mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 23 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 | 40.6% | 76.2 / 40.8 | 69 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 2,001,918 | 0 | A | C | 37.5% | 51.9 / 21.1 | 40 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,568,504 | 0 | T | G | 36.7% | 122.3 / 13.2 | 80 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 29,496 | 0 | T | A | 33.3% | 51.3 / 12.8 | 30 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 4,296,060 | 0 | C | T | 29.5% | 135.5 / 66.9 | 88 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 332,991 | 0 | G | T | 28.8% | 123.5 / 21.6 | 52 | L207F (TTG→TTT) | pdeL | DNA‑binding transcriptional activator/c‑di‑GMP phosphodiesterase PdeL |
| * | NC_000913 | 4,111,747 | 0 | G | T | 27.8% | 137.5 / 22.3 | 55 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 650,809 | 0 | T | G | 27.3% | 111.3 / 10.9 | 55 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 3,625,361 | 0 | T | C | 26.3% | 169.2 / 67.1 | 99 | N328N (AAT→AAC) | yhhI | putative transposase |
| * | NC_000913 | 3,926,366 | 0 | A | C | 25.0% | 163.7 / 17.0 | 76 | G30G (GGT→GGG) | mioC | flavoprotein MioC |
| * | NC_000913 | 3,625,364 | 0 | A | C | 24.7% | 155.9 / 88.9 | 93 | A329A (GCA→GCC) | yhhI | putative transposase |
| * | NC_000913 | 646,747 | 0 | T | G | 24.4% | 96.8 / 13.6 | 45 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 4,101,514 | 0 | G | T | 24.4% | 108.1 / 10.2 | 45 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 213,317 | 0 | G | A | 24.1% | 104.4 / 31.6 | 58 | P329P (CCG→CCA) | tilS | tRNA(Ile)‑lysidine synthetase |
| * | NC_000913 | 1,068,173 | 0 | T | G | 23.7% | 168.4 / 17.7 | 76 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 4,287,719 | 0 | T | A | 22.8% | 218.4 / 32.7 | 92 | intergenic (‑348/‑45) | acs/nrfA | acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 22.6% | 141.4 / 20.7 | 62 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,442,146 | 0 | A | G | 22.4% | 206.9 / 17.4 | 98 | S11P (TCC→CCC) | msrA | methionine sulfoxide reductase A |
| * | NC_000913 | 1,315,936 | 0 | T | A | 22.2% | 159.0 / 10.0 | 63 | K34* (AAA→TAA) | yciG | protein YciG |
| * | NC_000913 | 3,401,459 | 0 | T | C | 21.6% | 158.8 / 10.6 | 74 | D625G (GAT→GGT) | csrD | regulator of CsrB and CsrC decay |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1979489 | 65 (0.770) | 24 (0.290) | 15/276 | 3.1 | 27.0% | intergenic (‑274/‑264) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 4542682 = | 41 (0.490) | 12 (0.150) | 12/258 | 3.4 | 20.1% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 57 (0.730) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 1979486 = | 64 (0.760) | 25 (0.300) | 11/276 | 3.9 | 28.1% | 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 | 250706 = | 82 (0.980) | 4 (0.050) | 4/254 | 5.8 | 4.8% | pseudogene (635/756 nt) | lafU | flagellar system protein, promoterless fragment |
| ? | NC_000913 | 250755 = | 82 (1.060) | pseudogene (684/756 nt) | lafU | flagellar system protein, promoterless fragment | |||||
| * | ? | NC_000913 | = 1979489 | 65 (0.770) | 4 (0.050) | 4/276 | 6.1 | 5.8% | intergenic (‑274/‑264) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | = 2067353 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 2103191 = | 120 (1.430) | 3 (0.040) | 3/258 | 6.4 | 2.6% | pseudogene (199/446 nt) | wbbL | interrupted rhamnosyltransferase WbbL |
| ? | NC_000913 | = 2103187 | 115 (1.470) | pseudogene (203/446 nt) | wbbL | interrupted rhamnosyltransferase WbbL | |||||
| * | ? | NC_000913 | 3272338 = | 95 (1.130) | 3 (0.040) | 3/274 | 6.6 | 2.9% | coding (414/885 nt) | garR | tartronate semialdehyde reductase |
| ? | NC_000913 | 3272404 = | 104 (1.250) | coding (348/885 nt) | garR | tartronate semialdehyde reductase | |||||