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 26 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 | 45.0% | 108.6 / 97.5 | 129 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,568,504 | 0 | T | G | 34.6% | 281.2 / 36.5 | 164 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 4,111,747 | 0 | G | T | 32.5% | 165.8 / 48.3 | 77 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 3,556,207 | 0 | T | C | 32.0% | 74.8 / 20.2 | 50 | S215G (AGT→GGT) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 2,001,918 | 0 | A | C | 31.7% | 209.8 / 56.6 | 120 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 1,825,061 | 0 | G | A | 30.6% | 115.2 / 25.8 | 62 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 357,890 | 0 | C | A | 29.6% | 62.3 / 13.5 | 27 | L267F (TTG→TTT) | cynR | DNA‑binding transcriptional dual regulator CynR |
| * | NC_000913 | 501,575 | 0 | A | C | 29.0% | 121.9 / 18.3 | 62 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 4,111,752 | 0 | T | C | 28.3% | 162.4 / 20.3 | 92 | K155E (AAA→GAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,296,060 | 0 | C | T | 28.0% | 355.0 / 137.6 | 189 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 650,809 | 0 | T | G | 27.1% | 206.5 / 22.1 | 107 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 372,640 | 0 | T | G | 25.0% | 176.2 / 19.5 | 88 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 4,429,984 | 0 | T | G | 25.0% | 247.1 / 43.4 | 120 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 888,014 | 0 | T | G | 24.8% | 273.4 / 39.1 | 137 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 501,564 | 0 | A | C | 24.6% | 139.2 / 29.8 | 69 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| * | NC_000913 | 2,326,450 | 0 | T | G | 23.1% | 262.4 / 48.6 | 121 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 175,694 | 0 | T | G | 22.9% | 265.0 / 13.1 | 124 | G196G (GGT→GGG) | clcA | chloride:H(+) antiporter ClcA |
| * | NC_000913 | 501,572 | 0 | A | C | 22.6% | 137.7 / 12.0 | 62 | V556G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 1,491,098 | 0 | A | C | 22.3% | 267.0 / 15.9 | 121 | Y66S (TAC→TCC) | cybB | cytochrome b561 |
| * | NC_000913 | 753,125 | 0 | T | A | 21.7% | 223.8 / 24.4 | 92 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| Marginal new junction evidence (lowest skew 10 of 35 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4542682 = | 75 (0.540) | 14 (0.110) | 14/260 | 5.9 | 12.0% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 136 (1.040) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 1128952 = | 142 (1.020) | 12 (0.090) | 7/276 | 8.7 | 7.2% | coding (1114/1536 nt) | murJ | putative lipid II flippase MurJ |
| ? | NC_000913 | 1129064 = | 167 (1.200) | coding (1226/1536 nt) | murJ | putative lipid II flippase MurJ | |||||
| * | ? | NC_000913 | 2818058 = | 220 (1.570) | 9 (0.080) | 5/238 | 8.8 | 5.0% | intergenic (‑198/+1) | argQ/argZ | tRNA‑Arg/tRNA‑Arg |
| ? | NC_000913 | = 2818337 | 156 (1.310) | intergenic (‑63/+136) | argY/argV | tRNA‑Arg/tRNA‑Arg | |||||
| * | ? | NC_000913 | 608007 = | NA (NA) | 5 (0.040) | 4/226 | 9.1 | 3.6% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 134 (1.180) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | = 3388952 | 165 (1.180) | 6 (0.050) | 5/264 | 9.4 | 3.8% | coding (175/933 nt) | aaeA | aromatic carboxylic acid efflux pump membrane fusion protein |
| ? | NC_000913 | = 3389037 | 150 (1.130) | coding (90/933 nt) | aaeA | aromatic carboxylic acid efflux pump membrane fusion protein | |||||
| * | ? | NC_000913 | 224910 = | NA (NA) | 4 (0.030) | 4/262 | 9.9 | NA | noncoding (1140/1542 nt) | rrsH | 16S ribosomal RNA |
| ? | NC_000913 | 225157 = | NA (NA) | noncoding (1387/1542 nt) | rrsH | 16S ribosomal RNA | |||||
| * | ? | NC_000913 | 2817783 = | 145 (1.040) | 5 (0.040) | 3/238 | 10.0 | 3.4% | intergenic (‑280/+1) | yqaB/argQ | fructose‑1‑phosphatase/tRNA‑Arg |
| ? | NC_000913 | = 2818337 | 156 (1.310) | intergenic (‑63/+136) | argY/argV | tRNA‑Arg/tRNA‑Arg | |||||
| * | ? | NC_000913 | 2728258 = | NA (NA) | 4 (0.030) | 4/264 | 10.0 | NA | noncoding (927/2904 nt) | rrlG | 23S ribosomal RNA |
| ? | NC_000913 | 2728336 = | NA (NA) | noncoding (849/2904 nt) | rrlG | 23S ribosomal RNA | |||||
| * | ? | NC_000913 | = 226685 | 41 (0.290) | 4 (0.030) | 4/264 | 10.0 | 9.3% | noncoding (927/2904 nt) | rrlH | 23S ribosomal RNA |
| ? | NC_000913 | 2728336 = | NA (NA) | noncoding (849/2904 nt) | rrlG | 23S ribosomal RNA | |||||
| * | ? | NC_000913 | 4022727 = | 127 (0.910) | 4 (0.030) | 4/270 | 10.1 | 2.8% | coding (510/516 nt) | tatB | twin arginine protein translocation system ‑ TatB protein |
| ? | NC_000913 | = 4022918 | 156 (1.150) | coding (183/777 nt) | tatC | twin arginine protein translocation system ‑ TatC protein | |||||