mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| MC JC | 1,402,042 | Δ183,606 bp | [abgB]–[ydeP] | 176 genes [abgB], abgA, abgR, mcaS, smrA, ydaM, ydaN, fnrS, dbpA, ttcA, intR, ydaQ, ydaC, ralR, recT, recE, racC, ydaE, kilR, sieB, ydaF, ydaG, racR, ydaS, ydaT, ydaU, ydaV, ydaW, rzpR, rzoR, trkG, ynaK, ydaY, tmpR, lomR, insH1, lomR, stfR, tfaR, pinR, ynaE, ttcC, uspF, ompN, micC, pfo, ydbJ, hslJ, ldhA, ydbH, ynbE, ydbL, feaR, feaB, tynA, paaZ, paaA, paaB, paaC, paaD, paaE, paaF, paaG, paaH, paaI, paaJ, paaK, paaX, paaY, ynbG, ydbA, insD1, insC1, ydbA, insI1, ydbA, ydbC, ydbD, ynbA, ynbB, ynbC, ynbD, azoR, hrpA, ydcF, aldA, gapC, gapC, cybB, rydC, ydcA, hokB, mokB, sokB, trg, ydcI, ydcJ, opgD, ydcH, rimL, ydcK, tehA, tehB, ydcL, insP, insQ, ydcO, ydcN, ydcP, yncJ, hicA, hicB, ydcR, ydcS, ydcT, ydcU, ydcV, patD, yncL, ydcX, ydcY, ydcZ, mnaT, curA, mcbR, yncD, yncE, ansP, yncG, yncH, rhsE, ydcD, yncI, yncI, ydcC, pptA, yddH, nhoA, yddE, narV, narW, narY, narZ, narU, yddK, yddK, yddL, yddG, fdnG, fdnH, fdnI, yddM, adhP, maeA, sra, bdm, osmC, ddpF, ddpD, ddpC, ddpB, ddpA, ddpX, dosP, dosC, yddW, gadC, gadB, pqqL, yddB, yddA, ydeM, ydeN, ydeO, safA, [ydeP] |
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| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,173,363 | Δ2 bp | intergenic (‑1/+1) | gatC ← / ← gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,174,085 | G→A | pseudogene (194/914 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 3,560,455 | +G | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| MC JC | 3,936,337 | Δ902 bp | [rbsB] | [rbsB] | |
| RA | 3,937,351 | A→T | N20Y (AAT→TAT) | rbsK → | ribokinase |
| JC JC | 3,938,845 | IS2 (+) +5 bp | coding (619‑623/993 nt) | rbsR → | transcriptional repressor of ribose metabolism |
| RA | 3,967,666 | A→T | K417I (AAA→ATA) | rho → | transcription termination factor |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423818–3424232 | 3424499–3424238 | 7–682 | 32 [30] | [29] 31 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 9 (0.090) | 54 (0.590) | 40/448 | 1.1 | 78.0% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 22 (0.240) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 10 (0.100) | 64 (0.700) | 49/448 | 0.6 | 80.3% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 22 (0.240) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 72 (0.750) | 53/472 | 0.5 | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||