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 |
| RA | 67,887:1 | +G | 71.6% | coding (451/1503 nt) | araA ← | L‑arabinose isomerase |
| RA | 67,887:2 | +T | 71.6% | coding (451/1503 nt) | araA ← | L‑arabinose isomerase |
| RA | 154,817:1 | +G | 10.0% | coding (610/2598 nt) | htrE ← | putative outer membrane usher protein |
| RA | 222,300 | Δ1 bp | 6.5% | coding (346/1032 nt) | metN ← | DL‑methionine transporter subunit |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 711,107 | C→T | 5.3% | W120* (TGG→TAG) | fldA ← | flavodoxin 1 |
| RA | 738,600 | A→C | 6.0% | K170T (AAA→ACA) | ybfD → | H repeat‑associated putative transposase |
| RA | 741,501 | Δ1 bp | 6.2% | coding (1056/1482 nt) | dtpD ← | dipeptide and tripeptide permease D |
| RA | 962,674 | G→A | 5.5% | R227H (CGC→CAC) | rpsA → | 30S ribosomal subunit protein S1 |
| 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 | 1,350,329 | Δ1 bp | 5.5% | coding (711/789 nt) | fabI ← | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent |
| RA | 1,350,330 | Δ1 bp | 5.6% | coding (710/789 nt) | fabI ← | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent |
| 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 |
| JC | 2,023,796 | Δ5 bp | 67.9% | intergenic (+118/‑168) | fliR → / → rcsA | flagellar export pore protein/transcriptional regulator of colanic acid capsular biosynthesis |
| RA | 2,128,593 | A→G | 9.5% | V99A (GTG→GCG) | wcaF ← | putative acyl transferase |
| 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 | 2,316,681 | A→G | 100% | T169A (ACC→GCC) | rcsB → | response regulator in two‑component regulatory system with RcsC and YojN |
| RA | 2,655,794 | A→G | 5.3% | Y189H (TAC→CAC) | pepB ← | aminopeptidase B |
| RA | 2,967,533 | A→G | 11.1% | L301P (CTG→CCG) | ptsP ← | PEP‑protein phosphotransferase enzyme I; GAF domain containing protein |
| RA | 3,416,049 | A→G | 5.0% | E339E (GAA→GAG) | acrF → | multidrug efflux system protein |
| RA | 3,527,591 | C→T | 100% | Q375* (CAG→TAG) | yrfF → | putative RcsCDB‑response attenuator, inner membrane protein |
| RA | 3,550,108 | T→C | 5.6% | Q789R (CAG→CGG) | malP ← | maltodextrin phosphorylase |
| 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 |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| JC JC | 3,992,705 | IS5 (+) +4 bp | 100% | coding (1553‑1556/2547 nt) | cyaA → | adenylate cyclase |
| 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 | 4,186,262 | G→A | 34.1% | A305T (GCC→ACC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,296,060 | C→T | 18.1% | 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 | 4,573,987 | G→A | 6.1% | pseudogene (69/2937 nt) | yjiV → | pseudogene; conserved hypothetical protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2533734 | 2536367 | 2634 | 16 [13] | [14] 19 | ptsH–crr | ptsH,ptsI,crr |
| * | * | ÷ | NC_000913 | 3423855–3424232 | 3424401–3424239 | 8–547 | 16 [15] | [14] 17 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 381460 | 5 (0.080) | 3 (0.050) | 3/486 | NT | 37.8% | noncoding (201/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 381852 | NA (NA) | noncoding (593/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 15 (0.250) | 28 (0.490) | 27/460 | NT | 57.1% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 28 (0.490) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 13 (0.210) | 27 (0.470) | 23/460 | NT | 57.4% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 28 (0.490) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1644844 | 57 (0.930) | 4 (0.070) | 4/470 | NT | 6.2% | coding (59/252 nt) | rem | Qin prophage; uncharacterized protein |
| ? | NC_000913 | = 1645012 | 67 (1.150) | intergenic (‑110/+107) | rem/hokD | Qin prophage; uncharacterized protein/Qin prophage; small toxic polypeptide | |||||
| * | ? | NC_000913 | = 2214227 | 58 (0.950) | 4 (0.070) | 4/470 | NT | 5.3% | coding (418/1686 nt) | yehU | inner membrane putative sensory kinase in two‑component system with YehT |
| ? | NC_000913 | = 2214408 | 87 (1.490) | coding (237/1686 nt) | yehU | inner membrane putative sensory kinase in two‑component system with YehT | |||||
| * | ? | NC_000913 | 3620998 = | 46 (0.750) | 3 (0.050) | 3/470 | NT | 10.5% | coding (1807/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | 3763871 = | 7 (0.120) | coding (1689/4134 nt) | rhsA | Rhs protein with putative toxin 55 domain; putative polysaccharide synthesis/export protein; putative neighboring cell growth inhibitor | |||||