mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.0 revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 213,804 | T→C | 4.2% | L43L (TTA→TTG) | rof ← | modulator of Rho‑dependent transcription termination |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 290,635 | G→T | 4.9% | intergenic (+2/+14) | ykgS → / ← insB1 | pseudogene/IS1 transposase B |
| RA | 418,961 | Δ1 bp | 100% | coding (1073/1296 nt) | phoR → | sensory histidine kinase in two‑component regulatory system with PhoB |
| RA | 704,083 | C→A | 100% | A47E (GCG→GAG) | nagE → | N‑acetyl glucosamine specific PTS enzyme IIC, IIB, and IIA components |
| RA | 1,130,011 | T→A | 2.9% | S40C (AGT→TGT) | flgM ← | anti‑sigma factor for FliA (sigma 28) |
| RA | 1,157,900:1 | +A | 100% | coding (32/1434 nt) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| RA | 1,224,308 | T→A | 3.7% | T80S (ACC→TCC) | minE ← | cell division topological specificity factor |
| RA | 1,464,303 | G→A | 5.9% | W255* (TGG→TGA) | paaX → | transcriptional repressor of phenylacetic acid degradation paa operon, phenylacetyl‑CoA inducer |
| RA | 1,575,215 | C→T | 4.7% | intergenic (‑13/+32) | pqqL ← / ← yddB | putative periplasmic M16 family zinc metalloendopeptidase/putative TonB‑dependent outer membrane receptor |
| RA | 1,575,216 | G→A | 4.6% | intergenic (‑14/+31) | pqqL ← / ← yddB | putative periplasmic M16 family zinc metalloendopeptidase/putative TonB‑dependent outer membrane receptor |
| RA | 1,575,221 | T→C | 4.6% | intergenic (‑19/+26) | pqqL ← / ← yddB | putative periplasmic M16 family zinc metalloendopeptidase/putative TonB‑dependent outer membrane receptor |
| RA | 1,575,222 | A→G | 4.7% | intergenic (‑20/+25) | pqqL ← / ← yddB | putative periplasmic M16 family zinc metalloendopeptidase/putative TonB‑dependent outer membrane receptor |
| RA | 1,677,565 | Δ1 bp | 4.4% | coding (339/1533 nt) | pntA ← | pyridine nucleotide transhydrogenase, alpha subunit |
| RA | 1,726,390 | G→T | 100% | R123L (CGC→CTC) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| RA | 1,756,374 | G→A | 100% | G226D (GGC→GAC) | pykF → | pyruvate kinase I |
| RA | 1,836,422 | G→A | 3.4% | W117* (TGG→TAG) | ynjB → | putative ABC transporter periplasmic binding protein |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,066,465 | T→C | 100% | K286R (AAG→AGG) | insH1 ← | IS5 transposase and trans‑activator |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,304,520 | G→T | 7.9% | intergenic (+129/+586) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,521 | G→C | 6.5% | intergenic (+130/+585) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,535 | A→G | 8.0% | intergenic (+144/+571) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,538 | C→T | 9.2% | intergenic (+147/+568) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,547 | C→T | 9.7% | intergenic (+156/+559) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,534,205 | G→A | 2.8% | A48T (GCC→ACC) | ptsI → | PEP‑protein phosphotransferase of PTS system (enzyme I) |
| RA | 2,558,274 | A→T | 3.1% | I135N (ATC→AAC) | eutB ← | ethanolamine ammonia‑lyase, large subunit, heavy chain |
| RA | 2,738,923 | G→T | 3.5% | intergenic (+20/+23) | pheA → / ← tyrA | chorismate mutase and prephenate dehydratase, P‑protein/fused chorismate mutase T/prephenate dehydrogenase |
| RA | 2,738,924 | T→C | 3.5% | intergenic (+21/+22) | pheA → / ← tyrA | chorismate mutase and prephenate dehydratase, P‑protein/fused chorismate mutase T/prephenate dehydrogenase |
| RA | 2,738,925 | G→A | 3.4% | intergenic (+22/+21) | pheA → / ← tyrA | chorismate mutase and prephenate dehydratase, P‑protein/fused chorismate mutase T/prephenate dehydrogenase |
| RA | 2,738,926 | A→C | 3.5% | intergenic (+23/+20) | pheA → / ← tyrA | chorismate mutase and prephenate dehydratase, P‑protein/fused chorismate mutase T/prephenate dehydrogenase |
| RA | 2,801,863 | G→A | 3.8% | G173D (GGC→GAC) | nrdE → | ribonucleoside‑diphosphate reductase 2, alpha subunit |
| RA | 2,880,794 | A→G | 3.3% | Y85H (TAC→CAC) | casD ← | CRISP RNA (crRNA) containing Cascade antiviral complex protein |
| RA | 2,951,007 | C→T | 3.7% | A485T (GCC→ACC) | recD ← | exonuclease V (RecBCD complex), alpha chain |
| RA | 3,233,706 | A→G | 2.9% | intergenic (+25/+20) | fadH → / ← higA | 2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked/antitoxinof the HigB‑HigA toxin‑antitoxin system |
| RA | 3,444,515 | G→T | 3.6% | P8Q (CCG→CAG) | rplO ← | 50S ribosomal subunit protein L15 |
| RA | 3,523,475 | C→A | 2.9% | P203T (CCG→ACG) | mrcA → | penicillin‑binding protein 1a, murein transglycosylase and transpeptidase |
| RA | 3,538,206 | G→A | 2.6% | R275H (CGC→CAC) | yhgF → | putative transcriptional accessory protein |
| RA | 3,792,463 | A→T | 4.4% | S30T (TCT→ACT) | kbl ← | glycine C‑acetyltransferase |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| MC JC | 3,909,311 | Δ774 bp | 100% | [pstA]–[pstC] | [pstA], [pstC] | |
| RA | 3,922,564 | A→G | 5.6% | intergenic (‑125/+492) | atpI ← / ← rsmG | ATP synthase, membrane‑bound accessory factor/16S rRNA m(7)G527 methyltransferase, SAM‑dependent, glucose‑inhibited cell‑division protein |
| RA | 3,966,674 | C→T | 6.2% | R87C (CGC→TGC) | rho → | transcription termination factor |
| RA | 3,966,863 | G→A | 4.8% | G150S (GGT→AGT) | rho → | transcription termination factor |
| JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,097,730 | C→A | 4.0% | intergenic (‑283/‑5) | rhaB ← / → rhaS | rhamnulokinase/transcriptional activator of rhaBAD and rhaT |
| RA | 4,102,325 | A→C | 4.3% | T213P (ACC→CCC) ‡ | kdgT → | 2‑keto‑3‑deoxy‑D‑gluconate transporter |
| RA | 4,102,326 | C→A | 4.7% | T213N (ACC→AAC) ‡ | kdgT → | 2‑keto‑3‑deoxy‑D‑gluconate transporter |
| RA | 4,102,329 | T→G | 4.2% | I214S (ATT→AGT) | kdgT → | 2‑keto‑3‑deoxy‑D‑gluconate transporter |
| RA | 4,102,331 | G→C | 4.0% | D215H (GAT→CAT) ‡ | kdgT → | 2‑keto‑3‑deoxy‑D‑gluconate transporter |
| RA | 4,102,333 | T→A | 4.2% | D215E (GAT→GAA) ‡ | kdgT → | 2‑keto‑3‑deoxy‑D‑gluconate transporter |
| RA | 4,102,334 | T→A | 4.2% | L216M (TTG→ATG) ‡ | kdgT → | 2‑keto‑3‑deoxy‑D‑gluconate transporter |
| RA | 4,102,336 | G→C | 4.7% | L216F (TTG→TTC) ‡ | kdgT → | 2‑keto‑3‑deoxy‑D‑gluconate transporter |
| RA | 4,102,338 | C→A | 4.6% | T217N (ACT→AAT) | kdgT → | 2‑keto‑3‑deoxy‑D‑gluconate transporter |
| RA | 4,102,341 | T→G | 5.6% | V218G (GTG→GGG) ‡ | kdgT → | 2‑keto‑3‑deoxy‑D‑gluconate transporter |
| RA | 4,102,342 | G→T | 4.2% | V218V (GTG→GTT) ‡ | kdgT → | 2‑keto‑3‑deoxy‑D‑gluconate transporter |
| RA | 4,147,185 | A→T | 3.7% | T17S (ACT→TCT) | frwD → | putative enzyme IIB component of PTS |
| RA | 4,171,647 | A→C | 100% | noncoding (12/120 nt) | rrfB → | 5S ribosomal RNA of rrnB operon |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| JC | 4,189,484:1 | +CCGGC | 7.9% | coding (4136/4224 nt) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,189,484:2 | +C | 13.9% | coding (4136/4224 nt) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,189,512:1 | +C | 62.2% | coding (4164/4224 nt) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,296,154 | T→C | 25.7% | intergenic (+361/+283) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,189 | A→G | 41.0% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 48.6% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,443,278 | C→T | 3.6% | T299I (ACC→ATC) | tamA → | translocation and assembly module for autotransporter export, outer membrane subunit |
| RA | 4,516,903 | A→C | 2.9% | D272E (GAT→GAG) | fecR ← | anti‑sigma transmembrane signal transducer for ferric citrate transport, periplasmic FecA‑bound ferric citrate sensor and cytoplasmic FecI ECF sigma factor activator |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 954508 | 954856 | 349 | 43 [34] | [38] 40 | focA/ycaO | formate channel/ribosomal protein S12 methylthiotransferase accessory factor |
| * | * | ÷ | NC_000913 | 1211528 | 1212769 | 1242 | 40 [36] | [37] 39 | [icdC]–[ycgX] | [icdC], iraM, [ycgX] |
| * | * | ÷ | NC_000913 | 1299493 | 1300708 | 1216 | 40 [38] | [38] 40 | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| * | * | ÷ | NC_000913 | 1529876 | 1530536 | 661 | 42 [35] | [37] 42 | [rhsE]–ydcD | [rhsE], ydcD |
| * | * | ÷ | NC_000913 | 1640598 | 1641188 | 591 | 39 [33] | [38] 39 | essQ/cspB | Qin prophage, putative S lysis protein/Qin prophage, cold shock protein |
| * | * | ÷ | NC_000913 | 2469006 | 2469810 | 805 | 40 [35] | [34] 42 | [gtrB]–[gtrS] | [gtrB], [gtrS] |
| * | * | ÷ | NC_000913 | 3268693 | 3269662 | 970 | 39 [38] | [35] 39 | [yhaC] | [yhaC] |
| * | * | ÷ | NC_000913 | 3287039 | 3287436 | 398 | 39 [38] | [37] 40 | [yraH] | [yraH] |
| * | * | ÷ | NC_000913 | 4110664 | 4111543 | 880 | 41 [35] | [37] 40 | [cdh]–tpiA | [cdh], tpiA |
| * | * | ÷ | NC_000913 | 4476641 | 4477216 | 576 | 40 [38] | [36] 40 | yjgL | SopA‑central‑domain‑like hexapeptide repeat protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 81 (0.810) | 52/510 | NT | 98.8% | intergenic (+9/‑768) | crl/crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers |
| ? | NC_000913 | = 700605 | 1 (0.010) | coding (990/1221 nt) | nagC | N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor | |||||
| * | ? | NC_000913 | 257908 = | NA (NA) | 83 (0.830) | 65/510 | NT | 100% | intergenic (+9/‑768) | crl/crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers |
| ? | NC_000913 | = 1293039 | 0 (0.000) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | = 258675 | NA (NA) | 85 (0.850) | 64/510 | NT | 100% | intergenic (+776/‑1) | crl/crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers |
| ? | NC_000913 | 700597 = | 0 (0.000) | coding (998/1221 nt) | nagC | N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor | |||||
| * | ? | NC_000913 | = 1066842 | 93 (0.930) | 3 (0.030) | 3/490 | NT | 3.2% | intergenic (+16/+22) | agp/yccJ | glucose‑1‑phosphatase/inositol phosphatase/uncharacterized protein |
| ? | NC_000913 | = 1066847 | 94 (0.980) | intergenic (+21/+17) | agp/yccJ | glucose‑1‑phosphatase/inositol phosphatase/uncharacterized protein | |||||
| * | ? | NC_000913 | 1207790 = | 32 (0.320) | 62 (0.660) | 53/478 | NT | 67.4% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 30 (0.320) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 31 (0.310) | 81 (0.870) | 52/478 | NT | 73.3% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 30 (0.320) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 5 (0.050) | 78 (0.780) | 58/510 | NT | 94.0% | intergenic (‑110/‑495) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| ? | NC_000913 | = 1979270 | NA (NA) | intergenic (‑55/‑483) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 34 (0.350) | 28/502 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 1575208 = | 77 (0.770) | 4 (0.040) | 4/496 | NT | 5.1% | intergenic (‑6/+39) | pqqL/yddB | putative periplasmic M16 family zinc metalloendopeptidase/putative TonB‑dependent outer membrane receptor |
| ? | NC_000913 | 1575230 = | 73 (0.750) | intergenic (‑28/+17) | pqqL/yddB | putative periplasmic M16 family zinc metalloendopeptidase/putative TonB‑dependent outer membrane receptor | |||||
| * | ? | NC_000913 | = 1751528 | 109 (1.090) | 3 (0.030) | 3/496 | NT | 2.6% | coding (197/648 nt) | ydhW | FNR, Nar, NarP‑regulated protein, putative subunit of YdhYVWXUT oxidoreductase complex |
| ? | NC_000913 | = 1751544 | 118 (1.220) | coding (181/648 nt) | ydhW | FNR, Nar, NarP‑regulated protein, putative subunit of YdhYVWXUT oxidoreductase complex | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 41 (0.410) | 27/510 | NT | 100% | intergenic (‑271/‑267) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | 2101749 = | NA (NA) | intergenic (‑5/+146) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | = 1979489 | 0 (0.000) | 85 (0.850) | 56/510 | NT | 100% | intergenic (‑274/‑264) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | = 2290111 | NA (NA) | intergenic (‑32/+1) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system | |||||
| * | ? | NC_000913 | 2375822 = | 89 (0.890) | 3 (0.030) | 3/502 | NT | 3.3% | coding (139/963 nt) | menC | O‑succinylbenzoyl‑CoA synthase |
| ? | NC_000913 | = 2515611 | NA (NA) | intergenic (+170/+30) | insL1/yfeA | IS186 transposase/putative diguanylate cyclase | |||||
| * | ? | NC_000913 | = 2375834 | 87 (0.870) | 4 (0.040) | 4/504 | NT | 4.4% | coding (127/963 nt) | menC | O‑succinylbenzoyl‑CoA synthase |
| ? | NC_000913 | 2514275 = | NA (NA) | intergenic (+33/‑54) | nupC/insL1 | nucleoside (except guanosine) transporter/IS186 transposase | |||||
| * | ? | NC_000913 | 2738911 = | NA (NA) | 4 (0.040) | 4/486 | NT | NA | intergenic (+8/+35) | pheA/tyrA | chorismate mutase and prephenate dehydratase, P‑protein/fused chorismate mutase T/prephenate dehydrogenase |
| ? | NC_000913 | 2738939 = | NA (NA) | intergenic (+36/+7) | pheA/tyrA | chorismate mutase and prephenate dehydratase, P‑protein/fused chorismate mutase T/prephenate dehydrogenase | |||||
| * | ? | NC_000913 | 3216163 = | 124 (1.250) | 4 (0.040) | 4/490 | NT | 3.4% | coding (327/765 nt) | yqjH | putative siderophore interacting protein |
| ? | NC_000913 | 3216245 = | 105 (1.100) | coding (245/765 nt) | yqjH | putative siderophore interacting protein | |||||
| * | ? | NC_000913 | 4102316 = | 86 (0.860) | 4 (0.040) | 4/492 | NT | 4.5% | coding (628/984 nt) | kdgT | 2‑keto‑3‑deoxy‑D‑gluconate transporter |
| ? | NC_000913 | 4102352 = | 87 (0.910) | coding (664/984 nt) | kdgT | 2‑keto‑3‑deoxy‑D‑gluconate transporter | |||||
| * | ? | NC_000913 | 4171222 = | 0 (0.000) | 4 (0.040) | 4/504 | NT | 100% | noncoding (2583/2904 nt) | rrlB | 23S ribosomal RNA of rrnB operon |
| ? | NC_000913 | 4212633 = | NA (NA) | noncoding (2592/2904 nt) | rrlE | 23S ribosomal RNA of rrnE operon | |||||
| * | ? | NC_000913 | 4295831 = | NA (NA) | 7 (0.080) | 3/432 | NT | NA | intergenic (+38/+606) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| ? | NC_000913 | = 4296395 | NA (NA) | noncoding (562/602 nt) | RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites | |||||
| * | ? | NC_000913 | 4516892 = | 121 (1.220) | 5 (0.050) | 5/492 | NT | 4.1% | coding (827/954 nt) | fecR | anti‑sigma transmembrane signal transducer for ferric citrate transport, periplasmic FecA‑bound ferric citrate sensor and cytoplasmic FecI ECF sigma factor activator |
| ? | NC_000913 | 4516926 = | 117 (1.220) | coding (793/954 nt) | fecR | anti‑sigma transmembrane signal transducer for ferric citrate transport, periplasmic FecA‑bound ferric citrate sensor and cytoplasmic FecI ECF sigma factor activator | |||||