BRESEQ :: Marginal Predictions

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 674 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP006881	3,725,205	1	.	T	73.6%	110.3 / 44.7	57	intergenic (‑37/‑492)	U712_19205/U712_19210	Uncharacterized protein ywcI/Minor extracellular protease vpr
*	CP006881	2,010,244	0	T	A	66.0%	126.7 / 127.6	145	P63P (CCT→CCA)	U712_09940	UPF0361 protein yoqW
*	CP006881	2,010,247	0	T	G	63.7%	138.1 / 146.7	160	C64W (TGT→TGG)	U712_09940	UPF0361 protein yoqW
*	CP006881	2,010,217	0	T	C	62.6%	131.8 / 149.9	168	G54G (GGT→GGC)	U712_09940	UPF0361 protein yoqW
*	CP006881	2,010,202	0	T	C	61.5%	119.0 / 155.0	167	S49S (TCT→TCC)	U712_09940	UPF0361 protein yoqW
*	CP006881	2,010,268	0	T	C	60.5%	93.9 / 156.2	162	G71G (GGT→GGC)	U712_09940	UPF0361 protein yoqW
*	CP006881	1,947,474	0	T	C	60.2%	59.0 / 181.8	191	A913A (GCA→GCG)	U712_09655	Plipastatin synthase subunit A
*	CP006881	2,010,187	0	T	C	58.9%	107.0 / 183.6	186	I44I (ATT→ATC)	U712_09940	UPF0361 protein yoqW
*	CP006881	2,010,286	0	T	C	58.6%	71.3 / 160.2	157	A77A (GCT→GCC)	U712_09940	UPF0361 protein yoqW
*	CP006881	1,947,477	0	A	T	57.7%	25.3 / 196.6	194	R912R (CGT→CGA)	U712_09655	Plipastatin synthase subunit A
*	CP006881	1,947,480	0	C	G	57.7%	18.6 / 256.4	194	V911V (GTG→GTC)	U712_09655	Plipastatin synthase subunit A
*	CP006881	2,016,293	0	A	G	57.2%	102.2 / 194.8	188	G42G (GGT→GGC)	U712_09975	Putative UV‑damage repair protein uvrX
*	CP006881	2,026,290	0	G	C	56.8%	140.0 / 297.8	236	Q129E (CAG→GAG)	U712_10015	Uncharacterized protein yobM
*	CP006881	519,529	0	G	A	55.3%	31.3 / 141.5	123	intergenic (+184/‑65)	U712_02485/U712_02490	Hypothetical Protein/Hypothetical Protein
*	CP006881	2,026,299	0	T	A	55.2%	85.7 / 306.0	252	T126S (ACC→TCC)	U712_10015	Uncharacterized protein yobM
*	CP006881	2,010,333	0	G	T	54.9%	0.1 / 228.4	165	G93V (GGA→GTA)	U712_09940	UPF0361 protein yoqW
*	CP006881	2,016,775	0	C	T	54.6%	44.3 / 263.1	219	intergenic (‑123/+20)	U712_09980/U712_09985	Putative UV‑damage repair protein uvrX/Uncharacterized protein yozL
*	CP006881	2,025,410	0	G	T	53.8%	‑2.9 / 213.4	158	P134P (CCC→CCA)	U712_10010	UPF0720 protein yobL
*	CP006881	519,725	0	T	A	53.7%	21.8 / 298.4	229	V44V (GTT→GTA)	U712_02490	Hypothetical Protein
*	CP006881	1,863,255	0	A	G	53.5%	50.2 / 250.5	213	L46L (TTA→TTG)	U712_09275	putative deoxyuridine 5'‑triphosphate nucleotidohydrolase yncF

Marginal new junction evidence (sorted from low to high skew)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP006881	= 2179389	38 (0.420)	15 (0.170) +CATC	8/242	4.4	28.9%	intergenic (+35/+2)	U712_10905/U712_10910	UPF0750 membrane protein ypjC/Uncharacterized protein ypjB
*	?	CP006881	2179390 =	38 (0.410)	15 (0.170) +CATC	8/242	4.4	28.9%	intergenic (+36/+1)	U712_10905/U712_10910	UPF0750 membrane protein ypjC/Uncharacterized protein ypjB
*	?	CP006881	1157746 =	116 (1.260)	3 (0.030)	3/238	6.3	2.7%	coding (425/540 nt)	U712_05740	putative MFS‑type transporter yitZ
*	?	CP006881	= 1157742	106 (1.220)	3 (0.030)	3/238	6.3	2.7%	coding (421/540 nt)	U712_05740	putative MFS‑type transporter yitZ
*	?	CP006881	= 1988944	123 (1.330)	15 (0.170)	3/240	6.4	10.2%	coding (651/684 nt)	U712_09825	UPF0361 protein yoaM
*	?	CP006881	2010692 =	148 (1.690)	15 (0.170)	3/240	6.4	10.2%	coding (637/660 nt)	U712_09940	UPF0361 protein yoqW
*	?	pSIJ663_pHT315_araE_xy	= 5551	3126 (0.860)	14 (0.000)	12/242	10.6	0.46%	intergenic (+820/–)	ampR/–	–/–
*	?	pSIJ663_pHT315_araE_xy	9889 =	NA (NA)	14 (0.000)	12/242	10.6	0.46%	intergenic (+5158/–)	ampR/–	–/–