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 41 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,857,141	1	.	G	58.6%	56.7 / 40.4	29	coding (49/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	1,286,965	0	A	G	55.7%	‑1.5 / 66.7	61	intergenic (+439/+101)	narI/rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
*	NC_000913	2,857,148	0	G	.	55.2%	‑4.8 / 57.1	29	coding (56/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,147	0	A	.	53.6%	37.4 / 62.4	29	coding (55/2562 nt)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,144	0	C	T	52.2%	3.8 / 48.2	29	L18F (CTC→TTC) ‡	mutS	methyl‑directed mismatch repair protein
*	NC_000913	1,287,202	0	A	G	50.0%	‑3.5 / 26.7	22	noncoding (35/171 nt)	rttR	rtT sRNA, processed from tyrT transcript
*	NC_000913	1,287,215	0	T	C	50.0%	‑4.0 / 38.7	28	noncoding (22/171 nt)	rttR	rtT sRNA, processed from tyrT transcript
*	NC_000913	1,287,217	0	G	T	50.0%	4.2 / 48.3	28	noncoding (20/171 nt)	rttR	rtT sRNA, processed from tyrT transcript
*	NC_000913	1,287,220	0	A	G	48.0%	‑2.4 / 31.9	28	noncoding (17/171 nt)	rttR	rtT sRNA, processed from tyrT transcript
*	NC_000913	1,287,041	0	A	G	47.6%	6.5 / 25.0	21	intergenic (+515/+25)	narI/rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
*	NC_000913	1,287,219	0	G	A	46.2%	3.8 / 27.2	28	noncoding (18/171 nt)	rttR	rtT sRNA, processed from tyrT transcript
*	NC_000913	2,857,145	0	T	A	44.8%	10.5 / 38.5	29	L18H (CTC→CAC) ‡	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,146	0	C	G	44.8%	11.3 / 45.5	29	L18L (CTC→CTG) ‡	mutS	methyl‑directed mismatch repair protein
*	NC_000913	1,287,143	0	G	A	43.8%	‑6.5 / 13.5	16	noncoding (94/171 nt) P12S (CCA→TCA)	rttR tpr	rtT sRNA, processed from tyrT transcript protamine‑like protein
*	NC_000913	566,277	0	C	T	43.1%	29.0 / 52.9	52	pseudogene (100/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	566,205	0	T	C	43.1%	14.7 / 66.7	58	pseudogene (172/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
*	NC_000913	4,296,060	0	C	T	42.9%	27.2 / 41.7	42	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
*	NC_000913	2,857,142	0	A	G	41.4%	7.3 / 29.8	29	Y17C (TAT→TGT)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	2,857,143	0	T	A	41.4%	21.8 / 31.5	29	Y17* (TAT→TAA)	mutS	methyl‑directed mismatch repair protein
*	NC_000913	566,245	0	G	A	40.8%	34.3 / 47.6	49	pseudogene (132/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related

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	= 1287044	23 (0.600)	5 (0.130)	3/228	3.7	17.1%	intergenic (+518/+22)	narI/rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
	?	NC_000913	1287228 =	26 (0.680)					noncoding (9/171 nt)	rttR	rtT sRNA, processed from tyrT transcript