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 30 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 | 41.6% | 86.6 / 62.0 | 89 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 2,001,918 | 0 | A | C | 35.3% | 87.4 / 22.1 | 51 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 1,825,061 | 0 | G | A | 34.9% | 58.9 / 20.8 | 43 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 3,556,205 | 0 | A | C | 34.8% | 82.5 / 15.4 | 46 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 2,667,126 | 0 | A | C | 32.8% | 118.9 / 23.1 | 67 | Y241D (TAT→GAT) | hcaT | putative 3‑phenylpropionate transporter |
| * | NC_000913 | 3,556,207 | 0 | T | C | 32.6% | 74.6 / 21.3 | 49 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,111,747 | 0 | G | T | 31.5% | 109.4 / 36.0 | 54 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 445,558 | 0 | A | C | 28.9% | 68.9 / 18.9 | 38 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 2,326,450 | 0 | T | G | 28.8% | 124.7 / 35.6 | 67 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 28.2% | 197.0 / 80.6 | 110 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 3,404,215 | 0 | T | G | 27.1% | 140.6 / 32.6 | 70 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 4,568,504 | 0 | T | G | 26.4% | 292.4 / 17.1 | 130 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 4,111,752 | 0 | T | C | 25.4% | 129.2 / 12.1 | 67 | K155E (AAA→GAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 3,404,218 | 0 | T | G | 24.3% | 158.2 / 18.3 | 70 | G245G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 1,068,173 | 0 | T | G | 24.3% | 242.2 / 30.4 | 103 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 372,640 | 0 | T | G | 24.2% | 145.5 / 12.9 | 62 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 4,429,984 | 0 | T | G | 24.2% | 147.7 / 15.3 | 62 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 1,377,140 | 0 | A | C | 24.1% | 204.0 / 15.7 | 87 | K103N (AAA→AAC) | ycjS | putative oxidoreductase YcjS |
| * | NC_000913 | 501,575 | 0 | A | C | 23.8% | 96.5 / 10.3 | 42 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 2,236,876 | 0 | A | C | 23.8% | 181.0 / 25.9 | 80 | V293G (GTA→GGA) | mglC | D‑galactose/methyl‑galactoside ABC transporter membrane subunit |
| 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 | = 1207805 | 110 (1.010) | 23 (0.240) | 22/244 | 2.9 | 19.9% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 88 (0.910) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 7 (0.090) | 6/190 | 5.9 | NA | noncoding (33/34 nt) | other | REP31a |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 4542682 = | 76 (0.700) | 7 (0.070) | 7/258 | 6.9 | 8.5% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 79 (0.770) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 6 (0.080) | 4/202 | 7.2 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377430 = | NA (NA) | intergenic (+119/+105) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 5 (0.050) | 5/268 | 8.0 | NA | noncoding (33/34 nt) | other | REP31a |
| ? | NC_000913 | = 377387 | NA (NA) | intergenic (+76/+148) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 66625 | NA (NA) | 3 (0.030) | 3/236 | 8.5 | NA | noncoding (19/36 nt) | other | REP6b |
| ? | NC_000913 | = 72153 | NA (NA) | noncoding (17/37 nt) | other | REP7a | |||||
| * | ? | NC_000913 | 3736656 = | 161 (1.470) | 4 (0.040) | 3/256 | 8.9 | 2.5% | coding (522/825 nt) | bax | putative glycoside hydrolase Bax |
| ? | NC_000913 | = 3736652 | 157 (1.550) | coding (526/825 nt) | bax | putative glycoside hydrolase Bax | |||||
| * | ? | NC_000913 | = 227326 | NA (NA) | 3 (0.030) | 3/274 | 9.2 | NA | noncoding (1568/2904 nt) | rrlH | 23S ribosomal RNA |
| ? | NC_000913 | 227332 = | NA (NA) | noncoding (1574/2904 nt) | rrlH | 23S ribosomal RNA | |||||