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
*	NZ_CP025268	1,292,848	0	A	T	73.4%	245.4 / 222.1	348	noncoding (11/132 nt)	CXP41_RS06830	RtT sRNA
*	NZ_CP025268	1,292,810	0	G	A	60.3%	39.5 / inf	455	noncoding (49/132 nt)	CXP41_RS06830	RtT sRNA
*	NZ_CP025268	1,293,000	0	A	G	57.4%	94.7 / 305.5	246	noncoding (37/132 nt)	CXP41_RS06835	RtT sRNA
*	NZ_CP025268	1,292,991	0	C	T	52.5%	75.3 / 305.9	247	noncoding (46/132 nt)	CXP41_RS06835	RtT sRNA
*	NZ_CP025268	1,292,982	0	A	G	43.9%	96.3 / 276.8	249	noncoding (55/132 nt)	CXP41_RS06835	RtT sRNA
*	NZ_CP025268	2,233,239	0	T	A	36.7%	168.3 / 51.2	134	intergenic (+139/+234)	yohP/dusC	small membrane protein YohP/tRNA dihydrouridine(16) synthase DusC
*	NZ_CP025268	164,412	0	A	C	30.7%	127.5 / 32.0	140	intergenic (+47/‑149)	hrpB/mrcB	ATP‑dependent helicase HrpB/bifunctional glycosyl transferase/transpeptidase
*	NZ_CP025268	360,362	0	C	A	27.6%	226.8 / 15.3	159	E184* (GAA→TAA)	lacA	galactoside O‑acetyltransferase
*	NZ_CP025268	2,233,225	0	T	A	27.0%	209.7 / 36.1	129	intergenic (+125/+248)	yohP/dusC	small membrane protein YohP/tRNA dihydrouridine(16) synthase DusC
*	NZ_CP025268	2,233,248	0	G	C	26.9%	247.2 / 78.9	145	intergenic (+148/+225)	yohP/dusC	small membrane protein YohP/tRNA dihydrouridine(16) synthase DusC
*	NZ_CP025268	3,505,553	0	T	A	26.0%	472.1 / 39.5	237	intergenic (+84/+68)	phoB/yhfS	DNA‑binding transcriptional regulator FrlR/aminotransferase class I/II‑fold pyridoxal phosphate‑dependent enzyme
*	NZ_CP025268	360,371	0	C	A	23.9%	300.9 / 42.6	176	V181F (GTT→TTT)	lacA	galactoside O‑acetyltransferase
*	NZ_CP025268	164,395	0	A	T	23.4%	294.9 / 28.3	161	intergenic (+30/‑166)	hrpB/mrcB	ATP‑dependent helicase HrpB/bifunctional glycosyl transferase/transpeptidase
*	NZ_CP025268	3,505,559	0	T	A	22.5%	476.9 / 46.3	231	intergenic (+90/+62)	phoB/yhfS	DNA‑binding transcriptional regulator FrlR/aminotransferase class I/II‑fold pyridoxal phosphate‑dependent enzyme
*	NZ_CP025268	2,233,233	0	G	C	22.3%	238.9 / 32.5	121	intergenic (+133/+240)	yohP/dusC	small membrane protein YohP/tRNA dihydrouridine(16) synthase DusC
*	NZ_CP025268	107,386	0	A	T	22.1%	714.0 / 74.2	310	intergenic (+81/‑150)	lpxC/secM	UDP‑3‑O‑acyl‑N‑acetylglucosamine deacetylase/secA translation cis‑regulator SecM
*	NZ_CP025268	2,233,230	0	G	C	21.5%	244.1 / 23.8	121	intergenic (+130/+243)	yohP/dusC	small membrane protein YohP/tRNA dihydrouridine(16) synthase DusC
*	NZ_CP025268	3,505,561	0	T	A	21.5%	539.5 / 35.5	231	intergenic (+92/+60)	phoB/yhfS	DNA‑binding transcriptional regulator FrlR/aminotransferase class I/II‑fold pyridoxal phosphate‑dependent enzyme
*	NZ_CP025268	164,400	0	C	G	21.3%	326.6 / 36.4	152	intergenic (+35/‑161)	hrpB/mrcB	ATP‑dependent helicase HrpB/bifunctional glycosyl transferase/transpeptidase
*	NZ_CP025268	3,240,303	0	A	T	20.1%	468.9 / 33.8	202	intergenic (+73/‑326)	alx/sstT	TerC family membrane protein Alx/serine/threonine transporter SstT

Marginal new junction evidence (lowest skew 10 of 144 shown)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP025268	= 3743324	0 (0.000)	131 (0.210)	57/264	3.7	100%	intergenic (‑100/‑82)	yiaJ/galK	IclR family transcriptional regulator YiaJ/galactokinase
	?	NZ_CP025268	3744556 =	0 (0.000)					intergenic (+2/‑99)	galK/yiaK	galactokinase/3‑dehydro‑L‑gulonate 2‑dehydrogenase
*	?	NZ_CP025268	= 1214906	651 (1.050)	73 (0.130)	45/234	4.3	11.9%	coding (305/630 nt)	CXP41_RS06370	protein StfP
	?	NZ_CP025268	= 1216702	503 (0.930)					coding (57/540 nt)	CXP41_RS06385	phage tail protein
*	?	NZ_CP025268	695911 =	0 (0.000)	291 (0.520) +GAAGAAACAATC	42/242	4.9	55.5%	intergenic (‑33/+2)	CXP41_RS03680/CXP41_RS03685	tRNA‑Gln/tRNA‑Gln
	?	NZ_CP025268	= 696182	513 (0.830)					intergenic (‑1/+379)	CXP41_RS03695/asnB	tRNA‑Met/asparagine synthase B
*	?	NZ_CP025268	= 780065	431 (0.700)	28 (0.060)	18/192	7.9	10.6%	intergenic (+98/‑52)	CXP41_RS04095/CXP41_RS04100	tRNA‑Lys/tRNA‑Val
	?	NZ_CP025268	780858 =	160 (0.360)					intergenic (+1/‑276)	CXP41_RS04120/nadA	RtT sRNA/quinolinate synthase NadA
*	?	NZ_CP025268	= 4096272	455 (0.740)	19 (0.040)	16/184	8.1	5.0%	intergenic (‑78/+373)	rhaD/rhaA	rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase
	?	NZ_CP025268	4096641 =	408 (0.960)					intergenic (‑447/+4)	rhaD/rhaA	rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase
*	?	NZ_CP025268	= 2822378	426 (0.690)	34 (0.060)	18/226	9.0	8.9%	intergenic (‑83/+116)	CXP41_RS14790/CXP41_RS14795	tRNA‑Arg/tRNA‑Arg
	?	NZ_CP025268	2822513 =	331 (0.630)					noncoding (58/77 nt)	CXP41_RS14795	tRNA‑Arg
*	?	NZ_CP025268	= 2821963	437 (0.710)	26 (0.050)	17/226	9.3	6.9%	intergenic (‑82/+117)	CXP41_RS14780/CXP41_RS14785	tRNA‑Arg/tRNA‑Arg
	?	NZ_CP025268	2822513 =	331 (0.630)					noncoding (58/77 nt)	CXP41_RS14795	tRNA‑Arg
*	?	NZ_CP025268	4544596 =	21 (0.030)	30 (0.050)	17/248	9.9	18.3%	intergenic (+49/‑433)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP025268	4544910 =	248 (0.430)					intergenic (+363/‑119)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
*	?	NZ_CP025268	= 4297793	384 (0.620)	10 (0.020)	10/188	10.4	2.6%	intergenic (+76/+568)	gltP/yjcO	glutamate/aspartate:proton symporter GltP/Sel1 family TPR‑like repeat protein YjcO
	?	NZ_CP025268	4298359 =	466 (1.070)					intergenic (+642/+2)	gltP/yjcO	glutamate/aspartate:proton symporter GltP/Sel1 family TPR‑like repeat protein YjcO
*	?	NZ_CP025268	= 3913973	662 (1.070)	58 (0.100)	16/260	10.5	7.0%	coding (1615/1830 nt)	glmS	glutamine‑‑fructose‑6‑phosphate transaminase (isomerizing)
	?	NZ_CP025268	3915249 =	893 (1.480)					coding (339/1830 nt)	glmS	glutamine‑‑fructose‑6‑phosphate transaminase (isomerizing)