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 | 40.9% | 127.7 / 95.0 | 127 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 753,125 | 0 | T | A | 31.9% | 176.1 / 48.8 | 94 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 3,556,207 | 0 | T | C | 27.9% | 81.8 / 10.2 | 43 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 3,556,205 | 0 | A | C | 27.3% | 98.0 / 10.2 | 44 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 1,435,727 | 0 | G | A | 25.0% | 112.5 / 23.7 | 56 | intergenic (‑108/+33) | uspF/ompN | nucleotide binding filament protein/outer membrane porin N |
| * | NC_000913 | 3,740,909 | 0 | T | G | 24.7% | 165.9 / 15.1 | 73 | V402G (GTG→GGG) | avtA | valine‑‑pyruvate aminotransferase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 24.6% | 139.0 / 31.5 | 65 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 24.6% | 259.0 / 80.4 | 130 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,111,747 | 0 | G | T | 24.5% | 141.0 / 21.9 | 53 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 1,068,173 | 0 | T | G | 24.5% | 243.4 / 23.6 | 104 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 4,101,514 | 0 | G | T | 24.0% | 197.6 / 20.5 | 75 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 650,809 | 0 | T | G | 23.9% | 147.0 / 13.5 | 67 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 753,114 | 0 | G | T | 23.8% | 272.2 / 21.2 | 101 | intergenic (‑319/+71) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 1,550,663 | 0 | A | C | 23.5% | 117.6 / 15.9 | 51 | N68T (AAC→ACC) | fdnH | formate dehydrogenase N subunit beta |
| * | NC_000913 | 1,491,103 | 0 | A | C | 23.3% | 158.3 / 21.2 | 73 | T68P (ACC→CCC) | cybB | cytochrome b561 |
| * | NC_000913 | 3,206,435 | 0 | C | T | 22.4% | 102.5 / 13.3 | 49 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,568,504 | 0 | T | G | 22.3% | 303.1 / 19.0 | 133 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 2,001,918 | 0 | A | C | 20.6% | 180.5 / 11.2 | 68 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 3,926,366 | 0 | A | C | 20.4% | 267.6 / 24.3 | 108 | G30G (GGT→GGG) | mioC | flavoprotein MioC |
| Marginal new junction evidence (lowest skew 10 of 19 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 153 (1.320) | 20 (0.200) | 16/246 | 4.3 | 15.5% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 83 (0.810) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 147 (1.270) | 14 (0.140) | 14/246 | 4.8 | 11.7% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 81 (0.790) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 11 (0.140) | 8/192 | 5.5 | NA | noncoding (33/34 nt) | other | REP31a |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 374921 = | NA (NA) | 12 (0.150) | 7/192 | 5.9 | 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 | 374922 = | NA (NA) | 26 (0.240) | 9/262 | 6.7 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377329 = | NA (NA) | intergenic (+18/+206) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 340035 = | NA (NA) | 11 (0.100) | 8/276 | 7.3 | NA | coding (243/297 nt) | yahH | putative uncharacterized protein YahH |
| ? | NC_000913 | 377322 = | NA (NA) | intergenic (+11/+213) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 375023 = | NA (NA) | 9 (0.110) | 4/194 | 7.4 | 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 | 374922 = | NA (NA) | 6 (0.070) | 4/204 | 7.6 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377430 = | NA (NA) | intergenic (+119/+105) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 25796 | NA (NA) | 10 (0.090) | 7/276 | 7.7 | NA | noncoding (1/34 nt) | other | REP2b |
| ? | NC_000913 | 377322 = | NA (NA) | intergenic (+11/+213) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 375248 = | NA (NA) | 9 (0.090) | 4/240 | 8.5 | NA | noncoding (15/34 nt) | other | REP31g |
| ? | NC_000913 | 377507 = | NA (NA) | noncoding (16/34 nt) | other | REP32d | |||||