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 36 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 300,772 | 0 | C | A | 55.7% | 18.5 / 255.0 | 131 | G55C (GGT→TGT) | paoC | aldehyde dehydrogenase: molybdenum cofactor‑binding subunit |
| * | NC_000913 | 4,604,344 | 0 | C | T | 45.8% | 107.6 / 113.2 | 131 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,568,504 | 0 | T | G | 39.1% | 218.5 / 51.2 | 164 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 1,068,173 | 0 | T | G | 36.8% | 130.2 / 46.9 | 95 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 3,943,488 | 0 | T | G | 33.3% | 44.3 / 15.5 | 39 | noncoding (54/76 nt) | gltU | tRNA‑Glu |
| * | NC_000913 | 4,111,747 | 0 | G | T | 32.8% | 124.0 / 35.7 | 58 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 29,496 | 0 | T | A | 30.8% | 186.4 / 50.2 | 91 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 3,206,435 | 0 | C | T | 30.3% | 129.3 / 45.8 | 77 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 650,809 | 0 | T | G | 29.3% | 423.9 / 79.0 | 229 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 445,558 | 0 | A | C | 27.9% | 219.8 / 62.1 | 122 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 3,206,444 | 0 | T | A | 27.6% | 156.3 / 28.6 | 76 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 1,775,467 | 0 | A | C | 27.1% | 161.3 / 14.6 | 85 | intergenic (+23/‑120) | aroD/ydiF | 3‑dehydroquinate dehydratase/putative acetate‑CoA transferase |
| * | NC_000913 | 2,001,918 | 0 | A | C | 27.0% | 221.8 / 39.2 | 111 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,296,060 | 0 | C | T | 26.9% | 340.0 / 120.2 | 171 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 1,271,822 | 0 | T | G | 26.5% | 142.4 / 10.6 | 68 | T10P (ACC→CCC) | chaA | Na(+)/K(+):H(+) antiporter ChaA |
| * | NC_000913 | 1,550,663 | 0 | A | C | 26.3% | 110.8 / 16.0 | 57 | N68T (AAC→ACC) | fdnH | formate dehydrogenase N subunit beta |
| * | NC_000913 | 2,628,625 | 0 | A | C | 25.0% | 157.1 / 15.0 | 72 | V105G (GTC→GGC) | pdeF | cyclic di‑GMP phosphodiesterase PdeF |
| * | NC_000913 | 4,568,512 | 0 | C | A | 24.8% | 298.7 / 43.1 | 102 | R3L (CGT→CTT) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 4,098,155 | 0 | A | C | 24.5% | 200.3 / 12.9 | 98 | L140F (TTA→TTC) | rhaS | DNA‑binding transcriptional activator RhaS |
| * | NC_000913 | 1,621,118 | 0 | A | C | 24.2% | 141.8 / 15.7 | 66 | V7G (GTG→GGG) | eamA | cysteine/O‑acetylserine exporter EamA |
| Marginal new junction evidence (lowest skew 10 of 26 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 375203 = | NA (NA) | 22 (0.200) | 10/216 | 5.7 | NA | noncoding (17/36 nt) | other | REP31f |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 375001 = | NA (NA) | 20 (0.180) | 9/216 | 6.0 | NA | noncoding (17/36 nt) | other | REP31b |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 11 (0.110) | 7/190 | 6.1 | 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 | 4542682 = | 108 (0.760) | 12 (0.090) | 11/258 | 6.2 | 9.8% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 121 (0.910) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 10 (0.100) | 7/202 | 6.4 | 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 | 2765420 = | 185 (1.300) | 4 (0.040) | 4/188 | 7.5 | 2.9% | intergenic (‑267/+93) | abpA/yfjM | CP4‑57 prophage; anti‑bacteriophage protein/CP4‑57 prophage; protein YfjM |
| ? | NC_000913 | = 2765411 | 140 (1.440) | intergenic (‑258/+102) | abpA/yfjM | CP4‑57 prophage; anti‑bacteriophage protein/CP4‑57 prophage; protein YfjM | |||||
| * | ? | NC_000913 | 1411899 = | 126 (0.880) | 7 (0.060) | 5/224 | 7.8 | 6.4% | coding (50/936 nt) | ttcA | tRNA cytosine(32) 2‑sulfurtransferase TtcA |
| ? | NC_000913 | = 1434958 | 102 (0.880) | pseudogene (51/51 nt) | ttcC | putative tRNA 2‑thiocytidine (s(2)C32) synthase | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 10 (0.070) | 6/260 | 8.1 | 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 | 340035 = | NA (NA) | 9 (0.060) | 6/274 | 8.4 | 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 | = 375160 | NA (NA) | 8 (0.060) +T |
5/274 | 8.9 | NA | noncoding (28/34 nt) | other | REP31e |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||