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 | 119,988 | A→G | 2.7% | L236L (TTA→TTG) | ampE → | ampicillin resistance inner membrane protein, putative signaling protein in beta‑lactamase regulation |
| RA | 121,986 | Δ1 bp | 6.4% | intergenic (‑435/‑106) | aroP ← / → pdhR | aromatic amino acid transporter/pyruvate dehydrogenase complex repressor, autorepressor |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 375,121 | T→G | 5.6% | intergenic (+240/‑338) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 417,238 | Δ1 bp | 3.5% | coding (97/690 nt) | phoB → | response regulator in two‑component regulatory system with PhoR |
| RA | 417,239 | Δ1 bp | 3.4% | coding (98/690 nt) | phoB → | response regulator in two‑component regulatory system with PhoR |
| RA | 417,240 | Δ1 bp | 3.4% | coding (99/690 nt) | phoB → | response regulator in two‑component regulatory system with PhoR |
| JC | 417,368 | Δ5 bp | 100% | coding (227‑231/690 nt) | phoB → | response regulator in two‑component regulatory system with PhoR |
| RA | 701,378:1 | +T | 100% | coding (217/1221 nt) | nagC ← | N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor |
| RA | 704,008 | C→A | 100% | P22Q (CCG→CAG) | nagE → | N‑acetyl glucosamine specific PTS enzyme IIC, IIB, and IIA components |
| RA | 720,627 | A→T | 7.8% | L15F (TTA→TTT) | ybfK → | uncharacterized protein |
| RA | 738,514 | A→G | 3.2% | G141G (GGA→GGG) | ybfD → | H repeat‑associated putative transposase |
| RA | 879,966 | T→C | 4.4% | N172S (AAT→AGT) | gstB ← | glutathione S‑transferase |
| RA | 1,026,067 | G→A | 3.8% | G533R (GGA→AGA) | helD → | DNA helicase IV |
| RA | 1,101,043 | C→T | 3.9% | L214L (TTG→TTA) | csgG ← | curli production assembly/transport outer membrane lipoprotein |
| RA | 1,130,125 | T→A | 5.6% | S2C (AGT→TGT) | flgM ← | anti‑sigma factor for FliA (sigma 28) |
| RA | 1,131,260 | Δ1 bp | 4.4% | coding (243/417 nt) | flgB → | flagellar component of cell‑proximal portion of basal‑body rod |
| RA | 1,157,900:1 | +A | 100% | coding (32/1434 nt) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| RA | 1,269,450 | C→T | 7.0% | 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 | 6.3% | 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 |
| RA | 1,269,785 | G→A | 3.9% | T9I (ACT→ATT) | ldrB ← | toxic polypeptide, small |
| RA | 1,287,037 | C→T | 9.6% | intergenic (+511/+29) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,313,044 | A→G | 3.5% | F207S (TTT→TCT) | yciC ← | UPF0259 family inner membrane protein |
| RA | 1,360,647 | Δ1 bp | 3.6% | coding (262/1419 nt) | puuA ← | glutamate‑‑putrescine ligase |
| RA | 1,397,860 | Δ1 bp | 3.0% | coding (763/951 nt) | uspE ← | stress‑induced protein |
| RA | 1,466,258 | G→C | 6.1% | pseudogene (867/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,438 | T→G | 7.5% | pseudogene (1047/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,856 | A→G | 4.0% | pseudogene (1465/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,488,953 | C→T | 5.5% | A241V (GCG→GTG) | aldA → | aldehyde dehydrogenase A, NAD‑linked |
| RA | 1,521,460 | G→A | 4.5% | R536C (CGT→TGT) | yncD ← | putative iron outer membrane transporter |
| RA | 1,637,431 | A→G | 14.7% | K129E (AAA→GAA) | ydfO → | Qin prophage, uncharacterized protein |
| RA | 1,708,844 | C→G | 9.9% | A642A (GCC→GCG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,847 | G→A | 11.4% | E643E (GAG→GAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,854 | C→G | 10.2% | Q646E (CAA→GAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,726,169 | T→G | 100% | F49L (TTT→TTG) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| RA | 1,829,724:1 | +C | 4.3% | coding (11/1479 nt) | astD ← | succinylglutamic semialdehyde dehydrogenase |
| RA | 1,879,730 | C→A | 3.9% | Q73H (CAG→CAT) | yeaR ← | DUF1971 family protein, nitrate‑inducible |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,304,535 | A→G | 8.4% | intergenic (+144/+571) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,538 | C→T | 4.5% | intergenic (+147/+568) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,547 | C→T | 8.0% | intergenic (+156/+559) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,348,493 | T→C | 4.1% | L371S (TTG→TCG) | nrdB → | ribonucleoside‑diphosphate reductase 1, beta subunit, ferritin‑like protein |
| RA | 2,492,203 | C→T | 3.8% | L350L (TTG→TTA) | frc ← | formyl‑CoA transferase, NAD(P)‑binding |
| RA | 2,520,192 | A→G | 3.6% | I160T (ATC→ACC) | gltX ← | glutamyl‑tRNA synthetase |
| RA | 2,535,261 | C→T | 3.1% | R400C (CGT→TGT) | ptsI → | PEP‑protein phosphotransferase of PTS system (enzyme I) |
| RA | 2,567,330 | Δ1 bp | 5.6% | coding (776/1227 nt) | eutH ← | ethanolamine transporter |
| RA | 3,071,396 | A→G | 3.5% | intergenic (‑154/+61) | fbaA ← / ← pgk | fructose‑bisphosphate aldolase, class II/phosphoglycerate kinase |
| RA | 3,245,024 | A→G | 3.4% | intergenic (‑285/‑198) | uxaC ← / → exuT | uronate isomerase/hexuronate transporter |
| RA | 3,437,300:1 | +G | 4.4% | coding (785/1377 nt) | trkA → | NAD‑binding component of TrK potassium transporter |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| 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 | 4,296,189 | A→G | 31.4% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 33.1% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,267 | T→C | 16.8% | intergenic (+474/+170) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,285 | C→T | 8.1% | intergenic (+492/+152) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,325,889 | G→T | 4.4% | intergenic (‑147/+511) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,326,089 | T→G | 8.7% | intergenic (‑347/+311) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,326,148 | T→C | 11.2% | intergenic (‑406/+252) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,326,149 | G→A | 6.2% | intergenic (‑407/+251) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,386,905 | Δ1 bp | 3.4% | coding (2467/3324 nt) | mscM ← | mechanosensitive channel protein, miniconductance |
| RA | 4,537,832 | T→C | 4.4% | H312R (CAT→CGT) | nanM ← | N‑acetylneuraminic acid mutarotase |
| RA | 4,614,448 | C→T | 5.1% | intergenic (+187/+233) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| RA | 4,614,504 | T→C | 5.7% | intergenic (+243/+177) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| RA | 4,614,538 | T→G | 5.1% | intergenic (+277/+143) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| RA | 4,627,233 | G→T | 3.6% | G441W (GGG→TGG) | radA → | DNA repair protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1293040 | 1303172 | 10133 | 87 [0] | [8] 103 | tdk–[oppB] | tdk, insZ, insZ, insZ, adhE, ychE, oppA, [oppB] |
| * | * | ÷ | NC_000913 | 3423883–3424231 | 3424399–3424237 | 7–517 | 33 [32] | [30] 33 | rrlD | 23S ribosomal RNA of rrnD operon |
| * | * | ÷ | NC_000913 | 4110722 | 4111577 | 856 | 33 [32] | [32] 34 | tpiA | tpiA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 79 (0.820) | 59/514 | 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 | = 258674 | NA (NA) | 93 (0.970) | 66/512 | NT | 93.0% | intergenic (+775/‑2) | 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 | 1303173 = | 7 (0.070) | coding (275/921 nt) | oppB | oligopeptide ABC transporter permease | |||||
| * | ? | NC_000913 | 778042 = | 108 (1.120) | 3 (0.030) | 3/500 | NT | 2.6% | coding (303/1293 nt) | tolB | periplasmic protein |
| ? | NC_000913 | 778212 = | 122 (1.300) | coding (473/1293 nt) | tolB | periplasmic protein | |||||
| * | ? | NC_000913 | 1207790 = | 43 (0.450) | 41 (0.450) | 37/482 | NT | 50.5% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 40 (0.440) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 40 (0.420) | 59 (0.650) | 44/482 | NT | 60.4% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 40 (0.440) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 100 (1.040) | 69/514 | NT | 99.0% | intergenic (+146/‑127) | insH1/ynaJ | IS5 transposase and trans‑activator/DUF2534 family putative inner membrane protein |
| ? | NC_000913 | 1755755 = | 1 (0.010) | coding (58/1413 nt) | pykF | pyruvate kinase I | |||||
| * | ? | NC_000913 | 1411899 = | 96 (1.000) | 6 (0.070) | 6/462 | NT | 8.2% | coding (50/936 nt) | ttcA | tRNA s(2)C32 thioltransferase, iron sulfur cluster protein |
| ? | NC_000913 | = 1434958 | 48 (0.550) | pseudogene (51/51 nt) | ttcC | pseudogene, prophage Rac integration site ttcA duplication,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1517054 | 64 (0.660) | 3 (0.030) | 3/488 | NT | 4.5% | intergenic (+52/+45) | patD/yncL | gamma‑aminobutyraldehyde dehydrogenase/stress‑induced small inner membrane enterobacterial protein |
| ? | NC_000913 | = 1517063 | 66 (0.720) | intergenic (+61/+36) | patD/yncL | gamma‑aminobutyraldehyde dehydrogenase/stress‑induced small inner membrane enterobacterial protein | |||||
| * | ? | NC_000913 | = 1755758 | 1 (0.010) | 83 (0.860) | 58/514 | NT | 98.8% | coding (61/1413 nt) | pykF | pyruvate kinase I |
| ? | NC_000913 | = 2102943 | NA (NA) | intergenic (‑32/+1) | insH1/wbbL | IS5 transposase and trans‑activator/pseudogene, lipopolysaccharide biosynthesis protein | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 46 (0.480) | 32/514 | 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) | 65 (0.670) | 42/514 | 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 | = 3674138 | 111 (1.150) | 4 (0.040) | 4/494 | NT | 3.3% | coding (778/1014 nt) | yhjD | inner membrane putative BrbK family alternate lipid exporter |
| ? | NC_000913 | = 3674302 | 128 (1.380) | coding (942/1014 nt) | yhjD | inner membrane putative BrbK family alternate lipid exporter | |||||
| * | ? | NC_000913 | 4316638 = | 49 (0.510) | 4 (0.040) | 4/490 | NT | 6.9% | coding (582/1137 nt) | phnM | ribophosphonate triphosphate hydrolase |
| ? | NC_000913 | 4316824 = | 62 (0.680) | coding (396/1137 nt) | phnM | ribophosphonate triphosphate hydrolase | |||||