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 22 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 226,042 | 0 | T | . | 51.3% | 410.9 / inf | 270 | noncoding (284/2904 nt) | rrlH | 23S ribosomal RNA |
| * | NC_000913 | 226,041 | 0 | G | . | 51.1% | 416.9 / inf | 270 | noncoding (283/2904 nt) | rrlH | 23S ribosomal RNA |
| * | NC_000913 | 4,604,344 | 0 | C | T | 44.4% | 51.8 / 52.9 | 72 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 2,001,918 | 0 | A | C | 42.9% | 32.4 / 13.0 | 28 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 753,125 | 0 | T | A | 37.1% | 57.0 / 16.4 | 35 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,111,747 | 0 | G | T | 35.5% | 54.5 / 17.4 | 31 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 29,496 | 0 | T | A | 33.9% | 98.7 / 30.6 | 56 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 372,640 | 0 | T | G | 28.8% | 112.9 / 11.7 | 52 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 4,287,719 | 0 | T | A | 27.9% | 146.9 / 26.2 | 68 | intergenic (‑348/‑45) | acs/nrfA | acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase |
| * | NC_000913 | 646,747 | 0 | T | G | 27.8% | 75.6 / 10.1 | 36 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 4,340,050 | 0 | C | T | 26.8% | 87.4 / 34.1 | 56 | A158T (GCA→ACA) | adiA | arginine decarboxylase, degradative |
| * | NC_000913 | 445,558 | 0 | A | C | 25.8% | 58.1 / 12.1 | 31 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 3,404,218 | 0 | T | G | 25.5% | 102.1 / 11.3 | 47 | G245G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 3,401,459 | 0 | T | C | 25.0% | 115.3 / 10.9 | 60 | D625G (GAT→GGT) | csrD | regulator of CsrB and CsrC decay |
| * | NC_000913 | 4,101,514 | 0 | G | T | 25.0% | 126.8 / 18.9 | 52 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 1,577,123 | 0 | A | C | 23.9% | 171.2 / 10.5 | 71 | V166G (GTA→GGA) | yddB | putative TonB‑dependent receptor |
| * | NC_000913 | 646,760 | 0 | T | C | 23.7% | 73.9 / 11.3 | 38 | K250K (AAA→AAG) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 3,531,440 | 0 | A | C | 23.3% | 139.3 / 14.4 | 60 | Y334D (TAT→GAT) | yhgE | putative transport protein YhgE |
| * | NC_000913 | 2,326,450 | 0 | T | G | 21.9% | 94.5 / 15.0 | 41 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 2,782,509 | 0 | A | C | 21.8% | 207.7 / 15.9 | 87 | V73G (GTA→GGA) | ypjA | adhesin‑like autotransporter YpjA |
| Marginal new junction evidence (lowest skew 10 of 50 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 74 (1.000) | 14 (0.210) | 14/244 | 2.8 | 18.5% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 58 (0.890) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 375064 | NA (NA) | 13 (0.250) | 9/192 | 3.1 | 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 | 375183 = | NA (NA) | 16 (0.250) | 11/238 | 3.4 | NA | intergenic (+302/‑276) | 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 | 375124 = | NA (NA) | 21 (0.410) | 8/192 | 3.4 | 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 | |||||
| * | ? | NC_000913 | 375082 = | NA (NA) | 32 (0.500) | 9/238 | 3.9 | 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 | = 375165 | NA (NA) | 7 (0.140) | 6/192 | 4.1 | 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 | 375204 = | NA (NA) | 18 (0.240) +T |
9/274 | 4.4 | NA | noncoding (16/36 nt) | other | REP31f |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 340035 = | NA (NA) | 25 (0.340) | 9/274 | 4.4 | 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 | |||||
| * | ? | NC_000913 | = 25796 | NA (NA) | 12 (0.160) | 9/274 | 4.4 | NA | noncoding (1/34 nt) | other | REP2b |
| ? | NC_000913 | 377322 = | NA (NA) | intergenic (+11/+213) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 25 (0.360) | 8/260 | 4.5 | 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 | |||||