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 654 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	599,576	0	T	G	52.9%	54.3 / 102.2	68	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	357,890	0	C	A	50.0%	33.8 / 26.1	46	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	2,434,882	0	T	G	49.4%	96.7 / 35.8	77	Y252S (TAC→TCC)	truA	tRNA pseudouridine(38‑40) synthase
*	NC_000913	993,913	0	G	C	49.3%	103.9 / 29.8	69	G44G (GGC→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	436,516	0	C	A	49.2%	63.5 / 45.1	61	Q295K (CAA→AAA)	thiL	thiamine monophosphate kinase
*	NC_000913	993,904	0	A	C	47.6%	96.1 / 12.8	63	G47G (GGT→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	75,079	0	C	T	46.7%	54.0 / 49.8	60	L134L (CTG→CTA)	thiB	thiamine/thiamine pyrophosphate/thiamine monophosphate ABC transporter periplasmic binding protein
*	NC_000913	3,261,055	0	A	C	45.2%	121.1 / 14.1	75	V455G (GTG→GGG)	tdcE	pyruvate formate‑lyase 4/2‑ketobutyrate formate‑lyase
*	NC_000913	1,478,324	0	T	G	45.1%	126.3 / 35.8	82	G33G (GGT→GGG)	ynbB	putative CDP‑diglyceride synthase
*	NC_000913	2,678,039	0	T	G	45.1%	111.8 / 28.7	71	N108T (AAC→ACC)	yphE	putative sugar ABC transporter ATPase
*	NC_000913	357,880	0	T	C	44.9%	64.5 / 12.4	49	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	1,764,785	0	T	A	44.3%	84.5 / 37.9	71	intergenic (‑399/+149)	sufA/ydiH	Fe‑S cluster assembly protein/uncharacterized protein
*	NC_000913	2,326,450	0	T	G	43.2%	139.6 / 17.3	74	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	2,434,861	0	G	T	43.2%	129.4 / 42.4	81	P259Q (CCA→CAA)	truA	tRNA pseudouridine(38‑40) synthase
*	NC_000913	357,875	0	A	T	43.1%	61.2 / 25.4	51	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	3,423,290	0	A	C	43.1%	88.0 / 27.9	72	intergenic (+96/+133)	yhdZ/rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
*	NC_000913	1,604,237	0	C	T	43.0%	107.0 / 38.1	86	S64L (TCG→TTG)	lsrD	autoinducer 2 import system permease protein
*	NC_000913	941,713	0	T	G	42.6%	97.8 / 31.4	68	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	298,960	0	A	C	42.6%	75.6 / 25.2	55	Y659D (TAT→GAT)	paoC	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
*	NC_000913	4,056,115	0	A	C	42.5%	159.2 / 25.0	94	G75G (GGT→GGG)	glnL	sensory histidine kinase in two‑component regulatory system with GlnG

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	71 (0.860)	13 (0.180)	13/266	8.9	17.1%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	63 (0.860)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	72 (0.880)	13 (0.180)	13/266	8.9	16.8%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	65 (0.890)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	925901 =	61 (0.740)	13 (0.160) +C	10/296	11.6	20.0%	noncoding (71/88 nt)	serW	tRNA‑Ser
	?	NC_000913	= 1097399	44 (0.540)					intergenic (+570/+166)	ycdU/serX	putative inner membrane protein/tRNA‑Ser