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 (highest frequency 20 of 22 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,604,344 | 0 | C | T | 39.5% | 95.5 / 58.1 | 86 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,111,747 | 0 | G | T | 35.1% | 72.5 / 24.5 | 37 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 2,001,918 | 0 | A | C | 31.4% | 103.6 / 15.9 | 51 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,296,060 | 0 | C | T | 31.2% | 133.7 / 74.9 | 93 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 3,206,435 | 0 | C | T | 30.5% | 91.6 / 33.8 | 59 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 3,556,207 | 0 | T | C | 29.5% | 74.6 / 13.7 | 44 | S215G (AGT→GGT) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 650,809 | 0 | T | G | 27.4% | 140.7 / 13.3 | 63 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 4,628,649 | 0 | A | C | 27.4% | 172.4 / 13.3 | 73 | intergenic (+102/+206) | nadR/ettA | DNA‑binding transcriptional repressor/NMN adenylyltransferase NadR/energy‑dependent translational throttle protein EttA |
| * | NC_000913 | 1,825,061 | 0 | G | A | 27.3% | 79.1 / 15.3 | 44 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 888,014 | 0 | T | G | 27.0% | 156.3 / 23.1 | 74 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 3,608,719 | 0 | G | A | 26.7% | 76.9 / 12.1 | 45 | intergenic (+70/+32) | zntA/tusA | Zn(2(+))/Cd(2(+))/Pb(2(+)) exporting P‑type ATPase/sulfur transfer protein TusA |
| * | NC_000913 | 2,326,450 | 0 | T | G | 26.5% | 141.8 / 37.3 | 68 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 2,041,197 | 0 | C | A | 25.5% | 265.3 / 75.4 | 102 | intergenic (+79/‑178) | msrQ/zinT | periplasmic protein‑L‑methionine sulfoxide reductase heme binding subunit/metal‑binding protein ZinT |
| * | NC_000913 | 1,906,769 | 0 | A | C | 24.4% | 195.8 / 12.3 | 82 | Y98D (TAT→GAT) | rlmA | 23S rRNA m(1)G745 methyltransferase |
| * | NC_000913 | 3,943,488 | 0 | T | G | 24.0% | 93.3 / 12.1 | 50 | noncoding (54/76 nt) | gltU | tRNA‑Glu |
| * | NC_000913 | 4,568,504 | 0 | T | G | 23.3% | 242.6 / 11.3 | 103 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 753,125 | 0 | T | A | 23.2% | 125.3 / 15.0 | 56 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,287,719 | 0 | T | A | 23.1% | 148.2 / 23.2 | 65 | intergenic (‑348/‑45) | acs/nrfA | acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase |
| * | NC_000913 | 4,429,984 | 0 | T | G | 21.0% | 154.6 / 16.6 | 62 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 1,491,098 | 0 | A | C | 20.9% | 218.9 / 16.0 | 91 | Y66S (TAC→TCC) | cybB | cytochrome b561 |
| Marginal new junction evidence (lowest skew 10 of 31 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 375102 = | NA (NA) | 63 (0.820) | 15/216 | 3.1 | NA | noncoding (17/36 nt) | other | REP31d |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 26 (0.360) | 12/202 | 3.5 | 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 | 1207790 = | 96 (0.980) | 11 (0.130) | 11/244 | 4.5 | 11.7% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 81 (0.940) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 375064 | NA (NA) | 9 (0.130) | 6/192 | 5.1 | NA | noncoding (33/34 nt) | other | REP31c |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 375160 | NA (NA) | 37 (0.380) +T |
10/274 | 5.2 | NA | noncoding (28/34 nt) | other | REP31e |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 340035 = | NA (NA) | 13 (0.140) +GTCGTGCGCAG |
9/254 | 5.2 | NA | coding (243/297 nt) | yahH | putative uncharacterized protein YahH |
| ? | NC_000913 | 377433 = | NA (NA) | intergenic (+122/+102) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 4542682 = | 78 (0.800) | 10 (0.110) | 8/258 | 5.6 | 10.5% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 97 (1.060) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1207805 | 99 (1.010) | 6 (0.070) | 6/244 | 6.1 | 6.7% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 81 (0.940) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 375065 | NA (NA) | 3 (0.040) | 3/206 | 6.8 | NA | noncoding (34/34 nt) | other | REP31c |
| ? | NC_000913 | 3216680 = | NA (NA) | intergenic (‑189/‑99) | nfeF/nfeR | NADPH‑dependent ferric chelate reductase/DNA‑binding transcriptional repressor NfeR | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 13 (0.140) | 5/260 | 6.8 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377329 = | NA (NA) | intergenic (+18/+206) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||