breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
Predicted mutations | |||||
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evidence | position | mutation | annotation | gene | description |
RA | 191,125 | C→T | V83M (GTG→ATG) | PP_0166 ← | HlyD family secretion protein |
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 | 1,126,647 | +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 | 1,581,266 | G→T | A44D (GCC→GAC) | ttgB ← | efflux pump membrane protein TtgB |
RA | 1,795,651 | Δ1 bp | coding (464/504 nt) | PP_1600 → | Skp‑like 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 |
RA | 3,845,705 | +G | intergenic (‑72/+26) | PP_3394 ← / ← PP_3395 | 3‑hydroxy‑3‑methylglutaryl‑CoA lyase/LysR family transcriptional regulator |
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 | 4,682,024 | +A | coding (314/1431 nt) | mltD → | membrane‑bound lytic murein transglycosylase D |
RA | 4,738,324 | C→T | G16S (GGC→AGC) | sdhA ← | succinate dehydrogenase flavoprotein subunit |
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 | 5,621,706 | G→A | L194F (CTT→TTT) | PP_4940 ← | glycosyltransferase |
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 |
MC JC | 5,985,398 | Δ11 bp | coding (188‑198/405 nt) | PP_5244 ← | AraC family transcriptional regulator |
RA | 5,987,130 | T→G | I71S (ATC→AGC) | kefB‑III → | 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 | ||||||||||
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seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | NC_002947 | 171390–176275 | 176275 | 1–4886 | 6 [5] | [5] 7 | [PP_16SA]–[PP_5SA] | [PP_16SA],PP_23SA,[PP_5SA] |
* | * | ÷ | NC_002947 | 176676–181700 | 181700 | 1–5025 | 6 [3] | [4] 6 | PP_16SB–[PP_r01] | PP_16SB,PP_23SB,[PP_r01] |
* | * | ÷ | NC_002947 | 1367623 | 1367810 | 188 | 6 [5] | [5] 6 | PP_1193 | membrane protein |
* | * | ÷ | NC_002947 | 1370665 | 1370771 | 107 | 6 [5] | [5] 6 | PP_1195 | hypothetical protein |
* | * | ÷ | NC_002947 | 2299511 | 2299564 | 54 | 6 [5] | [4] 6 | sbcC | exonuclease subunit SbcC |
* | * | ÷ | NC_002947 | 2759345 | 2759520 | 176 | 6 [5] | [5] 6 | PP_2413 | GGDEF domain‑containing protein |
Unassigned new junction evidence | |||||||||||
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seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NC_002947 | 2301453 = | 0 (0.000) | 33 (1.300) | 22/284 | 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) | 21 (0.820) | 17/286 | 0.6 | 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 | = 2472115 | 9 (0.350) | 5 (0.200) | 5/276 | 2.6 | 27.4% | intergenic (+19/+130) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase |
? | NC_002947 | 2472313 = | 18 (0.730) | coding (1783/1851 nt) | PP_2167 | PhoD‑like phosphatase | |||||
* | ? | NC_002947 | = 2957080 | 15 (0.580) | 7 (0.280) | 7/280 | 2.1 | 26.7% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
? | NC_002947 | 2957165 = | 24 (0.960) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
* | ? | NC_002947 | = 5988771 | 16 (0.620) | 6 (0.240) | 6/274 | 2.3 | 24.9% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
? | NC_002947 | 5988963 = | 21 (0.860) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |