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 | 126,947 | G→T | R418L (CGT→CTT) | aceF → | pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2 |
| RA | 1,143,643 | T→G | Q242P (CAG→CCG) | rne ← | endoribonuclease; RNA‑binding protein;RNA degradosome binding protein |
| MC JC | 1,299,499 | Δ1,199 bp | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,413,542 | A→T | Y67N (TAT→AAT) | ydaC ← | DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein |
| RA | 1,793,898 | Δ1 bp | coding (212/552 nt) | btuE ← | glutathione peroxidase |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,093,040 | G→A | A215T (GCT→ACT) | hisC → | histidinol‑phosphate aminotransferase |
| RA | 3,623,585 | A→G | E63G (GAA→GGA) | yhhH → | putative NTF2 fold immunity protein for polymorphic toxin RhsB |
| RA | 4,116,703 | T→G | K173N (AAA→AAC) | glpK ← | glycerol kinase |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 257907 | 1 (0.010) | 92 (0.910) | 71/280 | 0.4 | 99.0% | 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 = | 1 (0.010) | 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 | 1207790 = | 28 (0.260) | 74 (0.770) | 54/264 | 1.1 | 80.9% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 10 (0.100) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 28 (0.260) | 84 (0.880) | 68/264 | 0.3 | 82.8% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 10 (0.100) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1469240 | NA (NA) | 78 (0.730) | 57/296 | 1.5 | 94.0% | intergenic (‑91/‑1) | insC1/ydbA | IS2 repressor TnpA/pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| ? | NC_000913 | = 1652258 | 5 (0.050) | pseudogene (708/1158 nt) | intQ | pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1651547 | NA (NA) | 106 (0.990) | 88/294 | 0.1 | 96.4% | intergenic (+10/‑4) | insD1/intQ | IS2 transposase TnpB;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related/pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related |
| ? | NC_000913 | 1652253 = | 4 (0.040) | pseudogene (703/1158 nt) | intQ | pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 2406857 = | 2 (0.020) | 110 (1.030) | 72/294 | 0.5 | 98.2% | intergenic (‑218/‑702) | lrhA/alaA | transcriptional repressor of flagellar, motility and chemotaxis genes/glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase |
| ? | NC_000913 | = 2997688 | NA (NA) | intergenic (‑90/+2) | insC1/ygeQ | IS2 repressor TnpA/pseudogene, glycosyl hydrolase family 15, part of T3SS PAI ETT2 remnant | |||||
| * | ? | NC_000913 | = 2406863 | 1 (0.010) | 97 (0.910) | 71/294 | 0.5 | 99.0% | intergenic (‑224/‑696) | lrhA/alaA | transcriptional repressor of flagellar, motility and chemotaxis genes/glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase |
| ? | NC_000913 | 2996360 = | NA (NA) | intergenic (‑2/+10) | ygeO/insD1 | pseudogene, orgA family, part of T3SS PAI ETT2 remnant/IS2 transposase TnpB | |||||
| * | ? | NC_000913 | 3186094 = | NA (NA) | 109 (1.020) | 81/296 | 0.2 | 95.6% | intergenic (+6/‑91) | yqiG/insC1 | pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein/IS2 repressor TnpA |
| ? | NC_000913 | 3485933 = | 5 (0.050) | intergenic (‑117/‑185) | yhfA/crp | OsmC family protein/cAMP‑activated global transcription factor, mediator of catabolite repression | |||||
| * | ? | NC_000913 | = 3187424 | NA (NA) | 108 (1.010) | 75/296 | 0.4 | 98.2% | intergenic (+11/‑1) | insD1/yqiG | IS2 transposase TnpB/pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein |
| ? | NC_000913 | = 3485937 | 2 (0.020) | intergenic (‑121/‑181) | yhfA/crp | OsmC family protein/cAMP‑activated global transcription factor, mediator of catabolite repression | |||||