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 | 47.6% | 53.1 / 61.4 | 83 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 1,825,061 | 0 | G | A | 34.1% | 63.2 / 20.7 | 44 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 650,809 | 0 | T | G | 30.2% | 104.3 / 19.1 | 63 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 4,568,504 | 0 | T | G | 29.4% | 241.9 / 11.9 | 128 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 3,745,397 | 0 | A | C | 29.3% | 91.3 / 11.7 | 59 | L198F (TTA→TTC) | yiaN | 2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ membrane subunit |
| * | NC_000913 | 4,101,507 | 0 | T | G | 27.5% | 165.6 / 19.6 | 80 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 646,747 | 0 | T | G | 27.3% | 78.3 / 19.3 | 44 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 372,640 | 0 | T | G | 26.8% | 134.6 / 14.6 | 71 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 2,001,918 | 0 | A | C | 25.9% | 173.9 / 23.1 | 81 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,429,984 | 0 | T | G | 25.3% | 164.6 / 16.2 | 75 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 3,206,435 | 0 | C | T | 25.0% | 97.0 / 18.7 | 52 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,628,649 | 0 | A | C | 24.6% | 117.2 / 16.5 | 57 | intergenic (+102/+206) | nadR/ettA | DNA‑binding transcriptional repressor/NMN adenylyltransferase NadR/energy‑dependent translational throttle protein EttA |
| * | NC_000913 | 2,326,450 | 0 | T | G | 23.7% | 210.0 / 39.4 | 97 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 29,496 | 0 | T | A | 23.4% | 156.1 / 24.0 | 64 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 2,667,126 | 0 | A | C | 23.3% | 180.6 / 10.1 | 87 | Y241D (TAT→GAT) | hcaT | putative 3‑phenylpropionate transporter |
| * | NC_000913 | 888,014 | 0 | T | G | 22.0% | 249.6 / 16.6 | 109 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 4,296,060 | 0 | C | T | 22.0% | 280.0 / 69.1 | 132 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 3,401,459 | 0 | T | C | 21.9% | 142.0 / 14.0 | 73 | D625G (GAT→GGT) | csrD | regulator of CsrB and CsrC decay |
| * | NC_000913 | 3,844,219 | 0 | T | G | 20.9% | 195.5 / 14.4 | 86 | F86V (TTT→GTT) | adeD | adenine deaminase |
| Marginal new junction evidence (lowest skew 10 of 24 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4542682 = | 66 (0.640) | 19 (0.200) | 18/260 | 3.7 | 18.4% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 107 (1.120) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 1979486 = | 96 (0.940) | 25 (0.240) | 12/278 | 5.4 | 20.7% | intergenic (‑271/‑267) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | 2101749 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1979489 | 102 (1.000) | 20 (0.200) | 9/278 | 6.4 | 16.4% | intergenic (‑274/‑264) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 313038 = | 165 (1.620) | 6 (0.060) | 4/276 | 8.6 | 3.5% | intergenic (‑261/+103) | ykgM/ykgR | putative ribosomal protein/putative membrane protein YkgR |
| ? | NC_000913 | = 1050545 | NA (NA) | noncoding (768/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | 257908 = | NA (NA) | 6 (0.060) | 4/276 | 8.6 | 3.5% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 313038 = | 165 (1.620) | intergenic (‑261/+103) | ykgM/ykgR | putative ribosomal protein/putative membrane protein YkgR | |||||
| * | ? | NC_000913 | 4492072 = | 180 (1.760) | 3 (0.030) | 3/262 | 8.9 | 2.0% | coding (454/1320 nt) | idnT | L‑idonate/5‑ketogluconate/gluconate transporter |
| ? | NC_000913 | 4492182 = | 128 (1.330) | coding (344/1320 nt) | idnT | L‑idonate/5‑ketogluconate/gluconate transporter | |||||
| * | ? | NC_000913 | = 3251266 | 115 (1.120) | 3 (0.030) | 3/262 | 8.9 | 2.7% | coding (243/987 nt) | yqjG | glutathionyl‑hydroquinone reductase YqjG |
| ? | NC_000913 | = 3251301 | 104 (1.080) | coding (278/987 nt) | yqjG | glutathionyl‑hydroquinone reductase YqjG | |||||
| * | ? | NC_000913 | 297744 = | 87 (0.850) | 3 (0.030) | 3/260 | 8.9 | 3.5% | coding (48/411 nt) | yagP | putative LysR family substrate binding domain‑containing protein YagP |
| ? | NC_000913 | 297848 = | 82 (0.860) | coding (879/957 nt) | paoD | molybdenum cofactor insertion chaperone for PaoABC | |||||
| * | ? | NC_000913 | = 268964 | 121 (1.180) | 3 (0.030) | 3/262 | 8.9 | 2.6% | intergenic (‑4/+325) | ykfA/perR | CP4‑6 prophage; putative GTP‑binding protein YkfA/putative transcriptional regulator PerR |
| ? | NC_000913 | = 269030 | 110 (1.140) | intergenic (‑70/+259) | ykfA/perR | CP4‑6 prophage; putative GTP‑binding protein YkfA/putative transcriptional regulator PerR | |||||
| * | ? | NC_000913 | 4207171 = | 118 (1.150) | 3 (0.030) | 3/266 | 9.0 | 2.6% | coding (362/1590 nt) | purH | bifunctional AICAR transformylase/IMP cyclohydrolase |
| ? | NC_000913 | 4211347 = | NA (NA) | noncoding (1305/2904 nt) | rrlE | 23S ribosomal RNA | |||||