mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 35,966 | A→T | 3.3% | L66* (TTA→TAA) | caiD ← | carnitinyl‑CoA dehydratase |
| RA | 75,586 | A→T | 4.8% | intergenic (‑106/+58) | thiB ← / ← sgrR | thiamine/thiamine pyrophosphate/thiamine monophosphate ABC transporter periplasmic binding protein/transcriptional DNA‑binding transcriptional activator of sgrS sRNA |
| RA | 160,600 | Δ1 bp | 3.4% | coding (5/456 nt) | dksA ← | transcriptional regulator of rRNA transcription, DnaK suppressor protein |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| JC | 700,783 | Δ9 bp | 9.3% | coding (804‑812/1221 nt) | nagC ← | N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor |
| RA | 701,374 | C→T | 6.8% | R74H (CGC→CAC) | nagC ← | N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor |
| RA | 747,670 | T→A | 5.5% | M34L (ATG→TTG) | abrB ← | regulator of aidB expression, inner membrane protein |
| RA | 1,158,377:1 | +A | 5.9% | coding (509/1434 nt) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| RA | 1,158,383 | G→A | 10.8% | W172* (TGG→TAG) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| JC | 1,159,286:1 | +GTA | 23.3% | coding (1418/1434 nt) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| 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 | 1,466,144 | G→T | 5.7% | pseudogene (753/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,210 | G→A | 5.7% | pseudogene (819/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 1,996,542 | Δ1 bp | 4.0% | coding (291/723 nt) | sdiA ← | quorum‑sensing transcriptional activator |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,173,325:1 | +T | 3.8% | pseudogene (38/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS,transport, Transport of small molecules: Carbohydrates, organic acids, alcohols, PTS system galactitol‑specific enzyme IIC |
| RA | 2,380,379 | T→C | 3.7% | E88G (GAA→GGA) | menF ← | isochorismate synthase 2 |
| RA | 2,696,566 | T→A | 3.9% | G256G (GGT→GGA) | mltF → | membrane‑bound lytic transglycosylase F, murein hydrolase |
| RA | 2,763,484 | A→G | 3.3% | S19P (TCG→CCG) | yfjK ← | radiation resistance protein, DEAD/H helicase‑like protein, CP4‑57 putative defective prophage |
| RA | 2,796,252 | A→C | 3.1% | D194A (GAT→GCT) | csiR → | transcriptional repressor of csiD |
| RA | 2,872,808 | A→T | 2.8% | L4Q (CTA→CAA) | ftsB ← | cell division protein |
| RA | 3,088,199 | C→A | 5.7% | intergenic (+341/‑83) | metK → / → galP | S‑adenosylmethionine synthetase/D‑galactose transporter |
| RA | 3,102,354 | T→A | 3.5% | K166I (AAA→ATA) | trmI ← | tRNA m(7)G46 methyltransferase, SAM‑dependent |
| RA | 3,380,049 | A→G | 3.4% | intergenic (‑54/‑140) | zapE ← / → yhcB | divisome ATPase/DUF1043 family inner membrane‑anchored protein |
| RA | 3,440,188 | Δ1 bp | 3.0% | coding (840/990 nt) | rpoA ← | RNA polymerase, alpha subunit |
| RA | 3,722,331 | T→C | 3.9% | Q689R (CAA→CGA) | glyS ← | glycine tRNA synthetase, beta subunit |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,869,795 | C→T | 2.6% | D140D (GAC→GAT) | cbrA → | colicin M resistance protein, FAD‑binding protein, putative oxidoreductase |
| RA | 3,872,322 | G→A | 3.2% | Q226* (CAA→TAA) | dgoD ← | D‑galactonate dehydratase |
| MC JC | 3,909,311 | Δ774 bp | 100% | [pstA]–[pstC] | [pstA], [pstC] | |
| RA | 3,935,819 | Δ1 bp | 3.7% | coding (533/966 nt) | rbsC → | D‑ribose ABC transporter permease |
| MC JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,127,598 | Δ1 bp | 2.9% | coding (296/609 nt) | yiiX ← | putative lipid binding hydrolase, DUF830 family protein |
| 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 | 4,296,189 | A→G | 47.0% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 49.8% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,305,527 | G→A | 4.0% | P358S (CCG→TCG) | yjcS ← | metallo‑beta‑lactamase superfamily protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423877–3424404 | 3424404 | 1–528 | 46 [42] | [43] 44 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 4110689 | 4111541 | 853 | 46 [43] | [41] 44 | tpiA | tpiA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 110 (1.010) | 61/524 | 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) | 4 (0.040) | 4/524 | NT | 3.5% | 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 = | 109 (1.000) | coding (998/1221 nt) | nagC | N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor | |||||
| * | ? | NC_000913 | 273955 = | NA (NA) | 10 (0.090) | 10/524 | NT | 9.0% | intergenic (+1/+146) | ykfC/insH1 | CP4‑6 prophage, conserved protein,Phage or Prophage Related/IS5 transposase and trans‑activator |
| ? | NC_000913 | = 701973 | 101 (0.930) | coding (779/1149 nt) | nagA | N‑acetylglucosamine‑6‑phosphate deacetylase | |||||
| * | ? | NC_000913 | = 275149 | NA (NA) | 4 (0.040) | 4/524 | NT | 3.9% | intergenic (‑32/‑176) | insH1/mmuP | IS5 transposase and trans‑activator/CP4‑6 prophage, putative S‑methylmethionine transporter |
| ? | NC_000913 | 701970 = | 99 (0.910) | coding (782/1149 nt) | nagA | N‑acetylglucosamine‑6‑phosphate deacetylase | |||||
| * | ? | NC_000913 | 608010 = | NA (NA) | 3 (0.030) | 3/520 | NT | 4.6% | intergenic (+22/‑55) | hokE/insL1 | toxic polypeptide, small/IS186 transposase |
| ? | NC_000913 | 1157803 = | 62 (0.570) | intergenic (+229/‑66) | ycfH/ptsG | putative DNase/fused glucose‑specific PTS enzymes: IIB component/IIC component | |||||
| * | ? | NC_000913 | 781577 = | 89 (0.820) | 5 (0.050) +G |
3/522 | NT | 5.7% | noncoding (1/76 nt) | lysQ | tRNA‑Lys |
| ? | NC_000913 | = 2521127 | 77 (0.710) | intergenic (+3/‑44) | valX/valY | tRNA‑Val/tRNA‑Val | |||||
| * | ? | NC_000913 | = 1159291 | 74 (0.680) | 4 (0.040) | 4/524 | NT | 5.1% | coding (1423/1434 nt) | ptsG | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| ? | NC_000913 | = 1651548 | NA (NA) | intergenic (+11/‑3) | insD1/intQ | IS2 transposase TnpB,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related/pseudogene, Qin prophage, phage integrase family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1207790 = | 66 (0.610) | 34 (0.330) | 27/492 | NT | 35.2% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 63 (0.620) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 61 (0.560) | 31 (0.300) | 28/492 | NT | 34.0% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 63 (0.620) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 0 (0.000) | 114 (1.050) | 74/524 | NT | 100% | 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 | 1411899 = | 86 (0.790) | 5 (0.050) | 5/472 | NT | 6.5% | coding (50/936 nt) | ttcA | tRNA s(2)C32 thioltransferase, iron sulfur cluster protein |
| ? | NC_000913 | = 1434958 | 67 (0.680) | pseudogene (51/51 nt) | ttcC | pseudogene, prophage Rac integration site ttcA duplication,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 74 (0.680) | 56/524 | 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) | 94 (0.860) | 61/524 | 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 | 4295831 = | NA (NA) | 7 (0.080) | 4/446 | 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 | |||||