mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 264,098 | G→T | L50L (CTC→CTA) | ykfH ← | uncharacterized protein |
| RA | 1,197,502 | C→T | G11R (GGA→AGA) | ymfD ← | e14 prophage; putative SAM‑dependent methyltransferase |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,173,363 | Δ2 bp | intergenic (‑1/+1) | gatC ← / ← gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,679,525 | G→T | A1074D (GCT→GAT) | yphG ← | DUF4380 domain‑containing TPR repeat protein |
| RA | 2,811,215 | Δ1 bp | coding (446/531 nt) | mprA → | transcriptional repressor of microcin B17 synthesis and multidrug efflux |
| RA | 3,413,571 | T→C | intergenic (‑106/‑293) | acrS ← / → acrE | acrAB operon transcriptional repressor/cytoplasmic membrane lipoprotein |
| RA | 3,560,455 | +G | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| MC JC | 3,580,806 | Δ2,622 bp | IS1‑mediated | ryhB–yrhA | ryhB, yhhY, yhhZ, yrhA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2995175 | 2995271 | 97 | 5 [4] | [4] 5 | ygeK/ygeN | pseudogene, response regulator family, part of T3SS PAI ETT2 remnant; putative 2‑component transcriptional regulator/pseudogene, orgB family, part of T3SS PAI ETT2 remnant |
| * | * | ÷ | NC_000913 | 3423723–3424234 | 3424599–3424238 | 5–877 | 5 [3] | [4] 7 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 27 (0.940) | 21/124 | 0.2 | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 2077808 = | 31 (1.010) | 10 (0.400) | 4/108 | 2.1 | 21.0% | coding (240/375 nt) | cbtA | CP4‑44 prophage; toxin of the YeeV‑YeeU toxin‑antitoxin system |
| ? | NC_000913 | 2077982 = | 50 (2.000) | pseudogene (43/168 nt) | yeeW | CP4‑44 prophage; uncharacterized protein;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 2158238 = | 13 (0.420) | 4 (0.140) | 3/122 | 2.7 | 25.8% | coding (2976/3123 nt) | mdtB | multidrug efflux system, subunit B |
| ? | NC_000913 | 2158297 = | 11 (0.390) | coding (3035/3123 nt) | mdtB | multidrug efflux system, subunit B | |||||
| * | ? | NC_000913 | 3620750 = | NA (NA) | 4 (0.130) | 3/128 | 2.8 | 100% | coding (1559/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | 3621165 = | 0 (0.000) | coding (1974/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | 3704467 = | 29 (0.950) | 7 (0.260) | 3/116 | 2.6 | 20.2% | coding (295/903 nt) | dppC | dipeptide/heme ABC transporter permease |
| ? | NC_000913 | 3704731 = | 30 (1.120) | coding (31/903 nt) | dppC | dipeptide/heme ABC transporter permease | |||||
| * | ? | NC_000913 | = 3831044 | 17 (0.550) | 8 (0.310) | 3/110 | 2.5 | 38.0% | coding (588/1710 nt) | yicH | putative inner membrane‑anchored periplasmic AsmA family protein |
| ? | NC_000913 | = 3831092 | 12 (0.470) | coding (636/1710 nt) | yicH | putative inner membrane‑anchored periplasmic AsmA family protein | |||||
| * | ? | NC_000913 | 3927418 = | 23 (0.750) | 5 (0.200) | 3/108 | 2.4 | 24.5% | coding (264/993 nt) | asnA | asparagine synthetase A |
| ? | NC_000913 | 3927457 = | 12 (0.480) | coding (303/993 nt) | asnA | asparagine synthetase A | |||||
| * | ? | NC_000913 | 4164667 = | 34 (1.110) | 7 (0.250) | 3/122 | 2.7 | 21.7% | coding (1029/1845 nt) | btuB | vitamin B12/cobalamin outer membrane transporter |
| ? | NC_000913 | 4164716 = | 19 (0.670) | coding (1078/1845 nt) | btuB | vitamin B12/cobalamin outer membrane transporter | |||||
| * | ? | NC_000913 | = 4392402 | 11 (0.360) | 3 (0.110) | 3/116 | 2.6 | 22.5% | noncoding (43/76 nt) | glyV | tRNA‑Gly |
| ? | NC_000913 | = 4392497 | 11 (0.410) | noncoding (26/76 nt) | glyX | tRNA‑Gly | |||||
| * | ? | NC_000913 | 4542682 = | 7 (0.230) | 6 (0.230) | 5/114 | 1.9 | 34.3% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 17 (0.640) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 4542690 | 7 (0.230) | 3 (0.110) | 3/114 | 2.5 | 20.7% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 17 (0.640) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||