mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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_000913 | 3,559,621 | 0 | C | T | 59.3% | 265.2 / inf | 438 | P452S (CCC→TCC) | rtcR | sigma 54‑dependent transcriptional regulator of rtcBA expression |
| * | NC_000913 | 3,946,246 | 0 | G | A | 58.1% | 48.9 / inf | 379 | noncoding (2543/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913 | 2,510,609 | 0 | C | T | 56.9% | 151.2 / inf | 357 | P327L (CCG→CTG) | yfeO | putative ion channel protein |
| * | NC_000913 | 3,587,531 | 0 | G | A | 56.8% | 180.0 / inf | 450 | L195F (CTC→TTC) | ugpQ | glycerophosphodiester phosphodiesterase, cytosolic |
| * | NC_000913 | 2,329,209 | 0 | A | G | 56.4% | 215.7 / inf | 394 | W197R (TGG→CGG) | yfaQ | tandem DUF2300 domain protein, putative host defense protein |
| * | NC_000913 | 3,815,879 | 1 | . | C | 56.3% | 731.4 / inf | 352 | pseudogene (3/48 nt) | rph | ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| * | NC_000913 | 4,517,355 | 0 | C | T | 56.0% | 138.2 / inf | 414 | Q121Q (CAG→CAA) | fecR | anti‑sigma transmembrane signal transducer for ferric citrate transport; periplasmic FecA‑bound ferric citrate sensor and cytoplasmic FecI ECF sigma factor activator |
| * | NC_000913 | 286,569 | 0 | G | A | 55.9% | 113.9 / inf | 356 | S392N (AGC→AAC) | yagG | CP4‑6 prophage; putative sugar transporter |
| * | NC_000913 | 4,320,079 | 0 | C | T | 55.7% | 120.9 / inf | 378 | Q195Q (CAG→CAA) | phnI | ribophosphonate triphosphate synthase complex putative catalytic subunit |
| * | NC_000913 | 2,041,411 | 0 | G | A | 55.3% | 136.8 / inf | 470 | G13S (GGT→AGT) | zinT | zinc and cadmium binding protein, periplasmic |
| * | NC_000913 | 784,677 | 0 | G | A | 55.3% | 112.2 / inf | 424 | A49A (GCC→GCT) | zitB | zinc efflux system |
| * | NC_000913 | 4,298,199 | 0 | C | T | 55.0% | 111.3 / inf | 441 | A390T (GCA→ACA) | fdhF | formate dehydrogenase‑H, selenopolypeptide subunit |
| * | NC_000913 | 4,401,607 | 0 | C | T | 55.0% | 133.4 / inf | 462 | T312T (ACC→ACT) | hflX | GTPase, stimulated by 50S subunit binding; Mn(2+) homeostasis regulator |
| * | NC_000913 | 3,193,351 | 0 | G | A | 54.8% | 124.1 / inf | 436 | G163E (GGG→GAG) | yqiK | PHB family membrane protein, function unknown |
| * | NC_000913 | 3,927,292 | 0 | T | C | 54.8% | 190.8 / inf | 448 | D46D (GAT→GAC) | asnA | asparagine synthetase A |
| * | NC_000913 | 3,176,625 | 0 | G | A | 54.6% | 117.8 / inf | 476 | S70F (TCC→TTC) | cpdA | 3',5' cAMP phosphodiesterase |
| * | NC_000913 | 306,023 | 0 | G | A | 54.5% | 117.1 / inf | 420 | T265T (ACC→ACT) | ecpD | polymerized tip adhesin of ECP fibers |
| * | NC_000913 | 1,401,893 | 0 | G | A | 54.4% | 90.3 / inf | 371 | Q455* (CAA→TAA) | abgB | p‑aminobenzoyl‑glutamate hydrolase, B subunit |
| * | NC_000913 | 313,543 | 0 | G | A | 54.3% | 111.4 / inf | 498 | intergenic (‑301/+173) | ykgR/ykgP | uncharacterized protein/pseudogene, oxidoreductase family |
| * | NC_000913 | 3,506,393 | 0 | T | C | 54.3% | 175.7 / inf | 410 | D315G (GAC→GGC) | yhfT | inner 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 | = 1673556 | 0 (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 | = 2174362 | 271 (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 | = 275149 | NA (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 | = 3964579 | 222 (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 | = 2558698 | 203 (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 | = 1673531 | 76 (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 | |||||