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 29 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 | 34.1% | 119.7 / 43.0 | 85 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 646,747 | 0 | T | G | 32.6% | 61.6 / 33.4 | 46 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 4,111,752 | 0 | T | C | 31.2% | 80.0 / 12.4 | 48 | K155E (AAA→GAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 3,206,435 | 0 | C | T | 31.1% | 70.6 / 27.6 | 45 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 2,001,918 | 0 | A | C | 30.5% | 105.8 / 23.1 | 59 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 1,825,061 | 0 | G | A | 30.3% | 62.2 / 12.6 | 33 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 4,568,504 | 0 | T | G | 30.2% | 268.1 / 21.1 | 141 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 650,809 | 0 | T | G | 27.1% | 117.8 / 12.6 | 59 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 4,111,747 | 0 | G | T | 27.0% | 99.6 / 17.0 | 37 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 3,556,207 | 0 | T | C | 26.8% | 78.8 / 10.2 | 41 | S215G (AGT→GGT) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 25.4% | 127.5 / 36.4 | 67 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 753,125 | 0 | T | A | 25.4% | 167.2 / 23.2 | 71 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,628,649 | 0 | A | C | 24.4% | 93.7 / 13.6 | 45 | intergenic (+102/+206) | nadR/ettA | DNA‑binding transcriptional repressor/NMN adenylyltransferase NadR/energy‑dependent translational throttle protein EttA |
| * | NC_000913 | 4,296,060 | 0 | C | T | 24.2% | 199.3 / 53.7 | 95 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,580,095 | 0 | A | C | 24.1% | 126.2 / 10.3 | 58 | G456G (GGT→GGG) | hsdS | type I restriction enzyme EcoKI specificity protein |
| * | NC_000913 | 3,206,444 | 0 | T | A | 24.0% | 105.1 / 20.0 | 50 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 646,760 | 0 | T | C | 23.7% | 71.6 / 11.9 | 38 | K250K (AAA→AAG) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 372,640 | 0 | T | G | 23.0% | 157.3 / 15.0 | 74 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 729,659 | 0 | T | G | 22.5% | 157.2 / 13.6 | 71 | V26G (GTA→GGA) | rhsC | rhs element protein RhsC |
| * | NC_000913 | 175,694 | 0 | T | G | 22.0% | 131.9 / 12.4 | 59 | G196G (GGT→GGG) | clcA | chloride:H(+) antiporter ClcA |
| Marginal new junction evidence (lowest skew 10 of 12 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4542682 = | 65 (0.720) | 12 (0.140) | 10/258 | 5.3 | 14.3% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 83 (0.990) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 3555970 = | 94 (1.040) | 8 (0.090) | 8/274 | 6.3 | 7.8% | coding (880/1017 nt) | rtcA | RNA 3'‑terminal phosphate cyclase |
| ? | NC_000913 | 3560457 = | 95 (1.060) | pseudogene (149/758 nt) | glpR | DNA‑binding transcriptional repressor GlpR | |||||
| * | ? | NC_000913 | = 4542690 | 64 (0.710) | 7 (0.080) | 7/258 | 6.4 | 9.0% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 82 (0.970) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 608007 = | NA (NA) | 6 (0.080) | 4/224 | 7.2 | 8.7% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 63 (0.860) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | 3279982 = | 77 (0.850) | 4 (0.050) | 4/262 | 7.9 | 5.1% | coding (1069/1281 nt) | kbaZ | tagatose‑1,6‑bisphosphate aldolase 1 subunit KbaZ |
| ? | NC_000913 | 3280074 = | 75 (0.880) | coding (1161/1281 nt) | kbaZ | tagatose‑1,6‑bisphosphate aldolase 1 subunit KbaZ | |||||
| * | ? | NC_000913 | = 2818188 | 101 (1.120) | 3 (0.040) +GTAAAGTAAGTTTCCCGA |
3/240 | 8.1 | 3.2% | intergenic (‑53/+10) | argZ/argY | tRNA‑Arg/tRNA‑Arg |
| ? | NC_000913 | = 2818550 | 106 (1.180) | intergenic (‑1/+3) | argV/serV | tRNA‑Arg/tRNA‑Ser | |||||
| * | ? | NC_000913 | = 156439 | 119 (1.320) | 4 (0.040) | 4/274 | 8.2 | 3.3% | coding (445/585 nt) | yadN | putative fimbrial protein YadN |
| ? | NC_000913 | 156443 = | 119 (1.330) | coding (441/585 nt) | yadN | putative fimbrial protein YadN | |||||
| * | ? | NC_000913 | = 375334 | NA (NA) | 3 (0.040) | 3/252 | 8.3 | NA | intergenic (+453/‑125) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 3392260 = | NA (NA) | noncoding (1/34 nt) | other | REP245e | |||||
| * | ? | NC_000913 | 272209 = | 122 (1.350) | 6 (0.070) | 3/258 | 8.5 | 5.0% | intergenic (+19/‑371) | insN/eyeA | CP4‑6 prophage; IS911A regulator fragment/CP4‑6 prophage; small RNA EyeA |
| ? | NC_000913 | 272342 = | 115 (1.360) | intergenic (+152/‑238) | insN/eyeA | CP4‑6 prophage; IS911A regulator fragment/CP4‑6 prophage; small RNA EyeA | |||||
| * | ? | NC_000913 | 230882 = | 71 (0.790) | 3 (0.040) | 3/260 | 8.5 | 3.9% | intergenic (‑1/‑240) | yafC/yafD | putative LysR family transcriptional regulator YafC/endonuclease/exonuclease/phosphatase domain‑containing protein YafD |
| ? | NC_000913 | 230989 = | 82 (0.970) | intergenic (‑108/‑133) | yafC/yafD | putative LysR family transcriptional regulator YafC/endonuclease/exonuclease/phosphatase domain‑containing protein YafD | |||||