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 | 79,455 | G→T | 4.2% | intergenic (‑2/+9) | leuD ← / ← leuC | 3‑isopropylmalate dehydratase small subunit/3‑isopropylmalate dehydratase large subunit |
| RA | 182,089 | G→A | 3.4% | M402I (ATG→ATA) | degP → | serine endoprotease (protease Do), membrane‑associated |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 287,906 | T→C | 5.0% | L373P (CTC→CCC) | yagH → | CP4‑6 prophage, putative xylosidase/arabinosidase |
| RA | 296,306 | A→G | 2.7% | V264A (GTG→GCG) | intF ← | CP4‑6 prophage, putative phage integrase |
| RA | 375,020 | T→G | 2.8% | intergenic (+139/‑439) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 408,219 | Δ1 bp | 2.5% | coding (43/285 nt) | yaiE → | UPF0345 family protein |
| RA | 411,240 | G→C | 2.5% | intergenic (+188/+57) | mak → / ← araJ | manno(fructo)kinase/L‑arabinose‑inducible putative transporter, MFS family |
| RA | 570,475 | A→T | 2.8% | intergenic (+47/‑418) | ybcK → / → ybcL | DLP12 prophage, putative recombinase/inactive polymorphonuclear leukocyte migration suppressor, DLP12 prophage, UPF0098 family secreted protein |
| RA | 737,442 | T→C | 2.5% | pseudogene (618/1137 nt) | ybfL → | pseudogene, DDE domain transposase family,putative factor, Not classified, putative receptor protein |
| RA | 767,138 | G→A | 2.7% | A385A (GCG→GCA) | mngA → | fused 2‑O‑a‑mannosyl‑D‑glycerate specific PTS enzymes: IIA component/IIB component/IIC component |
| RA | 833,429 | T→A | 2.7% | C120* (TGT→TGA) | dinG → | ATP‑dependent DNA helicase |
| RA | 873,620 | T→A | 4.2% | D214E (GAT→GAA) | yliE → | putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase |
| RA | 1,162,001 | Δ1 bp | 2.5% | coding (117/360 nt) | hinT → | purine nucleoside phosphoramidase, dadA activator protein |
| RA | 1,269,726 | C→T | 3.8% | G29S (GGC→AGC) | ldrB ← | toxic polypeptide, small |
| RA | 1,269,897 | T→G | 3.7% | noncoding (40/66 nt) | rdlB → | sRNA antisense regulator affects LdrB translation, proposed addiction module in LDR‑B repeat, with toxic peptide LdrB |
| RA | 1,272,996 | T→A | 2.5% | S164T (TCT→ACT) | chaC → | cation transport regulator |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,603,740 | A→G | 5.3% | E241G (GAG→GGG) | lsrC → | autoinducer 2 import system permease protein |
| RA | 1,708,847 | G→A | 7.0% | E643E (GAG→GAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,930 | C→A | 5.7% | P671Q (CCG→CAG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,876,124 | T→G | 2.9% | L151R (CTG→CGG) ‡ | yeaN → | putative MFS transporter, inner membrane protein |
| RA | 1,876,125 | G→A | 2.6% | L151L (CTG→CTA) ‡ | yeaN → | putative MFS transporter, inner membrane protein |
| RA | 1,876,126 | G→C | 2.5% | G152R (GGA→CGA) ‡ | yeaN → | putative MFS transporter, inner membrane protein |
| RA | 1,876,127 | G→C | 2.5% | G152A (GGA→GCA) ‡ | yeaN → | putative MFS transporter, inner membrane protein |
| RA | 1,876,130 | C→A | 2.8% | S153* (TCG→TAG) | yeaN → | putative MFS transporter, inner membrane protein |
| RA | 1,876,132 | G→C | 2.7% | A154P (GCT→CCT) ‡ | yeaN → | putative MFS transporter, inner membrane protein |
| RA | 1,876,134 | T→G | 3.3% | A154A (GCT→GCG) ‡ | yeaN → | putative MFS transporter, inner membrane protein |
| RA | 1,876,137 | G→C | 2.6% | M155I (ATG→ATC) | yeaN → | putative MFS transporter, inner membrane protein |
| RA | 1,876,138 | G→C | 2.6% | V156L (GTC→CTC) ‡ | yeaN → | putative MFS transporter, inner membrane protein |
| RA | 1,876,139 | T→C | 2.9% | V156A (GTC→GCC) ‡ | yeaN → | putative MFS transporter, inner membrane protein |
| RA | 1,876,140 | C→A | 2.6% | V156V (GTC→GTA) ‡ | yeaN → | putative MFS transporter, inner membrane protein |
| RA | 2,074,691 | C→G | 2.6% | intergenic (+33/‑88) | flu → / → yeeR | CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter/CP4‑44 prophage, putative membrane protein |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,304,796 | T→C | 16.1% | intergenic (+405/+310) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,686,631 | G→A | 2.8% | A267T (GCC→ACC) | hmp → | fused nitric oxide dioxygenase/dihydropteridine reductase 2 |
| RA | 3,194,295 | T→A | 4.4% | I478I (ATT→ATA) | yqiK → | PHB family membrane protein, function unknown |
| RA | 3,223,733 | Δ1 bp | 4.0% | coding (1103/3093 nt) | ebgA → | evolved beta‑D‑galactosidase, alpha subunit |
| RA | 3,233,262 | A→G | 5.8% | I534V (ATC→GTC) | fadH → | 2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked |
| RA | 3,375,924 | Δ1 bp | 3.0% | coding (1058/1368 nt) | dcuD → | putative transporter |
| RA | 3,490,643 | G→A | 2.7% | S62F (TCC→TTC) | pabA ← | aminodeoxychorismate synthase, subunit II |
| RA | 3,528,106 | T→G | 45.4% | L547R (CTG→CGG) | yrfF → | putative RcsCDB‑response attenuator, inner membrane protein |
| RA | 3,648,436 | Δ1 bp | 2.6% | intergenic (+60/‑91) | agrB → / → arsR | antisense sRNA antitoxin for the DinQ toxin/arsenical resistance operon transcriptional repressor, autorepressor |
| RA | 3,688,286 | A→C | 14.8% | V296G (GTG→GGG) | bcsC ← | cellulose synthase subunit |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,875,524 | G→T | 8.4% | V30F (GTT→TTT) | yidX → | putative lipoprotein |
| RA | 3,992,437 | T→G | 15.1% | L429* (TTA→TGA) | cyaA → | adenylate cyclase |
| JC | 3,992,468 | Δ4 bp | 6.3% | coding (1317‑1320/2547 nt) | cyaA → | adenylate cyclase |
| MC JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,160,473 | T→A | 2.7% | E106V (GAA→GTA) | sthA ← | pyridine nucleotide transhydrogenase, soluble |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,154 | T→C | 15.4% | intergenic (+361/+283) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,189 | A→G | 43.9% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 46.0% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,542,172 | G→A | 3.2% | L45L (CTG→CTA) | fimE → | tyrosine recombinase/inversion of on/off regulator of fimA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2533687 | 2536433 | 2747 | 83 [81] | [81] 84 | ptsH–[pdxK] | ptsH, ptsI, crr, [pdxK] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 142 (0.870) | 90/502 | 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 | 1207790 = | 64 (0.390) | 90 (0.590) | 70/470 | NT | 57.9% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 71 (0.460) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 64 (0.390) | 100 (0.650) | 67/470 | NT | 60.4% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 71 (0.460) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 1 (0.010) | 162 (0.990) | 88/502 | 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 | = 1978502 | 0 (0.000) | 66 (0.420) | 45/486 | NT | 100% | intergenic (‑305/+16) | flhD/insB1 | flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B |
| ? | NC_000913 | 1979279 = | 0 (0.000) | intergenic (‑64/‑474) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 85 (0.520) | 51/502 | 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) | 152 (0.930) | 81/502 | 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 | 2288917 = | NA (NA) | 90 (0.550) | 58/502 | NT | 60.4% | intergenic (‑5/+146) | yejO/insH1 | pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system/IS5 transposase and trans‑activator |
| ? | NC_000913 | 3526447 = | 59 (0.360) | intergenic (‑300/‑20) | nudE/yrfF | adenosine nucleotide hydrolase, Ap3A/Ap2A/ADP‑ribose/NADH hydrolase/putative RcsCDB‑response attenuator, inner membrane protein | |||||
| * | ? | NC_000913 | = 2290110 | NA (NA) | 91 (0.560) | 58/500 | NT | 60.8% | intergenic (‑31/+2) | 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 | = 3526451 | 59 (0.360) | intergenic (‑304/‑16) | nudE/yrfF | adenosine nucleotide hydrolase, Ap3A/Ap2A/ADP‑ribose/NADH hydrolase/putative RcsCDB‑response attenuator, inner membrane protein | |||||
| * | ? | NC_000913 | 2796363 = | 147 (0.900) | 4 (0.030) | 4/482 | NT | 2.7% | coding (422/450 nt) | ygaU | uncharacterized protein |
| ? | NC_000913 | 2796384 = | 144 (0.910) | coding (401/450 nt) | ygaU | uncharacterized protein | |||||
| * | ? | NC_000913 | 2997097 = | NA (NA) | 7 (0.040) | 4/496 | NT | 25.2% | coding (179/906 nt) | insD1 | IS2 transposase TnpB |
| ? | NC_000913 | 2997489 = | 21 (0.130) | coding (110/366 nt) | insC1 | IS2 repressor TnpA | |||||
| * | ? | NC_000913 | = 3619290 | 117 (0.710) | 7 (0.040) | 7/480 | NT | 7.7% | coding (100/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain, putative neighboring cell growth inhibitor |
| ? | NC_000913 | = 3619449 | 57 (0.360) | coding (259/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain, putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | = 3620050 | NA (NA) | 4 (0.030) | 4/474 | NT | 100% | coding (860/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain, putative neighboring cell growth inhibitor |
| ? | NC_000913 | = 3620502 | 0 (0.000) | coding (1312/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain, putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | 3845530 = | 162 (0.990) | 93 (0.590) | 69/482 | NT | 36.6% | coding (1568/1767 nt) | adeD | cryptic adenine deaminase |
| ? | NC_000913 | = 3992759 | 166 (1.050) | coding (1608/2547 nt) | cyaA | adenylate cyclase | |||||
| * | ? | NC_000913 | 4295831 = | NA (NA) | 13 (0.090) | 11/424 | 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 | |||||