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 | freq | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 345,296 | G→C | 10.2% | intergenic (+305/‑108) | yahL → / → yahM | uncharacterized protein/uncharacterized protein |
| RA | 375,168 | G→A | 6.0% | intergenic (+287/‑291) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 433,649 | T→G | 29.3% | G65G (GGT→GGG) | ribD → | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| RA | 445,570 | T→C | 21.8% | D366G (GAC→GGC) | yajR ← | putative transporter |
| JC JC | 458,790 | IS186 (–) +6 bp :: Δ1 bp | 44.3% | intergenic (+90/‑93) | clpX → / → lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| RA | 1,196,131 | G→A | 20.7% | A337T (GCC→ACC) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,305 | C→T | 46.0% | 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 | 1,383,710 | C→A | 25.2% | L84F (TTG→TTT) | ycjW ← | LacI family putative transcriptional repressor |
| RA | 1,576,077 | C→A | 15.0% | D515Y (GAT→TAT) | yddB ← | putative TonB‑dependent outer membrane receptor |
| RA | 1,596,176 | Δ1 bp | 5.6% | pseudogene (1812/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,803,853 | C→T | 5.2% | pseudogene (336/1476 nt) | arpB → | pseudogene, ankyrin repeats |
| 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 | 2,598,267 | T→C | 13.2% | E200G (GAG→GGG) | bamC ← | BamABCDE complex OM biogenesis lipoprotein |
| RA | 3,206,477 | T→A | 15.6% | S5R (AGT→AGA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,484 | C→A | 18.9% | Q8K (CAA→AAA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,518 | C→T | 10.9% | A19V (GCT→GTT) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| JC | 3,484,541 | Δ3 bp | 6.4% | coding (52‑54/870 nt) | prkB → | putative phosphoribulokinase |
| 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 | 3,751,537 | A→C | 15.8% | V111G (GTT→GGT) | yiaT ← | putative outer membrane protein |
| RA | 3,760,384 | A→C | 19.5% | V289G (GTG→GGG) | selA ← | selenocysteine synthase |
| RA | 3,782,913 | A→C | 18.2% | V250G (GTG→GGG) | gpsA ← | glycerol‑3‑phosphate dehydrogenase (NAD+) |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,862,661 | T→G | 26.5% | pseudogene (943/1617 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 |
| RA | 3,895,552 | A→C | 13.4% | V353G (GTG→GGG) | adeP ← | adenine permease, high affinity; adenine:H+ symporter |
| RA | 3,978,862 | A→C | 10.2% | T88P (ACC→CCC) | wzyE → | putative ECA polysaccharide chain elongation protein |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,094,489 | G→A | 5.0% | intergenic (‑217/+234) | rhaD ← / ← rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| RA | 4,145,065 | A→C | 11.9% | L357F (TTA→TTC) | pflD → | putative glycine radical domain‑containing pyruvate formate‑lyase |
| RA | 4,151,323 | A→G | 14.7% | A592A (GCT→GCC) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,219,539 | C→T | 8.0% | A315V (GCG→GTG) | aceK → | isocitrate dehydrogenase kinase/phosphatase |
| RA | 4,296,060 | C→T | 28.6% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 15.3% | 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 |
| RA | 4,392,453 | C→T | 5.7% | intergenic (+18/‑19) | glyV → / → glyX | tRNA‑Gly/tRNA‑Gly |
| RA | 4,392,456 | A→G | 6.0% | intergenic (+21/‑16) | glyV → / → glyX | tRNA‑Gly/tRNA‑Gly |
| RA | 4,630,340 | A→C | 17.3% | G61G (GGT→GGG) | ettA ← | energy‑dependent translational throttle A |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 300015 | 300221 | 207 | 37 [34] | [33] 35 | paoC | PaoABC aldehyde oxidoreductase, Moco‑containing subunit |
| * | * | ÷ | NC_000913 | 583216 | 583753 | 538 | 36 [33] | [32] 35 | [appY] | [appY] |
| * | * | ÷ | NC_000913 | 720875 | 721154 | 280 | 35 [33] | [34] 36 | [kdpE] | [kdpE] |
| * | * | ÷ | NC_000913 | 3798982 | 3799562 | 581 | 35 [32] | [31] 35 | [waaU]–[waaZ] | [waaU],[waaZ] |
| * | * | ÷ | NC_000913 | 3804699 | 3805189 | 491 | 35 [33] | [29] 37 | [waaS]–[waaP] | [waaS],[waaP] |
| * | * | ÷ | NC_000913 | 4233708 | 4235444 | 1737 | 35 [34] | [32] 35 | pgi | pgi |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 274254 | NA (NA) | 3 (0.030) | 3/428 | NT | NA | noncoding (896/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274258 = | NA (NA) | noncoding (892/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 458790 = | 55 (0.530) | 3 (0.030) | 3/424 | NT | 5.2% | intergenic (+90/‑98) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| ? | NC_000913 | = 609350 | NA (NA) | noncoding (1344/1345 nt) | IS186 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 22 (0.210) | 73 (0.750) | 52/398 | NT | 78.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 20 (0.200) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 23 (0.220) | 83 (0.850) | 62/398 | NT | 80.1% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 20 (0.200) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1877275 | 72 (0.680) | 4 (0.040) | 4/414 | NT | 5.4% | intergenic (+19/+3) | yeaO/yoaF | DUF488 family protein/DUF333 family outer membrane lipoprotein |
| ? | NC_000913 | = 1877290 | 71 (0.700) | coding (243/255 nt) | yoaF | DUF333 family outer membrane lipoprotein | |||||
| * | ? | NC_000913 | 2771956 = | 51 (0.490) | 7 (0.070) | 6/428 | NT | 12.1% | intergenic (+341/+46) | yfjT/yfjU | CP4‑57 prophage; putative periplasmic protein/CP4‑57 prophage; conserved protein;Phage or Prophage Related |
| ? | NC_000913 | = 2997691 | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 3427065 | NA (NA) | 5 (0.050) | 4/412 | NT | NA | intergenic (‑32/+11) | alaU/ileU | tRNA‑Ala/tRNA‑Ile |
| ? | NC_000913 | = 3427068 | NA (NA) | intergenic (‑35/+8) | alaU/ileU | tRNA‑Ala/tRNA‑Ile | |||||