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 432 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	501,575	0	A	C	44.1%	106.6 / 10.0	59	V555G (GTG→GGG)	ybaL	inner membrane putative NAD(P)‑binding transporter
*	NC_000913	1,157,289	0	A	G	43.8%	56.3 / 19.1	49	G171G (GGA→GGG)	ycfH	putative DNase
*	NC_000913	2,326,450	0	T	G	43.8%	104.2 / 16.2	65	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	501,564	0	A	C	43.1%	116.6 / 19.7	65	*559E (TAA→GAA)	ybaL	inner membrane putative NAD(P)‑binding transporter
*	NC_000913	1,097,581	0	A	G	42.9%	98.1 / 14.5	63	noncoding (72/88 nt)	serX	tRNA‑Ser
*	NC_000913	1,755,871	0	T	A	42.1%	39.8 / 21.6	38	G58G (GGT→GGA)	pykF	pyruvate kinase I
*	NC_000913	75,079	0	C	T	41.8%	69.1 / 39.1	55	L134L (CTG→CTA)	thiB	thiamine/thiamine pyrophosphate/thiamine monophosphate ABC transporter periplasmic binding protein
*	NC_000913	599,576	0	T	G	41.8%	104.3 / 11.3	55	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	357,890	0	C	A	41.7%	48.6 / 25.4	48	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	364,526	0	C	A	41.7%	79.9 / 21.9	60	G594C (GGC→TGC)	lacZ	beta‑D‑galactosidase
*	NC_000913	4,112,578	0	T	G	41.7%	110.9 / 14.2	61	G88G (GGT→GGG)	yiiR	DUF805 family putative inner membrane protein
*	NC_000913	1,861,866	0	G	T	41.4%	90.6 / 35.0	58	Q37K (CAA→AAA)	yeaC	DUF1315 family protein
*	NC_000913	2,252,660	0	G	T	41.4%	94.2 / 31.0	58	E321* (GAA→TAA)	yeiI	putative kinase
*	NC_000913	354,288	0	T	G	41.3%	105.9 / 16.6	63	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	3,508,657	0	A	G	40.6%	100.8 / 10.6	65	F386S (TTC→TCC)	yhfW	phosphopentomutase‑related metalloenzyme superfamily protein
*	NC_000913	4,538,101	0	G	T	40.6%	122.1 / 36.1	64	T222N (ACC→AAC)	nanM	N‑acetylneuraminic acid mutarotase
*	NC_000913	2,481,804	0	G	A	40.5%	109.7 / 35.5	75	P125S (CCA→TCA)	emrY	putative multidrug efflux system
*	NC_000913	4,538,109	0	A	C	40.3%	122.8 / 18.4	68	G219G (GGT→GGG)	nanM	N‑acetylneuraminic acid mutarotase
*	NC_000913	646,747	0	T	G	40.0%	109.1 / 12.6	61	T255P (ACC→CCC)	citG	2‑(5''‑triphosphoribosyl)‑3'‑dephosphocoenzyme‑A synthase
*	NC_000913	2,337,723	0	A	C	40.0%	138.8 / 20.0	76	G566G (GGT→GGG)	gyrA	DNA gyrase (type II topoisomerase), subunit A

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	1207790 =	47 (0.660)	25 (0.390)	24/266	3.7	35.5%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	49 (0.770)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	43 (0.600)	22 (0.340)	22/266	4.2	34.5%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	45 (0.700)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1411899 =	71 (0.990)	6 (0.100)	6/246	10.0	10.1%	coding (50/936 nt)	ttcA	tRNA s(2)C32 thioltransferase, iron sulfur cluster protein
	?	NC_000913	= 1434958	48 (0.810)					pseudogene (51/51 nt)	ttcC	pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related
*	?	NC_000913	= 1209618	60 (0.840)	19 (0.300)	3/268	13.0	23.3%	pseudogene (2/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
	?	NC_000913	2471897 =	71 (1.100)					pseudogene (226/579 nt)	yfdL	pseudogene, CPS‑53 (KpLE1) prophage;Phage or Prophage Related