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 | 3,364,975 | 1 | . | A | 46.5% | 392.6 / inf | 217 | coding (2169/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| * | NC_000913 | 4,604,344 | 0 | C | T | 39.4% | 70.1 / 46.7 | 66 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,111,747 | 0 | G | T | 36.7% | 54.4 / 17.8 | 30 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,568,504 | 0 | T | G | 35.9% | 112.4 / 10.8 | 64 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 4,296,060 | 0 | C | T | 32.7% | 78.2 / 46.3 | 55 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 3,206,435 | 0 | C | T | 32.4% | 47.0 / 17.7 | 34 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 1,825,061 | 0 | G | A | 32.1% | 41.9 / 13.3 | 28 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 3,556,205 | 0 | A | C | 31.7% | 80.5 / 11.0 | 41 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 2,001,918 | 0 | A | C | 30.8% | 72.1 / 13.4 | 39 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 3,556,207 | 0 | T | C | 29.3% | 74.4 / 10.0 | 41 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 753,125 | 0 | T | A | 28.6% | 70.6 / 13.1 | 35 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 26.1% | 95.1 / 20.0 | 46 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 376,401 | 0 | T | G | 25.9% | 107.1 / 12.7 | 54 | L315V (TTG→GTG) | mhpT | 3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| * | NC_000913 | 165,967 | 0 | C | T | 24.2% | 128.4 / 37.4 | 66 | A413V (GCC→GTC) | mrcB | peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcB |
| * | NC_000913 | 3,531,440 | 0 | A | C | 21.4% | 174.4 / 12.2 | 70 | Y334D (TAT→GAT) | yhgE | putative transport protein YhgE |
| * | NC_000913 | 4,492,710 | 0 | G | A | 21.4% | 117.9 / 26.2 | 56 | P214P (CCC→CCT) | idnO | 5‑keto‑D‑gluconate 5‑reductase |
| * | NC_000913 | 4,287,719 | 0 | T | A | 20.8% | 130.5 / 17.5 | 53 | intergenic (‑348/‑45) | acs/nrfA | acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase |
| 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 | = 4542690 | 35 (0.520) | 16 (0.260) | 13/258 | 3.0 | 27.9% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 50 (0.800) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 375165 | NA (NA) | 7 (0.150) | 7/192 | 3.6 | NA | noncoding (33/34 nt) | other | REP31e |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 375064 | NA (NA) | 8 (0.170) | 7/192 | 3.6 | NA | noncoding (33/34 nt) | other | REP31c |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 4373261 = | NA (NA) | 19 (0.350) | 7/226 | 4.1 | NA | intergenic (+99/+104) | yjeI/yjeJ | DUF4156 domain‑containing lipoprotein YjeI/protein YjeJ |
| ? | NC_000913 | 4374533 = | NA (NA) | intergenic (‑299/+96) | yjeJ/epmB | protein YjeJ/lysine 2,3‑aminomutase | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 13 (0.270) | 6/202 | 4.1 | 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 | = 375160 | NA (NA) | 12 (0.180) +T |
9/274 | 4.2 | NA | noncoding (28/34 nt) | other | REP31e |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 608007 = | NA (NA) | 6 (0.110) | 5/224 | 4.9 | 10.2% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 53 (0.980) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | 375082 = | NA (NA) | 11 (0.190) | 5/238 | 5.1 | NA | intergenic (+201/‑377) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377372 = | NA (NA) | noncoding (37/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | = 375261 | NA (NA) | 8 (0.120) +T |
6/274 | 5.2 | NA | noncoding (28/34 nt) | other | REP31g |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 375124 = | NA (NA) | 4 (0.090) | 3/192 | 5.2 | NA | intergenic (+243/‑335) | 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 | |||||