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 24 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 | 41.7% | 78.5 / 55.8 | 84 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 1,825,061 | 0 | G | A | 35.9% | 78.3 / 28.9 | 53 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 2,001,918 | 0 | A | C | 28.6% | 162.7 / 26.5 | 77 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,568,504 | 0 | T | G | 28.5% | 247.5 / 18.9 | 123 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 501,575 | 0 | A | C | 26.9% | 105.1 / 21.2 | 52 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 4,111,747 | 0 | G | T | 26.5% | 121.4 / 22.1 | 49 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 753,125 | 0 | T | A | 26.5% | 173.7 / 33.8 | 83 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 29,496 | 0 | T | A | 26.4% | 157.9 / 28.3 | 72 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 175,694 | 0 | T | G | 25.2% | 228.8 / 21.5 | 103 | G196G (GGT→GGG) | clcA | chloride:H(+) antiporter ClcA |
| * | NC_000913 | 372,640 | 0 | T | G | 25.0% | 172.6 / 23.3 | 80 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 3,608,719 | 0 | G | A | 25.0% | 126.6 / 14.5 | 64 | intergenic (+70/+32) | zntA/tusA | Zn(2(+))/Cd(2(+))/Pb(2(+)) exporting P‑type ATPase/sulfur transfer protein TusA |
| * | NC_000913 | 3,275,611 | 0 | A | C | 24.6% | 140.6 / 11.7 | 61 | E110D (GAA→GAC) | garD | galactarate dehydratase |
| * | NC_000913 | 4,111,752 | 0 | T | C | 23.9% | 126.5 / 11.6 | 67 | K155E (AAA→GAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 650,809 | 0 | T | G | 23.6% | 163.5 / 14.3 | 72 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 3,926,366 | 0 | A | C | 23.6% | 227.8 / 31.8 | 106 | G30G (GGT→GGG) | mioC | flavoprotein MioC |
| * | NC_000913 | 501,564 | 0 | A | C | 23.4% | 105.6 / 15.3 | 48 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| * | NC_000913 | 4,032,731 | 0 | T | G | 22.5% | 177.4 / 21.0 | 80 | G80G (GGT→GGG) | yigZ | IMPACT family member YigZ |
| * | NC_000913 | 4,296,060 | 0 | C | T | 21.9% | 316.5 / 78.1 | 146 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 3,401,459 | 0 | T | C | 21.6% | 221.0 / 19.0 | 102 | D625G (GAT→GGT) | csrD | regulator of CsrB and CsrC decay |
| * | NC_000913 | 1,825,056 | 0 | G | A | 21.4% | 98.1 / 10.6 | 42 | intergenic (‑119/+84) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| Marginal new junction evidence (lowest skew 10 of 11 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4542682 = | 89 (0.820) | 16 (0.160) | 14/260 | 5.1 | 15.6% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 90 (0.890) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 87 (0.810) | 9 (0.090) | 9/260 | 6.7 | 9.5% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 90 (0.890) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 608007 = | NA (NA) | 5 (0.060) | 4/226 | 8.3 | 5.8% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 81 (0.920) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | 1285619 = | 76 (0.700) | 4 (0.040) | 4/266 | 9.2 | 5.1% | coding (481/711 nt) | narJ | nitrate reductase 1 molybdenum cofactor assembly chaperone |
| ? | NC_000913 | = 1285615 | 75 (0.730) | coding (477/711 nt) | narJ | nitrate reductase 1 molybdenum cofactor assembly chaperone | |||||
| * | ? | NC_000913 | 1272758 = | 136 (1.260) | 3 (0.030) | 3/256 | 9.6 | 2.6% | coding (252/696 nt) | chaC | glutathione‑specific gamma‑glutamylcyclotransferase |
| ? | NC_000913 | 1273352 = | 97 (0.980) | coding (248/354 nt) | ychN | DsrE/F sulfur relay family protein YchN | |||||
| * | ? | NC_000913 | = 2874390 | 116 (1.070) | 3 (0.030) | 3/270 | 9.9 | 2.7% | coding (1030/1428 nt) | cysN | sulfate adenylyltransferase subunit 1 |
| ? | NC_000913 | 2874395 = | 106 (1.010) | coding (1025/1428 nt) | cysN | sulfate adenylyltransferase subunit 1 | |||||
| * | ? | NC_000913 | = 1466561 | 117 (1.080) | 4 (0.040) | 3/266 | 9.9 | 3.5% | pseudogene (1170/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment |
| ? | NC_000913 | = 1466747 | 111 (1.070) | pseudogene (1356/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment | |||||
| * | ? | NC_000913 | = 3553929 | 87 (0.810) | 3 (0.030) | 3/274 | 10.0 | 3.4% | coding (845/2706 nt) | malT | DNA‑binding transcriptional activator MalT |
| ? | NC_000913 | 3553990 = | 83 (0.780) | coding (906/2706 nt) | malT | DNA‑binding transcriptional activator MalT | |||||
| * | ? | NC_000913 | = 2054089 | 95 (0.880) | 3 (0.030) | 3/278 | 10.1 | 3.3% | coding (447/1317 nt) | shiA | shikimate:H(+) symporter |
| ? | NC_000913 | = 2054153 | 80 (0.740) | coding (511/1317 nt) | shiA | shikimate:H(+) symporter | |||||
| * | ? | NC_000913 | = 1979489 | 103 (0.950) | 11 (0.100) | 3/278 | 10.1 | 9.6% | intergenic (‑274/‑264) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||