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
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	380,013	0	G	.	50.0%	12.9 / 20.0	12	intergenic (‑132/+56)	frmR/yaiO	regulator protein that represses frmRAB operon/outer membrane protein
*	NC_000913	4,296,060	0	C	T	34.1%	39.7 / 36.0	44	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
*	NC_000913	4,277,225	0	G	A	26.9%	40.5 / 11.9	27	Y53Y (TAC→TAT) ‡	soxS	superoxide response regulon transcriptional activator; autoregulator
*	NC_000913	4,277,226	0	T	C	25.9%	38.9 / 13.4	27	Y53C (TAC→TGC) ‡	soxS	superoxide response regulon transcriptional activator; autoregulator
*	NC_000913	4,277,223	0	A	T	24.1%	51.1 / 10.3	29	I54N (ATT→AAT)	soxS	superoxide response regulon transcriptional activator; autoregulator
*	NC_000913	1,840,946	0	C	.	22.2%	42.4 / 10.1	18	coding (458/621 nt)	ynjF	CDP‑alcohol phosphatidyltransferase family inner membrane protein
*	NC_000913	4,520,500	0	A	.	21.7%	162.2 / 41.7	60	intergenic (‑176/+171)	yjhU/yjhF	putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter
*	NC_000913	4,520,504	1	.	T	21.3%	150.8 / 57.0	61	intergenic (‑180/+167)	yjhU/yjhF	putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter
*	NC_000913	3,376,265	0	G	C	21.3%	101.2 / 26.8	47	intergenic (+29/+14)	dcuD/sspB	putative transporter/ClpXP protease specificity enhancing factor
*	NC_000913	321,483	0	C	A	21.2%	77.1 / 14.6	33	intergenic (+402/‑125)	rclR/ykgE	reactive chlorine species (RCS)‑specific activator of the rcl genes/cysteine‑rich LutA family protein; putative electron transport chain YkgEFG component
*	NC_000913	321,484	0	A	T	21.2%	65.6 / 14.3	33	intergenic (+403/‑124)	rclR/ykgE	reactive chlorine species (RCS)‑specific activator of the rcl genes/cysteine‑rich LutA family protein; putative electron transport chain YkgEFG component
*	NC_000913	260,540	1	.	G	20.8%	54.3 / 19.5	24	coding (153/1104 nt)	proB	gamma‑glutamate kinase
*	NC_000913	2,888,820	0	T	C	20.7%	54.1 / 10.4	29	Q427R (CAG→CGG)	cysI	sulfite reductase, beta subunit, NAD(P)‑binding, heme‑binding
*	NC_000913	321,485	0	T	G	20.0%	72.4 / 16.5	35	intergenic (+404/‑123)	rclR/ykgE	reactive chlorine species (RCS)‑specific activator of the rcl genes/cysteine‑rich LutA family protein; putative electron transport chain YkgEFG component

Marginal new junction evidence (lowest skew 10 of 61 shown)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1972772 =	42 (1.220)	6 (0.190)	6/238	2.7	13.8%	intergenic (‑81/+64)	tar/cheW	methyl‑accepting chemotaxis protein II/purine‑binding chemotaxis protein
*	?	NC_000913	1972820 =	36 (1.120)	6 (0.190)	6/238	2.7	13.8%	intergenic (‑129/+16)	tar/cheW	methyl‑accepting chemotaxis protein II/purine‑binding chemotaxis protein
*	?	NC_000913	3154233 =	36 (1.040)	5 (0.160)	5/236	2.9	13.7%	intergenic (+11/+29)	yghB/yqhC	general envelope maintenance protein; DedA family inner membrane protein; putative multidrug efflux transporter/transcriptional activator of yqhD
*	?	NC_000913	3154259 =	30 (0.940)	5 (0.160)	5/236	2.9	13.7%	intergenic (+37/+3)	yghB/yqhC	general envelope maintenance protein; DedA family inner membrane protein; putative multidrug efflux transporter/transcriptional activator of yqhD
*	?	NC_000913	1411899 =	39 (1.130)	4 (0.150)	4/204	2.9	11.3%	coding (50/936 nt)	ttcA	tRNA s(2)C32 thioltransferase, iron sulfur cluster protein
*	?	NC_000913	= 1434958	32 (1.170)	4 (0.150)	4/204	2.9	11.3%	pseudogene (51/51 nt)	ttcC	pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related
*	?	NC_000913	= 303629	46 (1.330)	5 (0.160)	5/230	2.9	10.4%	intergenic (+24/+224)	yagU/ykgJ	DUF1440 family inner membrane acid resistance protein/UPF0153 cysteine cluster protein
*	?	NC_000913	= 303636	45 (1.450)	5 (0.160)	5/230	2.9	10.4%	intergenic (+31/+217)	yagU/ykgJ	DUF1440 family inner membrane acid resistance protein/UPF0153 cysteine cluster protein
*	?	NC_000913	= 4412115	60 (1.740)	5 (0.150)	5/244	3.0	8.3%	coding (137/399 nt)	yjfL	UPF0719 family inner membrane protein
*	?	NC_000913	= 4412132	54 (1.640)	5 (0.150)	5/244	3.0	8.3%	coding (154/399 nt)	yjfL	UPF0719 family inner membrane protein
*	?	NC_000913	4071224 =	52 (1.510)	5 (0.150)	5/244	3.0	8.7%	coding (533/1242 nt)	yihS	sulphoquinovose isomerase
*	?	NC_000913	4071255 =	56 (1.700)	5 (0.150)	5/244	3.0	8.7%	coding (502/1242 nt)	yihS	sulphoquinovose isomerase
*	?	NC_000913	3423318 =	32 (0.930)	5 (0.160)	5/238	3.0	15.0%	intergenic (+124/+105)	yhdZ/rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
*	?	NC_000913	3423341 =	27 (0.840)	5 (0.160)	5/238	3.0	15.0%	intergenic (+147/+82)	yhdZ/rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
*	?	NC_000913	2883264 =	38 (1.100)	5 (0.150)	5/242	3.0	12.8%	coding (875/1509 nt)	casA	CRISP RNA (crRNA) containing Cascade antiviral complex protein
*	?	NC_000913	2883296 =	32 (0.980)	5 (0.150)	5/242	3.0	12.8%	coding (843/1509 nt)	casA	CRISP RNA (crRNA) containing Cascade antiviral complex protein
*	?	NC_000913	= 2487982	29 (0.840)	5 (0.160)	5/238	3.0	15.2%	intergenic (+15/+41)	evgS/yfdE	hybrid sensory histidine kinase in two‑component regulatory system with EvgA/acetyl‑CoA:oxalate CoA‑transferase
*	?	NC_000913	= 2487991	29 (0.910)	5 (0.160)	5/238	3.0	15.2%	intergenic (+24/+32)	evgS/yfdE	hybrid sensory histidine kinase in two‑component regulatory system with EvgA/acetyl‑CoA:oxalate CoA‑transferase
*	?	NC_000913	= 4341795	38 (1.100)	4 (0.140)	4/220	3.1	11.7%	intergenic (‑167/‑116)	melR/melA	melibiose operon transcriptional regulator; autoregulator/alpha‑galactosidase, NAD(P)‑binding
*	?	NC_000913	= 4341815	28 (0.950)	4 (0.140)	4/220	3.1	11.7%	intergenic (‑187/‑96)	melR/melA	melibiose operon transcriptional regulator; autoregulator/alpha‑galactosidase, NAD(P)‑binding