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 |
| RA | 29,279 | (T)5→6 | intergenic (+84/‑372) | dapB → / → carA | dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 1,261,474 | C→A | Q134H (CAG→CAT) | prs ← | phosphoribosylpyrophosphate synthase |
| MC JC | 1,299,499 | Δ1,199 bp | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,019,460 | G→A | V359I (GTC→ATC) | fliK → | flagellar hook‑length control protein |
| 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 | 2,317,667 | T→G | E737A (GAA→GCA) | rcsC ← | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| RA | 2,632,046 | G→T | P164T (CCG→ACG) | guaA ← | GMP synthetase (glutamine aminotransferase) |
| RA | 3,002,530 | G→A | G729D (GGT→GAT) | xdhA → | xanthine dehydrogenase, molybdenum binding subunit |
| MC JC | 3,366,751 | Δ1,271 bp | IS5‑mediated | [yhcE]–[yhcG] | [yhcE], yhcF, [yhcG] |
| 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 |
| JC JC | 3,890,075 | IS5 (–) +4 bp | coding (1346‑1349/1416 nt) | tnaA → | tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent |
| RA | 4,044,390 | (T)6→5 | coding (192/1431 nt) | yihF → | DUF945 family protein |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| JC JC | 4,543,608 | Δ1 bp :: IS186 (+) +6 bp :: Δ1 bp | coding (494‑499/549 nt) | fimA → | major type 1 subunit fimbrin (pilin) |
| RA | 4,620,245 | C→A | P215T (CCG→ACG) | deoB → | phosphopentomutase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1708728 | 1708877–1708860 | 133–150 | 6 [5] | [5] 6 | rsxC | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| * | * | ÷ | NC_000913 | 3423785–3424234 | 3424546–3424239 | 6–762 | 6 [5] | [5] 9 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3514402 | 3515055 | 654 | 9 [4] | [0] 7 | rpe | D‑ribulose‑5‑phosphate 3‑epimerase |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 7 (0.190) | 24 (0.760) | 24/222 | 0.4 | 77.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 8 (0.250) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 7 (0.190) | 17 (0.540) | 17/222 | 0.9 | 70.7% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 8 (0.250) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1396531 = | NA (NA) | 11 (0.320) | 6/242 | 2.9 | NA | noncoding (488/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1428264 | NA (NA) | noncoding (531/1196 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1440443 | 16 (0.440) | 6 (0.180) | 6/240 | 2.9 | 28.5% | coding (342/3525 nt) | pfo | pyruvate‑flavodoxin oxidoreductase |
| ? | NC_000913 | = 1440464 | 15 (0.440) | coding (321/3525 nt) | pfo | pyruvate‑flavodoxin oxidoreductase | |||||
| * | ? | NC_000913 | 4542682 = | 57 (1.580) | 16 (0.480) | 16/236 | 1.1 | 24.6% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 45 (1.340) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 4542690 | 57 (1.580) | 14 (0.420) | 14/236 | 1.3 | 22.2% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 45 (1.340) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||