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

Predicted mutations
evidence	position	mutation	annotation	gene	description
MC JC	257,908	Δ776 bp		[crl]	[crl]
RA	924,050	T→G	F263V (TTT→GTT)	clpA →	ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity
MC JC	1,978,503	Δ776 bp		insB1–insA	insB1, insA
RA	2,173,363	Δ2 bp	intergenic (‑1/+1)	gatC ← / ← gatC	pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
RA	2,939,611	G→T	D82Y (GAT→TAT)	fucR →	l‑fucose operon activator
RA	3,560,455	+G	intergenic (‑2/+1)	glpR ← / ← glpR	pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon
RA	4,296,381	+GC	intergenic (+587/+55)	gltP → / ← yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	237107	237354	248	24 [21]	[23] 25	[yafT]	[yafT]
*	*	÷	NC_000913	583075	584621	1547	24 [23]	[22] 24	[tfaX]–appY	[tfaX],appY
*	*	÷	NC_000913	720784	721166	383	24 [20]	[23] 25	[ybfK]–[kdpE]	[ybfK],[kdpE]
*	*	÷	NC_000913	954528	954860	333	24 [23]	[20] 24	focA/ycaO	formate channel/ribosomal protein S12 methylthiotransferase accessory factor
*	*	÷	NC_000913	1196955	1197922	968	25 [22]	[23] 25	[ymfD]–[ymfE]	[ymfD],[ymfE]
*	*	÷	NC_000913	1211592	1212747	1156	24 [22]	[23] 26	iraM–[ycgX]	iraM,[ycgX]
*	*	÷	NC_000913	1299312	1300779	1468	24 [23]	[22] 24	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
*	*	÷	NC_000913	1526807	1527748	942	24 [23]	[23] 29	[yncG]–yncH	[yncG],yncH
*	*	÷	NC_000913	1529945	1530552	608	24 [23]	[23] 25	[ydcD]	[ydcD]
*	*	÷	NC_000913	1586509	1586808	300	24 [22]	[23] 24	ydeP/ydeQ	putative oxidoreductase/putative fimbrial‑like adhesin protein
*	*	÷	NC_000913	2033449	2034051	603	29 [22]	[22] 24	[yedR]–[yedS]	[yedR],rseX,[yedS]
*	*	÷	NC_000913	2103239	2104236	998	24 [20]	[20] 24	[wbbL]–[wbbK]	[wbbL],[wbbK]
*	*	÷	NC_000913	2469049	2469872	824	25 [22]	[22] 24	[gtrB]–[gtrS]	[gtrB],[gtrS]
*	*	÷	NC_000913	2469959	2470754	796	24 [23]	[23] 25	[gtrS]	[gtrS]
*	*	÷	NC_000913	2773297	2773967	671	24 [23]	[22] 24	[yfjW]	[yfjW]
*	*	÷	NC_000913	2903503	2904077	575	24 [23]	[23] 24	ygcE/queE	putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis
*	*	÷	NC_000913	2994976	2995537	562	24 [22]	[22] 24	[ygeK]–[ygeN]	[ygeK],[ygeN]
*	*	÷	NC_000913	3268720	3269741	1022	27 [22]	[23] 24	[yhaC]	[yhaC]
*	*	÷	NC_000913	3469789	3470193–3470164	376–405	24 [23]	[23] 24	[chiA]–[tufA]	[chiA],[tufA]
*	*	÷	NC_000913	3632049	3632344	296	24 [23]	[23] 25	yhiJ	DUF4049 family protein
*	*	÷	NC_000913	3769405	3770244	840	24 [22]	[23] 24	[yibV]–[yibH]	[yibV],yibV,yibU,yibU,[yibH]
*	*	÷	NC_000913	3796937	3798346	1410	25 [23]	[22] 25	[waaC]–[waaU]	[waaC],waaL,[waaU]
*	*	÷	NC_000913	3798572	3800270	1699	26 [20]	[23] 24	[waaU]–[waaY]	[waaU],waaZ,[waaY]
*	*	÷	NC_000913	3804155	3805189	1035	24 [23]	[22] 27	waaS–[waaP]	waaS,[waaP]
*	*	÷	NC_000913	4086792	4087049	258	25 [23]	[23] 24	[fdhD]–[yiiG]	[fdhD],[yiiG]
*	*	÷	NC_000913	4251455	4252084	630	25 [23]	[22] 24	yjbI	pseudogene, SopA‑related, pentapeptide repeats‑containing
*	*	÷	NC_000913	4268414	4269287	874	25 [23]	[22] 25	yjbS	yjbS
*	*	÷	NC_000913	4539527	4540004	478	25 [21]	[22] 24	nanC/fimB	N‑acetylnuraminic acid outer membrane channel protein/tyrosine recombinase/inversion of on/off regulator of fimA
*	*	÷	NC_000913	4541549	4542014	466	25 [18]	[23] 24	[fimB]	[fimB]

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1207790 =	11 (0.160)	65 (1.020)	49/506	0.2	87.1%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	9 (0.140)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	11 (0.160)	55 (0.860)	45/506	0.2	85.0%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	9 (0.140)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related