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_3_pae_pgi	4,295,320	0	C	T	25.0%	556.1 / 197.3	312	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
*	NC_000913_3_pae_pgi	526,796	0	C	G	23.6%	626.3 / 207.7	268	A1179G (GCG→GGG)	rhsD	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
*	NC_000913_3_pae_pgi	526,792	0	A	C	22.9%	566.3 / 199.8	282	S1178R (AGC→CGC)	rhsD	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
*	NC_000913_3_pae_pgi	526,800	0	A	G	22.2%	549.6 / 143.8	257	E1180E (GAA→GAG)	rhsD	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
*	NC_000913_3_pae_pgi	2,596,873	0	C	.	21.3%	576.0 / 184.9	212	intergenic (‑136/+32)	ypfJ/purC	putative neutral zinc metallopeptidase/phosphoribosylaminoimidazole‑succinocarboxamide synthetase

Marginal new junction evidence (lowest skew 10 of 331 shown)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	4541942 =	152 (0.790)	64 (0.360)	52/226	6.7	31.0%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913_3_pae_pgi	4542256 =	144 (0.810)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913_3_pae_pgi	= 4541950	151 (0.790)	62 (0.350)	50/226	7.1	30.5%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913_3_pae_pgi	= 4542246	143 (0.800)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913_3_pae_pgi	225456 =	12 (0.060)	61 (0.340)	42/226	9.1	82.4%	noncoding (76/77 nt)	ileV	tRNA‑Ile
	?	NC_000913_3_pae_pgi	225477 =	15 (0.080)					intergenic (+20/‑23)	ileV/alaV	tRNA‑Ile/tRNA‑Ala
*	?	NC_000913_3_pae_pgi	225468 =	16 (0.080)	60 (0.340)	41/226	9.3	80.2%	intergenic (+11/‑32)	ileV/alaV	tRNA‑Ile/tRNA‑Ala
	?	NC_000913_3_pae_pgi	= 3427068	NA (NA)					intergenic (‑35/+8)	alaU/ileU	tRNA‑Ala/tRNA‑Ile
*	?	NC_000913_3_pae_pgi	225456 =	12 (0.060)	65 (0.370)	41/226	9.3	85.4%	noncoding (76/77 nt)	ileV	tRNA‑Ile
	?	NC_000913_3_pae_pgi	= 3427056	NA (NA)					intergenic (‑23/+20)	alaU/ileU	tRNA‑Ala/tRNA‑Ile
*	?	NC_000913_3_pae_pgi	= 3427065	NA (NA)	64 (0.360)	40/226	9.6	NA	intergenic (‑32/+11)	alaU/ileU	tRNA‑Ala/tRNA‑Ile
	?	NC_000913_3_pae_pgi	= 3427068	NA (NA)					intergenic (‑35/+8)	alaU/ileU	tRNA‑Ala/tRNA‑Ile
*	?	NC_000913_3_pae_pgi	= 2068406	191 (0.990)	48 (0.290)	35/208	9.9	23.6%	pseudogene (14/159 nt)	yoeH	pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related
	?	NC_000913_3_pae_pgi	= 2068411	148 (0.900)					pseudogene (9/159 nt)	yoeH	pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related
*	?	NC_000913_3_pae_pgi	= 1207805	188 (0.980)	40 (0.240)	35/212	10.2	21.3%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913_3_pae_pgi	= 1209602	132 (0.790)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913_3_pae_pgi	1096961 =	212 (1.100)	39 (0.330) +47 bp	21/150	10.3	23.0%	intergenic (+132/+604)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
	?	NC_000913_3_pae_pgi	1097243 =	NA (NA)					intergenic (+414/+322)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
*	?	NC_000913_3_pae_pgi	1096961 =	212 (1.100)	37 (0.310) +47 bp	19/150	11.1	24.7%	intergenic (+132/+604)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
	?	NC_000913_3_pae_pgi	1097062 =	155 (0.810)					intergenic (+233/+503)	ycdU/serX	putative inner membrane protein/tRNA‑Ser