mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 4,604,344 | 0 | C | T | 43.5% | 79.1 / 69.9 | 93 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 2,001,918 | 0 | A | C | 34.8% | 105.7 / 36.2 | 69 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 1,825,061 | 0 | G | A | 33.3% | 50.8 / 13.1 | 33 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 3,206,435 | 0 | C | T | 33.3% | 83.5 / 36.2 | 60 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,429,984 | 0 | T | G | 29.2% | 137.9 / 26.2 | 72 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 1,068,173 | 0 | T | G | 28.2% | 150.8 / 29.2 | 79 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 1,550,663 | 0 | A | C | 26.6% | 138.5 / 17.6 | 64 | N68T (AAC→ACC) | fdnH | formate dehydrogenase N subunit beta |
| * | NC_000913 | 4,568,504 | 0 | T | G | 26.6% | 237.9 / 11.0 | 116 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 3,206,444 | 0 | T | A | 25.8% | 123.2 / 15.5 | 62 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 2,326,450 | 0 | T | G | 23.8% | 171.9 / 46.1 | 84 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 888,014 | 0 | T | G | 22.1% | 152.7 / 10.4 | 68 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 770,897 | 0 | T | G | 21.9% | 143.7 / 11.2 | 64 | intergenic (+286/‑561) | mngB/cydA | alpha‑mannosidase/cytochrome bd‑I ubiquinol oxidase subunit I |
| * | NC_000913 | 2,628,625 | 0 | A | C | 21.7% | 106.0 / 11.6 | 46 | V105G (GTC→GGC) | pdeF | cyclic di‑GMP phosphodiesterase PdeF |
| * | NC_000913 | 4,161,148 | 0 | G | A | 21.3% | 169.7 / 14.5 | 75 | E28K (GAA→AAA) | fabR | DNA‑binding transcriptional repressor FabR |
| * | NC_000913 | 29,496 | 0 | T | A | 21.3% | 139.5 / 18.2 | 61 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 753,125 | 0 | T | A | 21.2% | 162.9 / 15.8 | 66 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 2,782,509 | 0 | A | C | 21.0% | 221.5 / 15.4 | 100 | V73G (GTA→GGA) | ypjA | adhesin‑like autotransporter YpjA |
| 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 = | 121 (1.160) | 8 (0.090) | 8/244 | 6.5 | 7.0% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 105 (1.130) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 11 (0.140) | 4/202 | 7.4 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377430 = | NA (NA) | intergenic (+119/+105) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 4373295 = | NA (NA) | 10 (0.100) | 6/256 | 7.6 | NA | noncoding (2/34 nt) | other | REP328b |
| ? | NC_000913 | 4374499 = | NA (NA) | noncoding (1/34 nt) | other | REP329a | |||||
| * | ? | NC_000913 | = 1259644 | 101 (1.010) | 8 (0.080) +CCA |
4/258 | 8.7 | 7.3% | coding (1160/1680 nt) | dauA | aerobic C4‑dicarboxylate transporter DauA |
| ? | NC_000913 | 1259645 = | 102 (0.970) | coding (1159/1680 nt) | dauA | aerobic C4‑dicarboxylate transporter DauA | |||||
| * | ? | NC_000913 | = 1226728 | 113 (1.100) | 4 (0.040) +TGC |
4/266 | 8.9 | 3.5% | coding (129/369 nt) | ycgJ | PF05666 family protein YcgJ |
| ? | NC_000913 | 1226729 = | 114 (1.090) | coding (130/369 nt) | ycgJ | PF05666 family protein YcgJ | |||||
| * | ? | NC_000913 | = 3080504 | 94 (0.900) | 5 (0.050) | 4/274 | 9.0 | 5.8% | coding (1132/1992 nt) | tktA | transketolase 1 |
| ? | NC_000913 | = 3080680 | 68 (0.650) | coding (956/1992 nt) | tktA | transketolase 1 | |||||
| * | ? | NC_000913 | 1462089 = | 113 (1.080) | 4 (0.040) | 3/252 | 9.2 | 3.2% | coding (1197/1206 nt) | paaJ | beta‑ketoadipyl‑CoA thiolase |
| ? | NC_000913 | 1462223 = | 136 (1.420) | coding (99/1314 nt) | paaK | phenylacetate‑CoA ligase | |||||
| * | ? | NC_000913 | = 2719878 | 95 (0.910) | 3 (0.030) | 3/272 | 9.6 | 3.1% | coding (656/699 nt) | yfiP | conserved protein YfiP |
| ? | NC_000913 | 2719882 = | 96 (0.930) | coding (660/699 nt) | yfiP | conserved protein YfiP | |||||
| * | ? | NC_000913 | = 1054531 | 84 (0.800) | 3 (0.030) | 3/270 | 9.6 | 3.5% | coding (1648/2745 nt) | torS | sensory histidine kinase TorS |
| ? | NC_000913 | 1054535 = | 81 (0.790) | coding (1644/2745 nt) | torS | sensory histidine kinase TorS | |||||