mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.28.1 revision 52323b585d6f
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 100,838 | T→C | L246P (CTT→CCT) | gpsA → | glycerol‑3‑phosphate dehydrogenase (NAD(P)(+)) |
| MC JC | 163,135 | Δ95,041 bp | hokA–yhhJ | 83 genes hokA, cspA, yiaG, yiaF, ghrB, yiaD, bisC, yiaC, tag, yhjY, yhjX, eptB, ECDH1_RS00855, ECDH1_RS00860, dppA, ECDH1_RS00870, dppB, dppC, dppD, dppF, yhjV, ECDH1_RS00900, ldrD, bcsG, bcsF, bcsE, yhjR, ECDH1_RS00930, bcsA, bcsB, bcsZ, bcsC, yhjK, dctA, yhjJ, kdgK, ECDH1_RS00975, yhjH, yhjG, yhjE, yhjD, yhjC, yhjB, treF, yhjA, gadA, gadX, gadW, mdtF, mdtE, ECDH1_RS01045, gadE, hdeD, hdeA, hdeB, yhiD, dctR, slp, slp, insH1, ECDH1_RS01095, arsC, arsB, arsR, ECDH1_RS01115, ECDH1_RS01120, gor, rlmJ, prlC, rsmJ, tppB, uspA, uspB, pitA, yhiN, yhiM, ECDH1_RS01175, ECDH1_RS01180, ECDH1_RS01185, yhiJ, yhiI, rbbA, yhhJ |
|
| RA | 839,095 | Δ1 bp | coding (1001/1434 nt) | bglA ← | 6‑phospho‑beta‑glucosidase |
| RA | 915,795 | A→C | Q156P (CAG→CCG) | ptsP → | phosphoenolpyruvate‑protein phosphotransferase PtsP |
| RA | 1,299,401 | G→T | A389S (GCG→TCG) | aegA → | protein AegA |
| RA | 1,423,597 | T→A | pseudogene (1627/2646 nt) | yfcV → | fimbrial assembly protein |
| RA | 1,709,744 | G→T | G4C (GGT→TGT) | yegR → | hypothetical protein |
| RA | 1,768,973 | C→T | T168I (ACA→ATA) | wzxB → | polisoprenol‑linked O‑antigen transporter |
| RA | 1,779,915 | G→A | E54E (GAG→GAA) | wzzB → | chain length determinant protein |
| RA | 1,820,579 | G→A | L207F (CTT→TTT) | yeeN ← | transcriptional regulator |
| JC JC | 1,971,027 | repeat_region (+) +4 bp :: Δ3 bp | coding (141‑144/144 nt) | yobF → | DUF2527 domain‑containing protein |
| RA | 1,985,603 | G→T | D121Y (GAT→TAT) | yoaA → | ATP‑dependent helicase |
| RA | 2,122,777 | (T)5→4 | coding (4/1413 nt) | pykF ← | pyruvate kinase I |
| RA | 2,232,214 | Δ1 bp | intergenic (‑141/‑392) | flxA ← / → relB | protein FlxA/antitoxin RelB |
| RA | 2,244,937 | A→G | intergenic (‑81/+236) | pinQ ← / ← ydfK | Qin prophage; site‑specific recombinase/cold‑shock protein |
| RA | 2,352,449 | G→A | intergenic (‑218/‑49) | yncG ← / → ansP | glutathione S‑transferase/L‑asparagine permease |
| RA | 2,372,968 | G→A | D191N (GAT→AAT) | ydcO → | hypothetical protein |
| RA | 2,404,019 | +G | coding (239/861 nt) | ydbC ← | oxidoreductase |
| RA | 2,509,217 | G→A | S82L (TCA→TTA) | ycjM ← | alpha amylase catalytic domain family protein |
| RA | 2,573,476 | C→A | A146A (GCG→GCT) | oppF ← | oligopeptide transport ATP‑binding protein OppF |
| RA | 2,682,962 | T→A | intergenic (+90/+404) | ymfD → / ← icd | e14 prophage; SAM‑dependent methyltransferase/isocitrate dehydrogenase (NADP(+)) |
| RA | 3,154,902 | A→T | I274F (ATC→TTC) | kdpB → | potassium‑transporting ATPase B chain |
| RA | 3,297,355 | A→T | N28K (AAT→AAA) | appY ← | transcriptional regulator |
| JC | 3,520,073 | Δ107 bp | coding (765‑871/1170 nt) | prpC ← | 2‑methylcitrate synthase |
| RA | 3,668,924 | (T)5→6 | pseudogene (353/455 nt) | lpxA ← | hydroxymyristoyl‑ACP dehydratase |
| RA | 3,701,765 | Δ1 bp | coding (2129/2244 nt) | fhuA ← | ferrichrome‑iron receptor |
| RA | 3,795,806 | A→G | intergenic (+73/‑91) | sgrT → / → tbpA | transcriptional regulator SgrR/thiamine‑binding periplasmic protein |
| RA | 3,871,936 | G→A | S51F (TCT→TTT) | yjtD ← | RNA methyltransferase |
| RA | 3,894,823 | T→A | intergenic (‑23/+104) | deoA ← / ← deoC | thymidine phosphorylase/2‑deoxyribose‑5‑phosphate aldolase |
| RA | 3,913,413 | T→G | intergenic (+79/‑175) | yjjA → / → opgB | hypothetical protein/phosphoglycerol transferase I |
| RA | 3,980,009 | A→G | *86* (TAA→TAG) | yjhX → | hypothetical protein |
| RA | 4,137,730 | C→A | intergenic (‑24/+152) | sugE ← / ← ecnB | quaternary ammonium compound‑resistance protein SugE/entericidin B |
| RA | 4,173,457 | T→G | W169G (TGG→GGG) | melR → | melibiose operon regulatory protein |
| RA | 4,198,371 | C→T | Q337* (CAG→TAG) | phnM → | alpha‑D‑ribose 1‑methylphosphonate 5‑triphosphate diphosphatase |
| RA | 4,199,771 | T→G | V98G (GTT→GGT) | phnP → | phosphoribosyl 1,2‑cyclic phosphodiesterase |
| RA | 4,547,561 | C→G | A165P (GCA→CCA) | rho ← | transcription termination factor Rho |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | DH1 | = 2668875 | 160 (0.340) | 182 (0.440) | 130/268 | 2.1 | 52.8% | pseudogene (20/345 nt) | pinE | hypothetical protein |
| ? | DH1 | = 2670672 | 183 (0.440) | coding (306/789 nt) | stfP | integrase | |||||
| * | ? | DH1 | 2668875 = | 160 (0.380) | 167 (0.400) | 121/268 | 2.6 | 51.3% | pseudogene (20/345 nt) | pinE | hypothetical protein |
| ? | DH1 | 2670674 = | NA (NA) | noncoding (1/242 nt) | repeat_region | repeat region | |||||
| * | ? | DH1 | 3635058 = | 167 (0.360) | 412 (0.930) | 203/284 | 0.1 | 75.0% | coding (263/741 nt) | dnaQ | DNA polymerase III subunit epsilon |
| ? | DH1 | = 3635099 | 117 (0.260) | coding (222/741 nt) | dnaQ | DNA polymerase III subunit epsilon | |||||
| * | ? | DH1 | 3970034 = | 24 (0.050) | 542 (1.240) | 223/282 | 0.0 | 96.1% | intergenic (‑120/‑94) | fimA/ECDH1_RS19620 | type‑1 fimbrial protein, A chain/hypothetical protein |
| ? | DH1 | 3970348 = | 21 (0.050) | intergenic (+32/+48) | ECDH1_RS19620/fimE | hypothetical protein/tyrosine recombinase | |||||
| * | ? | DH1 | = 3970042 | 24 (0.050) | 597 (1.360) | 232/282 | 0.0 | 96.5% | intergenic (‑128/‑86) | fimA/ECDH1_RS19620 | type‑1 fimbrial protein, A chain/hypothetical protein |
| ? | DH1 | = 3970338 | 21 (0.050) | intergenic (+22/+58) | ECDH1_RS19620/fimE | hypothetical protein/tyrosine recombinase | |||||