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 | 148,372 | G→A | 2.8% | Q142* (CAG→TAG) | panC ← | pantothenate synthetase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 277,324 | A→G | 6.4% | S204G (AGC→GGC) | mmuM → | CP4‑6 prophage, S‑methylmethionine:homocysteine methyltransferase |
| RA | 418,428 | Δ1 bp | 2.7% | coding (540/1296 nt) | phoR → | sensory histidine kinase in two‑component regulatory system with PhoB |
| RA | 434,727 | T→C | 3.3% | N27N (AAT→AAC) | ribE → | riboflavin synthase beta chain |
| RA | 701,374 | C→T | 44.5% | R74H (CGC→CAC) | nagC ← | N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor |
| RA | 702,331 | Δ1 bp | 20.8% | coding (421/1149 nt) | nagA ← | N‑acetylglucosamine‑6‑phosphate deacetylase |
| RA | 1,158,384 | G→A | 30.5% | W172* (TGG→TGA) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| JC | 1,159,286:1 | +GTA | 55.8% | coding (1418/1434 nt) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| RA | 1,399,978 | Δ1 bp | 2.8% | coding (259/516 nt) | ogt ← | O‑6‑alkylguanine‑DNA:cysteine‑protein methyltransferase |
| RA | 1,466,210 | G→A | 5.5% | pseudogene (819/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,579 | G→C | 7.0% | pseudogene (1188/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,585 | T→C | 8.0% | pseudogene (1194/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,726 | G→A | 5.7% | pseudogene (1335/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| JC | 1,726,060:1 | (ACATCT)1→2 | 32.6% | coding (38/600 nt) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| JC | 1,726,392 | Δ16 bp | 11.3% | coding (370‑385/600 nt) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| RA | 1,726,507 | Δ1 bp | 27.4% | coding (485/600 nt) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| RA | 1,794,465 | Δ1 bp | 2.9% | coding (688/981 nt) | btuC ← | vitamin B12 ABC transporter permease |
| 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 | 2,204,075 | Δ1 bp | 2.6% | coding (106/318 nt) | yehK → | uncharacterized protein |
| RA | 2,274,537:1 | +C | 2.6% | coding (361/1095 nt) | yejB → | microcin C ABC transporter permease |
| RA | 2,304,686 | A→G | 6.0% | intergenic (+295/+420) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| JC | 2,765,454 | (TATGGCAC)6→5 | 3.6% | intergenic (‑303/+50) | yfjL ← / ← yfjM | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein/CP4‑57 prophage, uncharacterized protein |
| RA | 2,917,940 | A→T | 2.6% | intergenic (+129/+103) | barA → / ← gudD | hybrid sensory histidine kinase, in two‑component regulatory system with UvrY/D‑glucarate dehydratase 1 |
| RA | 2,977,594:1 | +C | 29.2% | coding (998/1032 nt) | galR → | galactose‑inducible d‑galactose regulon transcriptional repressor, autorepressor |
| RA | 3,004,822 | A→C | 54.0% | N321K (AAT→AAG) | ygeV ← | putative sigma‑54‑interacting transcriptional activator |
| RA | 3,006,180 | Δ1 bp | 2.6% | intergenic (‑396/‑80) | ygeV ← / → ygeW | putative sigma‑54‑interacting transcriptional activator/putative carbamoyltransferase |
| RA | 3,092,028 | C→T | 3.2% | R51R (CGC→CGT) | gshB → | glutathione synthetase |
| RA | 3,214,542 | Δ1 bp | 2.9% | coding (1498/1842 nt) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 3,233,262 | A→G | 9.4% | I534V (ATC→GTC) | fadH → | 2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked |
| RA | 3,412,964 | Δ1 bp | 2.5% | coding (500/663 nt) | acrS ← | acrAB operon transcriptional repressor |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,824,718 | A→G | 4.0% | S69G (AGC→GGC) | trmH → | tRNA mG18‑2'‑O‑methyltransferase, SAM‑dependent |
| MC JC | 3,909,311 | Δ774 bp | 100% | [pstA]–[pstC] | [pstA], [pstC] | |
| JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| 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 |
| RA | 4,295,833 | T→C | 5.9% | intergenic (+40/+604) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,059 | C→T | 10.4% | intergenic (+266/+378) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,154 | T→C | 10.6% | intergenic (+361/+283) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,189 | A→G | 38.2% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 43.0% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,472,296 | T→G | 14.0% | N34T (AAC→ACC) | pyrB ← | aspartate carbamoyltransferase, catalytic subunit |
| RA | 4,560,126 | A→G | 3.3% | F186L (TTT→CTT) | yjiH ← | nucleoside recognition pore and gate family putative inner membrane transporter |
| RA | 4,614,497 | C→T | 5.2% | intergenic (+236/+184) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423843–3424230 | 3424410–3424237 | 8–568 | 67 [66] | [63] 70 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 4110668 | 4111544 | 877 | 70 [64] | [66] 67 | [cdh]–tpiA | [cdh], tpiA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 153986 = | 111 (0.720) | 49 (0.320) | 38/522 | NT | 30.6% | coding (1441/2598 nt) | htrE | putative outer membrane usher protein |
| ? | NC_000913 | = 275149 | NA (NA) | intergenic (‑32/‑176) | insH1/mmuP | IS5 transposase and trans‑activator/CP4‑6 prophage, putative S‑methylmethionine transporter | |||||
| * | ? | NC_000913 | = 153989 | 108 (0.700) | 53 (0.350) | 37/522 | NT | 32.9% | coding (1438/2598 nt) | htrE | putative outer membrane usher protein |
| ? | NC_000913 | 273955 = | NA (NA) | intergenic (+1/+146) | ykfC/insH1 | CP4‑6 prophage, conserved protein,Phage or Prophage Related/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | 228016 = | NA (NA) | 7 (0.050) | 7/508 | NT | NA | noncoding (2258/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913 | 228041 = | NA (NA) | noncoding (2283/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | 257908 = | NA (NA) | 142 (0.930) | 82/522 | NT | 98.6% | 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 | 2 (0.010) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | = 275149 | NA (NA) | 9 (0.060) | 8/522 | NT | 4.2% | intergenic (‑32/‑176) | insH1/mmuP | IS5 transposase and trans‑activator/CP4‑6 prophage, putative S‑methylmethionine transporter |
| ? | NC_000913 | = 419062 | 205 (1.340) | coding (1174/1296 nt) | phoR | sensory histidine kinase in two‑component regulatory system with PhoB | |||||
| * | ? | NC_000913 | = 381689 | NA (NA) | 4 (0.030) | 4/504 | NT | NA | coding (339/366 nt) coding (16/906 nt) |
insC1 insD1 |
IS2 repressor TnpA IS2 transposase TnpB |
| ? | NC_000913 | = 381743 | NA (NA) | coding (70/906 nt) | insD1 | IS2 transposase TnpB | |||||
| * | ? | NC_000913 | = 555833 | 164 (1.070) | 5 (0.030) | 3/490 | NT | 3.3% | coding (1223/1386 nt) | cysS | cysteinyl‑tRNA synthetase |
| ? | NC_000913 | = 556784 | 143 (0.990) | coding (90/213 nt) | ybcJ | ribosome‑associated protein, putative RNA‑binding protein | |||||
| * | ? | NC_000913 | = 641354 | 107 (0.700) | 3 (0.020) | 3/508 | NT | 2.8% | intergenic (+36/+85) | ahpF/uspG | alkyl hydroperoxide reductase, F52a subunit, FAD/NAD(P)‑binding/universal stress protein UP12 |
| ? | NC_000913 | = 641366 | 107 (0.720) | intergenic (+48/+73) | ahpF/uspG | alkyl hydroperoxide reductase, F52a subunit, FAD/NAD(P)‑binding/universal stress protein UP12 | |||||
| * | ? | NC_000913 | = 696741 | 127 (0.830) | 4 (0.040) | 4/366 | NT | 3.9% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 109 (1.020) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | 1207790 = | 88 (0.570) | 59 (0.410) | 48/490 | NT | 39.4% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 99 (0.690) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 85 (0.550) | 58 (0.400) | 47/490 | NT | 39.4% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 99 (0.690) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 1 (0.010) | 164 (1.070) | 89/522 | NT | 99.4% | 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) | 109 (0.720) | 72/514 | 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 | 1979486 = | 0 (0.000) | 100 (0.650) | 65/522 | 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) | 132 (0.860) | 83/522 | 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 | = 2943598 | 149 (0.970) | 4 (0.030) | 3/506 | NT | 2.7% | coding (264/1206 nt) | csdA | cysteine sulfinate desulfinase |
| ? | NC_000913 | = 2943637 | 147 (0.990) | coding (303/1206 nt) | csdA | cysteine sulfinate desulfinase | |||||
| * | ? | NC_000913 | 3622014 = | 0 (0.000) | 3 (0.020) | 3/512 | NT | 2.6% | coding (2824/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain, putative neighboring cell growth inhibitor |
| ? | NC_000913 | 3765560 = | 228 (1.520) | coding (3379/4134 nt) | rhsA | Rhs protein with putative toxin 55 domain, putative polysaccharide synthesis/export protein, putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | = 4034101 | 165 (1.080) | 10 (0.070) | 8/504 | NT | 5.8% | coding (958/1452 nt) | trkH | potassium transporter |
| ? | NC_000913 | = 4034171 | 163 (1.100) | coding (1028/1452 nt) | trkH | potassium transporter | |||||
| * | ? | NC_000913 | 4295831 = | NA (NA) | 13 (0.100) | 6/444 | 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 | |||||