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 633 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	925,900	0	A	G	51.7%	63.9 / 87.6	58	noncoding (72/88 nt)	serW	tRNA‑Ser
*	NC_000913	357,890	0	C	A	51.6%	36.0 / 90.1	65	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	2,040,075	0	C	G	50.8%	33.4 / 76.7	62	L200V (CTG→GTG)	yedY	membrane‑anchored, periplasmic TMAO, DMSO reductase
*	NC_000913	357,880	0	T	C	50.0%	53.7 / 18.1	53	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	599,576	0	T	G	50.0%	71.2 / 38.6	64	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	213,341	0	A	G	49.4%	93.0 / 34.0	79	G337G (GGA→GGG)	tilS	tRNA(Ile)‑lysidine synthetase
*	NC_000913	599,579	0	T	G	48.4%	90.3 / 21.3	64	V289G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	2,252,646	0	T	G	46.6%	113.0 / 18.2	74	V316G (GTA→GGA)	yeiI	putative kinase
*	NC_000913	2,442,582	0	T	G	44.8%	100.4 / 13.2	68	G273G (GGT→GGG)	mnmC	fused 5‑methylaminomethyl‑2‑thiouridine‑forming enzyme methyltransferase and FAD‑dependent demodification enzyme
*	NC_000913	357,875	0	A	T	43.4%	62.1 / 22.7	55	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	354,288	0	T	G	43.2%	147.0 / 21.4	90	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	2,984,441	0	A	C	43.0%	145.1 / 30.7	86	G384G (GGT→GGG)	yqeF	short chain acyltransferase
*	NC_000913	1,097,581	0	A	G	42.9%	79.8 / 16.5	50	noncoding (72/88 nt)	serX	tRNA‑Ser
*	NC_000913	3,206,435	0	C	T	42.5%	110.4 / 62.2	94	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	4,536,197	0	A	T	42.5%	111.6 / 74.8	87	intergenic (+166/+417)	yjhR/nanS	pseudogene, helicase family; putative frameshift suppressor/9‑O‑acetyl N‑acetylneuraminic acid esterase
*	NC_000913	4,378,802	0	A	C	42.5%	141.6 / 11.0	73	V48G (GTA→GGA)	ampC	penicillin‑binding protein; beta‑lactamase, intrinsically weak
*	NC_000913	1,755,871	0	T	A	42.0%	65.4 / 32.9	50	G58G (GGT→GGA)	pykF	pyruvate kinase I
*	NC_000913	4,258,974	0	T	G	41.8%	178.9 / 26.8	104	G411G (GGT→GGG)	dinF	oxidative stress resistance protein; putative MATE family efflux pump; UV and mitomycin C inducible protein
*	NC_000913	1,684,749	0	A	C	41.5%	84.4 / 11.0	53	D164A (GAC→GCC)	tus	inhibitor of replication at Ter, DNA‑binding protein
*	NC_000913	4,538,109	0	A	C	41.1%	161.9 / 30.6	92	G219G (GGT→GGG)	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	= 4542690	135 (1.490)	5 (0.060)	5/280	6.8	4.0%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	111 (1.310)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	4542682 =	130 (1.440)	3 (0.040)	3/280	7.7	2.5%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	111 (1.310)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)