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 | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,604,344 | 0 | C | T | 41.2% | 66.0 / 46.8 | 68 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 753,125 | 0 | T | A | 34.0% | 91.2 / 30.5 | 53 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 650,809 | 0 | T | G | 30.2% | 59.7 / 15.9 | 43 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 4,111,747 | 0 | G | T | 29.7% | 97.9 / 15.4 | 37 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,568,504 | 0 | T | G | 29.6% | 144.5 / 11.5 | 81 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 501,564 | 0 | A | C | 29.0% | 45.5 / 15.2 | 31 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| * | NC_000913 | 3,206,435 | 0 | C | T | 27.5% | 71.2 / 19.8 | 40 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 1,550,663 | 0 | A | C | 26.2% | 76.8 / 13.0 | 42 | N68T (AAC→ACC) | fdnH | formate dehydrogenase N subunit beta |
| * | NC_000913 | 2,326,450 | 0 | T | G | 25.6% | 70.4 / 22.8 | 43 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 372,640 | 0 | T | G | 25.5% | 93.9 / 11.7 | 51 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 29,496 | 0 | T | A | 25.0% | 79.4 / 12.3 | 36 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 1,621,118 | 0 | A | C | 23.7% | 72.1 / 10.4 | 38 | V7G (GTG→GGG) | eamA | cysteine/O‑acetylserine exporter EamA |
| * | NC_000913 | 1,315,936 | 0 | T | A | 23.1% | 112.6 / 11.0 | 52 | K34* (AAA→TAA) | yciG | protein YciG |
| * | NC_000913 | 753,105 | 0 | A | T | 22.6% | 156.4 / 15.3 | 62 | intergenic (‑310/+80) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 3,401,459 | 0 | T | C | 22.6% | 126.3 / 14.1 | 62 | D625G (GAT→GGT) | csrD | regulator of CsrB and CsrC decay |
| * | NC_000913 | 3,240,985 | 0 | T | G | 21.8% | 114.0 / 10.2 | 55 | S348A (TCT→GCT) | sstT | serine/threonine:Na(+) symporter |
| * | NC_000913 | 3,135,775 | 0 | C | T | 21.2% | 145.9 / 11.3 | 66 | K199K (AAG→AAA) | pitB | metal phosphate:H(+) symporter PitB |
| * | NC_000913 | 2,001,918 | 0 | A | C | 21.1% | 108.3 / 12.7 | 52 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 2,483,268 | 0 | T | A | 20.4% | 141.2 / 12.4 | 54 | L24F (TTA→TTT) | emrK | tripartite efflux pump membrane fusion protein EmrK |
| 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 | 4542682 = | 68 (0.940) | 5 (0.070) | 5/258 | 5.9 | 7.5% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 59 (0.870) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 2304679 | NA (NA) | 4 (0.060) | 4/276 | 6.6 | NA | intergenic (+286/+429) | eco/mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase |
| ? | NC_000913 | 2304683 = | NA (NA) | intergenic (+290/+425) | eco/mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase | |||||
| * | ? | NC_000913 | 1997964 = | 93 (1.280) | 4 (0.060) | 3/260 | 6.9 | 4.9% | coding (516/669 nt) | tcyL | cystine ABC transporter membrane subunit |
| ? | NC_000913 | 1998031 = | 68 (0.990) | coding (449/669 nt) | tcyL | cystine ABC transporter membrane subunit | |||||
| * | ? | NC_000913 | = 4430326 | 70 (0.960) | 3 (0.040) | 3/270 | 7.1 | 4.2% | coding (463/1413 nt) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| ? | NC_000913 | = 4430404 | 70 (0.990) | coding (541/1413 nt) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter | |||||
| * | ? | NC_000913 | 718363 = | 100 (1.380) | 3 (0.040) | 3/272 | 7.1 | 4.0% | coding (2098/2199 nt) | speF | ornithine decarboxylase, degradative |
| ? | NC_000913 | = 718694 | 44 (0.620) | coding (1767/2199 nt) | speF | ornithine decarboxylase, degradative | |||||
| * | ? | NC_000913 | = 640523 | 42 (0.580) | 4 (0.060) | 3/274 | 7.1 | 6.8% | coding (771/1566 nt) | ahpF | alkyl hydroperoxide reductase, AhpF component |
| ? | NC_000913 | = 640712 | 68 (0.940) | coding (960/1566 nt) | ahpF | alkyl hydroperoxide reductase, AhpF component | |||||
| * | ? | NC_000913 | 337285 = | 59 (0.810) | 3 (0.040) | 3/274 | 7.1 | 5.2% | coding (508/1548 nt) | yahF | putative acyl‑CoA synthetase YahF |
| ? | NC_000913 | = 337474 | 51 (0.710) | coding (697/1548 nt) | yahF | putative acyl‑CoA synthetase YahF | |||||
| * | ? | NC_000913 | 2304683 = | NA (NA) | 6 (0.080) | 3/276 | 7.2 | NA | intergenic (+290/+425) | eco/mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase |
| ? | NC_000913 | = 2304905 | NA (NA) | intergenic (+512/+203) | eco/mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase | |||||
| * | ? | NC_000913 | = 2304679 | NA (NA) | 3 (0.040) | 3/276 | 7.2 | NA | intergenic (+286/+429) | eco/mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase |
| ? | NC_000913 | 2304909 = | NA (NA) | intergenic (+516/+199) | eco/mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase | |||||
| * | ? | NC_000913 | 2304570 = | NA (NA) | 6 (0.080) | 3/276 | 7.2 | NA | intergenic (+177/+538) | eco/mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase |
| ? | NC_000913 | = 2304905 | NA (NA) | intergenic (+512/+203) | eco/mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase | |||||