mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 30 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,745,397 | 0 | A | C | 32.8% | 51.9 / 13.0 | 63 | L198F (TTA→TTC) | yiaN | 2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ membrane subunit |
| * | NC_000913 | 3,875,532 | 0 | A | T | 30.8% | 58.7 / 24.0 | 53 | H32L (CAT→CTT) ‡ | yidX | putative lipoprotein YidX |
| * | NC_000913 | 884,184 | 0 | A | G | 29.3% | 111.5 / 11.1 | 83 | E171G (GAG→GGG) | mdfA | multidrug efflux pump MdfA/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 4,101,525 | 0 | C | T | 29.3% | 68.8 / 10.9 | 42 | intergenic (+95/‑165) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 4,027,233 | 0 | T | A | 29.0% | 108.9 / 16.6 | 62 | intergenic (+5/+376) | fre/fadA | NAD(P)H‑flavin reductase/3‑ketoacyl‑CoA thiolase |
| * | NC_000913 | 1,222,233 | 0 | G | A | 28.9% | 64.3 / 14.2 | 46 | intergenic (+3032/+72) | ymgF/ymgD | inner membrane protein YmgF/PF16456 family protein YmgD |
| * | NC_000913 | 599,576 | 0 | T | G | 28.4% | 136.2 / 12.5 | 88 | V288G (GTG→GGG) | cusA | copper/silver export system RND permease |
| * | NC_000913 | 3,875,521 | 0 | T | C | 28.3% | 72.3 / 22.0 | 55 | A28A (GCT→GCC) | yidX | putative lipoprotein YidX |
| * | NC_000913 | 2,001,911 | 0 | G | A | 28.3% | 73.7 / 14.3 | 46 | intergenic (‑122/+1) | fliA/fliX | RNA polymerase sigma factor FliA/small RNA FliX |
| * | NC_000913 | 743,705 | 0 | T | G | 27.5% | 121.1 / 13.1 | 81 | V38G (GTG→GGG) | pxpB | 5‑oxoprolinase component B |
| * | NC_000913 | 2,370,266 | 0 | T | G | 25.3% | 168.9 / 16.1 | 84 | G83G (GGT→GGG) | arnD | putative 4‑deoxy‑4‑formamido‑L‑arabinose‑phosphoundecaprenol deformylase ArnD |
| * | NC_000913 | 3,875,524 | 0 | G | C | 25.0% | 106.1 / 21.1 | 56 | L29L (CTG→CTC) | yidX | putative lipoprotein YidX |
| * | NC_000913 | 4,161,142 | 0 | C | A | 25.0% | 132.3 / 18.2 | 80 | Q26K (CAA→AAA) | fabR | DNA‑binding transcriptional repressor FabR |
| * | NC_000913 | 883,936 | 0 | A | G | 24.7% | 130.9 / 10.6 | 76 | G88G (GGA→GGG) | mdfA | multidrug efflux pump MdfA/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 3,875,531 | 0 | C | T | 24.5% | 80.0 / 16.4 | 53 | H32Y (CAT→TAT) ‡ | yidX | putative lipoprotein YidX |
| * | NC_000913 | 4,561,215 | 0 | G | A | 24.2% | 120.1 / 13.0 | 62 | E96K (GAA→AAA) | kptA | RNA 2'‑phosphotransferase |
| * | NC_000913 | 4,098,391 | 0 | A | C | 24.1% | 184.2 / 12.6 | 115 | Y219S (TAC→TCC) | rhaS | DNA‑binding transcriptional activator RhaS |
| * | NC_000913 | 1,015,516 | 0 | G | T | 23.6% | 95.3 / 14.5 | 55 | intergenic (+57/‑199) | pqiC/rmf | intermembrane transport lipoprotein PqiC/ribosome modulation factor |
| * | NC_000913 | 3,875,525 | 0 | G | T | 23.6% | 82.2 / 13.0 | 56 | V30F (GTT→TTT) | yidX | putative lipoprotein YidX |
| * | NC_000913 | 3,382,613 | 0 | A | T | 23.6% | 120.9 / 13.9 | 74 | L138F (TTA→TTT) | degS | serine endoprotease |
| 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 | = 15911 | NA (NA) | 19 (0.210) +TTTTTTCAA |
17/476 | 3.7 | NA | noncoding (525/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 15922 = | NA (NA) | noncoding (536/1345 nt) | IS186 | repeat region | |||||
| * | ? | NC_000913 | 257908 = | NA (NA) | 8 (0.080) | 8/494 | 5.9 | 8.9% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 258921 = | 82 (0.850) | pseudogene (246/331 nt) | crl | RNA polymerase holoenzyme assembly factor Crl | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 5 (0.050) | 5/494 | 7.0 | 17.2% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 4580649 = | 24 (0.250) | coding (814/1395 nt) | hsdS | type I restriction enzyme EcoKI specificity subunit | |||||
| * | ? | NC_000913 | 1094245 = | NA (NA) | 5 (0.050) | 5/492 | 7.0 | 5.6% | noncoding (1258/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 3429990 | 84 (0.880) | coding (34/258 nt) | yrdB | DUF1488 domain‑containing protein YrdB | |||||
| * | ? | NC_000913 | = 3584195 | NA (NA) | 4 (0.040) | 4/494 | 7.5 | 7.4% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 4542150 = | 50 (0.520) | coding (114/597 nt) | fimE | regulator for fimA | |||||
| * | ? | NC_000913 | = 258675 | NA (NA) | 4 (0.040) | 4/494 | 7.5 | 100% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 362204 = | 0 (0.000) | coding (976/1254 nt) | lacY | lactose permease | |||||
| * | ? | NC_000913 | 2375828 = | 102 (1.080) | 3 (0.030) | 3/486 | 7.9 | 2.9% | coding (135/963 nt) | menC | o‑succinylbenzoate synthase |
| ? | NC_000913 | = 2515617 | NA (NA) | noncoding (1345/1345 nt) | IS186 | repeat region | |||||
| * | ? | NC_000913 | = 2067353 | NA (NA) | 3 (0.030) | 3/482 | 7.9 | 11.4% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 4580649 = | 24 (0.250) | coding (814/1395 nt) | hsdS | type I restriction enzyme EcoKI specificity subunit | |||||
| * | ? | NC_000913 | = 4123882 | 85 (0.890) | 3 (0.030) | 3/492 | 8.0 | 3.5% | coding (575/1026 nt) | cytR | DNA‑binding transcriptional repressor CytR |
| ? | NC_000913 | 4123887 = | 82 (0.860) | coding (570/1026 nt) | cytR | DNA‑binding transcriptional repressor CytR | |||||
| * | ? | NC_000913 | = 3350563 | 62 (0.650) | 3 (0.030) | 3/494 | 8.0 | 4.6% | intergenic (‑104/‑14) | elbB/arcZ | low activity glyoxalase ElbB/small regulatory RNA ArcZ |
| ? | NC_000913 | = 3584195 | NA (NA) | noncoding (768/768 nt) | IS1 | repeat region | |||||