mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.27.1 revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 149,214 | C→T | A130T (GCC→ACC) | panB ← | 3‑methyl‑2‑oxobutanoate hydroxymethyltransferase |
| RA | 219,624 | A→G | C124C (TGT→TGC) | rcsF ← | putative outer membrane protein |
| RA | 232,959 | C→T | A333T (GCC→ACC) | mltD ← | putative membrane‑bound lytic murein transglycosylase D |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 321,564 | (G)7→6 | intergenic (+483/‑44) | rclR → / → ykgE | reactive chlorine species (RCS)‑specific activator of the rcl genes/cysteine‑rich LutA family protein; putative electron transport chain YkgEFG component |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | regulator protein that represses frmRAB operon/outer membrane protein |
| RA | 401,548 | (G)5→6 | coding (163/261 nt) | iraP → | anti‑RssB factor, RpoS stabilzer during Pi starvation; anti‑adapter protein |
| RA | 429,143 | C→T | G499G (GGC→GGT) | secD → | SecYEG protein translocase auxillary subunit |
| RA | 701,381 | (C)5→4 | coding (214/1221 nt) | nagC ← | N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor |
| RA | 701,958 | C→T | G265D (GGC→GAC) | nagA ← | N‑acetylglucosamine‑6‑phosphate deacetylase |
| RA | 703,652 | A→G | intergenic (‑41/‑292) | nagB ← / → nagE | glucosamine‑6‑phosphate deaminase/N‑acetyl glucosamine specific PTS enzyme IIC, IIB, and IIA components |
| RA | 902,610 | (T)6→7 | coding (379/732 nt) | artI ← | arginine transporter subunit |
| RA | 945,268 | A→G | V97A (GTA→GCA) | ycaC ← | putative isochorismatase family hydrolase |
| RA | 949,526 | C→T | A15T (GCC→ACC) | ycaN ← | LysR family putative transcriptional regulator |
| RA | 1,063,365 | A→G | R137R (CGT→CGC) | cbpA ← | DnaK co‑chaperone; curved DNA‑binding protein |
| RA | 1,119,438 | A→G | F4L (TTT→CTT) | yceO ← | uncharacterized protein |
| RA | 1,144,312 | A→G | V19A (GTA→GCA) | rne ← | endoribonuclease; RNA‑binding protein;RNA degradosome binding protein |
| RA | 1,170,795 | G→A | A1057V (GCG→GTG) | mfd ← | transcription‑repair coupling factor |
| RA | 1,331,289 | C→T | A81V (GCG→GTG) | topA → | DNA topoisomerase I, omega subunit |
| RA | 1,795,485 | G→A | A23V (GCC→GTC) | ihfA ← | integration host factor (IHF), DNA‑binding protein, alpha subunit |
| RA | 1,878,650 | T→C | S312S (AGT→AGC) | yeaP → | diguanylate cyclase |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| 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 | 2,359,914 | G→C | A80G (GCC→GGC) | rhmT ← | putative L‑rhamnonate transporter |
| RA | 2,462,889 | (C)9→10 | intergenic (+243/‑123) | fadL → / → yfdF | long‑chain fatty acid outer membrane transporter/uncharacterized protein |
| RA | 2,809,774 | (T)7→6 | coding (158/738 nt) | ygaZ → | putative L‑valine exporter, norvaline resistance protein |
| RA | 2,824,686 | G→A | A297A (GCC→GCT) | mltB ← | membrane‑bound lytic murein transglycosylase B |
| RA | 2,888,564 | T→C | T512T (ACA→ACG) | cysI ← | sulfite reductase, beta subunit, NAD(P)‑binding, heme‑binding |
| RA | 3,271,600 | (C)5→6 | coding (171/1146 nt) | garK ← | glycerate kinase I |
| RA | 3,346,530 | C→A | intergenic (+70/‑48) | hpf → / → ptsN | ribosome hibernation promoting factor HPF; stabilizes 100S dimers/sugar‑specific enzyme IIA component of PTS |
| RA | 3,361,426 | Δ1 bp | coding (251/765 nt) | gltF → | periplasmic protein |
| RA | 3,379,266 | (C)7→8 | coding (732/1128 nt) | zapE ← | divisome ATPase |
| 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 |
| MC JC | 3,582,206 | Δ1,222 bp | IS1‑mediated | [yhhZ]–yrhA | [yhhZ], yrhA |
| MC JC | 3,815,859 | Δ82 bp | [rph]–[rph] | [rph], [rph] | |
| RA | 3,931,183 | (G)7→8 | intergenic (‑90/‑133) | ravA ← / → kup | hexameric AAA+ MoxR family ATPase, putative molecular chaperone/potassium transporter |
| RA | 4,187,550 | C→T | A734V (GCG→GTG) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,397,557 | G→T | G49V (GGT→GTT) | mutL → | methyl‑directed mismatch repair protein |
| RA | 4,525,413 | (T)6→5 | coding (391/789 nt) | yjhI ← | putative DNA‑binding transcriptional regulator |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423767–3424547 | 3424547 | 1–781 | 25 [23] | [24] 28 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 63 (0.970) | 47/290 | 0.1 | 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 | |||||