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 | 1,095,512 | +A | coding (549/1494 nt) | rpoN ← | RNA polymerase sigma‑54 factor |
| RA | 1,126,647 | +C | intergenic (‑101/+48) | tdcG‑II ← / ← gcvP‑I | L‑serine dehydratase/glycine dehydrogenase |
| RA | 1,212,521 | C→T | intergenic (‑55/+133) | PP_1060 ← / ← PP_1061 | glutamate synthase large subunit/ATP‑dependent DNA helicase |
| 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 | 1,581,266 | G→T | A44D (GCC→GAC) | ttgB ← | efflux pump membrane protein TtgB |
| 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 | 2,202,220 | G→A | intergenic (+77/‑104) | PP_1946 → / → PP_1947 | short‑chain dehydrogenase/reductase family oxidoreductase/hypothetical protein |
| RA | 2,722,068 | C→T | Q197* (CAG→TAG) | PP_2382 → | putative transporter |
| RA | 2,921,460 | G→A | G3494R (GGG→AGG) | PP_2561 → | hemolysin‑type calcium‑binding bacteriocin |
| 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 | 4,718,040 | T→A | M202K (ATG→AAG) | fabB → | 3‑oxoacyl‑ACP synthase |
| 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 |
| 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 | 5,674,751 | +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 | 5,947,807 | C→A | V223L (GTG→TTG) | rho ← | transcription termination factor Rho |
| 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 |
| RA | 6,150,396 | C→T | intergenic (‑2580/‑594) | PP_5393 ← / → PP_5395 | metal‑binding chaperone/hypothetical protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_002947 | 171386–176276 | 176276 | 1–4891 | 8 [6] | [6] 7 | PP_16SA–[PP_5SA] | PP_16SA,PP_23SA,[PP_5SA] |
| * | * | ÷ | NC_002947 | 176666–181522 | 181522 | 1–4857 | 7 [6] | [6] 7 | PP_16SB–[PP_23SB] | PP_16SB,[PP_23SB] |
| * | * | ÷ | NC_002947 | 1124526 | 1124615 | 90 | 7 [6] | [6] 7 | gcvT‑I | aminomethyltransferase |
| * | * | ÷ | NC_002947 | 2299501 | 2299618 | 118 | 8 [6] | [6] 7 | sbcC | exonuclease subunit SbcC |
| * | * | ÷ | NC_002947 | 4808180 | 4808230 | 51 | 13 [0] | [6] 7 | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | * | ÷ | NC_002947 | 5525440–5525474 | 5525539 | 66–100 | 7 [5] | [4] 7 | PP_4858 | hypothetical protein |
| * | * | ÷ | NC_002947 | 5716209 | 5716350 | 142 | 7 [5] | [6] 7 | tatC‑II | Sec‑independent protein translocase protein |
| * | * | ÷ | NC_002947 | 6098363 | 6098486 | 124 | 7 [6] | [6] 7 | PP_5350 | RpiR family transcriptional regulator |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 181656 | 0 (0.000) | 6 (0.210) | 6/278 | 2.7 | 100% | intergenic (+122/‑11) | PP_23SB/PP_r01 | 23S ribosomal RNA/5S ribosomal RNA |
| ? | NC_002947 | = 1330343 | NA (NA) | intergenic (+125/‑7) | PP_23SE/PP_5SE | 23S ribosomal RNA/5S ribosomal RNA | |||||
| * | ? | NC_002947 | 1440000 = | NA (NA) | 32 (1.090) | 31/280 | 0.1 | 100% | intergenic (‑331/‑328) | yveA/PP_1260 | aspartate‑proton symporter/transposase |
| ? | NC_002947 | = 1844451 | 0 (0.000) | coding (343/2754 nt) | gacS | sensor protein GacS | |||||
| * | ? | NC_002947 | = 1441693 | NA (NA) | 31 (1.040) | 24/284 | 0.3 | 100% | intergenic (+37/+395) | PP_1260/ghrB | transposase/2‑ketoaldonate reductase/hydroxypyruvate/glyoxylate reductase |
| ? | NC_002947 | 1844449 = | 0 (0.000) | coding (345/2754 nt) | gacS | sensor protein GacS | |||||
| * | ? | NC_002947 | 2301453 = | 0 (0.000) | 31 (1.040) | 25/284 | 0.3 | 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) | 31 (1.040) | 26/286 | 0.3 | 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 | 22 (0.730) | 6 (0.210) | 6/280 | 2.7 | 21.3% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947 | 2957165 = | 23 (0.790) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947 | = 4808179 | 0 (0.000) | 5 (0.190) | 5/250 | 2.7 | 30.3% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5988949 | 23 (0.880) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | 5545321 = | NA (NA) | 37 (1.240) | 29/286 | 0.2 | 97.4% | intergenic (‑461/+416) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB |
| ? | NC_002947 | = 5621245 | 1 (0.030) | coding (19/774 nt) | PP_4939 | hypothetical protein | |||||
| * | ? | NC_002947 | = 5545666 | NA (NA) | 46 (1.550) | 31/284 | 0.1 | 97.9% | intergenic (‑806/+71) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB |
| ? | NC_002947 | 5621244 = | 1 (0.030) | coding (20/774 nt) | PP_4939 | hypothetical protein | |||||