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 |
| 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 |
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| 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 | 1,493,381 | T→C | L292L (TTA→TTG) | elaD ← | deubiquitinase |
| RA | 1,514,629 | C→T | intergenic (+88/‑132) | yfaY → / → rhmR | competence/damage‑inducible protein A/transcriptional regulator |
| RA | 1,618,508 | T→A | I6N (ATT→AAT) | psuG → | pseudouridine‑5'‑phosphate glycosidase |
| RA | 1,709,744 | G→T | G4C (GGT→TGT) | yegR → | hypothetical protein |
| RA | 1,755,118 | G→A | G14G (GGG→GGA) | cpsG → | phosphomannomutase |
| RA | 1,768,973 | C→T | T168I (ACA→ATA) | wzxB → | polisoprenol‑linked O‑antigen transporter |
| RA | 1,773,985 | (A)8→7 | coding (440/1119 nt) | wbbK → | hypothetical protein |
| 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 |
| RA | 1,885,611 | G→A | W125* (TGG→TAG) | pgsA → | CDP‑diacylglycerol‑‑glycerol‑3‑phosphate 3‑phosphatidyltransferase |
| 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 | 2,019,390 | T→A | I381N (ATC→AAC) | ydjK → | MFS sugar transporter membrane protein |
| 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 | 2,371,554 | C→A | L48F (TTG→TTT) | ydcP ← | peptidase |
| 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 | 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 |
| 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 | 3,781,762 | T→C | intergenic (‑19/+583) | mraZ ← / ← cra | division/cell wall cluster transcriptional repressor MraZ/catabolite repressor/activator |
| 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 |
| JC | 3,898,512 | Δ19 bp | intergenic (+163/+239) | yjjW → / ← yjjV | glycine radical enzyme activase/DNAse |
| RA | 3,913,413 | T→G | intergenic (+79/‑175) | yjjA → / → opgB | hypothetical protein/phosphoglycerol transferase I |
| RA | 3,935,805 | C→A | I255I (ATC→ATA) | mcrC → | protein mcrC |
| RA | 3,944,733 | T→C | I75T (ATT→ACT) | mdtM → | multidrug resistance protein MdtM |
| 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 | 4,204,741 | C→A | H381N (CAT→AAT) | alsA → | D‑allose import ATP‑binding protein AlsA |
| RA | 4,414,695 | G→A | A251T (GCA→ACA) | rhaT → | l‑rhamnose‑proton symporter |
| RA | 4,482,593 | C→A | E239D (GAG→GAT) | pepQ ← | Xaa‑Pro dipeptidase |
| 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 | 192 (0.390) | 194 (0.440) | 131/268 | 1.9 | 52.0% | pseudogene (20/345 nt) | pinE | hypothetical protein |
| ? | DH1 | = 2670672 | 187 (0.420) | coding (306/789 nt) | stfP | integrase | |||||
| * | ? | DH1 | 2668875 = | 189 (0.420) | 193 (0.430) | 130/268 | 2.0 | 50.7% | pseudogene (20/345 nt) | pinE | hypothetical protein |
| ? | DH1 | 2670674 = | NA (NA) | noncoding (1/242 nt) | repeat_region | repeat region | |||||
| * | ? | DH1 | 3635058 = | 137 (0.280) | 415 (0.880) | 207/284 | 0.1 | 77.1% | coding (263/741 nt) | dnaQ | DNA polymerase III subunit epsilon |
| ? | DH1 | = 3635099 | 117 (0.250) | coding (222/741 nt) | dnaQ | DNA polymerase III subunit epsilon | |||||