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 |
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 | 4,635,709 | C→T | G16D (GGT→GAT) | uvrY ← | BarA/UvrY two‑componenent system response regulator |
RA | 4,733,447 | A→G | Y730H (TAT→CAT) | sucA ← | 2‑oxoglutarate dehydrogenase subunit E1 |
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 | 5,948,277 | C→T | R66H (CGT→CAT) | rho ← | transcription termination factor Rho |
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 | 55549 | 55610 | 62 | 2 [1] | [1] 3 | PP_5423 | membrane protein |
* | * | ÷ | NC_002947 | 171377–172964 | 176273–172979 | 16–4897 | 2 [1] | [0] 2 | PP_16SA–[PP_5SA] | PP_16SA,PP_23SA,[PP_5SA] |
* | * | ÷ | NC_002947 | 176681–178394 | 181681–178409 | 16–5001 | 2 [1] | [1] 3 | PP_16SB–[PP_r01] | PP_16SB,PP_23SB,[PP_r01] |
* | * | ÷ | NC_002947 | 1180094 | 1180169 | 76 | 2 [1] | [1] 2 | PP_1033 | sulfatase domain‑containing protein |
* | * | ÷ | NC_002947 | 1370683 | 1370719 | 37 | 3 [1] | [0] 2 | PP_1195 | hypothetical protein |
* | * | ÷ | NC_002947 | 2005743 | 2005800 | 58 | 2 [1] | [1] 2 | PP_1788/PP_1789 | hypothetical protein/haloacid dehalogenase‑like family hydrolase |
* | * | ÷ | NC_002947 | 2087939 | 2088036 | 98 | 2 [1] | [1] 3 | PP_1865/aroH | transposase/3‑deoxy‑7‑phosphoheptulonate synthase |
* | * | ÷ | NC_002947 | 2109471 | 2109534 | 64 | 4 [1] | [0] 2 | PP_1882 | membrane protein |
* | * | ÷ | NC_002947 | 2182469 | 2182555 | 87 | 2 [1] | [1] 2 | PP_5487 | hypothetical protein |
* | * | ÷ | NC_002947 | 2185201 | 2185334 | 134 | 2 [1] | [1] 2 | PP_1936 | membrane protein |
* | * | ÷ | NC_002947 | 2599424 | 2599512 | 89 | 2 [0] | [1] 2 | PP_2277 | hypothetical protein |
* | * | ÷ | NC_002947 | 2837046 | 2837179 | 134 | 2 [1] | [1] 2 | [sad‑I] | [sad‑I] |
* | * | ÷ | NC_002947 | 3382852 | 3382876 | 25 | 2 [0] | [1] 2 | PP_5545/PP_5546 | hypothetical protein/hypothetical protein |
* | * | ÷ | NC_002947 | 3411408 | 3411509 | 102 | 2 [1] | [1] 3 | [PP_5550]–[PP_5551] | [PP_5550],[PP_5551] |
* | * | ÷ | NC_002947 | 3517331 | 3517413 | 83 | 2 [1] | [1] 3 | PP_5578 | hypothetical protein |
* | * | ÷ | NC_002947 | 3520268 | 3520360 | 93 | 2 [1] | [1] 2 | PP_5582 | hypothetical protein |
* | * | ÷ | NC_002947 | 3521321 | 3521418 | 98 | 2 [1] | [1] 2 | PP_5582/PP_5583 | hypothetical protein/hypothetical protein |
* | * | ÷ | NC_002947 | 3578813 | 3578839 | 27 | 3 [1] | [1] 2 | PP_5589 | rhs repeat‑associated core domain‑containing protein |
* | * | ÷ | NC_002947 | 3733549 | 3734281 | 733 | 16 [0] | [1] 2 | [PP_3300]–[PP_3301] | [PP_3300],[PP_3301] |
* | * | ÷ | NC_002947 | 3734487 | 3736072 | 1586 | 2 [1] | [0] 2 | [PP_3301]–[PP_3302] | [PP_3301],[PP_3302] |
* | * | ÷ | NC_002947 | 3736210 | 3739457 | 3248 | 2 [0] | [1] 2 | [PP_3302]–[PP_3303] | [PP_3302],[PP_3303] |
* | * | ÷ | NC_002947 | 3739502 | 3743303 | 3802 | 2 [1] | [1] 2 | [PP_3303]–[paoA] | [PP_3303],PP_3304,PP_3305,PP_3306,PP_3307,[paoA] |
* | * | ÷ | NC_002947 | 3743306 | 3744589 | 1284 | 2 [1] | [1] 2 | [paoA]–[paoB] | [paoA],[paoB] |
* | * | ÷ | NC_002947 | 3744737 | 3744906 | 170 | 2 [1] | [1] 2 | paoC | aromatic aldehyde dehydrogenase molybdopterin‑binding subunit |
* | * | ÷ | NC_002947 | 3745039 | 3751112 | 6074 | 2 [1] | [1] 2 | [paoC]–[PP_3316] | [paoC],kefB‑II,PP_3312,PP_3313,PP_3314,PP_3315,[PP_3316] |
* | * | ÷ | NC_002947 | 3751224 | 3752275 | 1052 | 2 [1] | [1] 2 | PP_3316 | chaperone‑associated ATPase |
* | * | ÷ | NC_002947 | 3752422 | 3752752 | 331 | 2 [1] | [1] 2 | PP_3316 | chaperone‑associated ATPase |
* | * | ÷ | NC_002947 | 3752855 | 3753313 | 459 | 2 [1] | [1] 2 | PP_3316 | chaperone‑associated ATPase |
* | * | ÷ | NC_002947 | 3753426 | 3754781 | 1356 | 2 [1] | [1] 2 | [PP_3316]–[PP_3319] | [PP_3316],PP_3317,PP_3318,[PP_3319] |
* | * | ÷ | NC_002947 | 3754850 | 3756211 | 1362 | 2 [1] | [1] 2 | PP_3319 | GGDEF domain‑containing sensory box protein |
* | * | ÷ | NC_002947 | 3756338 | 3757179 | 842 | 2 [1] | [1] 2 | [PP_3319]–[PP_3321] | [PP_3319],PP_3320,[PP_3321] |
* | * | ÷ | NC_002947 | 3757200 | 3759561 | 2362 | 2 [1] | [1] 2 | [PP_3321]–[folEB] | [PP_3321],hemBB,PP_3323,[folEB] |
* | * | ÷ | NC_002947 | 3759721 | 3759976 | 256 | 2 [1] | [1] 2 | folEB | GTP cyclohydrolase I |
* | * | ÷ | NC_002947 | 3760061 | 3761145 | 1085 | 2 [1] | [0] 2 | [folEB]–[PP_3325] | [folEB],[PP_3325] |
* | * | ÷ | NC_002947 | 3761374 | 3761938 | 565 | 2 [1] | [1] 2 | PP_3325 | ferric siderophore receptor |
* | * | ÷ | NC_002947 | 3762034 | 3764933 | 2900 | 2 [1] | [1] 2 | [PP_3325]–PP_3326 | [PP_3325],PP_3326 |
* | * | ÷ | NC_002947 | 3765008 | 3767079 | 2072 | 2 [1] | [1] 2 | PP_3328–[PP_3329] | PP_3328,PP_5599,[PP_3329] |
* | * | ÷ | NC_002947 | 3767098 | 3767872 | 775 | 2 [1] | [1] 2 | [PP_3329] | [PP_3329] |
* | * | ÷ | NC_002947 | 3767918 | 3768138 | 221 | 2 [1] | [0] 2 | [PP_5600] | [PP_5600] |
* | * | ÷ | NC_002947 | 3768404 | 3768836 | 433 | 2 [1] | [1] 2 | [PP_3330] | [PP_3330] |
* | * | ÷ | NC_002947 | 3768848 | 3769188 | 341 | 2 [1] | [1] 2 | PP_3330 | ferric siderophore receptor |
* | * | ÷ | NC_002947 | 3769473 | 3772051 | 2579 | 2 [1] | [0] 2 | [PP_3330]–[PP_3331] | [PP_3330],[PP_3331] |
* | * | ÷ | NC_002947 | 3772175 | 3773550 | 1376 | 3 [1] | [1] 2 | PP_3332–[PP_5743] | PP_3332,PP_3333,[PP_5743] |
* | * | ÷ | NC_002947 | 3773585 | 3773892 | 308 | 2 [1] | [1] 2 | PP_5743 | TonB‑dependent receptor protein |
* | * | ÷ | NC_002947 | 3774035 | 3774738 | 704 | 2 [1] | [1] 2 | [PP_5743]–[PP_3335] | [PP_5743],[PP_3335] |
* | * | ÷ | NC_002947 | 3774999 | 3775120 | 122 | 2 [1] | [1] 2 | [PP_3336] | [PP_3336] |
* | * | ÷ | NC_002947 | 3775330 | 3776527 | 1198 | 3 [1] | [1] 2 | [PP_3336]–[PP_3339] | [PP_3336],PP_3337,PP_3338,[PP_3339] |
* | * | ÷ | NC_002947 | 3776565 | 3777201 | 637 | 2 [1] | [1] 2 | [PP_3339]–[PP_3340] | [PP_3339],[PP_3340] |
* | * | ÷ | NC_002947 | 3777465 | 3778509 | 1045 | 2 [1] | [0] 2 | PP_3340 | TonB‑dependent receptor |
* | * | ÷ | NC_002947 | 3778635 | 3779485 | 851 | 2 [0] | [1] 2 | [PP_3340]–nikR | [PP_3340],nikR |
* | * | ÷ | NC_002947 | 3779614 | 3779705 | 92 | 2 [1] | [1] 2 | nikA | nickel ABC transporter substrate‑binding protein |
* | * | ÷ | NC_002947 | 3779798 | 3780143 | 346 | 2 [1] | [1] 2 | nikA | nickel ABC transporter substrate‑binding protein |
* | * | ÷ | NC_002947 | 3780189 | 3781558 | 1370 | 2 [1] | [0] 2 | [nikA]–[nikB] | [nikA],[nikB] |
* | * | ÷ | NC_002947 | 3781707 | 3784045 | 2339 | 2 [1] | [1] 2 | [nikB]–[nikE] | [nikB],nikC,nikD,[nikE] |
* | * | ÷ | NC_002947 | 3784118 | 3785940 | 1823 | 2 [1] | [1] 2 | [nikE]–[PP_3348] | [nikE],[PP_3348] |
* | * | ÷ | NC_002947 | 3786029 | 3787705 | 1677 | 2 [1] | [0] 2 | [mhpT]–[PP_3350] | [mhpT],[PP_3350] |
* | * | ÷ | NC_002947 | 3787834 | 3788578 | 745 | 2 [0] | [1] 2 | PP_3350 | hypothetical protein |
* | * | ÷ | NC_002947 | 3788625 | 3790412 | 1788 | 2 [1] | [1] 2 | [PP_3350]–[atsA] | [PP_3350],[atsA] |
* | * | ÷ | NC_002947 | 3790551 | 3790893 | 343 | 2 [1] | [1] 2 | [atsA]–[PP_3353] | [atsA],[PP_3353] |
* | * | ÷ | NC_002947 | 3791339 | 3793332 | 1994 | 2 [1] | [0] 16 | [PP_3353]–[PP_3355] | [PP_3353],PP_3354,[PP_3355] |
* | * | ÷ | NC_002947 | 4195165 | 4195318 | 154 | 3 [1] | [1] 2 | PP_3688 | hypothetical protein |
* | * | ÷ | NC_002947 | 4232624 | 4232643 | 20 | 2 [1] | [1] 3 | PP_3710 | hypothetical protein |
* | * | ÷ | NC_002947 | 4373414 | 4373445 | 32 | 3 [1] | [1] 2 | PP_3849 | hemolysin‑type calcium‑binding protein |
* | * | ÷ | NC_002947 | 4376687 | 4376743 | 57 | 2 [1] | [1] 2 | PP_3852 | BNR domain‑containing protein |
* | * | ÷ | NC_002947 | 4619128 | 4619582 | 455 | 3 [1] | [1] 2 | PP_5652/PP_5654 | hypothetical protein/phosphotriesterase |
* | * | ÷ | NC_002947 | 4624212 | 4624357 | 146 | 2 [1] | [1] 3 | PP_5654/PP_4091 | phosphotriesterase/transposase |
* | * | ÷ | NC_002947 | 4628394 | 4628517 | 124 | 2 [1] | [1] 2 | PP_4092/PP_5655 | transposase/hypothetical protein |
* | * | ÷ | NC_002947 | 4808163 | 4808235 | 73 | 4 [1] | [1] 2 | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
* | * | ÷ | NC_002947 | 5004572 | 5004642 | 71 | 2 [1] | [0] 2 | PP_4410 | hypothetical protein |
* | * | ÷ | NC_002947 | 5042356 | 5042450 | 95 | 2 [0] | [1] 2 | PP_4447 | hypothetical protein |
* | * | ÷ | NC_002947 | 5068711 | 5068815 | 105 | 2 [1] | [1] 3 | PP_4465 | porin |
* | * | ÷ | NC_002947 | 5603508 | 5603606 | 99 | 3 [1] | [1] 2 | PP_4925 | hypothetical protein |
Unassigned new junction evidence | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NC_002947 | = 1499458 | 35 (0.720) | 9 (0.190) | 8/280 | 1.1 | 24.8% | intergenic (+35/‑129) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
? | NC_002947 | = 1499495 | 20 (0.420) | intergenic (+72/‑92) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein | |||||
* | ? | NC_002947 | 2301453 = | 0 (0.000) | 38 (0.800) | 22/278 | 0.5 | 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) | 16 (0.330) | 16/280 | 0.7 | 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 | = 3733548 | 0 (0.000) | 16 (0.330) | 16/284 | 0.7 | 100% | coding (237/615 nt) | PP_3300 | Transcriptional regulator, tetR family |
? | NC_002947 | 3793333 = | 0 (0.000) | coding (1190/1191 nt) | PP_3355 | beta‑ketothiolase | |||||
* | ? | NC_002947 | 5545321 = | NA (NA) | 21 (0.440) | 21/280 | 0.5 | 100% | intergenic (‑461/+416) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB |
? | NC_002947 | = 5621245 | 0 (0.000) | coding (19/774 nt) | PP_4939 | hypothetical protein | |||||
* | ? | NC_002947 | = 5545666 | NA (NA) | 14 (0.290) | 12/278 | 0.9 | 100% | intergenic (‑806/+71) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB |
? | NC_002947 | 5621244 = | 0 (0.000) | coding (20/774 nt) | PP_4939 | hypothetical protein |