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 |
| RA | 278,744 | +A | intergenic (‑239/+75) | PP_0224 ← / ← sctC | DszC family monooxygenase/sulfur compound ABC transporter ATP‑binding protein |
| RA | 307,866 | +C | intergenic (+881/‑988) | hslO → / → PP_0254 | molecular chaperone HslO/hypothetical protein |
| RA | 336,125 | +T | coding (210/237 nt) | PP_0278 → | hypothetical protein |
| RA | 353,067 | A→G | intergenic (+34/+84) | hisF → / ← cbcV | imidazole glycerol phosphate synthase subunit HisF/choline/betaine/carnitine ABC transporter ATP binding protein |
| RA | 499,203 | A→G | intergenic (+47/‑249) | uhpA → / → PP_0411 | two‑component system response regulator UhpA/polyamine ABC transporter ATP‑binding protein |
| RA | 1,070,248 | +GA | intergenic (+48/+94) | aroP‑I → / ← PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| RA | 1,126,647 | +C | intergenic (‑101/+48) | tdcG‑II ← / ← gcvP‑I | L‑serine dehydratase/glycine dehydrogenase |
| RA | 1,419,549 | +C | intergenic (‑38/+98) | PP_1242 ← / ← PP_1244 | hypothetical protein/hypothetical protein |
| RA | 1,499,480 | 2 bp→AC | intergenic (+57/‑106) | trpS → / → zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| RA | 1,499,498 | 1 bp→CG | intergenic (+75/‑89) | trpS → / → zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| RA | 1,499,508 | +C | intergenic (+85/‑79) | trpS → / → zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| RA | 1,932,640 | +C | intergenic (‑107/+43) | rluA ← / ← minE | bifunctional tRNA pseudouridine(32) synthase TrmQ/ribosomal large subunit pseudouridine synthase RluA/cell division topological specificity factor |
| RA | 2,921,460 | G→A | G3494R (GGG→AGG) | PP_2561 → | hemolysin‑type calcium‑binding bacteriocin |
| MC JC | 2,982,976 | Δ197,125 bp | [PP_2608]–[PP_2790] | 180 genes [PP_2608], PP_2609, PP_2610, PP_2611, PP_2612, PP_2613, vgrG‑I, hcpC‑I, PP_2616, PP_2617, PP_2618, PP_2619, PP_2620, PP_2621, PP_2622, PP_2623, PP_2624, PP_2625, PP_2626, PP_2627, PP_2628, PP_2631, bcsG, PP_2633, PP_2634, bcsA, bcsB, bcsZ, PP_2638, dapA‑II, PP_2640, PP_2641, PP_2642, pcaY, mgtA, PP_2646, PP_2647, PP_2648, PP_2649, gbd, PP_2651, PP_2652, PP_2653, PP_5537, PP_2654, PP_2655, pstS, pstC, pstA, pstB‑I, PP_2660, PP_2661, PP_2662, PP_2663, PP_2664, agmR, PP_2666, PP_2667, PP_2668, PP_2669, PP_5538, PP_2671, exaE, PP_2673, qedH‑I, PP_2675, PP_2676, PP_2677, PP_2678, qedH‑II, aldB‑II, pqqD‑II, yiaY, PP_2683, PP_2684, PP_2685, PP_2686, PP_2687, PP_2688, PP_2689, PP_2690, PP_2691, PP_2692, PP_2693, PP_2694, PP_2695, metR‑II, PP_2697, metE, PP_2699, PP_2700, PP_2701, PP_2702, PP_2703, PP_2704, PP_2705, PP_2706, PP_2707, PP_2708, PP_2709, PP_2710, PP_2711, PP_2712, PP_2713, PP_2714, arsH, PP_2716, arsB‑II, arsR‑II, PP_2719, PP_2720, PP_2721, PP_2722, yhdF, PP_2724, pfpI, PP_2726, PP_2727, PP_2728, PP_2729, PP_2730, PP_2731, PP_2732, PP_2733, cfa, PP_2735, PP_2736, PP_2737, PP_2738, PP_2739, PP_2740, PP_2741, PP_2742, PP_2743, PP_2744, PP_2745, dmoA‑I, PP_2747, PP_2748, PP_2749, PP_2750, PP_2751, PP_2752, PP_2753, PP_2754, sfnB, PP_2756, PP_2757, PP_2758, rbsA‑II, PP_2760, PP_2761, sfnA, msuE, PP_2765, PP_2766, PP_2767, PP_2768, PP_2769, PP_2770, PP_2771, PP_2772, PP_2773, opuA, PP_2775, PP_2776, PP_2777, PP_2778, PP_2779, PP_2780, PP_2781, PP_2782, PP_2783, PP_2784, PP_2785, PP_2786, PP_2787, PP_2788, PP_2789, [PP_2790] |
|
| RA | 3,787,908 | Δ1 bp | coding (727/1392 nt) | PP_3350 ← | hypothetical protein |
| RA | 3,845,705 | +G | intergenic (‑72/+26) | PP_3394 ← / ← PP_3395 | 3‑hydroxy‑3‑methylglutaryl‑CoA lyase/LysR family transcriptional regulator |
| RA | 3,951,159 | T→C | intergenic (‑123/+72) | PP_3486 ← / ← PP_3487 | cytochrome c/hypothetical protein |
| RA | 3,951,161 | A→T | intergenic (‑125/+70) | PP_3486 ← / ← PP_3487 | cytochrome c/hypothetical protein |
| RA | 4,586,030 | 2 bp→TC | intergenic (+113/+101) | PP_4061 → / ← PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| RA | 4,586,035 | +G | intergenic (+118/+97) | PP_4061 → / ← PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| RA | 4,586,057 | +C | intergenic (+140/+75) | PP_4061 → / ← PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| RA | 4,715,145 | C→T | R126C (CGC→TGC) | PP_4173 → | two‑component system sensor histidine kinase/response regulator |
| RA | 4,740,811 | (T)7→6 | intergenic (+48/+705) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,740,816 | T→G | intergenic (+53/+700) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,740,819 | 2 bp→CT | intergenic (+56/+696) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,229 | A→C | intergenic (+466/+287) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,231 | C→G | intergenic (+468/+285) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,234 | C→T | intergenic (+471/+282) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,236 | 2 bp→TG | intergenic (+473/+279) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,239 | A→G | intergenic (+476/+277) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,243 | 3 bp→TGC | intergenic (+480/+271) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,255 | C→T | intergenic (+492/+261) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,257 | A→C | intergenic (+494/+259) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,260 | 2 bp→GC | intergenic (+497/+255) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,263 | A→C | intergenic (+500/+253) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,272 | A→G | intergenic (+509/+244) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,274 | A→C | intergenic (+511/+242) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,276 | G→C | intergenic (+513/+240) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,278 | C→T | intergenic (+515/+238) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,283 | +T | intergenic (+520/+233) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,289 | C→G | intergenic (+526/+227) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,292 | C→T | intergenic (+529/+224) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,294 | C→G | intergenic (+531/+222) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,296 | A→C | intergenic (+533/+220) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,298 | C→T | intergenic (+535/+218) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,964,741 | A→C | I206S (ATC→AGC) | fleQ ← | transcriptional regulator FleQ |
| JC | 4,980,585 | +GGC | intergenic (‑24/+44) | PP_4387 ← / ← flgE | hypothetical protein/flagellar hook protein FlgE |
| JC | 5,555,608 | +GCC | intergenic (‑84/+87) | PP_4887 ← / ← PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| RA | 5,603,056 | C→T | W142* (TGG→TGA) | PP_4924 ← | subtilase family serine protease |
| RA | 5,674,751 | +G | intergenic (+113/+27) | rhlE‑II → / ← yceI | ATP‑dependent RNA helicase/polyisoprene‑binding acidic stress response factor |
| RA | 5,674,753 | G→C | intergenic (+115/+25) | rhlE‑II → / ← yceI | ATP‑dependent RNA helicase/polyisoprene‑binding acidic stress response factor |
| JC | 5,681,415 | +CGGG | intergenic (‑133/+71) | PP_4986 ← / ← PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| RA | 5,986,841 | T→A | intergenic (+121/‑78) | PP_5245 → / → kefB‑III | AraC family transcriptional regulator/glutathione‑regulated potassium/H+ antiporter |
| RA | 6,013,885 | T→C | intergenic (+90/+20) | xpt → / ← PP_5266 | xanthine phosphoribosyltransferase/acetyl‑CoA hydrolase family protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_002947 | 171382–176275 | 176275 | 1–4894 | 6 [5] | [5] 7 | PP_16SA–[PP_5SA] | PP_16SA,PP_23SA,[PP_5SA] |
| * | * | ÷ | NC_002947 | 176676–181702 | 181702 | 1–5027 | 6 [5] | [5] 6 | PP_16SB–[PP_r01] | PP_16SB,PP_23SB,[PP_r01] |
| * | * | ÷ | NC_002947 | 1367584 | 1367808 | 225 | 6 [5] | [5] 6 | PP_1193 | membrane protein |
| * | * | ÷ | NC_002947 | 2837085 | 2837196 | 112 | 6 [5] | [5] 6 | sad‑I/PP_2489 | NAD+‑dependent succinate semialdehyde dehydrogenase/xenobiotic reductase |
| * | * | ÷ | NC_002947 | 4808130 | 4808248 | 119 | 6 [5] | [5] 6 | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 2086250 | NA (NA) | 6 (0.250) | 6/274 | 2.3 | NA | coding (365/1302 nt) | PP_1865 | transposase |
| ? | NC_002947 | = 2086296 | NA (NA) | coding (411/1302 nt) | PP_1865 | transposase | |||||
| * | ? | NC_002947 | 2301453 = | 0 (0.000) | 29 (1.150) | 19/284 | 0.4 | 100% | intergenic (‑97/‑234) | sbcD/PP_5497 | exonuclease subunit SbcD/rhs repeat‑associated core domain‑containing protein |
| ? | NC_002947 | 2925429 = | NA (NA) | intergenic (‑177/+388) | PP_2563/PP_2564 | antibiotic biosynthesis protein/quercetin 2,3‑dioxygenase | |||||
| * | ? | NC_002947 | = 2301454 | 0 (0.000) | 24 (0.940) | 18/286 | 0.5 | 100% | intergenic (‑98/‑233) | sbcD/PP_5497 | exonuclease subunit SbcD/rhs repeat‑associated core domain‑containing protein |
| ? | NC_002947 | 5545321 = | NA (NA) | intergenic (‑461/+416) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947 | = 2957080 | 16 (0.620) | 11 (0.440) | 11/280 | 1.2 | 44.5% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947 | 2957165 = | 12 (0.480) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||