breseq  version 0.29.0  revision 8f9c342918e4 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 305 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	226,384	0	A	T	79.2%	10.9 / 41.2	72	noncoding (626/2904 nt)	rrlH	23S ribosomal RNA of rrnH operon
*	NC_000913	226,387	0	G	C	78.8%	11.8 / 43.4	68	noncoding (629/2904 nt)	rrlH	23S ribosomal RNA of rrnH operon
*	NC_000913	226,392	0	C	G	78.5%	11.9 / 42.4	65	noncoding (634/2904 nt)	rrlH	23S ribosomal RNA of rrnH operon
*	NC_000913	226,381	0	C	G	78.4%	13.5 / 48.4	74	noncoding (623/2904 nt)	rrlH	23S ribosomal RNA of rrnH operon
*	NC_000913	226,310	0	T	G	77.4%	29.5 / 130.5	191	noncoding (552/2904 nt)	rrlH	23S ribosomal RNA of rrnH operon
*	NC_000913	226,309	0	G	A	77.0%	27.4 / 125.8	191	noncoding (551/2904 nt)	rrlH	23S ribosomal RNA of rrnH operon
*	NC_000913	226,378	0	G	T	76.9%	16.5 / 47.1	78	noncoding (620/2904 nt)	rrlH	23S ribosomal RNA of rrnH operon
*	NC_000913	226,307	0	G	T	76.7%	21.5 / 145.9	193	noncoding (549/2904 nt)	rrlH	23S ribosomal RNA of rrnH operon
*	NC_000913	226,308	0	C	T	76.6%	25.4 / 122.0	193	noncoding (550/2904 nt)	rrlH	23S ribosomal RNA of rrnH operon
*	NC_000913	226,299	0	A	C	76.5%	19.2 / 144.1	196	noncoding (541/2904 nt)	rrlH	23S ribosomal RNA of rrnH operon
*	NC_000913	226,301	0	G	A	76.5%	18.3 / 140.4	196	noncoding (543/2904 nt)	rrlH	23S ribosomal RNA of rrnH operon
*	NC_000913	226,371	0	A	T	76.5%	14.6 / 55.6	85	noncoding (613/2904 nt)	rrlH	23S ribosomal RNA of rrnH operon
*	NC_000913	226,305	0	A	.	76.4%	13.2 / 243.1	193	noncoding (547/2904 nt)	rrlH	23S ribosomal RNA of rrnH operon
*	NC_000913	226,354	0	T	A	76.3%	7.4 / 87.7	114	noncoding (596/2904 nt)	rrlH	23S ribosomal RNA of rrnH operon
*	NC_000913	226,363	0	G	C	76.1%	15.6 / 72.6	92	noncoding (605/2904 nt)	rrlH	23S ribosomal RNA of rrnH operon
*	NC_000913	226,278	0	G	A	75.3%	20.4 / 128.0	170	noncoding (520/2904 nt)	rrlH	23S ribosomal RNA of rrnH operon
*	NC_000913	226,262	0	A	T	75.2%	25.2 / 111.3	137	noncoding (504/2904 nt)	rrlH	23S ribosomal RNA of rrnH operon
*	NC_000913	226,357	0	A	G	75.0%	15.0 / 65.1	100	noncoding (599/2904 nt)	rrlH	23S ribosomal RNA of rrnH operon
*	NC_000913	226,280	0	A	G	74.7%	21.2 / 123.0	170	noncoding (522/2904 nt)	rrlH	23S ribosomal RNA of rrnH operon
*	NC_000913	226,248	0	C	A	71.9%	15.7 / 103.9	114	noncoding (490/2904 nt)	rrlH	23S ribosomal RNA of rrnH operon

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	= 3428662	11 (0.220)	41 (0.960) +25 bp	11/248	4.4	81.8%	noncoding (101/1542 nt)	rrsD	16S ribosomal RNA of rrnD operon
	?	NC_000913	3428694 =	NA (NA)					noncoding (69/1542 nt)	rrsD	16S ribosomal RNA of rrnD operon
*	?	NC_000913	= 2731057	55 (1.080)	41 (0.960) +25 bp	11/248	4.4	47.2%	noncoding (101/1542 nt)	rrsG	16S ribosomal RNA of rrnG operon
	?	NC_000913	2731089 =	NA (NA)					noncoding (69/1542 nt)	rrsG	16S ribosomal RNA of rrnG operon
*	?	NC_000913	4542682 =	66 (1.290)	4 (0.080)	4/280	8.7	6.2%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	59 (1.230)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)