breseq  version 0.27.1  revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 261 shown)
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,559,6210CT59.3% 265.2 / inf 438P452S (CCC→TCC) rtcRsigma 54‑dependent transcriptional regulator of rtcBA expression
*NC_0009133,946,2460GA58.1% 48.9 / inf 379noncoding (2543/2904 nt)rrlC23S ribosomal RNA of rrnC operon
*NC_0009132,510,6090CT56.9% 151.2 / inf 357P327L (CCG→CTG) yfeOputative ion channel protein
*NC_0009133,587,5310GA56.8% 180.0 / inf 450L195F (CTC→TTC) ugpQglycerophosphodiester phosphodiesterase, cytosolic
*NC_0009132,329,2090AG56.4% 215.7 / inf 394W197R (TGG→CGG) yfaQtandem DUF2300 domain protein, putative host defense protein
*NC_0009133,815,8791.C56.3% 731.4 / inf 352pseudogene (3/48 nt)rphribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH
*NC_0009134,517,3550CT56.0% 138.2 / inf 414Q121Q (CAG→CAAfecRanti‑sigma transmembrane signal transducer for ferric citrate transport; periplasmic FecA‑bound ferric citrate sensor and cytoplasmic FecI ECF sigma factor activator
*NC_000913286,5690GA55.9% 113.9 / inf 356S392N (AGC→AAC) yagGCP4‑6 prophage; putative sugar transporter
*NC_0009134,320,0790CT55.7% 120.9 / inf 378Q195Q (CAG→CAAphnIribophosphonate triphosphate synthase complex putative catalytic subunit
*NC_0009132,041,4110GA55.3% 136.8 / inf 470G13S (GGT→AGT) zinTzinc and cadmium binding protein, periplasmic
*NC_000913784,6770GA55.3% 112.2 / inf 424A49A (GCC→GCTzitBzinc efflux system
*NC_0009134,298,1990CT55.0% 111.3 / inf 441A390T (GCA→ACA) fdhFformate dehydrogenase‑H, selenopolypeptide subunit
*NC_0009134,401,6070CT55.0% 133.4 / inf 462T312T (ACC→ACThflXGTPase, stimulated by 50S subunit binding; Mn(2+) homeostasis regulator
*NC_0009133,193,3510GA54.8% 124.1 / inf 436G163E (GGG→GAG) yqiKPHB family membrane protein, function unknown
*NC_0009133,927,2920TC54.8% 190.8 / inf 448D46D (GAT→GACasnAasparagine synthetase A
*NC_0009133,176,6250GA54.6% 117.8 / inf 476S70F (TCC→TTC) cpdA3',5' cAMP phosphodiesterase
*NC_000913306,0230GA54.5% 117.1 / inf 420T265T (ACC→ACTecpDpolymerized tip adhesin of ECP fibers
*NC_0009131,401,8930GA54.4% 90.3 / inf 371Q455* (CAA→TAA) abgBp‑aminobenzoyl‑glutamate hydrolase, B subunit
*NC_000913313,5430GA54.3% 111.4 / inf 498intergenic (‑301/+173)ykgR/ykgPuncharacterized protein/pseudogene, oxidoreductase family
*NC_0009133,506,3930TC54.3% 175.7 / inf 410D315G (GAC→GGC) yhfTinner membrane protein

Marginal new junction evidence (lowest skew 10 of 82 shown)
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 3393149 =259 (0.590)242 (0.550) 158/300 3.0 48.3% coding (3110/3801 nt) yhdP DUF3971‑AsmA2 domains protein
?NC_000913 = 3584195 NA (NA)noncoding (768/768 nt) IS1 repeat region
* ? NC_000913 = 16735560 (0.000)245 (0.570) 156/296 3.0 100% intergenic (‑55/‑357) mdtJ/tqsA multidrug efflux system transporter/pheromone AI‑2 transporter
?NC_000913 1673677 = 0 (0.000)intergenic (‑176/‑236) mdtJ/tqsA multidrug efflux system transporter/pheromone AI‑2 transporter
* ? NC_000913 = 2174362271 (0.620)248 (0.570) 155/300 3.4 47.8% coding (205/285 nt) gatB galactitol‑specific enzyme IIB component of PTS
?NC_000913 = 2290113 NA (NA)noncoding (1/1195 nt) IS5 repeat region
* ? NC_000913 677185 =282 (0.640)223 (0.540) 145/284 3.5 46.4% coding (475/708 nt) ybeR uncharacterized protein
?NC_000913 = 677214 248 (0.600)coding (504/708 nt) ybeR uncharacterized protein
* ? NC_000913 1978503 =NA (NA)252 (0.580) 153/300 3.6 NA noncoding (768/768 nt) IS1 repeat region
?NC_000913 = 4434636 NA (NA)coding (1930/1944 nt) cpdB 2':3'‑cyclic‑nucleotide 2'‑phosphodiesterase
* ? NC_000913 = 275149NA (NA)228 (0.520) 152/300 3.7 47.9% noncoding (1/1195 nt) IS5 repeat region
?NC_000913 295082 = 248 (0.570)intergenic (‑283/+57) yagM/yagN CP4‑6 prophage; uncharacterized protein/CP4‑6 prophage; uncharacterized protein
* ? NC_000913 = 3964579222 (0.510)246 (0.580) 144/290 4.0 53.4% coding (1052/1266 nt) rhlB ATP‑dependent RNA helicase
?NC_000913 3964586 = 214 (0.510)coding (1045/1266 nt) rhlB ATP‑dependent RNA helicase
* ? NC_000913 = 2558698203 (0.460)206 (0.500) 141/284 4.0 51.3% intergenic (‑19/‑160) eutB/intZ ethanolamine ammonia‑lyase, large subunit, heavy chain/CPZ‑55 prophage; putative phage integrase
?NC_000913 2565489 = 199 (0.480)coding (1396/1404 nt) eutA reactivating factor for ethanolamine ammonia lyase
* ? NC_000913 = 167353176 (0.170)227 (0.520) 149/300 4.1 61.2% intergenic (‑30/‑382) mdtJ/tqsA multidrug efflux system transporter/pheromone AI‑2 transporter
?NC_000913 1676567 = 212 (0.480)coding (1337/1533 nt) pntA pyridine nucleotide transhydrogenase, alpha subunit
* ? NC_000913 2101749 =NA (NA)245 (0.560) 148/300 4.2 47.9% noncoding (1195/1195 nt) IS5 repeat region
?NC_000913 2174359 = 266 (0.610)coding (208/285 nt) gatB galactitol‑specific enzyme IIB component of PTS