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 25 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 | 41.6% | 144.0 / 94.9 | 137 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,206,435 | 0 | C | T | 34.9% | 84.1 / 37.6 | 63 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 1,825,061 | 0 | G | A | 32.8% | 104.6 / 28.9 | 67 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 4,568,504 | 0 | T | G | 32.3% | 357.2 / 36.0 | 199 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 3,206,444 | 0 | T | A | 30.6% | 106.2 / 22.6 | 62 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 1,775,467 | 0 | A | C | 28.8% | 141.0 / 10.7 | 73 | intergenic (+23/‑120) | aroD/ydiF | 3‑dehydroquinate dehydratase/putative acetate‑CoA transferase |
| * | NC_000913 | 2,667,126 | 0 | A | C | 27.4% | 220.7 / 28.4 | 113 | Y241D (TAT→GAT) | hcaT | putative 3‑phenylpropionate transporter |
| * | NC_000913 | 501,575 | 0 | A | C | 27.4% | 122.7 / 23.3 | 62 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 4,101,507 | 0 | T | G | 27.1% | 196.4 / 13.9 | 96 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 4,628,649 | 0 | A | C | 26.8% | 156.2 / 10.5 | 71 | intergenic (+102/+206) | nadR/ettA | DNA‑binding transcriptional repressor/NMN adenylyltransferase NadR/energy‑dependent translational throttle protein EttA |
| * | NC_000913 | 650,809 | 0 | T | G | 26.0% | 204.1 / 18.8 | 100 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 25.7% | 132.4 / 40.0 | 70 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 372,640 | 0 | T | G | 25.4% | 263.5 / 27.9 | 122 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 501,564 | 0 | A | C | 25.4% | 136.7 / 29.4 | 67 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| * | NC_000913 | 4,101,514 | 0 | G | T | 24.2% | 254.2 / 39.0 | 95 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 3,556,207 | 0 | T | C | 23.7% | 118.5 / 14.8 | 59 | S215G (AGT→GGT) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 2,001,918 | 0 | A | C | 23.0% | 201.3 / 23.9 | 87 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,098,155 | 0 | A | C | 23.0% | 295.6 / 19.6 | 135 | L140F (TTA→TTC) | rhaS | DNA‑binding transcriptional activator RhaS |
| * | NC_000913 | 888,014 | 0 | T | G | 22.7% | 202.7 / 11.3 | 89 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 4,111,747 | 0 | G | T | 22.2% | 153.7 / 16.5 | 54 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| 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 | = 1207805 | 100 (0.740) | 24 (0.200) | 20/246 | 4.1 | 23.0% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 72 (0.600) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 1207790 = | 119 (0.880) | 18 (0.150) | 16/246 | 5.0 | 16.7% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 74 (0.620) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 4542690 | 93 (0.690) | 9 (0.070) | 9/260 | 7.4 | 8.8% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 99 (0.780) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 608007 = | NA (NA) | 15 (0.140) | 7/226 | 7.4 | 10.4% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 129 (1.180) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | 4542682 = | 101 (0.750) | 7 (0.060) | 7/260 | 8.2 | 6.8% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 99 (0.780) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 2728258 = | NA (NA) | 8 (0.060) | 7/264 | 8.3 | NA | noncoding (927/2904 nt) | rrlG | 23S ribosomal RNA |
| ? | NC_000913 | 2728336 = | NA (NA) | noncoding (849/2904 nt) | rrlG | 23S ribosomal RNA | |||||
| * | ? | NC_000913 | = 226685 | 52 (0.380) | 8 (0.060) | 7/264 | 8.3 | 14.0% | noncoding (927/2904 nt) | rrlH | 23S ribosomal RNA |
| ? | NC_000913 | 2728336 = | NA (NA) | noncoding (849/2904 nt) | rrlG | 23S ribosomal RNA | |||||
| * | ? | NC_000913 | 1992602 = | 125 (0.920) | 4 (0.030) | 4/258 | 9.7 | 3.1% | coding (216/549 nt) | pgsA | phosphatidylglycerophosphate synthase |
| ? | NC_000913 | 1992748 = | 131 (1.040) | coding (70/549 nt) | pgsA | phosphatidylglycerophosphate synthase | |||||
| * | ? | NC_000913 | = 3660514 | 170 (1.260) | 4 (0.030) | 4/264 | 9.8 | 2.5% | coding (101/3114 nt) | mdtF | multidrug efflux pump RND permease MdtF |
| ? | NC_000913 | = 3660571 | 157 (1.220) | coding (158/3114 nt) | mdtF | multidrug efflux pump RND permease MdtF | |||||
| * | ? | NC_000913 | 2066566 = | 37 (0.270) | 4 (0.030) | 4/268 | 9.9 | 10.1% | noncoding (788/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 2102304 = | NA (NA) | noncoding (640/1195 nt) | IS5 | repeat region | |||||