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 34 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 | 40.8% | 122.2 / 90.9 | 121 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,943,488 | 0 | T | G | 33.3% | 53.2 / 10.9 | 42 | noncoding (54/76 nt) | gltU | tRNA‑Glu |
| * | NC_000913 | 2,326,450 | 0 | T | G | 32.0% | 131.7 / 68.9 | 100 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,101,507 | 0 | T | G | 30.1% | 121.3 / 13.5 | 73 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 753,125 | 0 | T | A | 29.7% | 193.6 / 40.6 | 91 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 1,825,061 | 0 | G | A | 29.6% | 99.9 / 19.2 | 54 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 650,809 | 0 | T | G | 29.0% | 151.1 / 35.9 | 93 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 4,111,747 | 0 | G | T | 29.0% | 165.6 / 33.6 | 62 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,568,504 | 0 | T | G | 28.9% | 229.4 / 17.5 | 128 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 3,556,207 | 0 | T | C | 28.6% | 111.3 / 23.1 | 63 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 3,745,397 | 0 | A | C | 28.0% | 124.9 / 10.8 | 75 | L198F (TTA→TTC) | yiaN | 2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ membrane subunit |
| * | NC_000913 | 4,429,984 | 0 | T | G | 27.8% | 164.1 / 43.1 | 97 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 1,550,663 | 0 | A | C | 27.7% | 109.8 / 20.3 | 65 | N68T (AAC→ACC) | fdnH | formate dehydrogenase N subunit beta |
| * | NC_000913 | 4,296,060 | 0 | C | T | 27.4% | 217.2 / 82.3 | 117 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 2,001,918 | 0 | A | C | 26.9% | 137.3 / 32.4 | 78 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 3,206,435 | 0 | C | T | 26.4% | 173.0 / 43.8 | 87 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 3,556,205 | 0 | A | C | 25.9% | 108.5 / 13.2 | 58 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 1,906,769 | 0 | A | C | 25.7% | 125.9 / 14.5 | 70 | Y98D (TAT→GAT) | rlmA | 23S rRNA m(1)G745 methyltransferase |
| * | NC_000913 | 1,491,098 | 0 | A | C | 24.4% | 167.2 / 16.8 | 90 | Y66S (TAC→TCC) | cybB | cytochrome b561 |
| * | NC_000913 | 4,628,649 | 0 | A | C | 23.7% | 156.8 / 14.0 | 76 | intergenic (+102/+206) | nadR/ettA | DNA‑binding transcriptional repressor/NMN adenylyltransferase NadR/energy‑dependent translational throttle protein EttA |
| Marginal new junction evidence (lowest skew 10 of 13 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4542682 = | 115 (0.880) | 9 (0.070) | 8/258 | 6.4 | 7.6% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 112 (0.920) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 1979486 = | 123 (0.950) | 41 (0.320) | 8/276 | 6.7 | 25.0% | intergenic (‑271/‑267) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | 2101749 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 4542690 | 108 (0.830) | 8 (0.070) | 7/258 | 6.8 | 7.0% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 112 (0.920) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4180665 = | 150 (1.150) | 5 (0.040) | 5/256 | 7.6 | 3.4% | coding (106/366 nt) | rplL | 50S ribosomal subunit protein L12 |
| ? | NC_000913 | = 4180661 | 144 (1.190) | coding (102/366 nt) | rplL | 50S ribosomal subunit protein L12 | |||||
| * | ? | NC_000913 | = 2070271 | NA (NA) | 5 (0.040) | 5/272 | 7.8 | 3.3% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 2313928 = | 145 (1.130) | coding (441/2673 nt) | rcsD | RcsD phosphotransferase | |||||
| * | ? | NC_000913 | = 3131340 | NA (NA) | 16 (0.120) | 5/276 | 7.9 | 16.5% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3145118 = | 81 (0.620) | coding (23/987 nt) | hybA | hydrogenase 2 iron‑sulfur protein | |||||
| * | ? | NC_000913 | 1363275 = | 89 (0.680) | 4 (0.030) | 4/276 | 8.4 | 4.0% | coding (533/1488 nt) | puuC | gamma‑glutamyl‑gamma‑aminobutyraldehyde dehydrogenase |
| ? | NC_000913 | = 1364505 | 103 (0.790) | coding (274/1281 nt) | puuB | gamma‑glutamylputrescine oxidase | |||||
| * | ? | NC_000913 | 1722616 = | 130 (1.000) | 3 (0.030) | 3/254 | 8.6 | 2.4% | coding (496/2013 nt) | ydhK | putative transporter YdhK |
| ? | NC_000913 | = 1722612 | 121 (1.010) | coding (492/2013 nt) | ydhK | putative transporter YdhK | |||||
| * | ? | NC_000913 | 3822609 = | 113 (0.870) | 3 (0.020) | 3/266 | 8.8 | 2.7% | coding (210/2109 nt) | spoT | bifunctional (p)ppGpp synthase/hydrolase SpoT |
| ? | NC_000913 | = 3822605 | 109 (0.870) | coding (206/2109 nt) | spoT | bifunctional (p)ppGpp synthase/hydrolase SpoT | |||||
| * | ? | NC_000913 | = 1427485 | 123 (0.950) | 3 (0.020) | 3/270 | 8.8 | 2.4% | pseudogene (97/210 nt) | lomR | Rac prophage; protein LomR_1 |
| ? | NC_000913 | 1427489 = | 122 (0.960) | pseudogene (101/210 nt) | lomR | Rac prophage; protein LomR_1 | |||||