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 | 129,186 | Δ1 bp | 4.5% | coding (1275/1425 nt) | lpd → | dihydrolipoyl dehydrogenase, E3 component of pyruvate and 2‑oxoglutarate dehydrogenases complexes, glycine cleavage system L protein, dihydrolipoamide dehydrogenase |
| RA | 129,187 | Δ1 bp | 4.5% | coding (1276/1425 nt) | lpd → | dihydrolipoyl dehydrogenase, E3 component of pyruvate and 2‑oxoglutarate dehydrogenases complexes, glycine cleavage system L protein, dihydrolipoamide dehydrogenase |
| RA | 129,188 | Δ1 bp | 4.5% | coding (1277/1425 nt) | lpd → | dihydrolipoyl dehydrogenase, E3 component of pyruvate and 2‑oxoglutarate dehydrogenases complexes, glycine cleavage system L protein, dihydrolipoamide dehydrogenase |
| RA | 129,190 | Δ1 bp | 4.5% | coding (1279/1425 nt) | lpd → | dihydrolipoyl dehydrogenase, E3 component of pyruvate and 2‑oxoglutarate dehydrogenases complexes, glycine cleavage system L protein, dihydrolipoamide dehydrogenase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 461,143 | T→C | 3.2% | I752I (ATT→ATC) | lon → | DNA‑binding ATP‑dependent protease La |
| RA | 701,811 | Δ1 bp | 11.6% | coding (941/1149 nt) | nagA ← | N‑acetylglucosamine‑6‑phosphate deacetylase |
| RA | 702,331 | Δ1 bp | 20.5% | coding (421/1149 nt) | nagA ← | N‑acetylglucosamine‑6‑phosphate deacetylase |
| RA | 705,052 | Δ1 bp | 3.3% | coding (1109/1947 nt) | nagE → | N‑acetyl glucosamine specific PTS enzyme IIC, IIB, and IIA components |
| RA | 705,053 | Δ1 bp | 3.3% | coding (1110/1947 nt) | nagE → | N‑acetyl glucosamine specific PTS enzyme IIC, IIB, and IIA components |
| RA | 705,054 | Δ1 bp | 3.3% | coding (1111/1947 nt) | nagE → | N‑acetyl glucosamine specific PTS enzyme IIC, IIB, and IIA components |
| RA | 705,055 | Δ1 bp | 3.3% | coding (1112/1947 nt) | nagE → | N‑acetyl glucosamine specific PTS enzyme IIC, IIB, and IIA components |
| RA | 705,056 | Δ1 bp | 3.3% | coding (1113/1947 nt) | nagE → | N‑acetyl glucosamine specific PTS enzyme IIC, IIB, and IIA components |
| RA | 923,469 | T→C | 4.6% | L69P (CTG→CCG) | clpA → | ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity |
| RA | 1,148,282 | T→A | 4.5% | L221* (TTA→TAA) | plsX → | putative phosphate acyltransferase |
| JC | 1,159,286:1 | +GTA | 8.3% | coding (1418/1434 nt) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| RA | 1,269,450 | C→T | 10.4% | intergenic (+61/+253) | rdlA → / ← ldrB | sRNA antisense regulator affects LdrA translation, proposed addiction module in LDR‑A repeat, with toxic peptide LdrA/toxic polypeptide, small |
| RA | 1,269,451 | G→T | 7.7% | intergenic (+62/+252) | rdlA → / ← ldrB | sRNA antisense regulator affects LdrA translation, proposed addiction module in LDR‑A repeat, with toxic peptide LdrA/toxic polypeptide, small |
| 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 | 1,549,913 | T→A | 3.7% | I838N (ATC→AAC) | fdnG → | formate dehydrogenase‑N, alpha subunit, nitrate‑inducible |
| RA | 1,726,004 | G→A | 29.8% | intergenic (‑84/‑19) | ydhL ← / → nemR | DUF1289 family protein/transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| RA | 1,726,155 | T→G | 49.4% | F45V (TTC→GTC) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| RA | 1,726,257 | G→T | 15.0% | E79* (GAA→TAA) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| 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 | 2,304,791 | C→T | 9.2% | intergenic (+400/+315) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,796 | T→C | 32.6% | intergenic (+405/+310) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,799 | G→A | 7.7% | intergenic (+408/+307) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,377,327 | A→G | 10.1% | G88G (GGT→GGC) | menH ← | 2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase |
| RA | 2,626,300 | T→G | 4.7% | G396G (GGT→GGG) | ppx → | exopolyphosphatase |
| JC | 2,765,454 | (TATGGCAC)6→5 | 5.4% | intergenic (‑303/+50) | yfjL ← / ← yfjM | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein/CP4‑57 prophage, uncharacterized protein |
| RA | 2,770,219 | G→A | 3.3% | G173G (GGG→GGA) | yfjR → | CP4‑57 prophage, putative DNA‑binding transcriptional regulator |
| RA | 2,814,419 | T→C | 4.3% | K105E (AAA→GAA) | luxS ← | S‑ribosylhomocysteine lyase |
| RA | 2,976,907 | A→C | 9.7% | E104A (GAG→GCG) | galR → | galactose‑inducible d‑galactose regulon transcriptional repressor, autorepressor |
| RA | 3,088,199 | C→A | 60.3% | intergenic (+341/‑83) | metK → / → galP | S‑adenosylmethionine synthetase/D‑galactose transporter |
| RA | 3,663,017 | A→G | 3.9% | N869D (AAT→GAT) | mdtF → | anaerobic multidrug efflux transporter, ArcA‑regulated |
| RA | 3,688,286 | A→C | 17.8% | V296G (GTG→GGG) | bcsC ← | cellulose synthase subunit |
| RA | 3,759,690 | G→A | 3.7% | D57D (GAC→GAT) | selB ← | selenocysteinyl‑tRNA‑specific translation factor |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,866,097 | A→G | 3.2% | L59P (CTG→CCG) | yidE ← | putative transporter |
| MC JC | 3,909,311 | Δ774 bp | 100% | [pstA]–[pstC] | [pstA], [pstC] | |
| MC 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 | 8.4% | intergenic (+40/+604) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,189 | A→G | 31.4% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,325,949 | A→G | 7.6% | intergenic (‑207/+451) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,332,310 | A→C | 10.7% | L322V (TTA→GTA) | basS ← | sensory histidine kinase in two‑component regulatory system with BasR |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423806–3424231 | 3424402–3424237 | 7–597 | 35 [34] | [34] 38 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 4110664 | 4111531 | 868 | 37 [34] | [34] 36 | [cdh]–tpiA | [cdh], tpiA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 228016 = | NA (NA) | 3 (0.030) | 3/510 | 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) | 81 (0.890) | 64/524 | 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 | 535503 = | 76 (0.840) | 3 (0.030) | 3/500 | NT | 3.9% | coding (1588/1782 nt) | gcl | glyoxylate carboligase |
| ? | NC_000913 | 535552 = | 74 (0.860) | coding (1637/1782 nt) | gcl | glyoxylate carboligase | |||||
| * | ? | NC_000913 | 1207790 = | 44 (0.490) | 36 (0.420) | 33/492 | NT | 46.4% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 42 (0.490) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 44 (0.490) | 26 (0.310) | 20/492 | NT | 38.4% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 42 (0.490) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 3 (0.030) | 80 (0.880) | 61/524 | NT | 96.4% | 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 | = 1877275 | 81 (0.890) | 3 (0.030) | 3/508 | NT | 3.6% | intergenic (+19/+3) | yeaO/yoaF | DUF488 family protein/DUF333 family outer membrane lipoprotein |
| ? | NC_000913 | = 1877290 | 84 (0.960) | coding (243/255 nt) | yoaF | DUF333 family outer membrane lipoprotein | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 46 (0.510) | 32/524 | 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) | 74 (0.820) | 50/524 | 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 | 2275830 = | 84 (0.930) | 3 (0.030) | 3/508 | NT | 3.6% | coding (560/1026 nt) | yejE | microcin C ABC transporter permease |
| ? | NC_000913 | 2275866 = | 80 (0.910) | coding (596/1026 nt) | yejE | microcin C ABC transporter permease | |||||
| * | ? | NC_000913 | 2996359 = | NA (NA) | 3 (0.030) | 3/524 | NT | 2.5% | intergenic (‑1/+11) | ygeO/insD1 | pseudogene, orgA family, part of T3SS PAI ETT2 remnant/IS2 transposase TnpB |
| ? | NC_000913 | = 3727434 | 116 (1.280) | coding (314/342 nt) | yiaB | YiaAB family inner membrane protein | |||||
| * | ? | NC_000913 | 3831818 = | 115 (1.270) | 4 (0.050) | 4/506 | NT | 3.7% | coding (1363/1710 nt) | yicH | putative inner membrane‑anchored periplasmic AsmA family protein |
| ? | NC_000913 | 3832393 = | 98 (1.120) | coding (2144/2319 nt) | yicI | putative alpha‑glucosidase | |||||
| * | ? | NC_000913 | 4295831 = | NA (NA) | 12 (0.160) | 5/446 | 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 | |||||