breseq  version 0.35.4  revision f352f80f4bc9 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 69 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	707,981	0	C	G	57.6%	7.8 / 43.3	50	intergenic (+224/‑353)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	2,470,436	0	C	A	56.5%	12.7 / 26.3	24	Q436K (CAA→AAA)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	4,378,973	0	G	C	55.6%	2.6 / 10.0	27	intergenic (‑29/+34)	ampC/frdD	beta‑lactamase/fumarate reductase membrane protein FrdD
*	NC_000913	454,919	0	G	T	54.5%	9.9 / 23.1	26	intergenic (+130/‑214)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	1,097,092	0	T	C	53.3%	‑4.4 / 11.9	18	intergenic (+263/+473)	ycdU/serX	uncharacterized protein YcdU/tRNA‑Ser
*	NC_000913	3,233,720	0	A	C	52.6%	1.0 / 15.2	19	intergenic (+37/+8)	fadH/higA	2,4‑dienoyl‑CoA reductase/antitoxin/DNA‑binding transcriptional repressor HigA
*	NC_000913	2,177,234	0	C	A	52.2%	‑6.2 / 15.1	38	intergenic (‑30/+278)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	454,866	0	G	T	52.0%	3.6 / 16.7	25	intergenic (+77/‑267)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	1,636,442	0	C	G	50.0%	22.8 / 13.6	33	intergenic (‑75/‑314)	nohA/ynfO	Qin prophage; putative prophage DNA‑packaging protein NohA/Qin prophage; protein YnfO
*	NC_000913	2,177,221	0	T	G	50.0%	9.1 / 20.1	34	intergenic (‑17/+291)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,177,228	0	C	G	50.0%	17.1 / 13.7	37	intergenic (‑24/+284)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,470,405	0	T	G	44.8%	17.7 / 17.1	29	V425V (GTT→GTG)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	454,934	0	A	C	44.0%	0.5 / 13.4	25	intergenic (+145/‑199)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	707,976	0	T	G	44.0%	24.4 / 22.5	50	intergenic (+219/‑358)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	2,470,472	0	G	T	42.3%	25.0 / 10.1	26	intergenic (+10/+605)	yfdI/yfdK	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase/CPS‑53 (KpLE1) prophage; putative tail fiber assembly protein YfdK
*	NC_000913	2,177,255	0	G	T	42.0%	19.1 / 28.6	50	intergenic (‑51/+257)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,470,411	0	A	T	41.4%	17.0 / 15.2	29	L427F (TTA→TTT)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	2,519,212	0	A	C	39.0%	37.0 / 15.0	41	intergenic (+7/+45)	yfeD/gltX	putative DNA‑binding transcriptional regulator YfeD/glutamate‑‑tRNA ligase
*	NC_000913	2,725,829	0	G	T	38.9%	49.3 / 18.1	36	intergenic (‑83/+240)	kgtP/rrfG	alpha‑ketoglutarate:H(+) symporter/5S ribosomal RNA
*	NC_000913	3,004,946	0	G	T	38.6%	48.3 / 20.3	45	Q281K (CAA→AAA)	ygeV	putative sigma(54)‑dependent transcriptional regulator YgeV

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	= 1207805	40 (0.640)	3 (0.050)	3/222	5.5	6.7%	coding (305/630 nt)	ycfK	e14 prophage; protein StfP
	?	NC_000913	= 1209602	49 (0.900)					pseudogene (54/537 nt)	stfE	e14 prophage; putative side tail fiber protein fragment
*	?	NC_000913	498254 =	55 (0.880)	3 (0.050)	3/254	6.1	4.6%	coding (200/963 nt)	hemH	ferrochelatase
	?	NC_000913	3665411 =	70 (1.120)					coding (400/825 nt)	gadX	DNA‑binding transcriptional dual regulator GadX