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 | 44.5% | 100.4 / 75.7 | 110 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,568,504 | 0 | T | G | 35.6% | 223.2 / 34.4 | 150 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 1,825,061 | 0 | G | A | 30.8% | 88.5 / 18.7 | 52 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 650,809 | 0 | T | G | 29.5% | 165.9 / 32.3 | 96 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 29,496 | 0 | T | A | 29.4% | 130.3 / 30.0 | 68 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 1,377,140 | 0 | A | C | 29.3% | 146.0 / 17.8 | 82 | K103N (AAA→AAC) | ycjS | putative oxidoreductase YcjS |
| * | NC_000913 | 2,001,918 | 0 | A | C | 29.2% | 133.5 / 26.8 | 72 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 888,014 | 0 | T | G | 27.5% | 138.6 / 13.3 | 70 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 4,296,060 | 0 | C | T | 25.9% | 240.7 / 86.4 | 131 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 2,667,126 | 0 | A | C | 24.7% | 193.8 / 18.9 | 97 | Y241D (TAT→GAT) | hcaT | putative 3‑phenylpropionate transporter |
| * | NC_000913 | 372,640 | 0 | T | G | 24.7% | 142.5 / 12.5 | 73 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 501,575 | 0 | A | C | 23.6% | 119.9 / 13.4 | 55 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 4,111,747 | 0 | G | T | 23.5% | 224.7 / 36.8 | 81 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 1,491,103 | 0 | A | C | 22.9% | 174.2 / 14.4 | 84 | T68P (ACC→CCC) | cybB | cytochrome b561 |
| * | NC_000913 | 4,098,155 | 0 | A | C | 22.7% | 273.6 / 12.2 | 129 | L140F (TTA→TTC) | rhaS | DNA‑binding transcriptional activator RhaS |
| * | NC_000913 | 3,926,366 | 0 | A | C | 22.3% | 257.2 / 23.7 | 112 | G30G (GGT→GGG) | mioC | flavoprotein MioC |
| * | NC_000913 | 1,068,173 | 0 | T | G | 22.2% | 243.1 / 21.2 | 108 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 753,125 | 0 | T | A | 21.6% | 228.8 / 22.0 | 88 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 1,775,467 | 0 | A | C | 21.6% | 188.3 / 12.1 | 88 | intergenic (+23/‑120) | aroD/ydiF | 3‑dehydroquinate dehydratase/putative acetate‑CoA transferase |
| * | NC_000913 | 3,240,985 | 0 | T | G | 21.5% | 252.7 / 28.0 | 107 | S348A (TCT→GCT) | sstT | serine/threonine:Na(+) symporter |
| Marginal new junction evidence (lowest skew 10 of 19 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4542690 | 106 (0.870) | 29 (0.260) | 25/260 | 3.1 | 18.9% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 150 (1.320) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 122 (1.000) | 23 (0.200) | 20/260 | 4.0 | 14.7% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 153 (1.350) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1300697 | NA (NA) | 26 (0.210) | 9/278 | 7.4 | 100% | intergenic (+150/‑485) | insH21/oppA | IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1979271 = | 0 (0.000) | intergenic (‑56/‑482) | insA‑5/uspC | IS1 protein InsA/universal stress protein C | |||||
| * | ? | NC_000913 | = 1978494 | 0 (0.000) | 21 (0.170) | 7/278 | 8.2 | 100% | intergenic (‑297/+24) | flhD/insB‑5 | DNA‑binding transcriptional dual regulator FlhD/IS1 protein InsB |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 3993987 | 135 (1.110) | 4 (0.030) | 4/264 | 9.4 | 3.1% | coding (73/321 nt) coding (138/486 nt) |
cyaY yzcX |
frataxin CyaY protein YzcX |
| ? | NC_000913 | = 3994080 | 120 (1.040) | coding (231/486 nt) | yzcX | protein YzcX | |||||
| * | ? | NC_000913 | 3217426 = | NA (NA) | 4 (0.030) | 4/276 | 9.7 | NA | intergenic (+24/+130) | nfeR/aer | DNA‑binding transcriptional repressor NfeR/aerotaxis sensor receptor, flavoprotein |
| ? | NC_000913 | 3217535 = | NA (NA) | intergenic (+133/+21) | nfeR/aer | DNA‑binding transcriptional repressor NfeR/aerotaxis sensor receptor, flavoprotein | |||||
| * | ? | NC_000913 | 1979271 = | 0 (0.000) | 6 (0.050) +T |
4/276 | 9.7 | 100% | intergenic (‑56/‑482) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | 2066156 = | NA (NA) | intergenic (‑392/+149) | cobU/insH‑6 | cobinamide‑P guanylyltransferase/cobinamide kinase/CP4‑44 prophage; IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | 3987746 = | 149 (1.230) | 3 (0.030) | 3/258 | 9.9 | 2.1% | coding (137/1197 nt) | hemY | protein HemY |
| ? | NC_000913 | 3988163 = | 139 (1.230) | coding (904/1182 nt) | hemX | PF04375 family protein HemX | |||||
| * | ? | NC_000913 | 3736656 = | 208 (1.710) | 3 (0.030) | 3/258 | 9.9 | 1.5% | coding (522/825 nt) | bax | putative glycoside hydrolase Bax |
| ? | NC_000913 | = 3736652 | 189 (1.680) | coding (526/825 nt) | bax | putative glycoside hydrolase Bax | |||||
| * | ? | NC_000913 | 1900765 = | 116 (0.950) | 3 (0.030) | 3/256 | 9.9 | 2.8% | coding (821/1557 nt) | yoaE | putative inner membrane protein |
| ? | NC_000913 | = 1900758 | 101 (0.900) | coding (828/1557 nt) | yoaE | putative inner membrane protein | |||||