mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.5 revision 9f368df52761
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 187,648 | T→A | Y154N (TAT→AAT) | PP_0164 → | conserved protein of unknown function |
| RA | 278,744 | +A | intergenic (‑239/+75) | PP_0224 ← / ← sctC | Monooxygenase, DszC family/sulfur compound ABC transporter ‑ ATP‑binding subunit |
| RA | 307,866 | +C | intergenic (+881/‑988) | hslO → / → 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) | hisF → / ← cbcV | Imidazole glycerol phosphate synthase subunit HisF/choline / betaine / carnitine ABC transporter ‑ ATP binding subunit |
| RA | 499,203 | A→G | intergenic (+47/‑249) | uhpA → / → PP_0411 | DNA‑binding response regulator UhpA/Polyamine ABC transporter, ATP‑binding protein |
| RA | 1,126,647 | +C | intergenic (‑101/+48) | tdcG‑II ← / ← gcvP‑I | L‑serine dehydratase/glycine dehydrogenase |
| MC JC | 1,164,572 | 830 bp→TCA | coding (4‑833/864 nt) | hexR ← | DNA‑binding transcriptional regulator |
| 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) | trpS → / → zapE | Tryptophan‑‑tRNA ligase/putative enzyme with nucleoside triphosphate hydrolase domain |
| RA | 1,499,498 | 1 bp→CG | intergenic (+75/‑89) | trpS → / → zapE | Tryptophan‑‑tRNA ligase/putative enzyme with nucleoside triphosphate hydrolase domain |
| RA | 1,499,508 | +C | intergenic (+85/‑79) | trpS → / → zapE | Tryptophan‑‑tRNA ligase/putative enzyme with nucleoside triphosphate hydrolase domain |
| MC JC | 1,709,370 | 2640 bp→7 bp | [ppc] | [ppc] | |
| RA | 1,932,640 | +C | intergenic (‑107/+43) | rluA ← / ← minE | 23S rRNA (746) and tRNA (32) pseudouridine synthase/Cell division topological specificity factor |
| MC JC | 2,032,505 | 1680 bp→8 bp | [pgi‑I] | [pgi‑I] | |
| RA | 2,935,792 | G→A | intergenic (+87/‑175) | PP_2568 → / → PP_2569 | Ring‑cleaving dioxygenase/Metabolite MFS transporter, MHS family |
| RA | 2,958,523 | C→T | A428V (GCA→GTA) | PP_2589 → | Aldehyde dehydrogenase family protein |
| RA | 3,137,784 | (T)9→8 | intergenic (+212/‑78) | PP_2753 → / → PP_2754 | putative Branched‑chain amino acid ABC transporter, ATP‑binding protein/putative OprD family outer membrane porin |
| RA | 3,845,705 | +G | intergenic (‑72/+26) | PP_3394 ← / ← PP_3395 | putative 3‑hydroxy‑3‑methylglutaryl‑CoA lyase/Transcriptional regulator, LysR family |
| RA | 3,951,159 | T→C | intergenic (‑123/+72) | PP_3486 ← / ← PP_3487 | putative cytochrome c/conserved exported protein of unknown function |
| RA | 3,951,161 | A→T | intergenic (‑125/+70) | PP_3486 ← / ← PP_3487 | putative cytochrome c/conserved exported protein of unknown function |
| RA | 4,025,384 | T→C | E105E (GAA→GAG) | emrA ← | multidrug efflux transport system ‑ membrane fusion protein |
| RA | 4,586,030 | 2 bp→TC | intergenic (+113/+101) | PP_4061 → / ← PP_4063 | conserved protein of unknown function/putative Long‑chain‑fatty‑acid‑CoA ligase |
| RA | 4,586,035 | +G | intergenic (+118/+97) | PP_4061 → / ← PP_4063 | conserved protein of unknown function/putative Long‑chain‑fatty‑acid‑CoA ligase |
| RA | 4,586,057 | +C | intergenic (+140/+75) | PP_4061 → / ← PP_4063 | conserved protein of unknown function/putative Long‑chain‑fatty‑acid‑CoA ligase |
| RA | 4,714,831 | C→A | A21D (GCC→GAC) | PP_4173 → | 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 | 4,741,228 | +C | intergenic (+465/+288) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,230 | A→G | intergenic (+467/+286) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,232 | C→T | intergenic (+469/+284) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,235 | C→T | intergenic (+472/+281) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,238 | C→G | intergenic (+475/+278) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,240 | 2 bp→CT | intergenic (+477/+275) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,246 | Δ1 bp | intergenic (+483/+270) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,254 | +T | intergenic (+491/+262) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,258 | A→G | intergenic (+495/+258) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,262 | Δ1 bp | intergenic (+499/+254) | 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 | 4,889,556 | G→A | intergenic (+2/‑151) | hyi → / → glxR | hydroxypyruvate isomerase/tartronate semialdehyde reductase |
| MC JC | 4,892,114 | 1412 bp→8 bp | coding (5‑1416/1416 nt) | pyk → | Pyruvate kinase |
| JC | 4,980,585 | +GGC | intergenic (‑24/+44) | PP_4387 ← / ← flgE | conserved exported protein of unknown function/Flagellar hook protein FlgE |
| MC JC | 5,342,745 | 1681 bp→8 bp | [pgi‑II] | [pgi‑II] | |
| JC | 5,555,608 | +GCC | intergenic (‑84/+87) | PP_4887 ← / ← PP_4888 | conserved protein of unknown function/putative methyl‑accepting chemotaxis transducer |
| RA | 5,674,751 | +G | intergenic (+113/+27) | rhlE‑II → / ← yceI | ATP‑dependent RNA helicase/polyisoprene‑binding protein, acidic stress response factor |
| RA | 5,674,753 | G→C | intergenic (+115/+25) | rhlE‑II → / ← yceI | ATP‑dependent RNA helicase/polyisoprene‑binding protein, acidic stress response factor |
| JC | 5,681,415 | +CGGG | intergenic (‑133/+71) | PP_4986 ← / ← PP_4987 | Channel protein, hemolysin III family/putative Chemotaxis protein |
| RA | 6,013,885 | T→C | intergenic (+90/+20) | xpt → / ← PP_5266 | Xanthine phosphoribosyltransferase/putative acetyl‑CoA hydrolase family protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | AE015451 | 1551214 | 1552909 | 1696 | 35 [33] | [33] 35 | [groL]–pykA | [groL],pykA |
| * | * | ÷ | AE015451 | 1644845 | 1647416 | 2572 | 35 [34] | [34] 36 | gcd–[oprB‑II] | gcd,[oprB‑II] |
| * | * | ÷ | AE015451 | 3276909 | 3278192 | 1284 | 35 [34] | [34] 36 | ampC | ampC |
| * | * | ÷ | AE015451 | 4236728 | 4239334 | 2607 | 35 [33] | [33] 35 | [catA‑I]–catR | [catA‑I],catC,catB,catR |
| * | * | ÷ | AE015451 | 5280859 | 5282499 | 1641 | 37 [33] | [34] 35 | [trmA]–[ypfJ] | [trmA],pcaG,pcaH,[ypfJ] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | AE015451 | 215580 = | NA (NA) | 72 (0.840) | 67/548 | 0.5 | 43.8% | coding (21086/26049 nt) | PP_0168 | putative surface adhesion protein |
| ? | AE015451 | = 2179377 | 93 (1.080) | intergenic (+176/+92) | PP_1931/PP_5486 | conserved protein of unknown function/conserved protein of unknown function | |||||
| * | ? | AE015451 | = 215584 | 0 (0.000) | 48 (0.560) | 47/548 | 1.7 | 52.8% | coding (21090/26049 nt) | PP_0168 | putative surface adhesion protein |
| ? | AE015451 | 2177703 = | 86 (1.000) | intergenic (+104/‑62) | PP_5485/PP_1931 | putative N‑acetyltransferase, GNAT domain/conserved protein of unknown function | |||||
| * | ? | AE015451 | 610901 = | NA (NA) | 73 (0.900) | 69/516 | 0.3 | 100% | intergenic (‑56/‑203) | PP_0525/PP_0526 | TonB‑dependent receptor, B12 family/transposase |
| ? | AE015451 | = 812297 | 0 (0.000) | intergenic (‑46/‑182) | PP_0698/PP_0699 | Transcriptional regulator, LysR family/Transporter, LysE family | |||||
| * | ? | AE015451 | 812296 = | 0 (0.000) | 115 (1.370) | 99/538 | 0.0 | 100% | intergenic (‑45/‑183) | PP_0698/PP_0699 | Transcriptional regulator, LysR family/Transporter, LysE family |
| ? | AE015451 | = 2436567 | NA (NA) | intergenic (+145/‑514) | PP_2134/fadB | transposase/enoyl‑CoA hydratase/3‑hydroxyacyl‑CoA dehydrogenase | |||||
| * | ? | AE015451 | 4896440 = | 0 (0.000) | 117 (1.450) | 81/516 | 0.1 | 100% | intergenic (+73/‑135) | PP_4304/sbp‑I | Cation transporter, VIC family/sulfate ABC transporter |
| ? | AE015451 | 5756808 = | NA (NA) | intergenic (+485/‑203) | glnG/PP_5050 | two‑component system DNA‑binding transcriptional dual regulator GlnL/GlnG/transposase | |||||
| * | ? | AE015451 | = 4896441 | 0 (0.000) | 88 (1.040) | 80/538 | 0.2 | 100% | intergenic (+74/‑134) | PP_4304/sbp‑I | Cation transporter, VIC family/sulfate ABC transporter |
| ? | AE015451 | = 5220211 | NA (NA) | intergenic (+145/+4) | PP_4599/moaB‑II | transposase/molybdenum cofactor biosynthesis protein B | |||||
| * | ? | AE015451 | 5513317 = | 0 (0.000) | 56 (0.690) | 54/516 | 0.9 | 100% | intergenic (+95/‑59) | urtD/urtE | putative Urea ABC transporter, ATP‑binding protein/putative Urea ABC transporter, ATP‑binding protein |
| ? | AE015451 | 5756808 = | NA (NA) | intergenic (+485/‑203) | glnG/PP_5050 | two‑component system DNA‑binding transcriptional dual regulator GlnL/GlnG/transposase | |||||
| * | ? | AE015451 | = 5513318 | 0 (0.000) | 78 (0.930) | 69/538 | 0.4 | 100% | intergenic (+96/‑58) | urtD/urtE | putative Urea ABC transporter, ATP‑binding protein/putative Urea ABC transporter, ATP‑binding protein |
| ? | AE015451 | = 5758121 | NA (NA) | intergenic (+145/+373) | PP_5050/PP_5051 | transposase/conserved protein of unknown function | |||||
| * | ? | AE015451 | = 5984436 | 46 (0.530) | 75 (0.930) | 69/516 | 0.3 | 63.6% | intergenic (+32/+57) | PP_5242/ycaC‑II | Sensor histidine kinase/GAF domain protein/putative hydrolase |
| ? | AE015451 | = 6039183 | NA (NA) | intergenic (‑203/+91) | PP_5290/pyrE | transposase/Orotate phosphoribosyltransferase | |||||
| * | ? | AE015451 | 5988787 = | 1 (0.010) | 98 (1.160) | 89/538 | 0.1 | 99.0% | intergenic (+81/‑465) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | AE015451 | 6037870 = | NA (NA) | intergenic (+72/+145) | argB/PP_5290 | Acetylglutamate kinase/transposase | |||||
| * | ? | AE015451 | = 5988788 | 1 (0.010) | 74 (0.920) | 65/516 | 0.4 | 98.8% | intergenic (+82/‑464) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | AE015451 | = 6039183 | NA (NA) | intergenic (‑203/+91) | PP_5290/pyrE | transposase/Orotate phosphoribosyltransferase | |||||