 / 23.5	58	intergenic (‑188/‑19)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	4,538,109	0	A	C	43.1%	115.9 / 24.6	72	G219G (GGT→GGG)	nanM	N‑acetylneuraminic acid mutarotase
*	NC_000913	3,465,167	0	G	T	42.9%	69.0 / 28.1	56	C29F (TGT→TTT)	gspM	general secretory pathway component, cryptic

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	51 (0.750)	12 (0.200)	12/266	7.1	19.8%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	52 (0.850)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	48 (0.700)	12 (0.200)	12/266	7.1	19.9%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	54 (0.890)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related