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 23 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 | 46.8% | 36.6 / 37.3 | 47 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 2,001,918 | 0 | A | C | 37.5% | 63.1 / 23.4 | 48 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 1,825,061 | 0 | G | A | 36.7% | 45.8 / 12.5 | 30 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 3,206,435 | 0 | C | T | 36.4% | 51.8 / 28.6 | 44 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 1,068,173 | 0 | T | G | 32.8% | 118.1 / 19.7 | 67 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 4,111,747 | 0 | G | T | 32.1% | 65.0 / 16.2 | 28 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,628,649 | 0 | A | C | 32.0% | 82.2 / 18.8 | 50 | intergenic (+102/+206) | nadR/ettA | DNA‑binding transcriptional repressor/NMN adenylyltransferase NadR/energy‑dependent translational throttle protein EttA |
| * | NC_000913 | 4,429,984 | 0 | T | G | 30.0% | 123.6 / 26.0 | 70 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 445,558 | 0 | A | C | 28.2% | 63.0 / 17.5 | 39 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 2,782,509 | 0 | A | C | 28.1% | 121.8 / 12.3 | 65 | V73G (GTA→GGA) | ypjA | adhesin‑like autotransporter YpjA |
| * | NC_000913 | 3,206,444 | 0 | T | A | 26.1% | 85.6 / 14.0 | 46 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 501,564 | 0 | A | C | 25.8% | 56.3 / 11.1 | 31 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| * | NC_000913 | 2,168,966 | 0 | A | C | 25.7% | 134.4 / 13.8 | 70 | I85I (ATA→ATC) | yegS | lipid kinase |
| * | NC_000913 | 3,404,215 | 0 | T | G | 24.6% | 139.7 / 24.1 | 69 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 1,621,118 | 0 | A | C | 24.4% | 77.4 / 11.8 | 41 | V7G (GTG→GGG) | eamA | cysteine/O‑acetylserine exporter EamA |
| * | NC_000913 | 3,404,218 | 0 | T | G | 23.9% | 138.6 / 17.5 | 67 | G245G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 3,401,459 | 0 | T | C | 23.8% | 159.2 / 18.4 | 81 | D625G (GAT→GGT) | csrD | regulator of CsrB and CsrC decay |
| * | NC_000913 | 29,496 | 0 | T | A | 23.6% | 138.5 / 18.6 | 55 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 650,809 | 0 | T | G | 23.6% | 187.0 / 19.1 | 89 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 21.6% | 108.2 / 18.9 | 51 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 374921 = | NA (NA) | 10 (0.200) | 5/190 | 4.8 | 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) | 4 (0.080) | 4/202 | 5.5 | 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 | 4542682 = | 78 (1.080) | 7 (0.100) | 6/258 | 5.6 | 9.0% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 68 (1.010) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 375023 = | NA (NA) | 8 (0.160) | 3/192 | 5.8 | 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 | 375248 = | NA (NA) | 8 (0.130) | 3/238 | 6.8 | NA | noncoding (15/34 nt) | other | REP31g |
| ? | NC_000913 | 377507 = | NA (NA) | noncoding (16/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | = 4598412 | 64 (0.890) | 4 (0.060) | 4/276 | 6.9 | 5.9% | coding (1030/2292 nt) | opgB | phosphoglycerol transferase I |
| ? | NC_000913 | 4598416 = | 63 (0.870) | coding (1026/2292 nt) | opgB | phosphoglycerol transferase I | |||||
| * | ? | NC_000913 | = 4542690 | 70 (0.970) | 3 (0.040) | 3/258 | 7.1 | 4.3% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 68 (1.010) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 806402 | 66 (0.910) | 3 (0.040) | 3/270 | 7.3 | 4.5% | coding (880/1284 nt) | ybhC | outer membrane lipoprotein YhbC |
| ? | NC_000913 | 806406 = | 64 (0.900) | coding (876/1284 nt) | ybhC | outer membrane lipoprotein YhbC | |||||
| * | ? | NC_000913 | 129294 = | 57 (0.790) | 3 (0.040) | 3/266 | 7.3 | 4.1% | coding (1383/1425 nt) | lpd | lipoamide dehydrogenase |
| ? | NC_000913 | = 3867271 | 86 (1.230) | coding (152/414 nt) | ibpA | small heat shock protein IbpA | |||||
| * | ? | NC_000913 | 340035 = | NA (NA) | 3 (0.040) | 3/274 | 7.4 | 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 | |||||