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 | 46.8% | 83.9 / 84.3 | 109 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 2,001,918 | 0 | A | C | 38.2% | 91.6 / 34.0 | 68 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 1,825,061 | 0 | G | A | 33.3% | 70.2 / 26.6 | 51 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 4,568,504 | 0 | T | G | 30.1% | 258.0 / 24.4 | 137 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 4,101,507 | 0 | T | G | 28.4% | 128.0 / 11.8 | 67 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 3,206,435 | 0 | C | T | 28.1% | 109.1 / 29.4 | 64 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 372,640 | 0 | T | G | 26.7% | 116.6 / 10.4 | 60 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 501,564 | 0 | A | C | 26.3% | 111.9 / 21.7 | 57 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| * | NC_000913 | 3,404,218 | 0 | T | G | 26.0% | 200.0 / 30.0 | 96 | G245G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 4,101,514 | 0 | G | T | 25.8% | 160.1 / 20.6 | 63 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 753,125 | 0 | T | A | 25.5% | 108.0 / 14.8 | 51 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 3,404,215 | 0 | T | G | 22.7% | 208.4 / 28.9 | 97 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 650,809 | 0 | T | G | 22.2% | 304.0 / 35.2 | 135 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 4,429,984 | 0 | T | G | 21.7% | 195.8 / 19.4 | 84 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 646,747 | 0 | T | G | 21.7% | 135.7 / 19.1 | 60 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 2,628,625 | 0 | A | C | 21.1% | 128.0 / 11.3 | 57 | V105G (GTC→GGC) | pdeF | cyclic di‑GMP phosphodiesterase PdeF |
| * | NC_000913 | 2,667,126 | 0 | A | C | 20.2% | 206.4 / 13.0 | 89 | Y241D (TAT→GAT) | hcaT | putative 3‑phenylpropionate transporter |
| * | NC_000913 | 2,326,450 | 0 | T | G | 20.0% | 279.7 / 43.5 | 120 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 3,619,268 | 0 | T | G | 20.0% | 221.0 / 12.9 | 95 | V26G (GTA→GGA) | rhsB | rhs element protein RhsB |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4542690 | 59 (0.470) | 9 (0.080) | 9/260 | 6.7 | 10.3% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 101 (0.870) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1978494 | 0 (0.000) | 6 (0.050) | 6/278 | 8.2 | 100% | intergenic (‑297/+24) | flhD/insB‑5 | DNA‑binding transcriptional dual regulator FlhD/IS1 protein InsB |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 4530888 = | 201 (1.620) | 6 (0.050) | 5/274 | 8.6 | 2.6% | coding (764/1122 nt) | sgcX | KpLE2 phage‑like element; putative endoglucanase with Zn‑dependent exopeptidase domain |
| ? | NC_000913 | 4530978 = | 254 (2.070) | coding (674/1122 nt) | sgcX | KpLE2 phage‑like element; putative endoglucanase with Zn‑dependent exopeptidase domain | |||||
| * | ? | NC_000913 | 4542682 = | 75 (0.600) | 4 (0.030) | 4/260 | 8.9 | 4.5% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 101 (0.870) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 3410758 = | 131 (1.050) | 5 (0.040) | 4/268 | 9.0 | 3.8% | coding (479/966 nt) | dusB | tRNA‑dihydrouridine synthase B |
| ? | NC_000913 | 3410835 = | 126 (1.050) | coding (556/966 nt) | dusB | tRNA‑dihydrouridine synthase B | |||||
| * | ? | NC_000913 | = 2771913 | 146 (1.170) | 4 (0.030) | 4/272 | 9.1 | 3.0% | coding (242/315 nt) | yfjU | CP4‑57 prophage; ArsC family protein YfjU |
| ? | NC_000913 | 2772151 = | 114 (0.940) | coding (4/315 nt) | yfjU | CP4‑57 prophage; ArsC family protein YfjU | |||||
| * | ? | NC_000913 | = 3899536 | 121 (0.970) | 3 (0.030) | 3/260 | 9.5 | 2.7% | coding (1042/1170 nt) | yieL | putative hydrolase YieL |
| ? | NC_000913 | = 3900485 | 107 (0.920) | coding (93/1170 nt) | yieL | putative hydrolase YieL | |||||
| * | ? | NC_000913 | 3698967 = | 146 (1.170) | 6 (0.050) | 3/260 | 9.5 | 3.9% | coding (754/1680 nt) | bcsG | cellulose phosphoethanolamine transferase |
| ? | NC_000913 | 3699059 = | 156 (1.340) | coding (846/1680 nt) | bcsG | cellulose phosphoethanolamine transferase | |||||
| * | ? | NC_000913 | = 4448731 | 137 (1.100) | 4 (0.030) | 3/274 | 9.8 | 2.7% | coding (40/351 nt) | chpB | endoribonuclease toxin ChpB |
| ? | NC_000913 | = 4448784 | 148 (1.210) | coding (93/351 nt) | chpB | endoribonuclease toxin ChpB | |||||
| * | ? | NC_000913 | = 1978494 | 0 (0.000) | 3 (0.020) | 3/278 | 9.8 | 100% | intergenic (‑297/+24) | flhD/insB‑5 | DNA‑binding transcriptional dual regulator FlhD/IS1 protein InsB |
| ? | NC_000913 | = 2067353 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||