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 | annotation | gene | description |
| RA | 278,744 | +A | intergenic (‑239/+75) | PP_0224 ← / ← PP_0225 | Monooxygenase, DszC family/sulfur compound ABC transporter ‑ ATP‑binding subunit |
| RA | 307,866 | +C | intergenic (+881/‑988) | PP_0252 → / → PP_0254 | 33 kDa chaperonin/conserved protein of unknown function |
| RA | 336,125 | +T | coding (210/237 nt) | PP_0278 → | conserved protein of unknown function |
| RA | 353,067 | A→G | intergenic (+34/+84) | PP_0293 → / ← PP_0294 | Imidazole glycerol phosphate synthase subunit HisF/choline / betaine / carnitine ABC transporter ‑ ATP binding subunit |
| RA | 499,203 | A→G | intergenic (+47/‑249) | PP_0410 → / → PP_0411 | DNA‑binding response regulator UhpA/Polyamine ABC transporter, ATP‑binding protein |
| RA | 1,070,248 | +GA | intergenic (+48/+94) | PP_0927 → / ← PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger related‑protein |
| RA | 1,126,647 | +C | intergenic (‑101/+48) | PP_0987 ← / ← PP_0988 | L‑serine dehydratase/glycine dehydrogenase |
| RA | 1,419,549 | +C | intergenic (‑38/+98) | PP_1242 ← / ← PP_1244 | conserved protein of unknown function/conserved protein of unknown function |
| RA | 1,499,480 | 2 bp→AC | intergenic (+57/‑106) | PP_1311 → / → PP_1312 | Tryptophan‑‑tRNA ligase/putative enzyme with nucleoside triphosphate hydrolase domain |
| RA | 1,499,498 | 1 bp→CG | intergenic (+75/‑89) | PP_1311 → / → PP_1312 | Tryptophan‑‑tRNA ligase/putative enzyme with nucleoside triphosphate hydrolase domain |
| RA | 1,499,508 | +C | intergenic (+85/‑79) | PP_1311 → / → PP_1312 | Tryptophan‑‑tRNA ligase/putative enzyme with nucleoside triphosphate hydrolase domain |
| RA | 1,646,782 | T→C | S2P (TCC→CCC) | araC (Ppu opt) → | L‑arabinonate dehydratase |
| RA | 1,938,272 | +C | intergenic (‑107/+43) | PP_1731 ← / ← PP_1732 | 23S rRNA (746) and tRNA (32) pseudouridine synthase/Cell division topological specificity factor |
| RA | 2,964,155 | C→T | A428V (GCA→GTA) | PP_2589 → | Aldehyde dehydrogenase family protein |
| RA | 3,074,368 | G→A | S592N (AGC→AAC) | PP_2679 → | quinoprotein ethanol dehydrogenase |
| RA | 3,283,603 | T→C | Y179C (TAC→TGC) | xylE (Ppu opt) ← | |
| RA | 3,284,241 | +T | intergenic (‑103/‑105) | xylE (Ppu opt) ← / → xylA (Ppu opt) | –/– |
| RA | 3,857,849 | +G | intergenic (‑72/+26) | PP_3394 ← / ← PP_3395 | putative 3‑hydroxy‑3‑methylglutaryl‑CoA lyase/Transcriptional regulator, LysR family |
| RA | 3,963,303 | T→C | intergenic (‑123/+72) | PP_3486 ← / ← PP_3487 | putative cytochrome c/conserved exported protein of unknown function |
| RA | 3,963,305 | A→T | intergenic (‑125/+70) | PP_3486 ← / ← PP_3487 | putative cytochrome c/conserved exported protein of unknown function |
| RA | 4,598,174 | 2 bp→TC | intergenic (+113/+101) | PP_4061 → / ← PP_4063 | conserved protein of unknown function/putative Long‑chain‑fatty‑acid‑CoA ligase |
| RA | 4,598,179 | +G | intergenic (+118/+97) | PP_4061 → / ← PP_4063 | conserved protein of unknown function/putative Long‑chain‑fatty‑acid‑CoA ligase |
| RA | 4,598,201 | +C | intergenic (+140/+75) | PP_4061 → / ← PP_4063 | conserved protein of unknown function/putative Long‑chain‑fatty‑acid‑CoA ligase |
| MC JC | 4,725,879 | Δ93 bp | coding (1967‑2059/2115 nt) | PP_4171 → | conserved exported protein of unknown function |
| RA | 4,752,955 | (T)7→6 | intergenic (+48/+705) | PP_4194 → / ← PP_4195 | citrate synthase/putative oxidoreductase |
| RA | 4,752,960 | T→G | intergenic (+53/+700) | PP_4194 → / ← PP_4195 | citrate synthase/putative oxidoreductase |
| RA | 4,752,963 | 2 bp→CT | intergenic (+56/+696) | PP_4194 → / ← PP_4195 | citrate synthase/putative oxidoreductase |
| RA | 4,753,373 | A→C | intergenic (+466/+287) | PP_4194 → / ← PP_4195 | citrate synthase/putative oxidoreductase |
| RA | 4,753,375 | C→G | intergenic (+468/+285) | PP_4194 → / ← PP_4195 | citrate synthase/putative oxidoreductase |
| RA | 4,753,378 | C→T | intergenic (+471/+282) | PP_4194 → / ← PP_4195 | citrate synthase/putative oxidoreductase |
| RA | 4,753,380 | 2 bp→TG | intergenic (+473/+279) | PP_4194 → / ← PP_4195 | citrate synthase/putative oxidoreductase |
| RA | 4,753,383 | A→G | intergenic (+476/+277) | PP_4194 → / ← PP_4195 | citrate synthase/putative oxidoreductase |
| RA | 4,753,387 | 3 bp→TGC | intergenic (+480/+271) | PP_4194 → / ← PP_4195 | citrate synthase/putative oxidoreductase |
| RA | 4,753,399 | C→T | intergenic (+492/+261) | PP_4194 → / ← PP_4195 | citrate synthase/putative oxidoreductase |
| RA | 4,753,401 | A→C | intergenic (+494/+259) | PP_4194 → / ← PP_4195 | citrate synthase/putative oxidoreductase |
| RA | 4,753,404 | 2 bp→GC | intergenic (+497/+255) | PP_4194 → / ← PP_4195 | citrate synthase/putative oxidoreductase |
| RA | 4,753,407 | A→C | intergenic (+500/+253) | PP_4194 → / ← PP_4195 | citrate synthase/putative oxidoreductase |
| RA | 4,753,416 | A→G | intergenic (+509/+244) | PP_4194 → / ← PP_4195 | citrate synthase/putative oxidoreductase |
| RA | 4,753,418 | A→C | intergenic (+511/+242) | PP_4194 → / ← PP_4195 | citrate synthase/putative oxidoreductase |
| RA | 4,753,420 | G→C | intergenic (+513/+240) | PP_4194 → / ← PP_4195 | citrate synthase/putative oxidoreductase |
| RA | 4,753,422 | C→T | intergenic (+515/+238) | PP_4194 → / ← PP_4195 | citrate synthase/putative oxidoreductase |
| RA | 4,753,427 | +T | intergenic (+520/+233) | PP_4194 → / ← PP_4195 | citrate synthase/putative oxidoreductase |
| RA | 4,753,433 | C→G | intergenic (+526/+227) | PP_4194 → / ← PP_4195 | citrate synthase/putative oxidoreductase |
| RA | 4,753,436 | C→T | intergenic (+529/+224) | PP_4194 → / ← PP_4195 | citrate synthase/putative oxidoreductase |
| RA | 4,753,438 | C→G | intergenic (+531/+222) | PP_4194 → / ← PP_4195 | citrate synthase/putative oxidoreductase |
| RA | 4,753,440 | A→C | intergenic (+533/+220) | PP_4194 → / ← PP_4195 | citrate synthase/putative oxidoreductase |
| RA | 4,753,442 | C→T | intergenic (+535/+218) | PP_4194 → / ← PP_4195 | citrate synthase/putative oxidoreductase |
| JC | 4,992,729 | +GGC | intergenic (‑24/+44) | PP_4387 ← / ← PP_4388 | conserved exported protein of unknown function/Flagellar hook protein FlgE |
| JC | 5,566,684 | +GCC | intergenic (‑84/+87) | PP_4887 ← / ← PP_4888 | conserved protein of unknown function/putative methyl‑accepting chemotaxis transducer |
| RA | 5,685,827 | +G | intergenic (+113/+27) | PP_4980 → / ← PP_4981 | ATP‑dependent RNA helicase/polyisoprene‑binding protein, acidic stress response factor |
| RA | 5,685,829 | G→C | intergenic (+115/+25) | PP_4980 → / ← PP_4981 | ATP‑dependent RNA helicase/polyisoprene‑binding protein, acidic stress response factor |
| JC | 5,692,491 | +CGGG | intergenic (‑133/+71) | PP_4986 ← / ← PP_4987 | Channel protein, hemolysin III family/putative Chemotaxis protein |
| RA | 6,024,961 | T→C | intergenic (+90/+20) | PP_5265 → / ← PP_5266 | Xanthine phosphoribosyltransferase/putative acetyl‑CoA hydrolase family protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | JE3692‑4 | 171329–176339 | 176339 | 1–5011 | 43 [41] | [40] 44 | PP_16SA–[PP_5SA] | PP_16SA,PP_23SA,[PP_5SA] |
| * | * | ÷ | JE3692‑4 | 176607–181731 | 181731 | 1–5125 | 46 [40] | [35] 43 | PP_16SB–[PP_r01] | PP_16SB,PP_23SB,[PP_r01] |
| * | * | ÷ | JE3692‑4 | 1652986 | 1652986 | 1 | 79 [0] | [0] 80 | nahF (Ppu opt)/PP_1445 | –/carbohydrate‑selective porin |
| * | * | ÷ | JE3692‑4 | 4820304 | 4820346 | 43 | 67 [0] | [40] 43 | PP_4234/PP_4235 | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | JE3692‑4 | = 652782 | 73 (0.700) | 52 (0.630) | 30/156 | 2.3 | 64.2% | coding (1961/1962 nt) | PP_0562 | Methyl‑accepting chemotaxis protein CtpL |
| ? | JE3692‑4 | = 4820303 | 0 (0.000) | intergenic (‑268/‑287) | PP_4234/PP_4235 | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | JE3692‑4 | = 1644999 | 0 (0.000) | 78 (0.760) | 58/194 | 0.7 | 100% | intergenic (‑258/‑188) | PP_1443/araE (Ppu opt) | DNA‑binding, ATP‑dependent protease/– |
| ? | JE3692‑4 | = 1652985 | 0 (0.000) | intergenic (+174/+34) | nahF (Ppu opt)/PP_1445 | –/carbohydrate‑selective porin | |||||
| * | ? | JE3692‑4 | 1644999 = | 0 (0.000) | 76 (0.740) | 58/194 | 0.7 | 100% | intergenic (‑258/‑188) | PP_1443/araE (Ppu opt) | DNA‑binding, ATP‑dependent protease/– |
| ? | JE3692‑4 | 1652987 = | 0 (0.000) | intergenic (+176/+32) | nahF (Ppu opt)/PP_1445 | –/carbohydrate‑selective porin | |||||
| * | ? | JE3692‑4 | = 4943879 | 32 (0.320) | 76 (0.770) +CCTTC |
59/176 | 0.4 | 70.9% | coding (483/741 nt) | PP_4341 | RNA polymerase sigma 28 (sigma F) factor for class III flagellar operons |
| ? | JE3692‑4 | 4943880 = | 32 (0.310) | coding (482/741 nt) | PP_4341 | RNA polymerase sigma 28 (sigma F) factor for class III flagellar operons | |||||