mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
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 | 1,529,218 | C→T | pseudogene (1317/2037 nt) | rhsE → | pseudogene, Rhs family |
| 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 |
| MC JC | 2,393,422 | Δ13 bp | coding (1613‑1625/1842 nt) | nuoL ← | NADH:ubiquinone oxidoreductase, membrane subunit L |
| RA | 3,316,730 | A→C | L266R (CTG→CGG) | nusA ← | transcription termination/antitermination L factor |
| 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 |
| RA | 4,296,384 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913_3_vch_pgi | 366193 | 366405 | 213 | 5 [4] | [4] 6 | [lacZ] | [lacZ] |
| * | * | ÷ | NC_000913_3_vch_pgi | 3423798–3424232 | 3424539–3424239 | 8–742 | 5 [4] | [4] 6 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_vch_pgi | = 228108 | NA (NA) | 8 (0.370) | 7/276 | 1.7 | NA | noncoding (2350/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913_3_vch_pgi | = 228124 | NA (NA) | noncoding (2366/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913_3_vch_pgi | 1207790 = | 2 (0.090) | 13 (0.660) | 12/252 | 0.7 | 79.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_vch_pgi | 1209619 = | 5 (0.250) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_vch_pgi | = 1207805 | 2 (0.090) | 16 (0.810) | 15/252 | 0.4 | 82.5% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_vch_pgi | = 1209602 | 5 (0.250) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_vch_pgi | = 1299498 | 0 (0.000) | 12 (0.560) | 12/276 | 0.8 | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913_3_vch_pgi | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913_3_vch_pgi | 1468798 = | NA (NA) | 4 (0.190) | 4/270 | 2.5 | NA | coding (29/906 nt) coding (352/366 nt) |
insD1 insC1 |
IS2 transposase TnpB IS2 repressor TnpA |
| ? | NC_000913_3_vch_pgi | 1468838 = | NA (NA) | coding (312/366 nt) | insC1 | IS2 repressor TnpA | |||||
| * | ? | NC_000913_3_vch_pgi | = 1718424 | 17 (0.770) | 4 (0.190) | 3/270 | 2.9 | 20.4% | intergenic (‑29/+69) | mliC/anmK | inhibitor of c‑type lysozyme, membrane‑bound; putative lipoprotein/anhydro‑N‑acetylmuramic acid kinase |
| ? | NC_000913_3_vch_pgi | = 1718429 | 15 (0.710) | intergenic (‑34/+64) | mliC/anmK | inhibitor of c‑type lysozyme, membrane‑bound; putative lipoprotein/anhydro‑N‑acetylmuramic acid kinase | |||||
| * | ? | NC_000913_3_vch_pgi | 2728214 = | NA (NA) | 5 (0.230) | 3/276 | 3.0 | NA | noncoding (971/2904 nt) | rrlG | 23S ribosomal RNA of rrnG operon |
| ? | NC_000913_3_vch_pgi | 2728240 = | NA (NA) | noncoding (945/2904 nt) | rrlG | 23S ribosomal RNA of rrnG operon | |||||
| * | ? | NC_000913_3_vch_pgi | 3134834 = | 15 (0.680) | 4 (0.190) | 4/266 | 2.5 | 20.5% | intergenic (+11/+38) | yghT/pitB | putative ATP‑binding protein/phosphate transporter |
| ? | NC_000913_3_vch_pgi | 3134863 = | 17 (0.820) | intergenic (+40/+9) | yghT/pitB | putative ATP‑binding protein/phosphate transporter | |||||
| * | ? | NC_000913_3_vch_pgi | = 3484043 | 14 (0.630) | 4 (0.190) | 4/274 | 2.5 | 23.2% | coding (842/1023 nt) | yheT | UPF0017 family putative hydrolase |
| ? | NC_000913_3_vch_pgi | = 3484049 | 13 (0.610) | coding (848/1023 nt) | yheT | UPF0017 family putative hydrolase | |||||
| * | ? | NC_000913_3_vch_pgi | 4317920 = | NA (NA) | 4 (0.190) | 4/270 | 2.5 | NA | noncoding (1/83 nt) | REP323 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP323 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913_3_vch_pgi | 4317952 = | NA (NA) | noncoding (33/83 nt) | REP323 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP323 (repetitive extragenic palindromic) element; contains 2 REP sequences | |||||
| * | ? | NC_000913_3_vch_pgi | 4344816 = | NA (NA) | 4 (0.190) | 4/266 | 2.5 | NA | intergenic (+23/+116) | melB/yjdF | melibiose:sodium symporter/DUF2238 family inner membrane protein |
| ? | NC_000913_3_vch_pgi | 4344845 = | NA (NA) | noncoding (28/95 nt) | RIP327 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP327 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||