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 | 4,568,504 | 0 | T | G | 41.7% | 220.9 / 21.9 | 133 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 3,556,207 | 0 | T | C | 36.4% | 61.2 / 15.1 | 44 | S215G (AGT→GGT) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,604,344 | 0 | C | T | 36.3% | 136.8 / 66.7 | 113 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 445,558 | 0 | A | C | 28.8% | 122.4 / 20.8 | 59 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 4,296,060 | 0 | C | T | 27.9% | 158.2 / 60.6 | 86 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 501,575 | 0 | A | C | 26.7% | 102.0 / 13.6 | 45 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 4,111,747 | 0 | G | T | 26.0% | 132.7 / 18.5 | 50 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 2,001,918 | 0 | A | C | 25.8% | 141.7 / 23.0 | 62 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 3,926,366 | 0 | A | C | 25.7% | 244.5 / 21.8 | 105 | G30G (GGT→GGG) | mioC | flavoprotein MioC |
| * | NC_000913 | 650,809 | 0 | T | G | 25.0% | 189.6 / 18.9 | 81 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 1,491,098 | 0 | A | C | 23.7% | 285.2 / 10.2 | 114 | Y66S (TAC→TCC) | cybB | cytochrome b561 |
| * | NC_000913 | 1,825,061 | 0 | G | A | 23.1% | 149.1 / 17.4 | 65 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 3,206,435 | 0 | C | T | 22.2% | 114.5 / 16.0 | 54 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,101,514 | 0 | G | T | 21.7% | 191.3 / 20.0 | 69 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 1,491,103 | 0 | A | C | 21.4% | 301.0 / 13.0 | 117 | T68P (ACC→CCC) | cybB | cytochrome b561 |
| * | NC_000913 | 646,747 | 0 | T | G | 20.3% | 162.2 / 25.0 | 64 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| 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 | = 1207805 | 114 (0.940) | 19 (0.180) | 19/246 | 3.3 | 15.7% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 104 (0.970) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 4542690 | 109 (0.900) | 8 (0.070) | 7/260 | 6.7 | 6.8% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 117 (1.030) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 1411899 = | 143 (1.180) | 4 (0.040) | 4/226 | 7.4 | 3.2% | coding (50/936 nt) | ttcA | tRNA cytosine(32) 2‑sulfurtransferase TtcA |
| ? | NC_000913 | = 1434958 | 124 (1.260) | pseudogene (51/51 nt) | ttcC | putative tRNA 2‑thiocytidine (s(2)C32) synthase | |||||
| * | ? | NC_000913 | 1658189 = | 143 (1.180) | 4 (0.030) | 4/262 | 8.1 | 2.9% | coding (121/2427 nt) | ynfE | putative selenate reductase YnfE |
| ? | NC_000913 | = 1658185 | 129 (1.130) | coding (117/2427 nt) | ynfE | putative selenate reductase YnfE | |||||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 16 (0.130) | 4/278 | 8.4 | 14.9% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3701929 = | 91 (0.750) | coding (940/1005 nt) | dppF | dipeptide ABC transporter ATP binding subunit DppF | |||||
| * | ? | NC_000913 | = 555833 | 110 (0.900) | 3 (0.030) | 3/246 | 8.4 | 2.6% | coding (1223/1386 nt) | cysS | cysteine‑‑tRNA ligase |
| ? | NC_000913 | = 556784 | 129 (1.200) | coding (90/213 nt) | ybcJ | putative RNA‑binding protein YbcJ | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 20 (0.160) | 3/278 | 8.9 | 17.5% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3701932 | 94 (0.770) | coding (937/1005 nt) | dppF | dipeptide ABC transporter ATP binding subunit DppF | |||||
| * | ? | NC_000913 | = 412086 | 105 (0.860) | 3 (0.020) | 3/276 | 8.9 | 2.8% | coding (396/1185 nt) | araJ | putative transport protein AraJ |
| ? | NC_000913 | 412090 = | 107 (0.890) | coding (392/1185 nt) | araJ | putative transport protein AraJ | |||||