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	28.1%	462.4 / 217.5	310	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
*	NC_000913_3_pae_pgi	3,781,152	0	A	G	27.3%	277.3 / 35.9	163	intergenic (+135/‑63)	lldD/trmL	L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent
*	NC_000913_3_pae_pgi	3,781,140	0	A	G	22.1%	287.2 / 13.1	143	intergenic (+123/‑75)	lldD/trmL	L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent

Marginal new junction evidence (lowest skew 10 of 1693 shown)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	1207790 =	179 (0.840)	56 (0.310)	40/164	6.3	30.7%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913_3_pae_pgi	1209619 =	103 (0.580)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913_3_pae_pgi	= 1207805	173 (0.810)	48 (0.270)	36/164	7.4	28.1%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913_3_pae_pgi	= 1209602	101 (0.560)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913_3_pae_pgi	= 1468681	NA (NA)	130 (1.100) +44 bp	11/108	12.0	57.4%	coding (146/906 nt)	insD1	IS2 transposase TnpB
	?	NC_000913_3_pae_pgi	1650843 =	175 (0.820)					intergenic (+1/‑2)	ydfE/insD1	Qin prophage; pseudogene;Phage or Prophage Related/IS2 transposase TnpB;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related
*	?	NC_000913_3_pae_pgi	= 228744	85 (0.400)	134 (0.670)	23/184	13.5	62.7%	intergenic (+82/‑12)	rrlH/rrfH	23S ribosomal RNA of rrnH operon/5S ribosomal RNA of rrnH operon
	?	NC_000913_3_pae_pgi	2726224 =	NA (NA)					intergenic (‑36/+57)	rrfG/rrlG	5S ribosomal RNA of rrnG operon/23S ribosomal RNA of rrnG operon
*	?	NC_000913_3_pae_pgi	2726200 =	NA (NA)	133 (0.660)	22/184	14.0	NA	intergenic (‑12/+81)	rrfG/rrlG	5S ribosomal RNA of rrnG operon/23S ribosomal RNA of rrnG operon
	?	NC_000913_3_pae_pgi	2726224 =	NA (NA)					intergenic (‑36/+57)	rrfG/rrlG	5S ribosomal RNA of rrnG operon/23S ribosomal RNA of rrnG operon
*	?	NC_000913_3_pae_pgi	3719794 =	251 (1.170)	35 (0.180)	19/178	14.8	13.3%	intergenic (+26/‑255)	yiaG/cspA	HTH_CROC1 family putative transcriptional regulator/RNA chaperone and antiterminator, cold‑inducible
	?	NC_000913_3_pae_pgi	3719816 =	230 (1.180)					intergenic (+48/‑233)	yiaG/cspA	HTH_CROC1 family putative transcriptional regulator/RNA chaperone and antiterminator, cold‑inducible
*	?	NC_000913_3_pae_pgi	= 381910	NA (NA)	68 (0.340)	20/184	14.9	NA	coding (237/906 nt)	insD1	IS2 transposase TnpB
	?	NC_000913_3_pae_pgi	= 381923	NA (NA)					coding (250/906 nt)	insD1	IS2 transposase TnpB
*	?	NC_000913_3_pae_pgi	= 274419	NA (NA)	109 (0.540)	19/186	15.5	NA	coding (699/1017 nt)	insH1	IS5 transposase and trans‑activator
	?	NC_000913_3_pae_pgi	= 274423	NA (NA)					coding (695/1017 nt)	insH1	IS5 transposase and trans‑activator
*	?	NC_000913_3_pae_pgi	= 381669	NA (NA)	64 (0.320)	18/182	15.6	NA	coding (319/366 nt)	insC1	IS2 repressor TnpA
	?	NC_000913_3_pae_pgi	= 381695	NA (NA)					coding (345/366 nt) coding (22/906 nt)	insC1 insD1	IS2 repressor TnpA IS2 transposase TnpB
*	?	NC_000913_3_pae_pgi	= 4541950	235 (1.100)	19 (0.100)	17/178	15.8	8.2%	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	213 (1.100)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)