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 | 1,529,185 | C→T | pseudogene (1284/2037 nt) | rhsE → | pseudogene, Rhs family |
| 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 |
| 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 | 3423733–3424567 | 3424567 | 1–835 | 37 [36] | [35] 37 | [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 | 1207790 = | 10 (0.120) | 47 (0.630) | 40/242 | 1.4 | 86.4% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_bme_pgi | 1209619 = | 6 (0.080) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_bme_pgi | = 1207805 | 10 (0.120) | 59 (0.780) | 51/242 | 0.6 | 88.8% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_bme_pgi | = 1209602 | 6 (0.080) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_bme_pgi | = 1299498 | 0 (0.000) | 81 (0.980) | 70/266 | 0.1 | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913_3_bme_pgi | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913_3_bme_pgi | = 1978502 | 2 (0.020) | 61 (0.760) | 56/258 | 0.5 | 98.5% | intergenic (‑305/+16) | flhD/insB1 | flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B |
| ? | NC_000913_3_bme_pgi | 1979279 = | 0 (0.000) | intergenic (‑64/‑474) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913_3_bme_pgi | = 1979270 | NA (NA) | 1526 (17.930) | 284/274 | -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 | 3583427 = | NA (NA) | 42 (0.800) +53 bp |
23/168 | 1.9 | NA | intergenic (+9/‑56) | yrhA/insA | pseudogene, interrupted by IS1E/IS1 repressor TnpA |
| ? | NC_000913_3_bme_pgi | 4235463 = | NA (NA) | noncoding (42/77 nt) | REP313 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP313 (repetitive extragenic palindromic) element; contains 2 REP sequences | |||||
| * | ? | NC_000913_3_bme_pgi | = 3584195 | NA (NA) | 1402 (16.470) | 284/274 | -0.0 | 94.2% | intergenic (+15/‑1) | insB1/yrhA | IS1 transposase B/pseudogene, interrupted by IS1E |
| ? | NC_000913_3_bme_pgi | 4221371 = | 86 (1.010) | coding (1117/2187 nt) | arpA | ankyrin repeat protein | |||||
| * | ? | NC_000913_3_bme_pgi | = 4229433 | NA (NA) | 95 (1.190) | 39/258 | 1.8 | NA | noncoding (58/70 nt) | REP312 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP312 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913_3_bme_pgi | = 4229438 | NA (NA) | noncoding (63/70 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) | 110 (1.370) | 39/258 | 1.8 | 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 | |||||