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 |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| JC JC | 485,977 | IS5 (–) +4 bp | 8.8% | coding (217‑220/648 nt) | acrR → | DNA‑binding transcriptional repressor AcrR |
| JC JC | 485,980 | IS1 (+) +9 bp | 23.2% | coding (220‑228/648 nt) | acrR → | DNA‑binding transcriptional repressor AcrR |
| MC JC | 1,397,381 | Δ13,756 bp | 100% | [ynaJ]–[ttcA] | 16 genes [ynaJ], uspE, fnr, ogt, abgT, abgB, abgA, abgR, mcaS, smrA, dgcM, zntB, fnrS, ynaL, dbpA, [ttcA] |
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| RA | 1,619,370 | T→A | 91.1% | V84E (GTG→GAG) | marR → | DNA‑binding transcriptional repressor MarR |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 3,214,380 | A→C | 15.2% | D445A (GAT→GCT) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| JC JC | 3,802,353 | IS1 (+) +9 bp | 10.4% | coding (698‑706/1020 nt) | waaO ← | UDP‑D‑glucose:(glucosyl)LPS alpha‑1,3‑glucosyltransferase |
| JC JC | 3,802,754 | IS5 (+) +4 bp | 16.2% | coding (302‑305/1020 nt) | waaO ← | UDP‑D‑glucose:(glucosyl)LPS alpha‑1,3‑glucosyltransferase |
| JC | 3,805,441 | Δ19 bp | 30.4% | coding (492‑510/798 nt) | waaP ← | lipopolysaccharide core heptose (I) kinase |
| JC JC | 3,807,700 | IS1 (–) +8 bp | 27.2% | coding (392‑399/1035 nt) | waaQ ← | lipopolysaccharide core heptosyltransferase 3 |
| RA | 4,296,060 | C→T | 23.6% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423691–3424234 | 3424599–3424238 | 5–909 | 53 [51] | [50] 53 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 56 (0.580) | 28 (0.360) | 22/144 | NT | 40.4% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 37 (0.470) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 57 (0.600) | 22 (0.280) | 21/144 | NT | 34.5% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 37 (0.470) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 1291702 = | 83 (0.870) | 8 (0.080) | 8/176 | NT | 8.8% | coding (246/909 nt) | galU | UTP‑‑glucose‑1‑phosphate uridylyltransferase |
| ? | NC_000913 | = 1979270 | NA (NA) | noncoding (1/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 85 (0.930) | 65/168 | NT | 100% | intergenic (+253/‑33) | ychE/insH21 | putative inner membrane protein/IS5 transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 4542682 = | 132 (1.380) | 38 (0.440) | 35/158 | NT | 25.1% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 109 (1.270) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 127 (1.330) | 48 (0.560) | 37/158 | NT | 30.1% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 109 (1.270) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||