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 455 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	50.0%	38.4 / 31.6	48	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	2,984,441	0	A	C	49.3%	87.1 / 32.1	69	G384G (GGT→GGG)	yqeF	short chain acyltransferase
*	NC_000913	811,721	0	T	G	47.9%	79.8 / 15.0	73	V67G (GTG→GGG)	bioC	malonyl‑ACP O‑methyltransferase, SAM‑dependent
*	NC_000913	4,538,109	0	A	C	47.6%	80.0 / 31.3	63	G219G (GGT→GGG)	nanM	N‑acetylneuraminic acid mutarotase
*	NC_000913	993,917	0	A	C	46.2%	92.7 / 18.2	65	V43G (GTG→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	1,825,056	0	G	A	46.2%	68.8 / 39.5	65	intergenic (‑119/+84)	ves/spy	cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced
*	NC_000913	4,042,993	0	C	T	46.2%	23.8 / 21.7	39	F193F (TTC→TTT)	srkA	Cpx stress response Thr/Ser protein kinase; MazF antagonist protein
*	NC_000913	1,376,505	0	A	C	45.6%	83.9 / 33.5	68	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
*	NC_000913	3,840,646	0	T	C	45.5%	68.5 / 33.2	67	D365G (GAT→GGT)	nepI	putative transporter
*	NC_000913	4,043,030	0	A	G	44.7%	43.9 / 10.2	38	N206D (AAT→GAT)	srkA	Cpx stress response Thr/Ser protein kinase; MazF antagonist protein
*	NC_000913	993,913	0	G	C	44.3%	100.8 / 31.1	70	G44G (GGC→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	3,508,657	0	A	G	44.3%	82.4 / 20.9	61	F386S (TTC→TCC)	yhfW	phosphopentomutase‑related metalloenzyme superfamily protein
*	NC_000913	1,222,233	0	G	A	44.1%	82.2 / 31.7	68	pseudogene (60/75 nt)	ycgH	pseudogene; putative ATP‑binding component of a transport system
*	NC_000913	357,880	0	T	C	44.0%	57.7 / 20.0	50	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	4,378,802	0	A	C	43.6%	96.3 / 11.8	55	V48G (GTA→GGA)	ampC	penicillin‑binding protein; beta‑lactamase, intrinsically weak
*	NC_000913	3,105,489	0	C	A	43.5%	97.9 / 33.1	62	Q353K (CAA→AAA)	mltC	membrane‑bound lytic murein transglycosylase C
*	NC_000913	4,346,675	0	T	G	43.5%	143.8 / 18.0	85	T218P (ACC→CCC)	fumB	anaerobic class I fumarate hydratase (fumarase B)
*	NC_000913	2,185,199	0	T	G	42.9%	97.6 / 21.6	63	T35P (ACC→CCC)	thiM	hydoxyethylthiazole kinase
*	NC_000913	3,813,272	0	C	T	42.6%	69.7 / 28.2	69	S181L (TCG→TTG)	dfp	fused 4'‑phosphopantothenoylcysteine decarboxylase/phosphopantothenoylcysteine synthetase, FMN‑binding
*	NC_000913	4,538,117	0	T	C	42.6%	78.6 / 21.8	62	N217D (AAT→GAT)	nanM	N‑acetylneuraminic acid mutarotase

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 =	79 (1.100)	7 (0.110)	6/266	9.9	10.3%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	51 (0.800)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	80 (1.110)	5 (0.080)	5/266	10.5	7.6%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	51 (0.800)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	381258 =	NA (NA)	8 (0.110)	5/296	11.4	NA	pseudogene (3/417 nt)	yaiX	pseudogene, interrupted by IS2A; hexapeptide transferase superfamily; putative transferase
	?	NC_000913	= 382589	NA (NA)					noncoding (1330/1331 nt)	IS2	repeat region
*	?	NC_000913	4498181 =	NA (NA)	7 (0.100)	5/298	11.5	NA	noncoding (1/1331 nt)	IS2	repeat region
	?	NC_000913	= 4499512	NA (NA)					intergenic (+12/+81)	insD1/yjgX	IS2 transposase TnpB/pseudogene fragment