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 |
| RA | 45,367 | C→T | 23.5% | S396S (AGC→AGT) | fixC → | putative oxidoreductase |
| RA | 222,958 | Δ1 bp | 100% | coding (126/576 nt) | gmhB → | D,D‑heptose 1,7‑bisphosphate phosphatase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 422,710 | C→A | 25.0% | R65S (CGT→AGT) | malZ → | maltodextrin glucosidase |
| RA | 588,114 | G→A | 14.8% | T947T (ACC→ACT) | nfrA ← | bacteriophage N4 receptor, outer membrane subunit |
| RA | 664,812 | C→T | 18.1% | G127R (GGG→AGG) | rlpA ← | septal ring protein, suppressor of prc, minor lipoprotein |
| RA | 665,576 | C→T | 14.8% | L246L (CTG→CTA) | mrdB ← | cell wall shape‑determining protein |
| RA | 672,388 | G→T | 28.6% | S799Y (TCC→TAC) | leuS ← | leucyl‑tRNA synthetase |
| RA | 678,469 | T→C | 22.2% | L352P (CTG→CCG) | djlB → | putative HscC co‑chaperone, uncharacterized J domain‑containing protein |
| RA | 681,014 | A→G | 25.0% | E268G (GAA→GGA) | djlC → | J domain‑containing HscC co‑chaperone; Hsc56 |
| RA | 714,866 | G→A | 16.7% | A437T (GCA→ACA) | pgm → | phosphoglucomutase |
| RA | 757,227 | C→A | 14.8% | L441M (CTG→ATG) | sdhA → | succinate dehydrogenase, flavoprotein subunit |
| RA | 934,532 | G→A | 14.8% | E437K (GAA→AAA) | ftsK → | DNA translocase at septal ring sorting daughter chromsomes |
| RA | 949,276 | T→C | 20.0% | N98S (AAT→AGT) | ycaN ← | LysR family putative transcriptional regulator |
| 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 | 1,434,787 | G→A | 26.7% | intergenic (‑563/+171) | ynaE ← / ← ttcC | cold shock protein, Rac prophage/pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related |
| RA | 1,728,796 | C→T | 19.0% | D150D (GAC→GAT) | rnt → | RNase T; exoribonuclease T; structured DNA 3' exonuclease; RNA processing; DNA repair |
| RA | 1,897,454 | A→G | 23.5% | T175A (ACC→GCC) | sdaA → | L‑serine dehydratase 1 |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,019,460 | G→A | 100% | V359I (GTC→ATC) | fliK → | flagellar hook‑length control 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 | 2,311,056 | T→A | 28.6% | H160L (CAC→CTC) | apbE ← | putative thiamine‑synthetic flavin transferase lipoprotein |
| JC JC | 2,375,828 | IS186 (+) +4 bp | 100% | coding (132‑135/963 nt) | menC ← | O‑succinylbenzoyl‑CoA synthase |
| RA | 2,508,936 | G→A | 27.3% | A164V (GCG→GTG) | glk ← | glucokinase |
| RA | 2,769,122 | C→T | 13.3% | A153V (GCG→GTG) | yfjQ → | CP4‑57 prophage; uncharacterized protein |
| RA | 2,832,057 | G→A | 21.0% | A78V (GCG→GTG) | norR ← | anaerobic nitric oxide reductase DNA‑binding transcriptional activator |
| RA | 2,904,212 | G→A | 100% | intergenic (+838/+535) | ygcE → / ← queE | putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis |
| RA | 2,958,329 | C→T | 26.7% | A186T (GCA→ACA) | ptrA ← | protease III |
| RA | 3,000,354 | G→A | 26.7% | D4N (GAT→AAT) | xdhA → | xanthine dehydrogenase, molybdenum binding subunit |
| RA | 3,124,303 | G→A | 13.3% | A386V (GCG→GTG) | glcF ← | glycolate oxidase 4Fe‑4S iron‑sulfur cluster subunit |
| RA | 3,174,776 | G→A | 20.0% | N207N (AAC→AAT) | parE ← | DNA topoisomerase IV, subunit B |
| RA | 3,223,190 | G→A | 22.2% | V186V (GTG→GTA) | ebgA → | evolved beta‑D‑galactosidase, alpha subunit |
| RA | 3,367,915 | C→T | 26.7% | T30M (ACG→ATG) | yhcG → | DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily |
| RA | 3,379,594 | G→A | 19.0% | A135V (GCC→GTC) | zapE ← | divisome ATPase |
| RA | 3,505,814 | C→T | 22.2% | A69A (GCG→GCA) | yhfS ← | FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein |
| 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 | 3,591,925 | C→T | 17.4% | G134D (GGC→GAC) | ugpB ← | sn‑glycerol‑3‑phosphate ABC transporter periplasmic binding protein |
| RA | 3,729,927 | T→C | 33.3% | H280R (CAT→CGT) | xylA ← | D‑xylose isomerase |
| JC JC | 3,890,075 | IS5 (–) +4 bp | 100% | coding (1346‑1349/1416 nt) | tnaA → | tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent |
| RA | 3,934,882 | G→A | 28.6% | A369T (GCC→ACC) | rbsA → | D‑ribose ABC transporter ATPase |
| JC JC | 3,966,263 | IS1 (+) +9 bp | 31.6% | intergenic (+173/‑146) | trxA → / → rho | thioredoxin 1/transcription termination factor |
| RA | 4,150,140 | G→A | 17.4% | G42G (GGC→GGT) | eptC ← | LPS heptose I phosphoethanolamine transferase |
| RA | 4,296,060 | C→T | 33.4% | 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 | 4,344,839 | C→A | 25.0% | intergenic (+49/+90) | melB → / ← yjdF | melibiose:sodium symporter/DUF2238 family inner membrane protein |
| RA | 4,406,129 | T→C | 100% | intergenic (+144/‑61) | purA → / → nsrR | adenylosuccinate synthetase/nitric oxide‑sensitive repressor for NO regulon |
| RA | 4,451,483 | G→A | 17.4% | P142P (CCG→CCA) | ytfR → | putative sugar ABC transporter ATPase |
| RA | 4,503,822 | A→G | 14.8% | intergenic (‑391/‑236) | insG ← / → yjhB | IS4 transposase/putative MFS transporter, membrane protein |
| JC JC | 4,640,551 | IS1 (–) +9 bp | 100% | intergenic (+9/‑383) | yjjY → / → yjtD | uncharacterized protein/putative methyltransferase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 773027 | 774183 | 1157 | 4 [1] | [1] 2 | cydB | cydB |
| * | * | ÷ | NC_000913 | 1037732 | 1038799 | 1068 | 3 [1] | [1] 2 | [cbdA] | [cbdA] |
| * | * | ÷ | NC_000913 | 1038888 | 1039098 | 211 | 2 [1] | [1] 2 | cbdA | cytochrome bd‑II oxidase, subunit I |
| * | * | ÷ | NC_000913 | 1039213 | 1039264 | 52 | 2 [1] | [0] 2 | cbdA | cytochrome bd‑II oxidase, subunit I |
| * | * | ÷ | NC_000913 | 1166089 | 1167405 | 1317 | 2 [0] | [1] 2 | [ndh] | [ndh] |
| * | * | ÷ | NC_000913 | 1292643 | 1292729 | 87 | 2 [1] | [0] 3 | hns | global DNA‑binding transcriptional dual regulator H‑NS |
| * | * | ÷ | NC_000913 | 1348106 | 1348112 | 7 | 2 [0] | [0] 3 | rnb | ribonuclease II |
| * | * | ÷ | NC_000913 | 3423766–3424234 | 3424542–3424238 | 5–777 | 3 [1] | [1] 4 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 1 (0.070) | 3 (0.230) | 3/246 | NT | 55.1% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 4 (0.310) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 1 (0.070) | 15 (1.150) | 12/246 | NT | 86.0% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 4 (0.310) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||