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 21 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 | 40.7% | 55.3 / 39.4 | 60 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,111,747 | 0 | G | T | 40.4% | 87.3 / 35.0 | 47 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 1,825,061 | 0 | G | A | 30.3% | 57.1 / 11.4 | 33 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 4,429,984 | 0 | T | G | 29.3% | 66.1 / 15.3 | 41 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 4,111,752 | 0 | T | C | 29.2% | 108.3 / 17.9 | 65 | K155E (AAA→GAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 3,206,435 | 0 | C | T | 26.7% | 51.8 / 11.3 | 30 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 1,068,173 | 0 | T | G | 24.6% | 116.0 / 16.9 | 61 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 445,558 | 0 | A | C | 24.4% | 84.3 / 12.1 | 46 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 650,809 | 0 | T | G | 24.4% | 154.9 / 22.1 | 82 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 753,125 | 0 | T | A | 24.1% | 121.5 / 16.1 | 54 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 372,640 | 0 | T | G | 23.5% | 136.1 / 14.1 | 68 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 4,101,525 | 0 | C | T | 23.4% | 143.7 / 10.3 | 64 | intergenic (+95/‑165) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 2,326,450 | 0 | T | G | 22.9% | 89.8 / 20.2 | 48 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 3,404,218 | 0 | T | G | 22.6% | 105.1 / 11.0 | 53 | G245G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 22.2% | 152.0 / 34.6 | 72 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 501,564 | 0 | A | C | 21.9% | 81.9 / 12.6 | 41 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| * | NC_000913 | 29,496 | 0 | T | A | 21.1% | 97.9 / 10.9 | 38 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 3,401,459 | 0 | T | C | 21.0% | 136.3 / 10.1 | 62 | D625G (GAT→GGT) | csrD | regulator of CsrB and CsrC decay |
| * | NC_000913 | 4,101,514 | 0 | G | T | 20.9% | 192.5 / 15.0 | 67 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 4,161,148 | 0 | G | A | 20.7% | 200.4 / 19.4 | 87 | E28K (GAA→AAA) | fabR | DNA‑binding transcriptional repressor FabR |
| Marginal new junction evidence (lowest skew 10 of 17 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4542682 = | 76 (0.990) | 11 (0.150) | 11/258 | 3.8 | 12.4% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 85 (1.190) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 1207790 = | 74 (0.960) | 12 (0.180) | 9/244 | 4.1 | 16.7% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 54 (0.800) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 758445 | NA (NA) | 16 (0.370) +60 bp |
4/156 | 4.2 | NA | noncoding (1/36 nt) | other | REP67a |
| ? | NC_000913 | = 2146639 | NA (NA) | intergenic (+56/+53) | dgcE/alkA | putative diguanylate cyclase DgcE/DNA‑3‑methyladenine glycosylase 2 | |||||
| * | ? | NC_000913 | 375023 = | NA (NA) | 8 (0.150) | 5/192 | 4.5 | NA | intergenic (+142/‑436) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377530 = | NA (NA) | intergenic (+219/+5) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 1207805 | 71 (0.930) | 6 (0.090) | 5/244 | 5.5 | 9.3% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 54 (0.800) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 3588424 = | 66 (0.860) | 5 (0.070) | 4/252 | 6.0 | 6.0% | coding (757/1071 nt) | ugpC | sn‑glycerol 3‑phosphate ABC transporter ATP binding subunit |
| ? | NC_000913 | 3589222 = | 96 (1.370) | coding (806/846 nt) | ugpE | sn‑glycerol 3‑phosphate ABC transporter membrane subunit UgpE | |||||
| * | ? | NC_000913 | = 4542690 | 67 (0.870) | 4 (0.060) | 4/258 | 6.1 | 5.1% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 85 (1.190) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4373261 = | NA (NA) | 5 (0.080) | 3/226 | 6.1 | NA | intergenic (+99/+104) | yjeI/yjeJ | DUF4156 domain‑containing lipoprotein YjeI/protein YjeJ |
| ? | NC_000913 | 4374533 = | NA (NA) | intergenic (‑299/+96) | yjeJ/epmB | protein YjeJ/lysine 2,3‑aminomutase | |||||
| * | ? | NC_000913 | 377321 = | NA (NA) | 5 (0.070) | 4/268 | 6.3 | NA | intergenic (+10/+214) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB |
| ? | NC_000913 | = 508817 | NA (NA) | noncoding (2/34 nt) | other | REP48e | |||||
| * | ? | NC_000913 | 375248 = | NA (NA) | 6 (0.090) | 3/238 | 6.3 | NA | noncoding (15/34 nt) | other | REP31g |
| ? | NC_000913 | 377507 = | NA (NA) | noncoding (16/34 nt) | other | REP32d | |||||