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 41 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	JE3692‑4	1,327,121	0	C	T	58.0%	11.1 / 196.8	144	intergenic (+97/‑196)	PP_16SE/PP_23SE	16S ribosomal RNA/23S ribosomal RNA
*	JE3692‑4	699,722	0	A	G	52.9%	‑1.0 / 128.6	88	intergenic (+115/‑129)	PP_t06/PP_23SD	tRNA‑Ala/23S ribosomal RNA
*	JE3692‑4	4,360,849	0	A	G	41.6%	103.5 / 170.2	125	intergenic (‑70/+404)	PP_3820/PP_3821	Group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase
*	JE3692‑4	4,630,642	0	A	G	37.9%	77.2 / 52.2	66	I85V (ATC→GTC)	PP_5652	conserved protein of unknown function, phage origin
*	JE3692‑4	195,634	0	C	T	36.5%	271.8 / 221.4	189	T380T (ACC→ACT)	PP_0168	putative surface adhesion protein
*	JE3692‑4	196,351	0	C	G	33.8%	306.4 / 247.0	210	T619T (ACC→ACG)	PP_0168	putative surface adhesion protein
*	JE3692‑4	681,281	0	C	G	33.3%	53.9 / 17.5	34	intergenic (+21/+48)	PP_0583/PP_0584	Transcriptional regulator, AraC family/Methyl‑accepting chemotaxis transducer
*	JE3692‑4	196,390	0	T	C	31.3%	286.3 / 148.3	167	D632D (GAT→GAC)	PP_0168	putative surface adhesion protein
*	JE3692‑4	2,184,203	0	T	C	31.1%	146.4 / 51.0	90	N269N (AAT→AAC)	PP_1931	conserved protein of unknown function
*	JE3692‑4	3,076,128	0	T	G	30.4%	115.3 / 10.3	56	intergenic (+64/‑290)	PP_2680/PP_2681	aldehyde dehydrogenase/coenzyme PQQ synthesis protein D
*	JE3692‑4	1,927,172	0	T	C	27.9%	78.8 / 14.6	43	intergenic (+15/+46)	PP_1720/PP_1721	Alcohol dehydrogenase, zinc‑containing/putative phosphoserine phosphatase
*	JE3692‑4	4,806,098	0	C	G	27.5%	165.9 / 39.1	83	intergenic (‑115/+41)	PP_4221/PP_4222	non‑ribosomal peptide synthetase (subunit of ferribactin synthase)/putative SyrP protein
*	JE3692‑4	884,008	0	A	G	26.7%	162.8 / 32.8	90	intergenic (+246/‑82)	PP_0766/PP_0767	conserved exported protein of unknown function/Transcriptional regulator, LuxR family
*	JE3692‑4	5,939,032	0	A	C	26.1%	232.6 / 20.0	112	intergenic (‑62/+91)	PP_5195/PP_5196	putative Iron ABC transporter, permease protein/putative iron(III);iron ABC transporter, periplasmic iron‑binding protein
*	JE3692‑4	5,301,739	0	G	C	26.0%	174.7 / 33.6	77	A244G (GCC→GGC)	PP_4663	conserved transmembrane protein of unknown function
*	JE3692‑4	324,670	0	C	T	25.2%	201.0 / 39.7	99	intergenic (‑430/‑45)	PP_0267/PP_0268	putative Outer membrane ferric siderophore receptor/outer‑membrane porin D
*	JE3692‑4	4,957,428	0	T	C	24.6%	167.8 / 26.7	66	intergenic (+644/+154)	PP_5673/PP_4352	putative D‑alanine‑‑D‑alanine ligase/flagellin export apparatus, substrate specificity protein
*	JE3692‑4	5,492,305	0	C	T	24.6%	118.1 / 21.0	66	R240C (CGC→TGC)	PP_4819	conserved protein of unknown function
*	JE3692‑4	5,834,172	0	C	G	24.4%	195.3 / 31.0	80	A11G (GCA→GGA)	PP_5101	coproporphyrinogen/heterocyclic compound oxidase(aerobic)
*	JE3692‑4	196,327	0	A	C	24.3%	433.9 / 173.7	222	T611T (ACA→ACC)	PP_0168	putative surface adhesion protein

Marginal new junction evidence (lowest skew 10 of 897 shown)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	JE3692‑4	= 173183	NA (NA)	26 (0.270)	15/182	6.8	NA	intergenic (+273/‑20)	PP_16SA/PP_23SA	16S ribosomal RNA/23S ribosomal RNA
	?	JE3692‑4	= 173194	NA (NA)					intergenic (+284/‑9)	PP_16SA/PP_23SA	16S ribosomal RNA/23S ribosomal RNA
*	?	JE3692‑4	= 2556265	NA (NA)	13 (0.130)	11/184	8.4	NA	intergenic (+160/‑84)	PP_t36/PP_23SF	tRNA‑Ala/23S ribosomal RNA
	?	JE3692‑4	= 2556295	NA (NA)					intergenic (+190/‑54)	PP_t36/PP_23SF	tRNA‑Ala/23S ribosomal RNA
*	?	JE3692‑4	5556293 =	NA (NA)	11 (0.110)	11/188	8.5	24.7%	noncoding (92/189 nt)	mobile_element	repeat region
	?	JE3692‑4	5556323 =	35 (0.330)					noncoding (62/189 nt)	mobile_element	repeat region
*	?	JE3692‑4	= 4820274	22 (0.210)	19 (0.190)	11/190	8.6	27.9%	intergenic (‑239/‑316)	PP_4234/PP_4235	Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2
	?	JE3692‑4	= 6000042	77 (0.760)					intergenic (+260/‑286)	PP_5246/PP_mr64	glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
*	?	JE3692‑4	= 528034	0 (0.000)	13 (0.130)	10/182	8.7	100%	noncoding (1272/2902 nt)	PP_23SC	23S ribosomal RNA
	?	JE3692‑4	= 528039	NA (NA)					noncoding (1277/2902 nt)	PP_23SC	23S ribosomal RNA
*	?	JE3692‑4	= 174474	NA (NA)	13 (0.130)	10/182	8.7	NA	noncoding (1272/2902 nt)	PP_23SA	23S ribosomal RNA
	?	JE3692‑4	= 174479	NA (NA)					noncoding (1277/2902 nt)	PP_23SA	23S ribosomal RNA
*	?	JE3692‑4	171653 =	NA (NA)	14 (0.140)	11/192	8.7	NA	noncoding (265/1522 nt)	PP_16SA	16S ribosomal RNA
	?	JE3692‑4	171682 =	NA (NA)					noncoding (294/1522 nt)	PP_16SA	16S ribosomal RNA
*	?	JE3692‑4	= 173119	NA (NA)	12 (0.120)	10/184	8.8	NA	intergenic (+209/‑84)	PP_16SA/PP_23SA	16S ribosomal RNA/23S ribosomal RNA
	?	JE3692‑4	= 173149	NA (NA)					intergenic (+239/‑54)	PP_16SA/PP_23SA	16S ribosomal RNA/23S ribosomal RNA
*	?	JE3692‑4	= 5465649	NA (NA)	10 (0.100)	10/188	8.9	22.9%	noncoding (1557/1674 nt)	mobile_element	repeat region
	?	JE3692‑4	5556323 =	35 (0.330)					noncoding (62/189 nt)	mobile_element	repeat region
*	?	JE3692‑4	2092551 =	NA (NA)	14 (0.140)	10/188	8.9	NA	noncoding (1156/1445 nt)	mobile_element	repeat region
	?	JE3692‑4	2092585 =	NA (NA)					noncoding (1190/1445 nt)	mobile_element	repeat region