BRESEQ :: Marginal Predictions

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

Marginal read alignment evidence
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_hsa_pgi	4,296,088	0	C	T	36.2%	46.7 / 63.3	69	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
*	NC_000913_3_hsa_pgi	225,467	0	G	T	32.0%	18.6 / 14.5	25	intergenic (+10/‑33)	ileV/alaV	tRNA‑Ile/tRNA‑Ala
*	NC_000913_3_hsa_pgi	225,466	0	C	G	30.4%	15.6 / 13.8	23	intergenic (+9/‑34)	ileV/alaV	tRNA‑Ile/tRNA‑Ala
*	NC_000913_3_hsa_pgi	1,286,983	0	A	G	25.0%	36.1 / 17.3	40	intergenic (+457/+83)	narI/rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
*	NC_000913_3_hsa_pgi	526,792	0	A	C	22.6%	183.7 / 36.2	103	S1178R (AGC→CGC)	rhsD	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
*	NC_000913_3_hsa_pgi	526,796	0	C	G	22.0%	197.5 / 53.3	101	A1179G (GCG→GGG)	rhsD	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
*	NC_000913_3_hsa_pgi	526,800	0	A	G	21.8%	193.4 / 50.7	102	E1180E (GAA→GAG)	rhsD	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
*	NC_000913_3_hsa_pgi	1,708,655	0	A	G	20.3%	95.8 / 19.0	66	E579E (GAA→GAG)	rsxC	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex

Marginal new junction evidence (lowest skew 10 of 231 shown)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_hsa_pgi	= 258675	NA (NA)	38 (0.380)	32/296	3.4	37.2%	intergenic (+776/‑1)	crl/crl	pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator;regulator; Surface structures; transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator;regulator; Surface structures; transcriptional regulator of cryptic csgA gene for curli surface fibers
*	?	NC_000913_3_hsa_pgi	314984 =	64 (0.630)	38 (0.380)	32/296	3.4	37.2%	pseudogene (628/872 nt)	eaeH	pseudogene, attaching and effacing protein homology;factor; Not classified
*	?	NC_000913_3_hsa_pgi	= 291401	NA (NA)	32 (0.320)	26/296	4.5	33.3%	intergenic (‑55/‑3)	insA/yagJ	IS1 repressor TnpA/CP4‑6 prophage; uncharacterized protein;Phage or Prophage Related
*	?	NC_000913_3_hsa_pgi	314984 =	64 (0.630)	32 (0.320)	26/296	4.5	33.3%	pseudogene (628/872 nt)	eaeH	pseudogene, attaching and effacing protein homology;factor; Not classified
*	?	NC_000913_3_hsa_pgi	257908 =	NA (NA)	23 (0.230)	23/296	5.1	24.7%	intergenic (+9/‑768)	crl/crl	pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator;regulator; Surface structures; transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator;regulator; Surface structures; transcriptional regulator of cryptic csgA gene for curli surface fibers
*	?	NC_000913_3_hsa_pgi	= 314992	70 (0.690)	23 (0.230)	23/296	5.1	24.7%	pseudogene (636/872 nt)	eaeH	pseudogene, attaching and effacing protein homology;factor; Not classified
*	?	NC_000913_3_hsa_pgi	= 314992	70 (0.690)	21 (0.210)	21/294	5.6	19.6%	pseudogene (636/872 nt)	eaeH	pseudogene, attaching and effacing protein homology;factor; Not classified
*	?	NC_000913_3_hsa_pgi	= 1050545	103 (1.030)	21 (0.210)	21/294	5.6	19.6%	intergenic (+15/+418)	insB1/cspH	IS1 transposase B/stress protein, member of the CspA‑family
*	?	NC_000913_3_hsa_pgi	314984 =	64 (0.630)	16 (0.160)	14/294	7.6	18.5%	pseudogene (628/872 nt)	eaeH	pseudogene, attaching and effacing protein homology;factor; Not classified
*	?	NC_000913_3_hsa_pgi	1049778 =	77 (0.770)	16 (0.160)	14/294	7.6	18.5%	intergenic (‑34/‑55)	gfcA/insA	O‑antigen capsule production threonine‑rich inner membrane protein/IS1 repressor TnpA
*	?	NC_000913_3_hsa_pgi	= 2947575	7 (0.070)	7 (0.100) +42 bp	7/212	8.1	20.5%	intergenic (+2/‑32)	metW/metV	tRNA‑Met/tRNA‑Met
*	?	NC_000913_3_hsa_pgi	= 2947757	69 (0.680)	7 (0.100) +42 bp	7/212	8.1	20.5%	coding (1254/1254 nt)	amiC	N‑acetylmuramoyl‑L‑alanine amidase
*	?	NC_000913_3_hsa_pgi	= 1028822	114 (1.130)	13 (0.130)	11/286	8.5	10.7%	coding (1148/1191 nt)	rlmI	23S rRNA m(5)C1962 methyltransferase, SAM‑dependent
*	?	NC_000913_3_hsa_pgi	= 1028857	108 (1.110)	13 (0.130)	11/286	8.5	10.7%	coding (1113/1191 nt)	rlmI	23S rRNA m(5)C1962 methyltransferase, SAM‑dependent
*	?	NC_000913_3_hsa_pgi	2700550 =	140 (1.390)	9 (0.100)	9/258	8.6	6.9%	noncoding (31/77 nt)	ohsC	sRNA antisense regulator of shoB toxin
*	?	NC_000913_3_hsa_pgi	2700601 =	121 (1.380)	9 (0.100)	9/258	8.6	6.9%	intergenic (+5/+17)	ohsC/acpS	sRNA antisense regulator of shoB toxin/holo‑[acyl‑carrier‑protein] synthase 1
*	?	NC_000913_3_hsa_pgi	1961815 =	100 (0.990)	14 (0.150)	10/276	8.6	12.8%	intergenic (+20/‑157)	argS/yecT	arginyl‑tRNA synthetase/uncharacterized protein
*	?	NC_000913_3_hsa_pgi	1961845 =	97 (1.030)	14 (0.150)	10/276	8.6	12.8%	intergenic (+50/‑127)	argS/yecT	arginyl‑tRNA synthetase/uncharacterized protein
*	?	NC_000913_3_hsa_pgi	= 2470479	148 (1.470)	12 (0.130)	9/278	9.1	8.1%	intergenic (+17/‑336)	gtrS/tfaS	serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage/pseudogene, CPS‑53 (KpLE1) prophage; tail fiber assembly protein fragment;Phage or Prophage Related
*	?	NC_000913_3_hsa_pgi	= 2470483	135 (1.430)	12 (0.130)	9/278	9.1	8.1%	intergenic (+21/‑332)	gtrS/tfaS	serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage/pseudogene, CPS‑53 (KpLE1) prophage; tail fiber assembly protein fragment;Phage or Prophage Related