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 | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,604,344 | 0 | C | T | 34.6% | 104.3 / 39.0 | 78 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 2,001,918 | 0 | A | C | 30.2% | 168.8 / 25.9 | 86 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,568,504 | 0 | T | G | 27.4% | 162.5 / 12.8 | 84 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 753,125 | 0 | T | A | 25.4% | 150.6 / 16.8 | 63 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 23.7% | 73.4 / 11.9 | 38 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 29,496 | 0 | T | A | 23.2% | 137.2 / 16.6 | 56 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 4,101,514 | 0 | G | T | 22.0% | 158.2 / 19.9 | 59 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 4,429,984 | 0 | T | G | 21.7% | 162.2 / 14.4 | 70 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 3,401,459 | 0 | T | C | 21.4% | 144.9 / 10.0 | 70 | D625G (GAT→GGT) | csrD | regulator of CsrB and CsrC decay |
| * | NC_000913 | 2,326,450 | 0 | T | G | 21.2% | 153.4 / 22.4 | 66 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,111,747 | 0 | G | T | 21.1% | 103.7 / 11.6 | 38 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,512,048 | 0 | A | C | 20.0% | 166.3 / 10.5 | 70 | L123V (TTG→GTG) | fecD | ferric citrate ABC transporter membrane subunit FecD |
| Marginal new junction evidence (lowest skew 10 of 29 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 125 (1.290) | 17 (0.200) | 16/246 | 3.6 | 16.2% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 65 (0.760) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 4542690 | 76 (0.790) | 17 (0.190) | 17/260 | 3.7 | 16.2% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 105 (1.160) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1207805 | 119 (1.230) | 14 (0.160) | 13/246 | 4.3 | 14.2% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 64 (0.750) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 608007 = | NA (NA) | 4 (0.050) | 4/226 | 7.2 | 4.3% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 88 (1.120) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | 2010203 = | 72 (0.740) | 5 (0.060) | 5/258 | 7.4 | 4.9% | coding (383/669 nt) | yedK | putative SOS response‑associated peptidase YedK |
| ? | NC_000913 | 2010392 = | 129 (1.440) | coding (572/669 nt) | yedK | putative SOS response‑associated peptidase YedK | |||||
| * | ? | NC_000913 | = 715563 | 68 (0.700) | 4 (0.040) | 4/258 | 7.9 | 5.2% | coding (152/495 nt) | ybfP | lipoprotein YbfP |
| ? | NC_000913 | = 715719 | 82 (0.910) | coding (308/495 nt) | ybfP | lipoprotein YbfP | |||||
| * | ? | NC_000913 | 1459405 = | 33 (0.340) | 5 (0.050) | 4/278 | 8.3 | 7.6% | coding (352/1428 nt) | paaH | 3‑hydroxyadipyl‑CoA dehydrogenase |
| ? | NC_000913 | 1459517 = | 88 (0.910) | coding (464/1428 nt) | paaH | 3‑hydroxyadipyl‑CoA dehydrogenase | |||||
| * | ? | NC_000913 | = 3129024 | 115 (1.190) | 3 (0.030) | 3/256 | 8.4 | 2.8% | coding (753/765 nt) | glcC | DNA‑binding transcriptional dual regulator GlcC |
| ? | NC_000913 | = 3129141 | 101 (1.130) | coding (1075/1173 nt) | yghO | putative DNA‑binding transcriptional regulator YghO | |||||
| * | ? | NC_000913 | = 4409634 | 81 (0.840) | 3 (0.030) | 3/258 | 8.5 | 3.5% | coding (360/732 nt) | rlmB | 23S rRNA 2'‑O‑ribose G2251 methyltransferase |
| ? | NC_000913 | = 4409697 | 89 (0.990) | coding (423/732 nt) | rlmB | 23S rRNA 2'‑O‑ribose G2251 methyltransferase | |||||
| * | ? | NC_000913 | 1088466 = | 115 (1.190) | 4 (0.040) | 3/260 | 8.5 | 3.7% | coding (1392/2019 nt) | pgaB | poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine N‑deacetylase and beta‑1,6 glycoside hydrolase |
| ? | NC_000913 | 1088571 = | 102 (1.130) | coding (1287/2019 nt) | pgaB | poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine N‑deacetylase and beta‑1,6 glycoside hydrolase | |||||