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 | 44.3% | 53.0 / 61.2 | 79 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 2,628,625 | 0 | A | C | 40.9% | 55.9 / 22.0 | 44 | V105G (GTC→GGC) | pdeF | cyclic di‑GMP phosphodiesterase PdeF |
| * | NC_000913 | 4,568,504 | 0 | T | G | 30.9% | 171.7 / 14.6 | 99 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 3,206,435 | 0 | C | T | 28.0% | 85.5 / 20.8 | 50 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,287,719 | 0 | T | A | 27.2% | 164.5 / 33.9 | 81 | intergenic (‑348/‑45) | acs/nrfA | acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase |
| * | NC_000913 | 650,809 | 0 | T | G | 25.7% | 149.3 / 13.2 | 70 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 2,782,509 | 0 | A | C | 25.3% | 182.5 / 17.8 | 87 | V73G (GTA→GGA) | ypjA | adhesin‑like autotransporter YpjA |
| * | NC_000913 | 2,001,918 | 0 | A | C | 24.5% | 117.3 / 14.9 | 54 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 175,694 | 0 | T | G | 23.9% | 200.6 / 16.4 | 92 | G196G (GGT→GGG) | clcA | chloride:H(+) antiporter ClcA |
| * | NC_000913 | 29,496 | 0 | T | A | 23.4% | 107.0 / 15.2 | 47 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 372,640 | 0 | T | G | 23.0% | 150.9 / 14.7 | 74 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 4,111,747 | 0 | G | T | 22.8% | 155.3 / 20.2 | 57 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 646,747 | 0 | T | G | 22.7% | 98.7 / 14.2 | 44 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 2,667,126 | 0 | A | C | 22.2% | 178.1 / 13.7 | 81 | Y241D (TAT→GAT) | hcaT | putative 3‑phenylpropionate transporter |
| * | NC_000913 | 4,296,060 | 0 | C | T | 22.1% | 216.3 / 55.5 | 104 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 3,404,215 | 0 | T | G | 21.1% | 134.0 / 11.6 | 57 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| Marginal new junction evidence (lowest skew 10 of 21 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 608007 = | NA (NA) | 18 (0.250) | 12/226 | 3.9 | 18.4% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 80 (1.110) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | 4542682 = | 87 (0.980) | 14 (0.170) | 13/260 | 4.3 | 14.0% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 91 (1.100) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 374921 = | NA (NA) | 6 (0.100) | 5/192 | 5.7 | 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 | 375023 = | NA (NA) | 7 (0.110) | 4/194 | 6.2 | 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 | 375248 = | NA (NA) | 9 (0.120) | 6/240 | 6.3 | NA | noncoding (15/34 nt) | other | REP31g |
| ? | NC_000913 | 377507 = | NA (NA) | noncoding (16/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | = 3686344 | 106 (1.190) | 4 (0.050) | 4/258 | 7.6 | 4.2% | coding (2830/3474 nt) | bcsC | cellulose biosynthesis protein BcsC |
| ? | NC_000913 | = 3686424 | 82 (1.000) | coding (2750/3474 nt) | bcsC | cellulose biosynthesis protein BcsC | |||||
| * | ? | NC_000913 | 2899588 = | 114 (1.280) | 4 (0.050) | 4/258 | 7.6 | 3.6% | coding (686/786 nt) | ygcW | putative deoxygluconate dehydrogenase |
| ? | NC_000913 | 2899697 = | 110 (1.340) | coding (577/786 nt) | ygcW | putative deoxygluconate dehydrogenase | |||||
| * | ? | NC_000913 | = 1049984 | NA (NA) | 5 (0.060) | 4/260 | 7.6 | 17.1% | noncoding (207/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 3583540 | 26 (0.290) | noncoding (113/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | 2086550 = | 98 (1.100) | 4 (0.050) | 4/270 | 7.8 | 4.5% | coding (513/1359 nt) | plaP | putrescine:H(+) symporter PlaP |
| ? | NC_000913 | = 2087351 | 74 (0.860) | coding (908/930 nt) | yeeY | putative DNA‑binding transcriptional regulator YeeY | |||||
| * | ? | NC_000913 | 729960 = | NA (NA) | 3 (0.040) | 3/256 | 8.1 | NA | coding (378/4194 nt) | rhsC | rhs element protein RhsC |
| ? | NC_000913 | 732054 = | NA (NA) | coding (2472/4194 nt) | rhsC | rhs element protein RhsC | |||||