breseq  version 0.32.1  revision aa8f2595a244 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 37 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,857,144	0	C	T	70.0%	29.2 / 37.3	37	L18F (CTC→TTC) ‡	mutS	methyl‑directed mismatch repair protein
*	NC_000913	4,171,557	0	C	A	65.2%	‑0.0 / 28.9	23	intergenic (+13/‑80)	rrlB/rrfB	23S ribosomal RNA of rrnB operon/5S ribosomal RNA of rrnB operon
*	NC_000913	1,286,965	0	A	G	64.6%	40.9 / 53.5	65	intergenic (+439/+101)	narI/rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
*	NC_000913	3,709,555	1	.	C	62.0%	202.3 / 125.0	92	coding (921/1692 nt)	eptB	KDO phosphoethanolamine transferase, Ca(2+)‑inducible
*	NC_000913	2,857,142	0	A	G	56.8%	13.9 / 38.4	37	Y17C (TAT→TGT)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,143	0	T	A	56.8%	10.9 / 52.9	37	Y17* (TAT→TAA)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,145	0	T	A	56.8%	9.7 / 53.3	37	L18H (CTC→CAC) ‡	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,146	0	C	G	56.8%	12.5 / 61.3	37	L18L (CTC→CTG) ‡	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,147	0	A	T	56.8%	65.8 / 53.2	37	coding (55/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,148	0	G	C	56.8%	66.7 / 56.1	37	coding (56/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	730,796	0	G	C	56.1%	‑4.2 / 96.4	57	G405A (GGC→GCC)	rhsC	Rhs protein with putative toxin domain, putative neighboring cell growth inhibitor
*	NC_000913	3,728,077	0	G	A	48.3%	19.9 / 109.8	87	A432V (GCG→GTG)	xylB	xylulokinase
*	NC_000913	566,245	0	G	A	47.2%	23.0 / 84.9	72	pseudogene (132/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	3,755,411	0	T	.	46.9%	144.2 / 135.3	81	coding (1101/1539 nt)	aldB	aldehyde dehydrogenase B
*	NC_000913	1,287,044	0	G	A	45.5%	7.6 / 22.0	22	intergenic (+518/+22)	narI/rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
*	NC_000913	1,287,220	0	A	G	43.5%	7.8 / 25.9	25	noncoding (17/171 nt)	rttR	rtT sRNA, processed from tyrT transcript
*	NC_000913	2,857,141	1	.	G	43.2%	0.1 / 70.7	37	coding (49/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	1,287,052	0	A	G	42.9%	3.1 / 22.4	21	intergenic (+526/+14)	narI/rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
*	NC_000913	566,277	0	C	T	42.0%	53.4 / 86.6	81	pseudogene (100/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	1,287,048	0	A	C	41.7%	11.1 / 38.8	24	intergenic (+522/+18)	narI/rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript

Marginal new junction evidence (sorted from low to high skew)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1286708 =	33 (0.620)	7 (0.160)	6/176	3.4	23.9%	intergenic (+182/+358)	narI/rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
	?	NC_000913	= 1287241	18 (0.420)					intergenic (‑5/+3)	rttR/tyrV	rtT sRNA, processed from tyrT transcript/tRNA‑Tyr
*	?	NC_000913	= 184206	39 (0.740)	4 (0.080) +TGTAA	4/208	4.7	9.9%	intergenic (‑111/+51)	yaeH/yaeI	UPF0325 family protein/phosphodiesterase with model substrate bis‑pNPP
	?	NC_000913	= 184256	37 (0.700)					intergenic (‑161/+1)	yaeH/yaeI	UPF0325 family protein/phosphodiesterase with model substrate bis‑pNPP
*	?	NC_000913	= 3081460	48 (0.910)	3 (0.060)	3/218	5.4	6.3%	coding (176/1992 nt)	tktA	transketolase 1, thiamine triphosphate‑binding
	?	NC_000913	= 3081522	41 (0.770)					coding (114/1992 nt)	tktA	transketolase 1, thiamine triphosphate‑binding