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 31 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 | 43.2% | 80.5 / 60.0 | 88 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 646,747 | 0 | T | G | 35.1% | 82.1 / 32.6 | 57 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 35.0% | 98.7 / 74.2 | 81 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 3,206,435 | 0 | C | T | 34.5% | 62.3 / 31.5 | 55 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 2,001,918 | 0 | A | C | 32.1% | 94.4 / 23.7 | 56 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 1,293,599 | 0 | A | G | 31.2% | 118.6 / 77.4 | 93 | N25D (AAT→GAT) | tdk | thymidine/deoxyuridine kinase |
| * | NC_000913 | 4,101,514 | 0 | G | T | 30.9% | 121.7 / 27.6 | 55 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 4,223,593 | 0 | T | G | 29.4% | 135.7 / 11.6 | 68 | K12N (AAA→AAC) | iclR | DNA‑binding transcriptional repressor IclR |
| * | NC_000913 | 29,496 | 0 | T | A | 29.3% | 126.8 / 24.8 | 58 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 4,111,747 | 0 | G | T | 29.2% | 115.7 / 21.6 | 48 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 3,206,444 | 0 | T | A | 28.3% | 84.3 / 20.6 | 53 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,568,504 | 0 | T | G | 28.2% | 222.4 / 15.1 | 110 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 2,326,450 | 0 | T | G | 28.1% | 120.5 / 31.4 | 64 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 370,876 | 0 | C | G | 27.7% | 115.7 / 10.9 | 47 | S200R (AGC→AGG) ‡ | mhpB | 3‑carboxyethylcatechol 2,3‑dioxygenase |
| * | NC_000913 | 1,912,478 | 0 | C | T | 26.0% | 128.8 / 48.8 | 77 | Q33Q (CAG→CAA) | htpX | zinc dependent endoprotease |
| * | NC_000913 | 650,809 | 0 | T | G | 25.4% | 156.4 / 15.3 | 71 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 646,760 | 0 | T | C | 24.0% | 149.6 / 26.1 | 76 | K250K (AAA→AAG) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 4,287,719 | 0 | T | A | 23.5% | 161.7 / 23.6 | 68 | intergenic (‑348/‑45) | acs/nrfA | acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase |
| * | NC_000913 | 1,428,271 | 0 | A | C | 22.5% | 613.5 / 229.2 | 262 | S152S (TCT→TCG) | insH‑5 | Rac prophage; IS5 transposase and trans‑activator |
| * | NC_000913 | 4,098,155 | 0 | A | C | 22.2% | 271.2 / 11.3 | 117 | L140F (TTA→TTC) | rhaS | DNA‑binding transcriptional activator RhaS |
| Marginal new junction evidence (lowest skew 10 of 16 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 374963 | NA (NA) | 19 (0.280) | 12/188 | 3.3 | NA | noncoding (33/34 nt) | other | REP31a |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 1207805 | 102 (1.040) | 16 (0.190) | 15/242 | 3.7 | 16.3% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 74 (0.860) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 374921 = | NA (NA) | 10 (0.150) | 7/188 | 4.8 | NA | intergenic (+40/‑538) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377531 = | NA (NA) | intergenic (+220/+4) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 4542682 = | 45 (0.460) | 10 (0.110) | 9/256 | 5.5 | 15.7% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 65 (0.710) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 375023 = | NA (NA) | 8 (0.120) | 5/190 | 5.7 | 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 | = 375246 | NA (NA) | 8 (0.090) +GAACGCCTTATCCGGT |
6/242 | 6.3 | NA | noncoding (13/34 nt) | other | REP31g |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 375248 = | NA (NA) | 8 (0.100) | 5/236 | 6.6 | NA | noncoding (15/34 nt) | other | REP31g |
| ? | NC_000913 | 377507 = | NA (NA) | noncoding (16/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | = 4445546 | 105 (1.070) | 8 (0.080) | 6/274 | 6.9 | 7.1% | coding (1435/3780 nt) | tamB | translocation and assembly module subunit TamB |
| ? | NC_000913 | 4445550 = | 104 (1.060) | coding (1439/3780 nt) | tamB | translocation and assembly module subunit TamB | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 6 (0.080) | 3/200 | 6.9 | 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 | 374922 = | NA (NA) | 10 (0.110) | 5/258 | 7.0 | 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 | |||||