breseq  version 0.35.4  revision f352f80f4bc9 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 136 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	580,431	0	T	A	76.9%	9.9 / 12.4	26	I125I (ATT→ATA) ‡	nohB	bacteriophage DNA packaging protein
*	NC_000913	1,634,019	0	T	C	65.8%	37.8 / 37.4	41	I125V (ATT→GTT) ‡	nohA	NohA
*	NC_000913	580,429	0	A	G	64.5%	28.4 / 27.5	31	I125V (ATT→GTT) ‡	nohB	bacteriophage DNA packaging protein
*	NC_000913	580,425	0	T	A	62.2%	44.1 / 48.2	45	G123G (GGT→GGA)	nohB	bacteriophage DNA packaging protein
*	NC_000913	3,192,873	0	T	C	59.7%	298.4 / inf	457	intergenic (+332/+88)	b3051/b3052	putative membrane protein/putative kinase
*	NC_000913	3,192,891	0	C	T	58.7%	351.2 / inf	443	intergenic (+350/+70)	b3051/b3052	putative membrane protein/putative kinase
*	NC_000913	3,192,907	0	A	T	56.0%	234.7 / inf	440	intergenic (+366/+54)	b3051/b3052	putative membrane protein/putative kinase
*	NC_000913	3,192,905	0	C	A	55.6%	26.0 / inf	438	intergenic (+364/+56)	b3051/b3052	putative membrane protein/putative kinase
*	NC_000913	1,634,023	0	A	T	55.1%	63.5 / 72.7	49	G123G (GGT→GGA)	nohA	NohA
*	NC_000913	580,422	0	A	C	54.5%	73.9 / 76.5	55	A122A (GCA→GCC)	nohB	bacteriophage DNA packaging protein
*	NC_000913	580,419	0	C	G	54.2%	98.1 / 112.1	72	I121M (ATC→ATG)	nohB	bacteriophage DNA packaging protein
*	NC_000913	580,509	0	G	C	53.5%	144.4 / 166.2	101	L151L (CTG→CTC)	nohB	bacteriophage DNA packaging protein
*	NC_000913	580,512	0	A	G	52.4%	134.8 / 149.4	103	K152K (AAA→AAG)	nohB	bacteriophage DNA packaging protein
*	NC_000913	1,634,026	0	T	G	50.0%	85.4 / 104.9	54	A122A (GCA→GCC)	nohA	NohA
*	NC_000913	1,949,411	0	A	C	49.7%	143.8 / inf	499	N197H (AAC→CAC)	yecD	hypothetical protein
*	NC_000913	1,949,410	0	C	T	49.4%	27.2 / inf	501	L196L (CTC→CTT)	yecD	hypothetical protein
*	NC_000913	3,192,619	0	A	C	48.5%	151.4 / inf	521	intergenic (+78/+342)	b3051/b3052	putative membrane protein/putative kinase
*	NC_000913	1,949,356	0	T	C	48.2%	76.4 / inf	487	S178S (AGT→AGC)	yecD	hypothetical protein
*	NC_000913	1,949,436	0	A	G	48.1%	88.2 / inf	423	L6L (CTA→CTG)	yecE	hypothetical protein
*	NC_000913	580,513	0	C	A	47.8%	202.1 / 168.7	111	R153R (CGG→AGG)	nohB	bacteriophage DNA packaging 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	1207013 =	177 (0.690)	90 (0.420)	66/152	4.4	39.3%	coding (290/630 nt)	ycfK	hypothetical protein
	?	NC_000913	1208842 =	132 (0.620)					coding (40/540 nt)	b1157	putative tail fiber protein
*	?	NC_000913	= 1207028	160 (0.620)	88 (0.410)	65/152	4.6	40.8%	coding (305/630 nt)	ycfK	hypothetical protein
	?	NC_000913	= 1208825	124 (0.580)					coding (57/540 nt)	b1157	putative tail fiber protein
*	?	NC_000913	= 4008398	74 (0.290)	49 (0.200) +AAGA	21/172	19.0	40.6%	coding (481/516 nt)	b4555	hypothetical protein
	?	NC_000913	4008399 =	74 (0.290)					coding (482/516 nt)	b4555	hypothetical protein
*	?	NC_000913	= 1208841	193 (0.750)	15 (0.070)	10/154	23.3	7.4%	coding (41/540 nt)	b1157	putative tail fiber protein
	?	NC_000913	2469917 =	212 (0.980)					coding (166/519 nt)	yfdL	putative RNA polymerase beta
*	?	NC_000913	= 2875930	0 (0.000)	4 (0.020) +G	4/182	30.5	100%	intergenic (+289/+662)	iap/ygbF	Iap/hypothetical protein
	?	NC_000913	2875993 =	0 (0.000)					intergenic (+352/+599)	iap/ygbF	Iap/hypothetical protein