mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.32.0 revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 433,649 | T→G | 29.9% | G65G (GGT→GGG) | ribD → | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| RA | 1,196,305 | C→T | 100% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,478,306 | A→T | 22.9% | L27F (TTA→TTT) | ynbB → | putative CDP‑diglyceride synthase |
| RA | 1,865,874 | T→C | 10.4% | E200G (GAG→GGG) | mipA ← | scaffolding protein for murein synthesizing machinery |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 3,206,436 | G→A | 29.3% | intergenic (‑182/‑25) | ttdR ← / → ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,481 | G→A | 31.5% | K7K (AAG→AAA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,482 | C→A | 21.4% | Q8K (CAA→AAA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,760,383 | A→C | 29.8% | V289G (GTG→GGG) | selA ← | selenocysteine synthase |
| RA | 3,782,916 | G→A | 22.8% | L249L (CTG→TTG) | gpsA ← | glycerol‑3‑phosphate dehydrogenase (NAD+) |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,862,672 | G→A | 43.7% | pseudogene (931/1617 nt) | glvC ← | pseudogene, arbutin specific enzyme IIC component of PTS,enzyme, Transport of small molecules: Carbohydrates, organic acids, alcohols, PTS system, arbutin‑like IIB component, PTS system, arbutin‑like IIC component |
| MC JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,267 | T→C | 14.7% | intergenic (+474/+170) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,568,566 | T→A | 17.2% | intergenic (‑46/‑433) | mdtM ← / → yjiP | multidrug efflux system protein/pseudogene, transposase_31 family protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1209603 | 1209618 | 16 | 39 [0] | [0] 47 | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related |
| * | * | ÷ | NC_000913 | 3423880–3424230 | 3424417–3424236 | 7–538 | 9 [8] | [7] 9 | rrlD | 23S ribosomal RNA of rrnD operon |
| * | * | ÷ | NC_000913 | 3769633 | 3769903 | 271 | 9 [8] | [8] 9 | [yibV]–yibV | [yibV], yibV |
| * | * | ÷ | NC_000913 | 4233768 | 4235397 | 1630 | 11 [7] | [8] 9 | pgi | glucosephosphate isomerase |
| * | * | ÷ | NC_000913 | 4476841 | 4477094 | 254 | 9 [8] | [8] 10 | yjgL | SopA‑central‑domain‑like hexapeptide repeat protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 54 (1.110) | 43/438 | NT | 100% | intergenic (+9/‑768) | 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 | = 1293039 | 0 (0.000) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | 458787 = | 8 (0.160) | 44 (0.920) | 33/432 | NT | 84.8% | intergenic (+87/‑101) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| ? | NC_000913 | 608011 = | NA (NA) | intergenic (+23/‑54) | hokE/insL1 | toxic polypeptide, small/IS186 transposase | |||||
| * | ? | NC_000913 | = 458799 | 8 (0.160) | 36 (0.750) | 29/430 | NT | 82.1% | intergenic (+99/‑89) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| ? | NC_000913 | = 609347 | NA (NA) | intergenic (+170/+112) | insL1/entD | IS186 transposase/phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex | |||||
| * | ? | NC_000913 | 458873 = | 10 (0.210) | 11 (0.230) | 10/438 | NT | 52.4% | intergenic (+173/‑15) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| ? | NC_000913 | = 575785 | NA (NA) | intergenic (‑32/+1) | insH1/nmpC | IS5 transposase and trans‑activator/DLP12 prophage, truncated outer membrane porin (pseudogene),IS, phage, Tn, Phage or Prophage Related, outer membrane porin protein, locus of qsr prophage | |||||
| * | ? | NC_000913 | = 458877 | 12 (0.250) | 12 (0.250) | 9/436 | NT | 50.1% | intergenic (+177/‑11) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| ? | NC_000913 | 574592 = | NA (NA) | intergenic (‑6/+145) | nmpC/insH1 | DLP12 prophage, truncated outer membrane porin (pseudogene),IS, phage, Tn, Phage or Prophage Related, outer membrane porin protein, locus of qsr prophage/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | 1207790 = | 8 (0.160) | 40 (0.890) | 32/406 | NT | 91.5% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 0 (0.000) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 8 (0.160) | 33 (0.730) | 29/406 | NT | 89.9% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 0 (0.000) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 1 (0.020) | 65 (1.340) | 51/438 | NT | 98.5% | intergenic (‑110/‑495) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| ? | NC_000913 | = 1979270 | NA (NA) | intergenic (‑55/‑483) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 19 (0.390) | 16/438 | NT | 100% | intergenic (‑271/‑267) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | 2101749 = | NA (NA) | intergenic (‑5/+146) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | = 1979489 | 0 (0.000) | 40 (0.820) | 34/438 | NT | 100% | intergenic (‑274/‑264) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | = 2290111 | NA (NA) | intergenic (‑32/+1) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system | |||||
| * | ? | NC_000913 | 2288917 = | NA (NA) | 8 (0.160) | 8/438 | NT | 23.5% | intergenic (‑5/+146) | yejO/insH1 | pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system/IS5 transposase and trans‑activator |
| ? | NC_000913 | = 3836841 | 26 (0.540) | intergenic (+286/‑111) | yicT/setC | pseudogene/putative arabinose efflux transporter | |||||
| * | ? | NC_000913 | = 3032400 | 54 (1.110) | 3 (0.060) | 3/424 | NT | 5.5% | coding (1036/1449 nt) | uacT | uric acid permease |
| ? | NC_000913 | = 3032403 | 50 (1.060) | coding (1039/1449 nt) | uacT | uric acid permease | |||||
| * | ? | NC_000913 | = 3653229 | NA (NA) | 22 (0.450) | 20/438 | NT | 56.4% | intergenic (‑32/‑1) | insH1/yhiS | IS5 transposase and trans‑activator/pseudogene |
| ? | NC_000913 | 3836838 = | 17 (0.350) | intergenic (+283/‑114) | yicT/setC | pseudogene/putative arabinose efflux transporter | |||||