mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 433,649 | T→G | 27.9% | G65G (GGT→GGG) | ribD → | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| JC JC | 458,790 | IS186 (–) +6 bp :: Δ1 bp | 88.9% | intergenic (+90/‑93) | clpX → / → lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| JC JC | 458,873 | IS5 (–) +4 bp | 57.4% | intergenic (+173/‑12) | clpX → / → lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| RA | 1,196,305 | C→T | 100% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,865,874 | T→C | 10.4% | E200G (GAG→GGG) | mipA ← | scaffolding protein for murein synthesizing machinery |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 3,206,438 | G→A | 30.6% | intergenic (‑182/‑25) | ttdR ← / → ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,484 | C→A | 22.3% | Q8K (CAA→AAA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,560,455:1 | +G | 100% | 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 | 3,782,917 | G→A | 22.8% | L249L (CTG→TTG) | gpsA ← | glycerol‑3‑phosphate dehydrogenase (NAD+) |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| JC JC | 3,836,839 | IS5 (–) +4 bp | 50.0% | intergenic (+283/‑111) | yicT → / → setC | pseudogene/putative arabinose efflux transporter |
| RA | 3,862,673 | G→A | 43.7% | pseudogene (931/1617 nt) | glvC ← | pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,060 | C→T | 19.7% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 20.3% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | 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 | 1209603 | 1209618 | 16 | 39 [0] | [0] 47 | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related |
| * | * | ÷ | NC_000913 | 3423882–3424232 | 3424419–3424238 | 7–538 | 9 [8] | [7] 9 | rrlD | 23S ribosomal RNA of rrnD operon |
| * | * | ÷ | NC_000913 | 3769634 | 3769904 | 271 | 9 [8] | [8] 9 | [yibV]–yibV | [yibV],yibV |
| * | * | ÷ | NC_000913 | 4233769 | 4235454 | 1686 | 10 [6] | [7] 9 | [pgi] | [pgi] |
| * | * | ÷ | NC_000913 | 4476840 | 4477093 | 254 | 9 [8] | [8] 10 | yjgL | SopA‑central‑domain‑like hexapeptide repeat protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 8 (0.170) | 40 (0.890) | 32/406 | NT | 91.5% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 0 (0.000) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 8 (0.170) | 33 (0.740) | 29/406 | NT | 89.9% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 0 (0.000) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 3032402 | 52 (1.080) | 3 (0.060) | 3/424 | NT | 5.8% | coding (1036/1449 nt) | uacT | uric acid permease |
| ? | NC_000913 | = 3032405 | 48 (1.030) | coding (1039/1449 nt) | uacT | uric acid permease | |||||