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 21 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 | 38.5% | 119.8 / 61.3 | 104 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,556,205 | 0 | A | C | 35.1% | 58.7 / 11.2 | 37 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 753,125 | 0 | T | A | 34.4% | 102.9 / 30.3 | 61 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 3,556,207 | 0 | T | C | 30.8% | 62.1 / 12.0 | 39 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 2,001,918 | 0 | A | C | 30.4% | 96.6 / 23.8 | 56 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,568,504 | 0 | T | G | 30.4% | 202.0 / 21.0 | 113 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 4,032,731 | 0 | T | G | 29.5% | 113.7 / 13.7 | 61 | G80G (GGT→GGG) | yigZ | IMPACT family member YigZ |
| * | NC_000913 | 1,825,061 | 0 | G | A | 29.2% | 87.5 / 14.3 | 49 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 372,640 | 0 | T | G | 28.6% | 114.7 / 16.0 | 63 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 646,747 | 0 | T | G | 26.0% | 93.8 / 20.9 | 50 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 4,111,747 | 0 | G | T | 25.9% | 145.7 / 24.3 | 54 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,628,649 | 0 | A | C | 25.7% | 162.6 / 13.7 | 74 | intergenic (+102/+206) | nadR/ettA | DNA‑binding transcriptional repressor/NMN adenylyltransferase NadR/energy‑dependent translational throttle protein EttA |
| * | NC_000913 | 3,531,440 | 0 | A | C | 24.6% | 264.5 / 30.3 | 122 | Y334D (TAT→GAT) | yhgE | putative transport protein YhgE |
| * | NC_000913 | 3,206,435 | 0 | C | T | 24.5% | 103.1 / 19.7 | 53 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,223,593 | 0 | T | G | 24.2% | 210.0 / 16.9 | 91 | K12N (AAA→AAC) | iclR | DNA‑binding transcriptional repressor IclR |
| * | NC_000913 | 388,336 | 0 | A | C | 23.8% | 221.8 / 12.3 | 106 | N181T (AAC→ACC) | tauD | taurine dioxygenase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 23.5% | 235.8 / 65.9 | 115 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,429,984 | 0 | T | G | 21.1% | 229.4 / 18.0 | 95 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 753,114 | 0 | G | T | 21.0% | 160.6 / 10.2 | 62 | intergenic (‑319/+71) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 29,496 | 0 | T | A | 20.8% | 125.8 / 11.1 | 48 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| Marginal new junction evidence (lowest skew 10 of 24 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 115 (1.070) | 20 (0.210) | 19/246 | 3.3 | 18.1% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 80 (0.840) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 97 (0.900) | 16 (0.170) | 14/246 | 4.3 | 16.4% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 78 (0.820) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 4542690 | 80 (0.750) | 14 (0.140) | 14/260 | 4.6 | 14.6% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 89 (0.890) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 90 (0.840) | 10 (0.100) | 8/260 | 6.4 | 10.4% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 89 (0.890) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 12 (0.110) | 5/278 | 8.0 | 10.6% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1979489 | 101 (0.940) | intergenic (‑274/‑264) | insA‑5/uspC | IS1 protein InsA/universal stress protein C | |||||
| * | ? | NC_000913 | 802244 = | 129 (1.200) | 4 (0.040) | 4/256 | 8.1 | 3.5% | coding (358/1434 nt) | ybhI | putative tricarboxylate transporter |
| ? | NC_000913 | 802354 = | 102 (1.030) | coding (468/1434 nt) | ybhI | putative tricarboxylate transporter | |||||
| * | ? | NC_000913 | 3831969 = | 111 (1.030) | 4 (0.040) | 4/258 | 8.2 | 3.8% | coding (1513/1710 nt) | yicH | AsmA famly protein YicH |
| ? | NC_000913 | 3832036 = | 98 (0.980) | coding (1580/1710 nt) | yicH | AsmA famly protein YicH | |||||
| * | ? | NC_000913 | 4068618 = | 142 (1.320) | 3 (0.030) | 3/254 | 8.7 | 2.1% | coding (659/2037 nt) | yihQ | sulfoquinovosidase |
| ? | NC_000913 | 4068736 = | 153 (1.560) | coding (541/2037 nt) | yihQ | sulfoquinovosidase | |||||
| * | ? | NC_000913 | 3736656 = | 134 (1.250) | 3 (0.030) | 3/258 | 8.8 | 2.3% | coding (522/825 nt) | bax | putative glycoside hydrolase Bax |
| ? | NC_000913 | = 3736652 | 131 (1.320) | coding (526/825 nt) | bax | putative glycoside hydrolase Bax | |||||
| * | ? | NC_000913 | = 3499593 | 83 (0.770) | 3 (0.030) | 3/258 | 8.8 | 3.4% | coding (146/168 nt) | yhfL | DUF4223 domain‑containing lipoprotein YhfL |
| ? | NC_000913 | 3500068 = | 91 (0.910) | coding (159/1338 nt) | frlA | fructoselysine/psicoselysine transporter | |||||