mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.26.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 859 | G→T | 7.5% | A175S (GCG→TCG) | thrA → | Bifunctional aspartokinase/homoserine dehydrogenase 1 |
| RA | 101,138 | C→T | 6.7% | A125V (GCC→GTC) | murC → | UDP‑N‑acetylmuramate:L‑alanine ligase |
| RA | 268,810 | T→C | 6.6% | S51G (AGT→GGT) | ykfA ← | CP4‑6 prophage; putative GTP‑binding protein |
| RA | 286,698 | C→T | 6.0% | A435V (GCC→GTC) | yagG → | CP4‑6 prophage; putative sugar transporter |
| RA | 300,196 | A→G | 56.3% | F247L (TTC→CTC) | paoC ← | PaoABC aldehyde oxidoreductase, Moco‑containing subunit |
| RA | 323,369 | G→A | 57.9% | V344V (GTG→GTA) | ykgF → | ferridoxin‑like LutB family protein; putative electron transport chain YkgEFG component |
| RA | 463,152 | C→T | 7.6% | A413V (GCC→GTC) | ppiD → | periplasmic folding chaperone, has an inactive PPIase domain |
| RA | 791,937 | A→G | 16.9% | V40A (GTA→GCA) | galE ← | UDP‑galactose‑4‑epimerase |
| RA | 1,055,493 | G→A | 49.0% | A229V (GCA→GTA) | torS ← | hybrid sensory histidine kinase in two‑component regulatory system with TorR |
| RA | 1,529,218 | C→T | 100% | pseudogene (1317/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,756,826 | G→A | 12.7% | A377T (GCT→ACT) | pykF → | pyruvate kinase I |
| RA | 1,930,894 | G→A | 22.6% | G5D (GGC→GAC) | purT → | phosphoribosylglycinamide formyltransferase 2 |
| RA | 1,987,038 | C→T | 17.4% | G38G (GGC→GGT) | ftnB → | ferritin B, putative ferrous iron reservoir |
| RA | 2,096,876 | T→C | 17.0% | V88A (GTG→GCG) | hisI → | phosphoribosyl‑AMP cyclohydrolase and phosphoribosyl‑ATP pyrophosphatase |
| RA | 2,131,557 | G→A | 6.4% | R172C (CGC→TGC) | wcaC ← | putative glycosyl transferase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 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 | 2,230,157 | G→A | 49.6% | L77L (CTG→TTG) | dusC ← | tRNA‑dihydrouridine synthase C |
| RA | 2,241,183 | G→A | 5.2% | S162S (AGC→AGT) | galS ← | galactose‑ and fucose‑inducible galactose regulon transcriptional isorepressor; mgl operon transcriptional repressor; autorepressor |
| RA | 2,304,798 | T→C | 8.1% | intergenic (+405/+310) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,394,953 | T→C | 5.4% | I32V (ATC→GTC) | nuoL ← | NADH:ubiquinone oxidoreductase, membrane subunit L |
| RA | 2,426,060 | A→G | 24.9% | G243G (GGT→GGC) | hisJ ← | histidine ABC transporter periplasmic binding protein |
| RA | 2,437,733 | G→A | 5.2% | A40V (GCG→GTG) | pdxB ← | erythronate‑4‑phosphate dehydrogenase |
| RA | 2,453,414 | T→G | 9.2% | pseudogene (1588/2646 nt) | yfcU ← | pseudogene, FimD fimbrial export usher family;putative membrane; Not classified; putative outer membrane protein |
| RA | 2,502,577 | G→A | 25.2% | P637S (CCG→TCG) | fryA ← | putative PTS enzyme: Hpr, enzyme I and IIA components |
| RA | 2,756,933 | G→A | 37.3% | E259K (GAG→AAG) | intA → | CP4‑57 prophage; integrase |
| RA | 2,757,236 | G→A | 37.3% | A360T (GCG→ACG) | intA → | CP4‑57 prophage; integrase |
| RA | 2,810,759 | G→A | 11.2% | intergenic (+80/‑11) | ygaH → / → mprA | putative L‑valine exporter, norvaline resistance protein/transcriptional repressor of microcin B17 synthesis and multidrug efflux |
| RA | 2,832,018 | T→C | 11.2% | D91G (GAC→GGC) | norR ← | anaerobic nitric oxide reductase DNA‑binding transcriptional activator |
| JC | 2,911,480 | Δ12 bp | 4.9% | coding (2161‑2172/2235 nt) | relA ← | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| RA | 2,913,536 | C→T | 18.5% | W39* (TGG→TAG) | relA ← | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| RA | 3,124,889 | G→A | 11.4% | R191* (CGA→TGA) | glcF ← | glycolate oxidase 4Fe‑4S iron‑sulfur cluster subunit |
| RA | 3,198,419 | G→A | 13.0% | A408V (GCG→GTG) | glnE ← | fused deadenylyltransferase/adenylyltransferase for glutamine synthetase |
| RA | 3,305,873 | A→G | 18.6% | intergenic (‑56/+98) | mtr ← / ← deaD | tryptophan transporter of high affinity/ATP‑dependent RNA helicase |
| RA | 3,560,455 | +G | 100% | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,563,700 | C→A | 10.7% | intergenic (+182/+87) | glpD → / ← yzgL | sn‑glycerol‑3‑phosphate dehydrogenase, aerobic, FAD/NAD(P)‑binding/pseudogene, periplasmic solute binding protein homology |
| RA | 3,748,468 | T→C | 22.4% | L462P (CTG→CCG) | lyxK → | L‑xylulose kinase |
| RA | 3,815,809 | +A | 6.9% | intergenic (‑41/+25) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| RA | 3,932,937 | G→A | 5.8% | G541D (GGT→GAT) | kup → | potassium transporter |
| RA | 3,951,559 | +A | 91.5% | pseudogene (18/663 nt) | ilvG → | pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive; acetolactate synthase II, large subunit, cryptic, interrupted |
| RA | 3,964,825 | C→T | 5.4% | C269Y (TGT→TAT) | rhlB ← | ATP‑dependent RNA helicase |
| RA | 4,187,507 | A→C | 100% | N720H (AAC→CAC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,296,060 | C→T | 5.1% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,155 | T→C | 6.2% | intergenic (+361/+281) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→G | 17.7% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 22.3% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 26.9% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 12.0% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380 | +C | 92.7% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380 | +G | 92.7% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,325,948 | A→G | 5.2% | intergenic (‑207/+451) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,367,579 | A→G | 9.6% | V250A (GTG→GCG) | aspA ← | aspartate ammonia‑lyase |
| JC | 4,397,612 | Δ6 bp | 26.1% | coding (201‑206/1848 nt) | mutL → | methyl‑directed mismatch repair protein |
| Unassigned new junction evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 257907 | 0 (0.000) | 113 (0.770) | 71/522 | NT | 100% | intergenic (+8/‑769) | 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 | 258684 = | 0 (0.000) | pseudogene (9/331 nt) | crl | 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 | = 609351 | NA (NA) | 7 (0.050) | 7/530 | NT | 4.4% | noncoding (1345/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | = 1393461 | 153 (1.020) | coding (235/1614 nt) | mppA | murein tripeptide (L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit | |||||
| * | ? | NC_000913 | 1207790 = | 84 (0.550) | 41 (0.290) | 29/506 | NT | 36.0% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 67 (0.470) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 74 (0.490) | 38 (0.270) | 32/506 | NT | 35.7% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 67 (0.470) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293196 = | 291 (1.940) | 3 (0.020) | 3/538 | NT | 1.0% | intergenic (‑274/‑331) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| ? | NC_000913 | = 1300693 | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1293199 | 291 (1.940) | 3 (0.020) | 3/538 | NT | 1.0% | intergenic (‑277/‑328) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| ? | NC_000913 | 1299499 = | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1299498 | 1 (0.010) | 125 (0.840) | 80/530 | NT | 99.6% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 69 (0.470) | 54/522 | 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 | |||||