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 | 4,538,211 | 0 | G | T | 54.9% | 2.7 / 248.9 | 133 | F185L (TTC→TTA) | nanM | N‑acetylneuraminate mutarotase |
| * | NC_000913 | 4,604,344 | 0 | C | T | 39.5% | 151.1 / 77.7 | 124 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 1,825,061 | 0 | G | A | 35.0% | 85.4 / 34.9 | 60 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 2,001,918 | 0 | A | C | 32.6% | 167.7 / 41.5 | 89 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,111,747 | 0 | G | T | 32.4% | 149.1 / 43.9 | 68 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 3,556,205 | 0 | A | C | 28.8% | 133.0 / 12.8 | 59 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 29,496 | 0 | T | A | 28.1% | 197.5 / 41.7 | 96 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 3,206,435 | 0 | C | T | 25.7% | 133.0 / 29.6 | 70 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 2,326,450 | 0 | T | G | 24.5% | 219.2 / 50.5 | 98 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 1,491,098 | 0 | A | C | 24.4% | 270.2 / 20.6 | 119 | Y66S (TAC→TCC) | cybB | cytochrome b561 |
| * | NC_000913 | 4,628,649 | 0 | A | C | 24.1% | 202.1 / 19.8 | 83 | intergenic (+102/+206) | nadR/ettA | DNA‑binding transcriptional repressor/NMN adenylyltransferase NadR/energy‑dependent translational throttle protein EttA |
| * | NC_000913 | 4,568,504 | 0 | T | G | 23.6% | 422.5 / 23.6 | 180 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 175,694 | 0 | T | G | 23.6% | 258.0 / 14.2 | 106 | G196G (GGT→GGG) | clcA | chloride:H(+) antiporter ClcA |
| * | NC_000913 | 3,556,207 | 0 | T | C | 22.9% | 123.7 / 14.2 | 61 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 650,809 | 0 | T | G | 22.9% | 250.5 / 23.0 | 105 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 2,628,625 | 0 | A | C | 22.6% | 202.9 / 30.3 | 84 | V105G (GTC→GGC) | pdeF | cyclic di‑GMP phosphodiesterase PdeF |
| * | NC_000913 | 4,111,752 | 0 | T | C | 21.7% | 179.2 / 12.2 | 83 | K155E (AAA→GAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 445,558 | 0 | A | C | 21.1% | 175.1 / 22.2 | 71 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 4,223,593 | 0 | T | G | 20.9% | 348.0 / 13.6 | 134 | K12N (AAA→AAC) | iclR | DNA‑binding transcriptional repressor IclR |
| * | NC_000913 | 3,745,397 | 0 | A | C | 20.5% | 238.7 / 12.6 | 113 | L198F (TTA→TTC) | yiaN | 2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ membrane subunit |
| Marginal new junction evidence (lowest skew 10 of 27 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4542682 = | 101 (0.680) | 20 (0.140) | 17/258 | 5.9 | 16.2% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 113 (0.810) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 375102 = | NA (NA) | 15 (0.130) | 13/216 | 6.0 | NA | noncoding (17/36 nt) | other | REP31d |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | = 4542690 | 94 (0.630) | 16 (0.120) | 15/258 | 6.4 | 13.8% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 112 (0.810) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 375203 = | NA (NA) | 12 (0.100) | 11/216 | 6.6 | NA | noncoding (17/36 nt) | other | REP31f |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 375001 = | NA (NA) | 7 (0.060) | 6/216 | 8.7 | NA | noncoding (17/36 nt) | other | REP31b |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 2518092 = | 133 (0.890) | 7 (0.050) | 7/240 | 8.9 | 6.0% | noncoding (25/76 nt) | alaX | tRNA‑Ala |
| ? | NC_000913 | 2521076 = | 102 (0.790) | noncoding (26/76 nt) | valX | tRNA‑Val | |||||
| * | ? | NC_000913 | = 375160 | NA (NA) | 10 (0.070) +T |
7/274 | 9.7 | NA | noncoding (28/34 nt) | other | REP31e |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 3 (0.030) | 3/202 | 10.1 | 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 | = 3588435 | 146 (0.980) | 6 (0.040) | 5/252 | 10.3 | 3.4% | coding (746/1071 nt) | ugpC | sn‑glycerol 3‑phosphate ABC transporter ATP binding subunit |
| ? | NC_000913 | = 3589209 | 209 (1.540) | coding (819/846 nt) | ugpE | sn‑glycerol 3‑phosphate ABC transporter membrane subunit UgpE | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 5 (0.040) | 5/260 | 10.5 | 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 | |||||