mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 22 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 753,125 | 0 | T | A | 35.3% | 77.1 / 26.1 | 51 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 34.6% | 103.3 / 53.9 | 78 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,604,344 | 0 | C | T | 34.5% | 120.7 / 47.2 | 87 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,296,060 | 0 | C | T | 32.2% | 129.2 / 75.6 | 90 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 3,556,207 | 0 | T | C | 31.4% | 80.9 / 19.8 | 51 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 770,897 | 0 | T | G | 30.9% | 117.8 / 16.1 | 68 | intergenic (+286/‑561) | mngB/cydA | alpha‑mannosidase/cytochrome bd‑I ubiquinol oxidase subunit I |
| * | NC_000913 | 3,556,205 | 0 | A | C | 30.6% | 80.7 / 21.9 | 49 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,111,747 | 0 | G | T | 28.1% | 146.1 / 26.8 | 57 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 2,628,625 | 0 | A | C | 27.1% | 112.4 / 22.3 | 59 | V105G (GTC→GGC) | pdeF | cyclic di‑GMP phosphodiesterase PdeF |
| * | NC_000913 | 445,558 | 0 | A | C | 26.9% | 87.1 / 27.5 | 52 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 4,287,719 | 0 | T | A | 25.6% | 176.6 / 37.8 | 86 | intergenic (‑348/‑45) | acs/nrfA | acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase |
| * | NC_000913 | 4,101,507 | 0 | T | G | 25.4% | 138.6 / 10.5 | 67 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 1,377,140 | 0 | A | C | 24.4% | 189.7 / 15.3 | 90 | K103N (AAA→AAC) | ycjS | putative oxidoreductase YcjS |
| * | NC_000913 | 1,550,663 | 0 | A | C | 23.5% | 105.9 / 11.5 | 51 | N68T (AAC→ACC) | fdnH | formate dehydrogenase N subunit beta |
| * | NC_000913 | 4,568,504 | 0 | T | G | 23.0% | 289.8 / 15.5 | 137 | 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 | 21.8% | 121.3 / 13.6 | 55 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 3,206,435 | 0 | C | T | 21.7% | 99.2 / 13.0 | 46 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 2,236,876 | 0 | A | C | 20.6% | 214.9 / 16.6 | 92 | V293G (GTA→GGA) | mglC | D‑galactose/methyl‑galactoside ABC transporter membrane subunit |
| * | NC_000913 | 3,404,218 | 0 | T | G | 20.5% | 180.0 / 16.7 | 78 | G245G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 375,100 | 1 | . | C | 20.2% | 246.5 / 90.6 | 94 | intergenic (+219/‑359) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| Marginal new junction evidence (lowest skew 10 of 22 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 142 (1.280) | 19 (0.190) | 14/244 | 4.1 | 15.7% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 78 (0.800) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 375023 = | NA (NA) | 25 (0.320) | 8/192 | 4.7 | 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 | = 374963 | NA (NA) | 16 (0.210) | 8/190 | 4.7 | 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) | 25 (0.330) | 8/190 | 4.7 | 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 | = 1207805 | 144 (1.300) | 11 (0.110) | 11/244 | 4.8 | 9.7% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 78 (0.800) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 4542690 | 62 (0.560) | 12 (0.120) | 11/258 | 5.1 | 14.6% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 82 (0.790) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 375248 = | NA (NA) | 25 (0.260) | 8/238 | 5.6 | NA | noncoding (15/34 nt) | other | REP31g |
| ? | NC_000913 | 377507 = | NA (NA) | noncoding (16/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 4542682 = | 66 (0.590) | 7 (0.070) | 7/258 | 6.3 | 8.9% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 82 (0.790) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 377321 = | NA (NA) | 15 (0.140) | 7/274 | 6.6 | NA | intergenic (+10/+214) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB |
| ? | NC_000913 | 4325851 = | NA (NA) | intergenic (‑110/+548) | yjdN/yjdM | conserved protein YjdN/conserved protein YjdM | |||||
| * | ? | NC_000913 | = 375160 | NA (NA) | 10 (0.090) +T |
7/274 | 6.6 | NA | noncoding (28/34 nt) | other | REP31e |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||