mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.26.1
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] | |
| JC JC | 1,879,829 | Δ1 :: IS186 (+) +6 bp :: Δ1 | coding (115‑120/360 nt) | yeaR ← | DUF1971 family protein, nitrate‑inducible |
| RA | 2,019,460 | G→A | V359I (GTC→ATC) | fliK → | flagellar hook‑length control protein |
| RA | 2,108,006 | A→T | D108E (GAT→GAA) | glf ← | UDP‑galactopyranose mutase, FAD/NAD(P)‑binding |
| 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 | 3,222,566 | C→A | intergenic (+117/‑67) | ebgR → / → ebgA | transcriptional repressor/evolved beta‑D‑galactosidase, 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 |
| JC JC | 3,890,075 | IS5 (–) +4 bp | coding (1346‑1349/1416 nt) | tnaA → | tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent |
| RA | 3,966,720 | C→T | R102C (CGC→TGC) | rho → | transcription termination factor |
| 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 :: IS186 (+) +6 bp :: Δ1 | coding (494‑499/549 nt) | fimA → | major type 1 subunit fimbrin (pilin) |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 583085 | 583876 | 792 | 56 [46] | [50] 58 | [tfaX]–[appY] | [tfaX], [appY] |
| * | * | ÷ | NC_000913 | 720880 | 721157 | 278 | 53 [49] | [51] 53 | [kdpE] | [kdpE] |
| * | * | ÷ | NC_000913 | 1978409 | 1979305 | 897 | 57 [47] | [41] 53 | insB1–insA | insB1, insA |
| * | * | ÷ | NC_000913 | 2469122 | 2469829 | 708 | 65 [45] | [50] 57 | [gtrB]–[gtrS] | [gtrB], [gtrS] |
| * | * | ÷ | NC_000913 | 3268771 | 3269509 | 739 | 52 [50] | [49] 53 | yhaC | pentapetide repeats‑related protein |
| * | * | ÷ | NC_000913 | 3423742–3424234 | 3424552–3424238 | 5–811 | 52 [51] | [51] 52 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| * | * | ÷ | NC_000913 | 3455378 | 3455795 | 418 | 52 [48] | [51] 54 | [gspA]–[gspC] | [gspA], [gspC] |
| * | * | ÷ | NC_000913 | 3653659 | 3653783 | 125 | 52 [51] | [45] 53 | [yhiS] | [yhiS] |
| * | * | ÷ | NC_000913 | 3799033 | 3799369 | 337 | 69 [37] | [39] 59 | [waaU]–[waaZ] | [waaU], [waaZ] |
| * | * | ÷ | NC_000913 | 4476754 | 4477156 | 403 | 57 [44] | [45] 55 | yjgL | SopA‑central‑domain‑like hexapeptide repeat protein |
| * | * | ÷ | NC_000913 | 4572169 | 4572338 | 170 | 55 [44] | [51] 52 | yjiS/yjiT | DUF1127 family protein/pseudogene |
| Unassigned new junction evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 5 (0.040) | 110 (1.040) | 50/268 | 0.8 | 93.8% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 10 (0.090) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 5 (0.040) | 80 (0.760) | 48/268 | 0.9 | 91.7% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 10 (0.090) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 3670423 = | 141 (1.190) | 115 (0.980) | 69/298 | 0.3 | 44.6% | coding (832/1650 nt) | treF | cytoplasmic trehalase |
| ? | NC_000913 | = 3873421 | 146 (1.250) | coding (192/618 nt) | dgoA | 2‑oxo‑3‑deoxygalactonate 6‑phosphate aldolase | |||||