mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 |
| RA | 70,289 | G→T | 9.3% | intergenic (‑241/‑98) | araB ← / → araC | ribulokinase/DNA‑binding transcriptional dual regulator AraC |
| RA | 70,581 | C→T | 8.3% | V65V (GTC→GTT) | araC → | DNA‑binding transcriptional dual regulator AraC |
| RA | 71,079 | C→T | 6.4% | R231R (CGC→CGT) | araC → | DNA‑binding transcriptional dual regulator AraC |
| RA | 71,082 | T→C | 5.5% | I232I (ATT→ATC) | araC → | DNA‑binding transcriptional dual regulator AraC |
| RA | 71,085 | T→C | 5.3% | S233S (AGT→AGC) | araC → | DNA‑binding transcriptional dual regulator AraC |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| 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 | 2,868,098 | IS5 (+) +4 bp | 7.3% | coding (653‑656/1140 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 | 33.4% | 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 | 4,542,002 | IS1 (–) +9 bp | 13.2% | intergenic (+443/‑27) | fimB → / → fimE | regulator for fimA/regulator for fimA |
| JC JC | 4,542,161 | IS5 (–) +4 bp | 9.6% | coding (125‑128/597 nt) | fimE → | regulator for fimA |
| JC JC | 4,542,237 | IS1 (–) +9 bp | 13.2% | coding (201‑209/597 nt) | fimE → | regulator for fimA |
| JC JC | 4,542,308 | IS5 (–) +4 bp | 18.5% | coding (272‑275/597 nt) | fimE → | regulator for fimA |
| JC JC | 4,542,448 | IS5 (–) +4 bp | 13.6% | coding (412‑415/597 nt) | fimE → | regulator for fimA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423696–3424235 | 3424591–3424238 | 4–896 | 49 [48] | [47] 50 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 807339 | 5 (0.060) | 69 (0.810) | 50/176 | NT | 95.2% | intergenic (‑58/+94) | ybhC/ybhB | outer membrane lipoprotein YhbC/putative kinase inhibitor |
| ? | NC_000913 | 4171877 = | 2 (0.020) | intergenic (+121/‑180) | rrfB/murB | 5S ribosomal RNA/UDP‑N‑acetylenolpyruvoylglucosamine reductase | |||||
| * | ? | NC_000913 | 1207790 = | 41 (0.480) | 32 (0.460) | 29/144 | NT | 44.9% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 45 (0.650) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 43 (0.500) | 16 (0.230) | 14/144 | NT | 28.5% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 45 (0.650) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 72 (0.890) | 56/168 | 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 = | 20 (0.230) | 63 (0.820) | 51/158 | NT | 76.9% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 20 (0.260) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 21 (0.250) | 96 (1.260) | 72/158 | NT | 83.2% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 20 (0.260) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||