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 | 14,116 | A→G | 6.3% | intergenic (+37/‑52) | dnaK → / → dnaJ | chaperone Hsp70, with co‑chaperone DnaJ/chaperone Hsp40, DnaK co‑chaperone |
| RA | 14,119 | G→A | 6.1% | intergenic (+40/‑49) | dnaK → / → dnaJ | chaperone Hsp70, with co‑chaperone DnaJ/chaperone Hsp40, DnaK co‑chaperone |
| RA | 14,124 | T→A | 6.2% | intergenic (+45/‑44) | dnaK → / → dnaJ | chaperone Hsp70, with co‑chaperone DnaJ/chaperone Hsp40, DnaK co‑chaperone |
| RA | 14,129 | T→C | 6.5% | intergenic (+50/‑39) | dnaK → / → dnaJ | chaperone Hsp70, with co‑chaperone DnaJ/chaperone Hsp40, DnaK co‑chaperone |
| RA | 14,132 | C→T | 6.4% | intergenic (+53/‑36) | dnaK → / → dnaJ | chaperone Hsp70, with co‑chaperone DnaJ/chaperone Hsp40, DnaK co‑chaperone |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 357,692 | C→A | 5.1% | intergenic (+238/+99) | codA → / ← cynR | cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor |
| RA | 526,792 | A→C | 24.1% | S1178R (AGC→CGC) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 526,796 | C→G | 24.0% | A1179G (GCG→GGG) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 526,800 | A→G | 23.4% | E1180E (GAA→GAG) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 659,204 | C→T | 5.1% | intergenic (+54/+47) | tatE → / ← lipA | TatABCE protein translocation system subunit/lipoate synthase |
| RA | 659,205 | A→T | 5.4% | intergenic (+55/+46) | tatE → / ← lipA | TatABCE protein translocation system subunit/lipoate synthase |
| RA | 659,206 | A→T | 5.0% | intergenic (+56/+45) | tatE → / ← lipA | TatABCE protein translocation system subunit/lipoate synthase |
| RA | 659,207 | A→G | 5.2% | intergenic (+57/+44) | tatE → / ← lipA | TatABCE protein translocation system subunit/lipoate synthase |
| RA | 712,875:1 | +C | 100% | intergenic (‑73/‑112) | ybfF ← / → seqA | acyl‑CoA esterase/negative modulator of initiation of replication |
| RA | 747,895 | C→G | 5.3% | intergenic (‑126/+26) | abrB ← / ← ybgO | regulator of aidB expression; inner membrane protein/putative fimbrial protein |
| RA | 747,897 | G→C | 5.5% | intergenic (‑128/+24) | abrB ← / ← ybgO | regulator of aidB expression; inner membrane protein/putative fimbrial protein |
| RA | 747,900 | G→C | 5.5% | intergenic (‑131/+21) | abrB ← / ← ybgO | regulator of aidB expression; inner membrane protein/putative fimbrial protein |
| RA | 747,902 | C→G | 5.3% | intergenic (‑133/+19) | abrB ← / ← ybgO | regulator of aidB expression; inner membrane protein/putative fimbrial protein |
| RA | 1,097,158 | C→T | 9.8% | intergenic (+329/+407) | ycdU → / ← serX | putative inner membrane protein/tRNA‑Ser |
| RA | 1,141,153 | A→G | 5.3% | intergenic (+167/+29) | flgL → / ← rne | flagellar hook‑filament junction protein/endoribonuclease; RNA‑binding protein;RNA degradosome binding protein |
| RA | 1,529,175 | T→C | 100% | pseudogene (1274/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,180 | T→C | 100% | pseudogene (1279/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,185 | C→T | 100% | pseudogene (1284/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,203 | C→A | 100% | pseudogene (1302/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,218 | C→T | 100% | pseudogene (1317/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,666,470 | C→A | 5.0% | L386I (CTA→ATA) | clcB → | H(+)/Cl(‑) exchange transporter |
| RA | 1,873,691 | T→C | 5.3% | S40P (TCA→CCA) | yeaK → | aminoacyl‑tRNA editing domain protein |
| RA | 1,873,694 | G→C | 5.3% | E41Q (GAA→CAA) ‡ | yeaK → | aminoacyl‑tRNA editing domain protein |
| RA | 1,873,695 | A→G | 5.6% | E41G (GAA→GGA) ‡ | yeaK → | aminoacyl‑tRNA editing domain protein |
| RA | 1,873,700 | C→T | 5.2% | R43C (CGT→TGT) ‡ | yeaK → | aminoacyl‑tRNA editing domain protein |
| RA | 1,873,701 | G→C | 5.4% | R43P (CGT→CCT) ‡ | yeaK → | aminoacyl‑tRNA editing domain protein |
| RA | 1,873,704 | G→A | 5.2% | G44D (GGC→GAC) | yeaK → | aminoacyl‑tRNA editing domain protein |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| 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 | 2,317,011 | A→T | 5.2% | intergenic (+184/+16) | rcsB → / ← rcsC | response regulator in two‑component regulatory system with RcsC and YojN/hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| RA | 2,317,012 | A→T | 5.2% | intergenic (+185/+15) | rcsB → / ← rcsC | response regulator in two‑component regulatory system with RcsC and YojN/hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| RA | 2,317,018 | T→G | 5.2% | intergenic (+191/+9) | rcsB → / ← rcsC | response regulator in two‑component regulatory system with RcsC and YojN/hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| RA | 2,894,856 | C→A | 5.4% | intergenic (+85/+63) | ygcP → / ← ygcQ | putative antiterminator regulatory protein/putative flavoprotein |
| 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 | 3,608,695 | C→G | 8.4% | intergenic (+46/+56) | zntA → / ← tusA | zinc, cobalt and lead efflux system/mnm(5)‑s(2)U34‑tRNA 2‑thiolation sulfurtransferase |
| RA | 3,700,416 | T→C | 5.2% | intergenic (+215/‑147) | rdlD → / → yhjV | sRNA antisense regulator affects LdrD translation; proposed addiction module in LDR‑D repeat, with toxic peptide LdrD/putative transporter |
| RA | 3,700,418 | G→A | 5.0% | intergenic (+217/‑145) | rdlD → / → yhjV | sRNA antisense regulator affects LdrD translation; proposed addiction module in LDR‑D repeat, with toxic peptide LdrD/putative transporter |
| RA | 3,700,419 | T→C | 5.0% | intergenic (+218/‑144) | rdlD → / → yhjV | sRNA antisense regulator affects LdrD translation; proposed addiction module in LDR‑D repeat, with toxic peptide LdrD/putative transporter |
| RA | 3,700,421 | G→A | 5.4% | intergenic (+220/‑142) | rdlD → / → yhjV | sRNA antisense regulator affects LdrD translation; proposed addiction module in LDR‑D repeat, with toxic peptide LdrD/putative transporter |
| RA | 3,918,291 | C→T | 5.7% | intergenic (‑26/+25) | atpG ← / ← atpA | F1 sector of membrane‑bound ATP synthase, gamma subunit/F1 sector of membrane‑bound ATP synthase, alpha subunit |
| RA | 3,918,296 | C→T | 6.4% | intergenic (‑31/+20) | atpG ← / ← atpA | F1 sector of membrane‑bound ATP synthase, gamma subunit/F1 sector of membrane‑bound ATP synthase, alpha subunit |
| RA | 3,918,299 | A→G | 6.3% | intergenic (‑34/+17) | atpG ← / ← atpA | F1 sector of membrane‑bound ATP synthase, gamma subunit/F1 sector of membrane‑bound ATP synthase, alpha subunit |
| RA | 3,918,304 | A→G | 6.2% | intergenic (‑39/+12) | atpG ← / ← atpA | F1 sector of membrane‑bound ATP synthase, gamma subunit/F1 sector of membrane‑bound ATP synthase, alpha subunit |
| RA | 4,296,190 | A→G | 18.3% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 16.7% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 32.0% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 21.0% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,303 | A→G | 8.5% | intergenic (+509/+133) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,304 | A→C | 5.8% | intergenic (+510/+132) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +C | 94.8% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:2 | +G | 94.8% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,593,430 | G→T | 5.2% | V431V (GTC→GTA) ‡ | lgoT ← | putative L‑galactonate:H+ symporter |
| RA | 4,593,431 | A→G | 5.2% | V431A (GTC→GCC) ‡ | lgoT ← | putative L‑galactonate:H+ symporter |
| RA | 4,593,434 | C→T | 5.2% | C430Y (TGC→TAC) ‡ | lgoT ← | putative L‑galactonate:H+ symporter |
| RA | 4,593,435 | A→C | 5.1% | C430G (TGC→GGC) ‡ | lgoT ← | putative L‑galactonate:H+ symporter |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423733–3424234 | 3424553–3424238 | 5–821 | 90 [89] | [89] 90 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 90 (0.610) | 29 (0.210) | 28/532 | NT | 23.8% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 101 (0.730) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 91 (0.620) | 25 (0.180) | 25/532 | NT | 21.1% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 101 (0.730) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 161 (1.110) | 129/556 | 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 | |||||