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 140 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,765,459	1	.	C	73.6%	265.6 / 98.2	110	intergenic (+83/‑272)	yfjO/b2632	hypothetical protein/putative GTP‑binding protein
*	NC_000913	580,498	0	G	A	71.8%	21.9 / 25.0	39	V148I (GTT→ATT)	nohB	bacteriophage DNA packaging protein
*	NC_000913	1,634,019	0	T	C	71.0%	18.0 / 19.1	31	I125V (ATT→GTT)	nohA	NohA
*	NC_000913	580,429	0	A	G	68.0%	20.6 / 19.3	25	I125V (ATT→GTT)	nohB	bacteriophage DNA packaging protein
*	NC_000913	580,419	0	C	G	61.0%	84.7 / 100.0	77	I121M (ATC→ATG)	nohB	bacteriophage DNA packaging protein
*	NC_000913	580,422	0	A	C	60.0%	67.3 / 74.0	62	A122A (GCA→GCC)	nohB	bacteriophage DNA packaging protein
*	NC_000913	580,425	0	T	A	59.6%	51.0 / 56.7	47	G123G (GGT→GGA)	nohB	bacteriophage DNA packaging protein
*	NC_000913	1,634,023	0	A	T	59.5%	37.9 / 44.4	37	G123G (GGT→GGA)	nohA	NohA
*	NC_000913	3,192,625	0	T	A	54.2%	157.9 / inf	409	intergenic (+84/+336)	b3051/b3052	putative membrane protein/putative kinase
*	NC_000913	3,192,626	0	T	C	54.0%	37.8 / inf	409	intergenic (+85/+335)	b3051/b3052	putative membrane protein/putative kinase
*	NC_000913	3,192,619	0	A	C	53.7%	316.0 / inf	441	intergenic (+78/+342)	b3051/b3052	putative membrane protein/putative kinase
*	NC_000913	3,192,609	0	A	G	53.5%	28.4 / inf	410	intergenic (+68/+352)	b3051/b3052	putative membrane protein/putative kinase
*	NC_000913	3,192,635	0	A	G	53.3%	15.0 / inf	412	intergenic (+94/+326)	b3051/b3052	putative membrane protein/putative kinase
*	NC_000913	3,192,647	0	G	C	51.0%	25.6 / inf	384	intergenic (+106/+314)	b3051/b3052	putative membrane protein/putative kinase
*	NC_000913	3,192,891	0	C	T	50.1%	74.0 / inf	393	intergenic (+350/+70)	b3051/b3052	putative membrane protein/putative kinase
*	NC_000913	3,192,873	0	T	C	49.6%	56.7 / inf	403	intergenic (+332/+88)	b3051/b3052	putative membrane protein/putative kinase
*	NC_000913	3,192,665	0	C	T	49.2%	32.9 / inf	359	intergenic (+124/+296)	b3051/b3052	putative membrane protein/putative kinase
*	NC_000913	1,949,344	0	G	A	48.3%	10.9 / inf	410	Q174Q (CAG→CAA)	yecD	hypothetical protein
*	NC_000913	3,192,907	0	A	T	47.9%	73.3 / inf	401	intergenic (+366/+54)	b3051/b3052	putative membrane protein/putative kinase
*	NC_000913	1,949,359	0	C	T	47.7%	1.8 / inf	438	I179I (ATC→ATT)	yecD	hypothetical 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	= 4008398	75 (0.310)	54 (0.230) +AAGA	26/172	17.5	42.7%	coding (481/516 nt)	b4555	hypothetical protein
	?	NC_000913	4008399 =	75 (0.300)					coding (482/516 nt)	b4555	hypothetical protein
*	?	NC_000913	4540250 =	73 (0.290)	19 (0.080)	17/166	21.1	15.0%	intergenic (+49/‑433)	fimE/fimA	FimE/major type 1 subunit fimbrin
	?	NC_000913	4540564 =	150 (0.670)					intergenic (+363/‑119)	fimE/fimA	FimE/major type 1 subunit fimbrin
*	?	NC_000913	= 4540258	75 (0.300)	11 (0.050)	11/166	24.7	9.2%	intergenic (+57/‑425)	fimE/fimA	FimE/major type 1 subunit fimbrin
	?	NC_000913	= 4540554	150 (0.670)					intergenic (+353/‑129)	fimE/fimA	FimE/major type 1 subunit fimbrin
*	?	NC_000913	= 957330	278 (1.120)	3 (0.010)	3/180	32.7	1.1%	coding (455/1089 nt)	serC	3‑phosphoserine aminotransferase
	?	NC_000913	= 957344	284 (1.170)					coding (469/1089 nt)	serC	3‑phosphoserine aminotransferase