mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 13,957 | A→T | M599L (ATG→TTG) | dnaK → | chaperone Hsp70, with co‑chaperone DnaJ |
| RA | 101,342 | C→T | T193I (ACC→ATC) | murC → | UDP‑N‑acetylmuramate:L‑alanine ligase |
| RA | 145,691 | C→T | A204V (GCC→GTC) | yadE → | putative polysaccharide deacetylase lipoprotein |
| RA | 243,264 | C→T | G14S (GGC→AGC) | fadE ← | acyl coenzyme A dehydrogenase |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 342,567 | +G | intergenic (+60/‑317) | yahJ → / → yahK | putative metallo‑dependent hydrolase domain deaminase/broad specificity NADPH‑dependent aldehyde reductase, Zn‑containing |
| RA | 345,973 | (G)5→4 | coding (365/672 nt) | yahN ← | amino acid exporter for proline, lysine, glutamate, homoserine |
| RA | 459,607 | A→G | E240E (GAA→GAG) | lon → | DNA‑binding ATP‑dependent protease La |
| RA | 696,177 | T→C | N359N (AAT→AAC) | ubiF → | 2‑octaprenyl‑3‑methyl‑6‑methoxy‑1,4‑benzoquinol oxygenase |
| RA | 706,591 | G→A | E167K (GAA→AAA) | glnS → | glutamyl‑tRNA synthetase |
| RA | 714,588 | C→T | A344V (GCC→GTC) | pgm → | phosphoglucomutase |
| RA | 723,678 | A→G | V246A (GTG→GCG) | kdpD ← | fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein |
| RA | 833,768 | C→T | S233S (AGC→AGT) | dinG → | ATP‑dependent DNA helicase |
| JC JC | 1,293,036 | IS2 (+) +5 bp | intergenic (‑114/‑487) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| RA | 1,461,981 | T→C | G363G (GGT→GGC) | paaJ → | 3‑oxoadipyl‑CoA/3‑oxo‑5,6‑dehydrosuberyl‑CoA thiolase |
| RA | 1,624,020 | G→A | intergenic (‑170/+85) | dgcZ ← / ← ydeI | diguanylate cyclase, zinc‑sensing/hydrogen peroxide resistance OB fold protein; putative periplasmic protein |
| RA | 1,875,056 | (C)6→7 | coding (521/822 nt) | yeaM ← | putative DNA‑binding transcriptional regulator |
| RA | 1,883,993 | A→G | Y269C (TAC→TGC) | yeaV → | putative transporter |
| RA | 1,932,950 | T→C | E552G (GAA→GGA) | edd ← | 6‑phosphogluconate dehydratase |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,090,136 | (G)5→6 | intergenic (+90/‑56) | hisL → / → hisG | his operon leader peptide/ATP phosphoribosyltransferase |
| RA | 2,173,363 | Δ2 bp | intergenic (‑1/+1) | gatC ← / ← gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,245,958 | C→T | R271H (CGC→CAC) | cirA ← | colicin IA outer membrane receptor and translocator; ferric iron‑catecholate transporter |
| RA | 2,267,405 | A→G | I387M (ATA→ATG) | yeiQ → | putative NAD‑dependent D‑mannonate oxidoreductase |
| RA | 2,304,838 | A→G | intergenic (+445/+270) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,490,115 | T→C | R24R (AGA→AGG) | yfdV ← | putative transporter |
| RA | 2,567,248 | G→C | A287G (GCG→GGG) | eutH ← | ethanolamine transporter |
| RA | 2,608,927 | T→C | D147D (GAT→GAC) | hyfG → | hydrogenase 4, subunit |
| RA | 2,653,277 | T→C | Y262H (TAC→CAC) | sseA → | 3‑mercaptopyruvate sulfurtransferase |
| RA | 2,779,038 | G→A | A1230V (GCC→GTC) | ypjA ← | adhesin‑like autotransporter |
| RA | 2,809,774 | (T)7→6 | coding (158/738 nt) | ygaZ → | putative L‑valine exporter, norvaline resistance protein |
| RA | 3,024,934 | T→C | L195S (TTA→TCA) | xanQ → | xanthine permease |
| RA | 3,136,947 | C→T | V526M (GTG→ATG) | gss ← | glutathionylspermidine amidase and glutathionylspermidine synthetase |
| RA | 3,173,566 | G→C | R611G (CGC→GGC) | parE ← | DNA topoisomerase IV, subunit B |
| RA | 3,240,984 | (G)7→8 | coding (1041/1245 nt) | sstT → | sodium:serine/threonine symporter |
| RA | 3,279,878 | A→G | D322G (GAC→GGC) | kbaZ → | tagatose 6‑phosphate aldolase 1, kbaZ subunit |
| RA | 3,560,455 | +G | 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 | 3,568,561 | C→T | A256A (GCG→GCA) | glgC ← | glucose‑1‑phosphate adenylyltransferase |
| RA | 3,661,667 | T→C | R418R (CGT→CGC) | mdtF → | anaerobic multidrug efflux transporter, ArcA‑regulated |
| RA | 3,663,901 | T→C | T240A (ACC→GCC) | gadW ← | transcriptional activator of gadA and gadBC; repressor of gadX |
| MC JC | 3,815,859 | Δ82 bp | [rph]–[rph] | [rph], [rph] | |
| RA | 3,928,131 | T→C | V326A (GTC→GCC) | asnA → | asparagine synthetase A |
| RA | 4,135,739 | T→C | V635V (GTT→GTC) | katG → | catalase‑peroxidase HPI, heme b‑containing |
| RA | 4,136,037 | C→T | intergenic (+22/‑71) | katG → / → yijE | catalase‑peroxidase HPI, heme b‑containing/EamA‑like transporter family protein |
| RA | 4,183,258 | G→A | E672K (GAA→AAA) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,282,608 | A→G | G156G (GGT→GGC) | yjcF ← | pentapeptide repeats protein |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,397,649 | Δ1 bp | coding (238/1848 nt) | mutL → | methyl‑directed mismatch repair protein |
| RA | 4,438,767 | C→T | A166T (GCG→ACG) | ytfJ ← | putative transcriptional regulator |
| RA | 4,451,758 | A→G | Q234R (CAG→CGG) | ytfR → | putative sugar ABC transporter ATPase |
| RA | 4,477,982 | A→G | G110G (GGT→GGC) | argI ← | ornithine carbamoyltransferase 1 |
| RA | 4,506,193 | (A)8→9 | coding (907/1119 nt) | yjhC → | GFO/IDH/MOCA family putative oxidoreductase. NAD(P)‑dependent |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423713–3424577 | 3424577 | 1–865 | 106 [101] | [104] 105 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 19 (0.090) | 132 (0.790) | 86/166 | 0.5 | 91.4% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 9 (0.050) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 18 (0.090) | 133 (0.790) | 83/166 | 0.6 | 91.7% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 9 (0.050) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 204 (1.060) | 116/190 | 0.1 | 100% | 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 | |||||