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 591 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,378,802	0	A	C	70.6%	0.1 / 31.5	34	V48G (GTA→GGA)	ampC	penicillin‑binding protein; beta‑lactamase, intrinsically weak
*	NC_000913	993,917	0	A	C	49.3%	97.1 / 32.0	75	V43G (GTG→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	357,890	0	C	A	48.9%	21.2 / 40.0	47	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	4,378,796	0	T	A	48.8%	35.4 / 24.8	41	Y50F (TAT→TTT)	ampC	penicillin‑binding protein; beta‑lactamase, intrinsically weak
*	NC_000913	993,904	0	A	C	48.0%	128.0 / 17.0	77	G47G (GGT→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	1,825,056	0	G	A	47.1%	37.4 / 17.1	34	intergenic (‑119/+84)	ves/spy	cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced
*	NC_000913	2,326,450	0	T	G	47.1%	112.5 / 11.8	68	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	599,576	0	T	G	46.7%	114.7 / 25.6	76	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	2,421,443	0	A	C	46.0%	101.6 / 13.4	63	Y40S (TAC→TCC)	folX	D‑erythro‑7,8‑dihydroneopterin triphosphate 2'‑epimerase and dihydroneopterin aldolase
*	NC_000913	993,913	0	G	C	45.5%	119.7 / 32.8	77	G44G (GGC→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	925,900	0	A	G	45.2%	57.8 / 15.8	42	noncoding (72/88 nt)	serW	tRNA‑Ser
*	NC_000913	357,880	0	T	C	44.9%	60.4 / 17.3	49	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	2,434,861	0	G	T	44.7%	104.8 / 40.3	76	P259Q (CCA→CAA)	truA	tRNA pseudouridine(38‑40) synthase
*	NC_000913	436,516	0	C	A	44.6%	94.4 / 39.1	65	Q295K (CAA→AAA)	thiL	thiamine monophosphate kinase
*	NC_000913	2,421,437	0	T	C	44.6%	87.5 / 20.3	65	I38T (ATC→ACC)	folX	D‑erythro‑7,8‑dihydroneopterin triphosphate 2'‑epimerase and dihydroneopterin aldolase
*	NC_000913	1,825,061	0	G	A	44.4%	40.9 / 17.2	36	intergenic (‑124/+79)	ves/spy	cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced
*	NC_000913	2,483,268	0	T	A	44.4%	31.3 / 17.5	36	L24F (TTA→TTT)	emrK	multidrug resistance efflux pump membrane fusion protein
*	NC_000913	4,378,794	0	G	A	43.6%	40.5 / 14.9	41	Q51* (CAG→TAG)	ampC	penicillin‑binding protein; beta‑lactamase, intrinsically weak
*	NC_000913	1,356,201	0	T	G	43.4%	144.2 / 18.6	76	T304P (ACC→CCC)	sapA	antimicrobial peptide transport ABC transporter periplasmic binding protein
*	NC_000913	3,133,302	0	T	G	43.3%	129.7 / 10.3	67	H219P (CAC→CCC)	yghS	putative ATP‑binding protein

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	4542682 =	26 (0.340)	3 (0.040)	3/280	11.7	8.9%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	37 (0.520)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)