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 | 4,296,268 | 0 | T | C | 40.0% | 9.4 / 13.1 | 15 | intergenic (+474/+168) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,604,344 | 0 | C | T | 37.4% | 219.5 / 102.7 | 166 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 2,001,918 | 0 | A | C | 35.0% | 172.1 / 44.0 | 97 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 3,206,435 | 0 | C | T | 35.0% | 121.2 / 73.7 | 100 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,111,747 | 0 | G | T | 30.3% | 231.0 / 60.2 | 99 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 3,206,444 | 0 | T | A | 27.3% | 176.7 / 40.9 | 99 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,568,504 | 0 | T | G | 25.9% | 388.6 / 24.6 | 176 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 4,111,752 | 0 | T | C | 25.6% | 238.2 / 28.4 | 121 | K155E (AAA→GAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,287,719 | 0 | T | A | 25.4% | 285.4 / 69.0 | 142 | intergenic (‑348/‑45) | acs/nrfA | acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase |
| * | NC_000913 | 372,640 | 0 | T | G | 24.2% | 226.2 / 26.4 | 99 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 1,825,061 | 0 | G | A | 24.1% | 176.8 / 28.2 | 83 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 1,911,754 | 0 | T | G | 23.9% | 157.7 / 13.1 | 67 | T275P (ACC→CCC) | htpX | zinc dependent endoprotease |
| * | NC_000913 | 650,809 | 0 | T | G | 23.8% | 335.9 / 44.6 | 143 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 3,556,207 | 0 | T | C | 23.5% | 181.1 / 23.9 | 85 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 29,496 | 0 | T | A | 23.4% | 261.5 / 42.3 | 111 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 646,747 | 0 | T | G | 23.4% | 259.5 / 51.1 | 112 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 4,429,984 | 0 | T | G | 22.8% | 371.8 / 50.2 | 150 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 2,628,625 | 0 | A | C | 22.4% | 142.2 / 17.1 | 58 | V105G (GTC→GGC) | pdeF | cyclic di‑GMP phosphodiesterase PdeF |
| * | NC_000913 | 3,404,215 | 0 | T | G | 22.1% | 455.2 / 54.6 | 181 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 3,556,205 | 0 | A | C | 21.9% | 214.7 / 13.6 | 82 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| Marginal new junction evidence (lowest skew 10 of 36 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4542690 | 94 (0.500) | 31 (0.180) | 27/256 | 3.9 | 18.1% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 192 (1.100) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 115 (0.610) | 27 (0.150) | 21/256 | 4.9 | 15.3% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 192 (1.100) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 375102 = | NA (NA) | 12 (0.080) | 10/214 | 6.8 | NA | noncoding (17/36 nt) | other | REP31d |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 375203 = | NA (NA) | 9 (0.060) | 9/214 | 7.1 | NA | noncoding (17/36 nt) | other | REP31f |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 2765420 = | 249 (1.330) | 6 (0.050) | 6/186 | 7.6 | 3.3% | intergenic (‑267/+93) | abpA/yfjM | CP4‑57 prophage; anti‑bacteriophage protein/CP4‑57 prophage; protein YfjM |
| ? | NC_000913 | = 2765411 | 182 (1.430) | intergenic (‑258/+102) | abpA/yfjM | CP4‑57 prophage; anti‑bacteriophage protein/CP4‑57 prophage; protein YfjM | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 8 (0.060) | 6/188 | 7.7 | 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 | 375001 = | NA (NA) | 4 (0.030) | 4/214 | 9.4 | NA | noncoding (17/36 nt) | other | REP31b |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 3 (0.020) | 3/200 | 9.6 | 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 | = 16731 | NA (NA) | 4 (0.030) | 4/222 | 9.6 | 3.8% | noncoding (1345/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | = 2514272 | 100 (0.660) | intergenic (+28/‑59) | nupC/insL‑3 | nucleoside:H(+) symporter NupC/putative IS186/IS421 transposase | |||||
| * | ? | NC_000913 | 545672 = | 206 (1.100) | 5 (0.030) | 5/254 | 9.7 | 2.5% | coding (692/1050 nt) | allD | ureidoglycolate dehydrogenase |
| ? | NC_000913 | = 545668 | 197 (1.130) | coding (696/1050 nt) | allD | ureidoglycolate dehydrogenase | |||||