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 24 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,604,344 | 0 | C | T | 44.3% | 42.8 / 44.6 | 61 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 226,041 | 0 | G | . | 39.6% | 503.3 / inf | 235 | noncoding (283/2904 nt) | rrlH | 23S ribosomal RNA |
| * | NC_000913 | 226,042 | 0 | T | . | 39.6% | 465.6 / inf | 235 | noncoding (284/2904 nt) | rrlH | 23S ribosomal RNA |
| * | NC_000913 | 3,556,207 | 0 | T | C | 37.5% | 66.7 / 31.1 | 56 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 3,556,205 | 0 | A | C | 36.8% | 75.9 / 24.9 | 57 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 1,825,061 | 0 | G | A | 36.4% | 42.1 / 20.2 | 33 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 3,206,435 | 0 | C | T | 35.9% | 67.7 / 37.1 | 53 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,101,507 | 0 | T | G | 33.9% | 95.2 / 17.0 | 63 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 650,809 | 0 | T | G | 31.5% | 75.9 / 20.8 | 54 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 2,001,918 | 0 | A | C | 30.8% | 82.1 / 18.3 | 52 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 372,640 | 0 | T | G | 29.8% | 72.3 / 16.6 | 47 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 3,206,444 | 0 | T | A | 29.6% | 90.1 / 27.2 | 54 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,111,747 | 0 | G | T | 28.8% | 138.8 / 26.3 | 52 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,296,060 | 0 | C | T | 28.6% | 161.5 / 66.7 | 91 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,568,504 | 0 | T | G | 28.3% | 184.1 / 12.9 | 99 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 753,125 | 0 | T | A | 27.8% | 121.4 / 18.6 | 54 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 27.8% | 86.7 / 28.7 | 54 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,101,514 | 0 | G | T | 26.6% | 175.5 / 18.9 | 64 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 29,496 | 0 | T | A | 23.8% | 103.1 / 11.0 | 42 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 3,240,985 | 0 | T | G | 23.7% | 119.3 / 12.6 | 59 | S348A (TCT→GCT) | sstT | serine/threonine:Na(+) 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 | = 374963 | NA (NA) | 7 (0.120) | 7/190 | 4.1 | 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 | = 1207805 | 86 (1.050) | 12 (0.170) | 10/244 | 4.2 | 14.0% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 72 (0.990) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 375102 = | NA (NA) | 19 (0.300) | 8/216 | 4.3 | NA | noncoding (17/36 nt) | other | REP31d |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | = 375246 | NA (NA) | 9 (0.120) +GAACGCCTTATCCGGT |
7/244 | 5.1 | NA | noncoding (13/34 nt) | other | REP31g |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | = 4542690 | 48 (0.580) | 6 (0.080) | 6/258 | 5.7 | 10.1% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 62 (0.810) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 375059 | NA (NA) | 6 (0.070) +T |
6/274 | 6.0 | NA | noncoding (28/34 nt) | other | REP31c |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 4 (0.070) | 3/202 | 6.1 | 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 | 4512054 = | 61 (0.740) | 4 (0.050) | 4/256 | 6.6 | 5.2% | coding (361/957 nt) | fecD | ferric citrate ABC transporter membrane subunit FecD |
| ? | NC_000913 | 4512149 = | 88 (1.160) | coding (266/957 nt) | fecD | ferric citrate ABC transporter membrane subunit FecD | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 5 (0.060) | 4/260 | 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 | = 374963 | NA (NA) | 4 (0.050) | 4/268 | 6.8 | NA | noncoding (33/34 nt) | other | REP31a |
| ? | NC_000913 | = 377387 | NA (NA) | intergenic (+76/+148) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||