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 27 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,568,504 | 0 | T | G | 34.3% | 107.9 / 16.3 | 70 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 29,496 | 0 | T | A | 32.2% | 114.9 / 31.0 | 59 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 3,206,435 | 0 | C | T | 32.2% | 90.3 / 38.8 | 59 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 1,825,061 | 0 | G | A | 32.1% | 98.2 / 24.6 | 56 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 372,640 | 0 | T | G | 30.9% | 93.7 / 17.3 | 55 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 4,604,344 | 0 | C | T | 30.4% | 111.6 / 32.7 | 69 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 2,001,918 | 0 | A | C | 28.8% | 125.7 / 22.8 | 67 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 2,326,450 | 0 | T | G | 28.3% | 106.2 / 31.9 | 60 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 3,206,444 | 0 | T | A | 27.9% | 117.6 / 26.2 | 61 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 3,745,397 | 0 | A | C | 26.8% | 97.7 / 10.5 | 56 | L198F (TTA→TTC) | yiaN | 2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ membrane subunit |
| * | NC_000913 | 3,240,985 | 0 | T | G | 26.4% | 106.3 / 16.0 | 53 | S348A (TCT→GCT) | sstT | serine/threonine:Na(+) symporter |
| * | NC_000913 | 888,014 | 0 | T | G | 26.2% | 123.1 / 12.9 | 61 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 646,747 | 0 | T | G | 26.2% | 81.0 / 15.9 | 42 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 1,068,173 | 0 | T | G | 25.8% | 129.4 / 17.6 | 62 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 1,825,056 | 0 | G | A | 25.5% | 105.7 / 12.4 | 47 | intergenic (‑119/+84) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 4,628,649 | 0 | A | C | 25.5% | 97.0 / 11.0 | 47 | intergenic (+102/+206) | nadR/ettA | DNA‑binding transcriptional repressor/NMN adenylyltransferase NadR/energy‑dependent translational throttle protein EttA |
| * | NC_000913 | 646,760 | 0 | T | C | 25.0% | 75.4 / 10.5 | 40 | K250K (AAA→AAG) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 4,568,512 | 0 | C | A | 25.0% | 136.2 / 19.3 | 48 | R3L (CGT→CTT) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 2,782,509 | 0 | A | C | 24.6% | 130.8 / 12.2 | 65 | V73G (GTA→GGA) | ypjA | adhesin‑like autotransporter YpjA |
| * | NC_000913 | 3,926,366 | 0 | A | C | 23.8% | 127.9 / 17.4 | 63 | G30G (GGT→GGG) | mioC | flavoprotein MioC |
| Marginal new junction evidence (lowest skew 10 of 16 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 608007 = | NA (NA) | 4 (0.070) | 4/224 | 6.8 | 5.6% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 68 (1.110) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | = 1876615 | 65 (0.860) | 4 (0.060) | 4/258 | 7.5 | 5.1% | coding (943/1182 nt) | nimT | 2‑nitroimidazole exporter |
| ? | NC_000913 | = 1876823 | 88 (1.240) | coding (1151/1182 nt) | nimT | 2‑nitroimidazole exporter | |||||
| * | ? | NC_000913 | 3392170 = | NA (NA) | 4 (0.050) +GCA |
4/270 | 7.7 | 5.8% | noncoding (2/34 nt) | other | REP245c |
| ? | NC_000913 | = 3392625 | 67 (0.880) | coding (3634/3801 nt) | yhdP | AsmA2 domain‑containing protein | |||||
| * | ? | NC_000913 | = 3367875 | 117 (1.540) | 4 (0.050) | 4/270 | 7.7 | 3.4% | coding (49/1128 nt) | yhcG | DUF1016 domain‑containing protein YhcG |
| ? | NC_000913 | 3367879 = | 115 (1.550) | coding (53/1128 nt) | yhcG | DUF1016 domain‑containing protein YhcG | |||||
| * | ? | NC_000913 | = 206980 | 80 (1.060) | 4 (0.050) | 4/276 | 7.8 | 4.9% | coding (1855/3483 nt) | dnaE | DNA polymerase III subunit alpha |
| ? | NC_000913 | 212761 = | 74 (0.980) | coding (431/1299 nt) | tilS | tRNA(Ile)‑lysidine synthetase | |||||
| * | ? | NC_000913 | = 65182 | 84 (1.110) | 4 (0.050) | 4/272 | 7.8 | 4.7% | coding (599/2352 nt) | polB | DNA polymerase II |
| ? | NC_000913 | = 65254 | 78 (1.040) | coding (527/2352 nt) | polB | DNA polymerase II | |||||
| * | ? | NC_000913 | 1992602 = | 67 (0.880) | 3 (0.040) | 3/256 | 8.0 | 4.1% | coding (216/549 nt) | pgsA | phosphatidylglycerophosphate synthase |
| ? | NC_000913 | 1992748 = | 77 (1.100) | coding (70/549 nt) | pgsA | phosphatidylglycerophosphate synthase | |||||
| * | ? | NC_000913 | = 4542690 | 70 (0.920) | 3 (0.040) | 3/258 | 8.1 | 4.3% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 69 (0.970) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 790031 = | 79 (1.040) | 3 (0.040) | 3/258 | 8.1 | 4.5% | coding (999/1047 nt) | galT | galactose‑1‑phosphate uridylyltransferase |
| ? | NC_000913 | 790126 = | 54 (0.760) | coding (904/1047 nt) | galT | galactose‑1‑phosphate uridylyltransferase | |||||
| * | ? | NC_000913 | 3782021 = | 90 (1.190) | 3 (0.040) | 3/266 | 8.2 | 3.6% | coding (542/822 nt) | cysE | serine acetyltransferase |
| ? | NC_000913 | 3782214 = | 74 (1.010) | coding (349/822 nt) | cysE | serine acetyltransferase | |||||