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] | |
| 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 | 1,529,203 | C→A | pseudogene (1302/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,218 | C→T | pseudogene (1317/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,927,949 | A→C | R297R (CGT→CGG) | ptrB ← | protease II |
| 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 | 3,316,893 | C→T | E212K (GAA→AAA) | nusA ← | transcription termination/antitermination L factor |
| RA | 3,440,086 | C→A | G315V (GGC→GTC) | rpoA ← | RNA polymerase, alpha subunit |
| 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 | 4,235,408 | Δ1 bp | intergenic (‑2175/‑499) | lysC ← / → yjbE | lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein |
| RA | 4,296,382 | +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_bme_pgi | 3423764–3424234 | 3424531–3424238 | 5–768 | 10 [8] | [8] 9 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_bme_pgi | = 225998 | NA (NA) | 9 (0.250) | 9/236 | 2.7 | NA | noncoding (240/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913_3_bme_pgi | = 226015 | NA (NA) | noncoding (257/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913_3_bme_pgi | = 227052 | 22 (0.590) | 12 (0.340) | 10/232 | 2.4 | 36.4% | noncoding (1294/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913_3_bme_pgi | 2727910 = | NA (NA) | noncoding (1275/2904 nt) | rrlG | 23S ribosomal RNA of rrnG operon | |||||
| * | ? | NC_000913_3_bme_pgi | = 258676 | NA (NA) | 13 (0.580) +48 bp |
7/148 | 1.9 | NA | pseudogene (1/331 nt) | crl | 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_3_bme_pgi | 837584 = | NA (NA) | noncoding (46/123 nt) | REP77 (repetitive extragenic palindromic) element; contains 3 REP sequences | REP77 (repetitive extragenic palindromic) element; contains 3 REP sequences | |||||
| * | ? | NC_000913_3_bme_pgi | 1096961 = | 32 (0.860) | 13 (0.570) +47 bp |
11/150 | 1.1 | 39.8% | intergenic (+132/+604) | ycdU/serX | putative inner membrane protein/tRNA‑Ser |
| ? | NC_000913_3_bme_pgi | 1097243 = | NA (NA) | intergenic (+414/+322) | ycdU/serX | putative inner membrane protein/tRNA‑Ser | |||||
| * | ? | NC_000913_3_bme_pgi | 1207790 = | 9 (0.240) | 21 (0.650) | 18/212 | 0.9 | 76.6% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_bme_pgi | 1209619 = | 5 (0.160) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_bme_pgi | = 1207805 | 9 (0.240) | 25 (0.780) | 23/212 | 0.5 | 79.6% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_bme_pgi | = 1209602 | 5 (0.160) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_bme_pgi | 1552071 = | NA (NA) | 12 (0.360) | 12/220 | 1.8 | NA | noncoding (1/97 nt) | RIP120 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP120 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913_3_bme_pgi | 1552279 = | NA (NA) | noncoding (31/97 nt) | RIP121 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP121 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913_3_bme_pgi | = 1979270 | NA (NA) | 739 (19.950) | 236/244 | 0.0 | NA | intergenic (‑55/‑483) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913_3_bme_pgi | = 4235548 | NA (NA) | intergenic (‑2315/‑359) | lysC/yjbE | lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein | |||||
| * | ? | NC_000913_3_bme_pgi | 2304591 = | NA (NA) | 13 (0.370) | 9/230 | 2.6 | 26.1% | noncoding (175/655 nt) | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences |
| ? | NC_000913_3_bme_pgi | 2304609 = | 39 (1.050) | noncoding (193/655 nt) | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | |||||
| * | ? | NC_000913_3_bme_pgi | = 3584195 | NA (NA) | 696 (18.790) | 222/244 | 0.0 | 94.3% | intergenic (+15/‑1) | insB1/yrhA | IS1 transposase B/pseudogene, interrupted by IS1E |
| ? | NC_000913_3_bme_pgi | 4221371 = | 42 (1.130) | coding (1117/2187 nt) | arpA | ankyrin repeat protein | |||||
| * | ? | NC_000913_3_bme_pgi | 3950444 = | 23 (0.620) | 9 (0.260) | 9/230 | 2.6 | 31.2% | intergenic (+24/‑63) | ilvL/ilvX | ilvG operon leader peptide/uncharacterized protein |
| ? | NC_000913_3_bme_pgi | 3950470 = | 18 (0.520) | intergenic (+50/‑37) | ilvL/ilvX | ilvG operon leader peptide/uncharacterized protein | |||||
| * | ? | NC_000913_3_bme_pgi | = 4040683 | 22 (0.590) | 12 (0.330) | 10/240 | 2.5 | 29.8% | intergenic (+47/+223) | rrfA/mobB | 5S ribosomal RNA of rrnA operon/molybdopterin‑guanine dinucleotide biosynthesis protein B |
| ? | NC_000913_3_bme_pgi | = 4213162 | 35 (0.960) | intergenic (+3/‑72) | rrfE/yjaA | 5S ribosomal RNA of rrnE operon/stress‑induced protein | |||||
| * | ? | NC_000913_3_bme_pgi | 4040769 = | 20 (0.540) | 8 (0.230) | 8/228 | 2.8 | 29.8% | intergenic (+133/+137) | rrfA/mobB | 5S ribosomal RNA of rrnA operon/molybdopterin‑guanine dinucleotide biosynthesis protein B |
| ? | NC_000913_3_bme_pgi | 4040790 = | 19 (0.550) | intergenic (+154/+116) | rrfA/mobB | 5S ribosomal RNA of rrnA operon/molybdopterin‑guanine dinucleotide biosynthesis protein B | |||||
| * | ? | NC_000913_3_bme_pgi | 4229380 = | NA (NA) | 26 (0.740) | 20/230 | 0.9 | NA | noncoding (5/70 nt) | REP312 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP312 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913_3_bme_pgi | 4229413 = | NA (NA) | noncoding (38/70 nt) | REP312 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP312 (repetitive extragenic palindromic) element; contains 2 REP sequences | |||||
| * | ? | NC_000913_3_bme_pgi | 4235376 = | NA (NA) | 28 (0.810) | 17/228 | 1.2 | NA | intergenic (‑2143/‑531) | lysC/yjbE | lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein |
| ? | NC_000913_3_bme_pgi | 4235396 = | NA (NA) | intergenic (‑2163/‑511) | lysC/yjbE | lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein | |||||
| * | ? | NC_000913_3_bme_pgi | 4235426 = | NA (NA) | 9 (0.260) | 9/230 | 2.6 | NA | noncoding (5/77 nt) | REP313 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP313 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913_3_bme_pgi | 4235456 = | NA (NA) | noncoding (35/77 nt) | REP313 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP313 (repetitive extragenic palindromic) element; contains 2 REP sequences | |||||