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 | 1,292,997 | IS1 (+) +9 bp | 17.9% | intergenic (‑75/‑522) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| 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] |
|
| 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 |
| JC JC | 2,867,842 | IS1 (–) +9 bp | 31.2% | coding (904‑912/1140 nt) | nlpD ← | murein hydrolase activator NlpD |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| JC JC | 3,899,395 | IS1 (–) +9 bp | 100% | intergenic (‑2/+5) | yieK ← / ← yieL | putative glucosamine‑6‑phosphate deaminase YieK/putative hydrolase YieL |
| RA | 4,296,060 | C→T | 31.3% | 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 |
| JC JC | 4,542,578 | IS1 (+) +9 bp | 17.5% | coding (542‑550/597 nt) | fimE → | regulator for fimA |
| JC JC | 4,542,831 | IS5 (–) +4 bp | 26.2% | intergenic (+198/‑281) | fimE → / → fimA | regulator for fimA/type 1 fimbriae major subunit |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423693–3424234 | 3424598–3424238 | 5–906 | 72 [71] | [71] 74 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 807339 | 6 (0.050) | 90 (0.750) | 65/176 | NT | 93.8% | intergenic (‑58/+94) | ybhC/ybhB | outer membrane lipoprotein YhbC/putative kinase inhibitor |
| ? | NC_000913 | 4171877 = | 6 (0.050) | intergenic (+121/‑180) | rrfB/murB | 5S ribosomal RNA/UDP‑N‑acetylenolpyruvoylglucosamine reductase | |||||
| * | ? | NC_000913 | = 1050545 | NA (NA) | 12 (0.100) | 12/174 | NT | 12.2% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 1292998 = | 86 (0.730) | intergenic (‑76/‑529) | hns/tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase | |||||
| * | ? | NC_000913 | 1207790 = | 61 (0.510) | 45 (0.460) | 38/144 | NT | 49.8% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 41 (0.420) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 58 (0.490) | 36 (0.370) | 28/144 | NT | 44.9% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 41 (0.420) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 108 (0.950) | 74/168 | 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 | = 2290113 | NA (NA) | 10 (0.080) | 5/176 | NT | 6.0% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 4542161 = | 156 (1.310) | coding (125/597 nt) | fimE | regulator for fimA | |||||
| * | ? | NC_000913 | 3583428 = | NA (NA) | 7 (0.060) | 6/172 | NT | 5.9% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 4542577 = | 102 (0.970) | coding (541/597 nt) | fimE | regulator for fimA | |||||
| * | ? | NC_000913 | 4542682 = | 49 (0.410) | 107 (1.000) | 70/158 | NT | 72.6% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 37 (0.350) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 47 (0.390) | 96 (0.900) | 70/158 | NT | 70.8% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 37 (0.350) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||