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 | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 417,391 | G→C | A84P (GCC→CCC) | phoB → | response regulator in two‑component regulatory system with PhoR |
| RA | 702,066 | G→C | P229R (CCT→CGT) | nagA ← | N‑acetylglucosamine‑6‑phosphate deacetylase |
| RA | 1,158,384 | G→A | W172* (TGG→TGA) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| 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 | 1,726,507 | Δ1 bp | coding (485/600 nt) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,132,787 | A→C | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,977,594 | +C | coding (998/1032 nt) | galR → | galactose‑inducible d‑galactose regulon transcriptional repressor, autorepressor |
| MC JC | 3,815,858 | Δ82 bp | [rph]–[rph] | [rph], [rph] | |
| MC JC | 3,909,311 | Δ774 bp | [pstA]–[pstC] | [pstA], [pstC] | |
| JC | 4,001,644 | Δ5 bp | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,184,542 | C→A | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,583,863 | C→T | R967H (CGT→CAT) | hsdR ← | endonuclease R Type I restriction enzyme |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423753–3424232 | 3424530–3424237 | 6–778 | 10 [9] | [9] 10 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| * | * | ÷ | NC_000913 | 3762360–3764071 | 3765192–3764079 | 9–2833 | 10 [8] | [9] 10 | rhsA | Rhs protein with putative toxin 55 domain, putative polysaccharide synthesis/export protein, putative neighboring cell growth inhibitor |
| * | * | ÷ | NC_000913 | 4110752 | 4111476 | 725 | 10 [9] | [8] 10 | tpiA | triosephosphate isomerase |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 153986 = | 1 (0.030) | 54 (1.800) | 34/284 | 0.0 | 98.2% | coding (1441/2598 nt) | htrE | putative outer membrane usher protein |
| ? | NC_000913 | = 275149 | NA (NA) | intergenic (‑32/‑176) | insH1/mmuP | IS5 transposase and trans‑activator/CP4‑6 prophage, putative S‑methylmethionine transporter | |||||
| * | ? | NC_000913 | = 153989 | 0 (0.000) | 23 (0.770) | 19/284 | 0.5 | 100% | coding (1438/2598 nt) | htrE | putative outer membrane usher protein |
| ? | NC_000913 | 273955 = | NA (NA) | intergenic (+1/+146) | ykfC/insH1 | CP4‑6 prophage, conserved protein,Phage or Prophage Related/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | 257908 = | NA (NA) | 27 (0.900) | 23/284 | 0.3 | 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 | 1207790 = | 7 (0.230) | 18 (0.680) | 16/252 | 0.6 | 76.3% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 5 (0.190) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 7 (0.230) | 18 (0.680) | 16/252 | 0.6 | 76.3% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 5 (0.190) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 2 (0.070) | 43 (1.430) | 35/284 | 0.0 | 95.6% | 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) | 41 (1.370) | 29/284 | 0.1 | 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 | 3 (0.100) | 21 (0.700) | 20/284 | 0.5 | 87.5% | 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 | 2375822 = | 1 (0.030) | 21 (0.720) | 18/276 | 0.6 | 95.6% | coding (139/963 nt) | menC | O‑succinylbenzoyl‑CoA synthase |
| ? | NC_000913 | = 2515611 | NA (NA) | intergenic (+170/+30) | insL1/yfeA | IS186 transposase/putative diguanylate cyclase | |||||
| * | ? | NC_000913 | = 2375833 | 1 (0.030) | 31 (1.060) | 21/276 | 0.4 | 97.0% | coding (128/963 nt) | menC | O‑succinylbenzoyl‑CoA synthase |
| ? | NC_000913 | 2514275 = | NA (NA) | intergenic (+33/‑54) | nupC/insL1 | nucleoside (except guanosine) transporter/IS186 transposase | |||||