breseq  version 0.33.1  revision 8505477f25b3 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000731	81	N→G	100%	intergenic (–/‑151)	– / → repA	–/replication protein A
JC	CP000731	6,552	+28 bp	100%	intergenic (+1069/‑419)	cadX → / → USA300HOU_pUSA300HOUMR0010	cadmium efflux regulator/MarR family transcriptional regulator
RA	CP000731	25,663	Δ1 bp	100%	coding (316/333 nt)	USA300HOU_pUSA300HOUMR0031 →	hypothetical protein
RA	USA300TCH1516_ALE	222,846	C→A	21.0%	G143V (GGG→GTG)	ptsG_1 ←	PTS system glucose‑specific EIICBA component
RA	USA300TCH1516_ALE	1,306,605	G→T	33.3%	G223V (GGA→GTA)	phaB →	Acetoacetyl‑CoA reductase
RA	USA300TCH1516_ALE	1,354,081	C→A	25.0%	E242* (GAA→TAA)	USA300HOU_RS06735 ←	hypothetical protein
RA	USA300TCH1516_ALE	1,416,458	A→T	100%	I216N (ATT→AAT)	oppD_4 ←	Oligopeptide transport ATP‑binding protein OppD
RA	USA300TCH1516_ALE	1,513,930	A→T	100%	L413F (TTA→TTT)	USA300HOU_RS07375 →	hypothetical protein
RA	USA300TCH1516_ALE	1,646,189	G→C	100%	A155G (GCA→GGA)	ypdF ←	Aminopeptidase YpdF
RA	USA300TCH1516_ALE	2,010,363	C→T	100%	C146Y (TGT→TAT)	USA300HOU_RS10125 ←	Putative multidrug export ATP‑binding/permease protein
RA	USA300TCH1516_ALE	2,010,695	T→A	33.5%	L35L (CTA→CTT)	USA300HOU_RS10125 ←	Putative multidrug export ATP‑binding/permease protein
RA	USA300TCH1516_ALE	2,139,469	T→C	30.8%	N31S (AAC→AGC)	USA300HOU_RS10910 ←	hypothetical protein
RA	USA300TCH1516_ALE	2,139,474	T→A	30.4%	G29G (GGA→GGT)	USA300HOU_RS10910 ←	hypothetical protein
RA	USA300TCH1516_ALE	2,139,498	T→C	30.8%	V21V (GTA→GTG)	USA300HOU_RS10910 ←	hypothetical protein
RA	USA300TCH1516_ALE	2,139,504	C→A	36.3%	L19L (CTG→CTT)	USA300HOU_RS10910 ←	hypothetical protein
RA	USA300TCH1516_ALE	2,139,513	A→T	36.4%	I16I (ATT→ATA)	USA300HOU_RS10910 ←	hypothetical protein
RA	USA300TCH1516_ALE	2,279,705	G→A	100%	A943V (GCA→GTA)	ebh_3 ←	Extracellular matrix‑binding protein ebh
RA	USA300TCH1516_ALE	2,532,298	A→T	100%	T15T (ACA→ACT)	femA_3 →	Aminoacyltransferase FemA

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	USA300TCH1516_ALE	463494	463512	19	2 [1]	[1] 2	lpl2_1	putative lipoprotein
*	*	÷	USA300TCH1516_ALE	983737	983785	49	2 [1]	[0] 2	[USA300TCH1516_00912]	[USA300TCH1516_00912]
*	*	÷	USA300TCH1516_ALE	983976	984019	44	2 [1]	[1] 2	USA300TCH1516_00912/USA300HOU_RS04865	hypothetical protein/65 kDa membrane protein
*	*	÷	USA300TCH1516_ALE	1043361	1043390	30	2 [0]	[1] 3	catD/yfmC_1	Putative oxidoreductase CatD/Fe(3+)‑citrate‑binding protein YfmC
*	*	÷	USA300TCH1516_ALE	1045148	1045210	63	2 [0]	[1] 3	USA300HOU_RS05170/rimI_2	hypothetical protein/N‑alpha‑acetyltransferase RimI
*	*	÷	USA300TCH1516_ALE	1072623	1072628	6	3 [1]	[1] 3	folD	Bifunctional protein FolD protein
*	*	÷	USA300TCH1516_ALE	1166331	1166471	141	2 [1]	[0] 2	[USA300HOU_RS05790]	[USA300HOU_RS05790]
*	*	÷	USA300TCH1516_ALE	1248291	1248329	39	2 [1]	[1] 2	smc_2	Chromosome partition protein Smc
*	*	÷	USA300TCH1516_ALE	1320703	1320717	15	2 [1]	[0] 2	mutS_1	DNA mismatch repair protein MutS
*	*	÷	USA300TCH1516_ALE	1337231	1337284	54	2 [1]	[1] 2	glnA	Glutamine synthetase
*	*	÷	USA300TCH1516_ALE	1345403	1345583	181	2 [1]	[1] 2	[USA300HOU_RS06680]	[USA300HOU_RS06680]
*	*	÷	USA300TCH1516_ALE	1400136	1400194	59	2 [1]	[1] 2	[dinB1]	[dinB1]
*	*	÷	USA300TCH1516_ALE	1515745	1515806	62	2 [1]	[1] 2	[rlmL]	[rlmL]
*	*	÷	USA300TCH1516_ALE	1655866	1655923	58	2 [1]	[1] 2	epsF	Type II secretion system protein F
*	*	÷	USA300TCH1516_ALE	1894340	1894397	58	2 [1]	[1] 2	ytpA/putB	Phospholipase YtpA/Proline dehydrogenase 2
*	*	÷	USA300TCH1516_ALE	2203636	2203696	61	3 [1]	[0] 2	[murF_2]	[murF_2]