mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
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 | 262,894 | G→A | 6.9% | noncoding (24/76 nt) | thrW → | tRNA‑Thr |
| RA | 354,812 | C→T | 100% | intergenic (+220/‑110) | prpE → / → codB | propionate‑‑CoA ligase/cytosine transporter |
| RA | 421,608 | T→G | 12.4% | V208G (GTG→GGG) | proY → | proline‑specific permease |
| RA | 433,649 | T→G | 28.5% | G65G (GGT→GGG) | ribD → | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| RA | 509,371 | A→C | 14.8% | V670G (GTG→GGG) | copA ← | copper transporter |
| RA | 1,089,222 | G→A | 100% | D212D (GAC→GAT) | pgaB ← | poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine (PGA) N‑deacetylase outer membrane export lipoprotein |
| JC JC | 1,293,008 | IS1 (+) +9 bp | 92.7% | intergenic (‑86/‑511) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| RA | 1,466,210 | G→A | 5.6% | pseudogene (819/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (+) +6 bp :: Δ1 bp | 100% | coding (115‑120/360 nt) | yeaR ← | DUF1971 family protein, nitrate‑inducible |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| JC JC | 1,995,341 | IS5 (–) +4 bp | 13.4% | coding (16‑19/657 nt) | uvrY ← | response regulator in two‑component regulatory system with BarA |
| JC JC | 1,995,398 | IS5 (–) +4 bp | 32.9% | intergenic (‑39/‑417) | uvrY ← / → yecF | response regulator in two‑component regulatory system with BarA/DUF2594 family protein |
| RA | 2,149,907 | A→C | 22.2% | V360G (GTG→GGG) | yegI ← | protein kinase‑related putative non‑specific DNA‑binding protein |
| RA | 2,151,689 | G→T | 50.3% | intergenic (+43/+22) | yegJ → / ← yegK | uncharacterized protein/ser/thr phosphatase‑related protein |
| 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 | 2,304,523 | G→C | 5.5% | intergenic (+130/+585) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,818,145 | T→C | 12.0% | intergenic (‑10/+53) | argZ ← / ← argY | tRNA‑Arg/tRNA‑Arg |
| RA | 2,818,151 | T→C | 7.2% | intergenic (‑16/+47) | argZ ← / ← argY | tRNA‑Arg/tRNA‑Arg |
| RA | 2,828,510 | G→T | 10.7% | M258I (ATG→ATT) | srlD → | sorbitol‑6‑phosphate dehydrogenase |
| JC JC | 2,876,678 | IS5 (+) +4 bp | 17.9% | coding (98‑101/1038 nt) | iap → | aminopeptidase in alkaline phosphatase isozyme conversion |
| JC JC | 2,916,566 | IS1 (–) +9 bp | 13.0% | coding (1510‑1518/2757 nt) | barA → | hybrid sensory histidine kinase, in two‑component regulatory system with UvrY |
| RA | 2,986,652 | T→G | 88.9% | V269G (GTC→GGC) | yqeG → | putative transporter |
| 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 | 3,782,913 | A→C | 22.0% | V250G (GTG→GGG) | gpsA ← | glycerol‑3‑phosphate dehydrogenase (NAD+) |
| RA | 3,798,652 | Δ1 bp | 100% | coding (661/1074 nt) | waaU ← | lipopolysaccharide core biosynthesis |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,862,661 | T→G | 21.7% | 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 | 3,862,662 | T→G | 25.6% | pseudogene (942/1617 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 | 3,862,674:1 | +A | 6.9% | pseudogene (930/1617 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 | 4,183,597 | G→T | 100% | D785Y (GAC→TAC) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,060 | C→T | 31.4% | intergenic (+266/+376) | 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 | 4,325,948 | A→G | 5.9% | intergenic (‑207/+451) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,571,096 | A→G | 26.4% | L160P (CTC→CCC) | yjiR ← | putative DNA‑binding transcriptional regulator/putative aminotransferase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423827–3424233 | 3424468–3424238 | 6–642 | 29 [27] | [26] 29 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 26 (0.250) | 60 (0.640) | 46/364 | NT | 71.5% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 24 (0.260) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 27 (0.260) | 50 (0.530) | 39/364 | NT | 67.2% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 24 (0.260) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1242594 | 77 (0.760) | 8 (0.090) | 8/360 | NT | 10.3% | coding (487/915 nt) | ldcA | murein tetrapeptide carboxypeptidase; LD‑carboxypeptidase A |
| ? | NC_000913 | = 1242576 | 69 (0.740) | coding (505/915 nt) | ldcA | murein tetrapeptide carboxypeptidase; LD‑carboxypeptidase A | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 57 (0.570) | 41/388 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 80 (0.820) | 52/380 | NT | 100% | intergenic (‑305/+16) | flhD/insB1 | flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B |
| ? | NC_000913 | 1979279 = | 0 (0.000) | intergenic (‑64/‑474) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | = 1995401 | 58 (0.570) | 10 (0.100) | 10/396 | NT | 14.7% | intergenic (‑42/‑417) | uvrY/yecF | response regulator in two‑component regulatory system with BarA/DUF2594 family protein |
| ? | NC_000913 | = 2102943 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 2807474 = | 58 (0.570) | 4 (0.040) | 4/378 | NT | 5.1% | coding (343/993 nt) | proX | glycine betaine/proline ABC transporter periplasmic binding protein; cold shock protein |
| ? | NC_000913 | 2807610 = | 94 (0.970) | coding (479/993 nt) | proX | glycine betaine/proline ABC transporter periplasmic binding protein; cold shock protein | |||||
| * | ? | NC_000913 | 3289715 = | 119 (1.170) | 6 (0.060) | 4/374 | NT | 5.2% | coding (902/2517 nt) | yraJ | putative outer membrane protein |
| ? | NC_000913 | 3289835 = | 105 (1.090) | coding (1022/2517 nt) | yraJ | putative outer membrane protein | |||||
| * | ? | NC_000913 | 3621989 = | NA (NA) | 5 (0.050) | 3/380 | NT | 100% | coding (2798/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | 3622012 = | 0 (0.000) | coding (2821/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | = 3670238 | 122 (1.200) | 10 (0.100) | 8/384 | NT | 7.6% | coding (647/1650 nt) | treF | cytoplasmic trehalase |
| ? | NC_000913 | = 3670407 | 124 (1.250) | coding (816/1650 nt) | treF | cytoplasmic trehalase | |||||