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 | 51,782 | Δ1 bp | 3.2% | coding (649/822 nt) | rsmA ← | 16S rRNA m(6)A1518, m(6)A1519 dimethyltransferase, SAM‑dependent |
| RA | 126,147 | T→G | 4.3% | A151A (GCT→GCG) | aceF → | pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2 |
| RA | 197,491 | A→G | 4.4% | K316E (AAA→GAA) | rseP → | inner membrane zinc RIP metalloprotease, RpoE activator, by degrading RseA, cleaved signal peptide endoprotease |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 349,926 | A→C | 3.2% | intergenic (+354/‑86) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 357,626 | C→T | 4.8% | intergenic (+172/+165) | codA → / ← cynR | cytosine/isoguanine deaminase/transcriptional activator of cyn operon, autorepressor |
| RA | 357,627 | C→A | 4.6% | intergenic (+173/+164) | codA → / ← cynR | cytosine/isoguanine deaminase/transcriptional activator of cyn operon, autorepressor |
| RA | 375,247 | A→G | 4.4% | intergenic (+366/‑212) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 453,477 | A→G | 4.8% | A23A (GCT→GCC) | ampG ← | muropeptide transporter |
| RA | 618,763:1 | +C | 4.7% | coding (510/1134 nt) | fepE → | regulator of length of O‑antigen component of lipopolysaccharide chains |
| RA | 737,478 | A→C | 3.2% | pseudogene (654/1137 nt) | ybfL → | pseudogene, DDE domain transposase family,putative factor, Not classified, putative receptor protein |
| RA | 737,479 | G→A | 3.2% | pseudogene (655/1137 nt) | ybfL → | pseudogene, DDE domain transposase family,putative factor, Not classified, putative receptor protein |
| RA | 790,024 | G→A | 3.6% | R336C (CGC→TGC) | galT ← | galactose‑1‑phosphate uridylyltransferase |
| RA | 831,186 | T→C | 3.2% | R105R (CGT→CGC) | rhlE → | ATP‑dependent RNA helicase |
| RA | 843,920 | T→C | 4.2% | I521V (ATC→GTC) | ybiO ← | mechanosensitive channel protein, intermediate conductance |
| RA | 1,058,601 | G→A | 4.2% | C173Y (TGT→TAT) | torC → | trimethylamine N‑oxide (TMAO) reductase I, cytochrome c‑type subunit |
| RA | 1,185,260 | A→T | 3.0% | F112Y (TTT→TAT) | potA ← | spermidine/putrescine ABC transporter ATPase |
| RA | 1,188,685 | Δ1 bp | 3.4% | coding (1092/1461 nt) | phoQ ← | sensory histidine kinase in two‑component regulatory system with PhoP |
| RA | 1,188,686 | Δ1 bp | 3.4% | coding (1091/1461 nt) | phoQ ← | sensory histidine kinase in two‑component regulatory system with PhoP |
| RA | 1,196,305 | C→T | 100% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase |
| RA | 1,269,191 | T→C | 4.0% | S29G (AGC→GGC) | ldrA ← | toxic polypeptide, small |
| RA | 1,269,231 | T→C | 5.1% | A15A (GCA→GCG) | ldrA ← | toxic polypeptide, small |
| RA | 1,269,250 | A→G | 3.8% | I9T (ATT→ACT) | ldrA ← | toxic polypeptide, small |
| RA | 1,269,856 | G→T | 8.2% | intergenic (‑46/‑2) | ldrB ← / → rdlB | toxic polypeptide, small/sRNA antisense regulator affects LdrB translation, proposed addiction module in LDR‑B repeat, with toxic peptide LdrB |
| RA | 1,269,859:1 | +T | 5.3% | noncoding (2/66 nt) | rdlB → | sRNA antisense regulator affects LdrB translation, proposed addiction module in LDR‑B repeat, with toxic peptide LdrB |
| RA | 1,286,793 | A→G | 6.0% | intergenic (+267/+273) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,287,009 | A→T | 7.1% | intergenic (+483/+57) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| 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 | 1,421,843 | T→C | 4.5% | V242A (GTG→GCG) | ydaU → | Rac prophage, conserved protein |
| RA | 1,542,625 | T→C | 3.4% | intergenic (‑35/+47) | narZ ← / ← narU | nitrate reductase 2 (NRZ), alpha subunit/nitrate/nitrite transporter |
| RA | 1,670,910 | T→C | 4.2% | A404A (GCT→GCC) | ynfM → | putative arabinose efflux transporter |
| RA | 1,696,637 | T→A | 3.3% | D139V (GAT→GTT) | uidR ← | transcriptional repressor |
| RA | 1,708,930 | C→A | 7.4% | P671Q (CCG→CAG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,723,150 | Δ1 bp | 3.5% | coding (1030/2013 nt) | ydhK → | putative efflux protein (PET) component of YdhJK efflux pump |
| RA | 1,723,151 | Δ1 bp | 3.5% | coding (1031/2013 nt) | ydhK → | putative efflux protein (PET) component of YdhJK efflux pump |
| RA | 1,837,764 | T→A | 3.6% | S185T (TCC→ACC) | ynjC → | putative ABC transporter permease |
| RA | 1,855,397 | T→A | 3.8% | Y192F (TAC→TTC) | ydjG ← | methylglyoxal reductase, NADH‑dependent |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 1,988,454 | A→G | 5.8% | N78S (AAC→AGC) | yecR → | lipoprotein, function unknown |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,304,521 | G→C | 7.0% | intergenic (+130/+585) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,430,911 | Δ1 bp | 3.4% | intergenic (‑150/+109) | cvpA ← / ← dedD | colicin V production protein/membrane‑anchored periplasmic protein involved in septation |
| RA | 2,490,735 | Δ1 bp | 6.9% | coding (1214/1695 nt) | oxc ← | oxalyl CoA decarboxylase, ThDP‑dependent |
| RA | 2,600,617 | Δ1 bp | 13.4% | coding (142/471 nt) | bcp → | peroxiredoxin, thiol peroxidase, thioredoxin‑dependent |
| RA | 2,799,463 | T→C | 3.7% | L101S (TTA→TCA) | alaE → | alanine exporter, alanine‑inducible, stress‑responsive |
| RA | 2,870,021 | Δ1 bp | 4.2% | coding (252/762 nt) | umpG ← | broad specificity 5'(3')‑nucleotidase and polyphosphatase |
| RA | 2,916,722 | A→G | 3.7% | L556L (TTA→TTG) | barA → | hybrid sensory histidine kinase, in two‑component regulatory system with UvrY |
| RA | 3,213,424 | T→G | 7.2% | I127S (ATC→AGC) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 3,213,427 | A→C | 4.3% | N128T (AAC→ACC) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 3,213,790 | T→G | 14.0% | I249S (ATC→AGC) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 3,326,011 | A→G | 3.3% | L308P (CTG→CCG) | ftsH ← | protease, ATP‑dependent zinc‑metallo |
| RA | 3,346,329 | A→G | 3.5% | T53T (ACA→ACG) | hpf → | ribosome hibernation promoting factor HPF, stabilizes 100S dimers |
| RA | 3,486,712 | G→A | 16.1% | A199T (GCA→ACA) | crp → | cAMP‑activated global transcription factor, mediator of catabolite repression |
| RA | 3,626,971 | Δ1 bp | 2.6% | coding (2567/2736 nt) | rbbA ← | ribosome‑associated ATPase: ATP‑binding protein/ATP‑binding membrane protein |
| RA | 3,733,461 | Δ1 bp | 3.4% | coding (1262/1542 nt) | xylG → | D‑xylose ABC transporter dual domain ATPase |
| RA | 3,769,856 | T→A | 33.3% | intergenic (+74/‑91) | yibV → / → yibU | pseudogene, putative cryptic Rhs immunity protein/pseudogene, H repeat‑associated protein |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,824,336 | A→G | 4.1% | A646A (GCA→GCG) | spoT → | bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
| RA | 3,863,229 | C→A | 2.7% | pseudogene (374/1617 nt) | glvC ← | pseudogene, arbutin specific enzyme IIC component of PTS,enzyme, Transport of small molecules: Carbohydrates, organic acids, alcohols, PTS system, arbutin‑like IIB component, PTS system, arbutin‑like IIC component |
| RA | 3,872,580 | A→G | 3.3% | F140L (TTC→CTC) | dgoD ← | D‑galactonate dehydratase |
| MC JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,016,056 | T→C | 3.7% | Q38R (CAA→CGA) | ysgA ← | putative carboxymethylenebutenolidase |
| RA | 4,044,938 | T→C | 3.9% | D247D (GAT→GAC) | yihF → | DUF945 family protein |
| RA | 4,048,109 | A→G | 4.3% | Y382C (TAT→TGT) | polA → | 5' to 3' DNA polymerase and 3' to 5'/5' to 3' exonuclease |
| RA | 4,073,770 | G→A | 3.3% | V11V (GTG→GTA) | yihV → | 6‑deoxy‑6‑sulphofructose kinase |
| RA | 4,097,572 | A→G | 3.4% | intergenic (‑125/‑163) | rhaB ← / → rhaS | rhamnulokinase/transcriptional activator of rhaBAD and rhaT |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,277,819 | G→T | 100% | G118* (GGA→TGA) | soxR → | redox‑sensitive transcriptional activator of soxS, autorepressor |
| RA | 4,295,833 | T→C | 7.3% | intergenic (+40/+604) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,059 | C→T | 6.4% | intergenic (+266/+378) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,154 | T→C | 13.3% | intergenic (+361/+283) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,189 | A→G | 41.3% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 42.7% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,325,889 | G→T | 4.5% | intergenic (‑147/+511) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,326,042 | C→T | 5.4% | intergenic (‑300/+358) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,326,048 | C→T | 8.2% | intergenic (‑306/+352) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,326,089 | T→G | 9.0% | intergenic (‑347/+311) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,326,142 | T→C | 10.4% | intergenic (‑400/+258) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,326,148 | T→C | 8.7% | intergenic (‑406/+252) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,326,149 | G→A | 4.6% | intergenic (‑407/+251) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,337,431 | A→G | 2.9% | M167T (ATG→ACG) | adiY ← | adi system transcriptional activator |
| RA | 4,363,718 | C→T | 3.9% | A442A (GCG→GCA) | dsbD ← | thiol:disulfide interchange protein and activator of DsbC |
| RA | 4,460,034 | T→A | 3.9% | E111V (GAA→GTA) | nrdG ← | anaerobic ribonucleotide reductase activating protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423847–3424229 | 3424420–3424237 | 9–574 | 41 [40] | [40] 41 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 4233705 | 4235541 | 1837 | 41 [39] | [39] 43 | pgi | pgi |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 66 (0.650) | 53/516 | 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 | 273955 = | NA (NA) | 20 (0.200) | 20/516 | NT | 15.6% | intergenic (+1/+146) | ykfC/insH1 | CP4‑6 prophage, conserved protein,Phage or Prophage Related/IS5 transposase and trans‑activator |
| ? | NC_000913 | 348458 = | 108 (1.070) | intergenic (‑15/‑224) | prpR/prpB | propionate catabolism operon regulatory protein/2‑methylisocitrate lyase | |||||
| * | ? | NC_000913 | = 275148 | NA (NA) | 9 (0.090) | 9/514 | NT | 8.0% | intergenic (‑31/‑177) | insH1/mmuP | IS5 transposase and trans‑activator/CP4‑6 prophage, putative S‑methylmethionine transporter |
| ? | NC_000913 | = 348462 | 104 (1.030) | intergenic (‑19/‑220) | prpR/prpB | propionate catabolism operon regulatory protein/2‑methylisocitrate lyase | |||||
| * | ? | NC_000913 | 458787 = | 4 (0.040) | 65 (0.650) | 50/510 | NT | 94.3% | intergenic (+87/‑101) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| ? | NC_000913 | 608011 = | NA (NA) | intergenic (+23/‑54) | hokE/insL1 | toxic polypeptide, small/IS186 transposase | |||||
| * | ? | NC_000913 | = 458799 | 1 (0.010) | 103 (1.040) | 70/508 | NT | 99.1% | intergenic (+99/‑89) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| ? | NC_000913 | = 609347 | NA (NA) | intergenic (+170/+112) | insL1/entD | IS186 transposase/phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex | |||||
| * | ? | NC_000913 | = 515492 | 115 (1.140) | 3 (0.030) | 3/492 | NT | 2.7% | coding (282/918 nt) | qmcA | PHB domain membrane‑anchored putative protease |
| ? | NC_000913 | = 515480 | 106 (1.100) | coding (294/918 nt) | qmcA | PHB domain membrane‑anchored putative protease | |||||
| * | ? | NC_000913 | 762116 = | 128 (1.270) | 5 (0.050) | 3/488 | NT | 3.7% | coding (595/1218 nt) | sucB | dihydrolipoyltranssuccinase |
| ? | NC_000913 | 762340 = | 136 (1.420) | coding (819/1218 nt) | sucB | dihydrolipoyltranssuccinase | |||||
| * | ? | NC_000913 | 1207790 = | 25 (0.250) | 55 (0.580) | 43/484 | NT | 63.4% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 40 (0.420) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 26 (0.260) | 70 (0.740) | 50/484 | NT | 68.5% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 40 (0.420) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 1 (0.010) | 93 (0.920) | 63/516 | NT | 98.9% | 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 | = 1517054 | 70 (0.690) | 3 (0.030) | 3/490 | NT | 4.2% | intergenic (+52/+45) | patD/yncL | gamma‑aminobutyraldehyde dehydrogenase/stress‑induced small inner membrane enterobacterial protein |
| ? | NC_000913 | = 1517063 | 72 (0.750) | intergenic (+61/+36) | patD/yncL | gamma‑aminobutyraldehyde dehydrogenase/stress‑induced small inner membrane enterobacterial protein | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 49 (0.480) | 36/516 | 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) | 93 (0.920) | 60/516 | 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 | 2438760 = | 104 (1.030) | 3 (0.030) | 3/510 | NT | 2.6% | coding (813/996 nt) | flk | putative flagella assembly protein |
| ? | NC_000913 | 2439230 = | 118 (1.180) | coding (889/1179 nt) | yfcJ | putative arabinose efflux transporter | |||||
| * | ? | NC_000913 | 3186094 = | NA (NA) | 67 (0.660) | 46/516 | NT | 100% | intergenic (+6/‑91) | yqiG/insC1 | pseudogene, fimbrial export usher family,putative membrane, Not classified, putative membrane protein/IS2 repressor TnpA |
| ? | NC_000913 | = 4049915 | 0 (0.000) | noncoding (18/109 nt) | spf | Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent | |||||
| * | ? | NC_000913 | 4049911 = | 0 (0.000) | 85 (0.840) | 63/516 | NT | 100% | noncoding (14/109 nt) | spf | Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent |
| ? | NC_000913 | = 4499512 | NA (NA) | intergenic (+11/+82) | insD1/yjgX | IS2 transposase TnpB/pseudogene fragment | |||||
| * | ? | NC_000913 | 4295831 = | NA (NA) | 10 (0.120) | 8/438 | 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 | |||||