mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 83,587 | A→C | 9.2% | intergenic (‑58/+35) | leuA ← / ← leuL | 2‑isopropylmalate synthase/leu operon leader peptide |
| RA | 83,590 | G→T | 10.4% | intergenic (‑61/+32) | leuA ← / ← leuL | 2‑isopropylmalate synthase/leu operon leader peptide |
| RA | 152,311 | T→C | 5.6% | T168A (ACA→GCA) | yadM ← | putative fimbrial‑like adhesin protein |
| RA | 239,250 | C→T | 5.4% | pseudogene (145/273 nt) | yafF → | pseudogene, H repeat‑associated protein |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 289,257 | T→A | 11.1% | intergenic (‑95/+44) | yagI ← / ← argF | CP4‑6 prophage; putative DNA‑binding transcriptional regulator/ornithine carbamoyltransferase 2, chain F; CP4‑6 prophage |
| RA | 624,666 | A→C | 5.2% | intergenic (‑156/‑219) | fepB ← / → entC | ferrienterobactin ABC transporter periplasmic binding protein/isochorismate synthase 1 |
| RA | 665,094 | G→C | 9.8% | P33A (CCT→GCT) | rlpA ← | septal ring protein, suppressor of prc, minor lipoprotein |
| JC | 755,487 | +AGCGGGT | 9.1% | coding (311/390 nt) | sdhC → | succinate dehydrogenase, membrane subunit, binds cytochrome b556 |
| RA | 756,099 | T→C | 68.7% | W65R (TGG→CGG) | sdhA → | succinate dehydrogenase, flavoprotein subunit |
| RA | 758,306 | T→G | 10.8% | C206W (TGT→TGG) | sdhB → | succinate dehydrogenase, FeS subunit |
| RA | 759,121 | T→G | 7.2% | F139C (TTC→TGC) | sucA → | 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding |
| RA | 781,254 | A→T | 9.7% | intergenic (+32/‑115) | lysY → / → lysZ | tRNA‑Lys/tRNA‑Lys |
| RA | 915,080 | G→C | 5.5% | intergenic (‑223/+272) | ybjE ← / ← aqpZ | putative transporter/aquaporin Z |
| RA | 915,081 | G→C | 5.5% | intergenic (‑224/+271) | ybjE ← / ← aqpZ | putative transporter/aquaporin Z |
| RA | 1,306,787 | G→A | 7.3% | intergenic (+19/+34) | oppF → / ← yciU | oligopeptide ABC transporter ATPase/UPF0263 family protein |
| RA | 1,306,788 | T→C | 7.3% | intergenic (+20/+33) | oppF → / ← yciU | oligopeptide ABC transporter ATPase/UPF0263 family protein |
| RA | 1,466,630 | G→C | 12.7% | pseudogene (1239/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,639 | C→T | 16.4% | pseudogene (1248/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,542,421 | G→T | 5.1% | S57Y (TCC→TAC) | narZ ← | nitrate reductase 2 (NRZ), alpha subunit |
| RA | 1,708,309 | A→T | 6.5% | Q464L (CAG→CTG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,662 | C→G | 5.8% | Q582E (CAA→GAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,748,830 | C→T | 5.3% | A244T (GCC→ACC) | ydhT ← | FNR, Nar, NarP‑regulated protein; putative subunit of YdhYVWXUT oxidoreductase complex |
| 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 |
| 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 | 2,267,752 | G→A | 5.5% | intergenic (+41/‑77) | yeiQ → / → yeiR | putative NAD‑dependent D‑mannonate oxidoreductase/Zn‑stimulated GTPase involved in zinc homeostasis; mutants are cadmium and EDTA sensitive; Zn(2+) binding protein |
| RA | 2,282,966 | G→A | 5.7% | Q328* (CAG→TAG) | yejK ← | spermidine nucleoid‑associated protein |
| RA | 2,304,649 | C→T | 9.4% | intergenic (+256/+459) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,363,448 | A→G | 5.2% | D62D (GAT→GAC) ‡ | yfaY ← | inactive PncC family protein |
| RA | 2,363,449 | T→C | 5.0% | D62G (GAT→GGT) ‡ | yfaY ← | inactive PncC family protein |
| RA | 2,363,452 | G→A | 5.1% | A61V (GCC→GTC) ‡ | yfaY ← | inactive PncC family protein |
| RA | 2,363,453 | C→T | 5.1% | A61T (GCC→ACC) ‡ | yfaY ← | inactive PncC family protein |
| RA | 2,543,119 | C→A | 5.7% | W137L (TGG→TTG) | cysP ← | thiosulfate‑binding protein |
| RA | 2,556,501 | C→T | 5.0% | G266D (GGC→GAC) | eutC ← | ethanolamine ammonia‑lyase, small subunit (light chain) |
| RA | 2,596,873 | Δ1 bp | 9.4% | intergenic (‑136/+32) | ypfJ ← / ← purC | putative neutral zinc metallopeptidase/phosphoribosylaminoimidazole‑succinocarboxamide synthetase |
| RA | 2,596,878:1 | +G | 8.6% | intergenic (‑141/+27) | ypfJ ← / ← purC | putative neutral zinc metallopeptidase/phosphoribosylaminoimidazole‑succinocarboxamide synthetase |
| RA | 2,741,991 | T→C | 5.3% | I39I (ATT→ATC) | yfiR → | putative periplasmic inhibitor of YfiN activity |
| RA | 2,817,774 | A→T | 10.2% | intergenic (‑271/+10) | yqaB ← / ← argQ | fructose‑1‑P and 6‑phosphogluconate phosphatase/tRNA‑Arg |
| RA | 2,818,046 | A→G | 18.7% | intergenic (‑186/+13) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,818,049 | T→A | 16.0% | intergenic (‑189/+10) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,913,956 | T→C | 5.1% | K349E (AAG→GAG) | rlmD ← | 23S rRNA m(5)U1939 methyltransferase, SAM‑dependent |
| RA | 3,059,703 | A→T | 7.2% | intergenic (‑2/‑50) | yqfE ← / → argP | pseudogene, LysR family/transcriptional regulator for arginine transport and DNA replication genes; replication initiation inhibitor |
| RA | 3,059,704 | A→T | 7.8% | intergenic (‑3/‑49) | yqfE ← / → argP | pseudogene, LysR family/transcriptional regulator for arginine transport and DNA replication genes; replication initiation inhibitor |
| RA | 3,163,148 | C→T | 6.4% | G112S (GGC→AGC) | plsC ← | 1‑acyl‑sn‑glycerol‑3‑phosphate acyltransferase |
| RA | 3,194,996 | G→A | 5.0% | intergenic (‑131/+103) | sibD ← / ← sibE | sRNA antisense regulator of toxic IbsD protein/sRNA antisense regulator of toxic IbsE protein |
| RA | 3,246,561 | T→G | 6.5% | intergenic (+39/‑91) | exuT → / → exuR | hexuronate transporter/hexuronate regulon transcriptional repressor; autorepressor |
| RA | 3,246,562 | C→A | 6.4% | intergenic (+40/‑90) | exuT → / → exuR | hexuronate transporter/hexuronate regulon transcriptional repressor; autorepressor |
| RA | 3,246,563 | T→G | 6.4% | intergenic (+41/‑89) | exuT → / → exuR | hexuronate transporter/hexuronate regulon transcriptional repressor; autorepressor |
| RA | 3,246,564 | C→A | 6.4% | intergenic (+42/‑88) | exuT → / → exuR | hexuronate transporter/hexuronate regulon transcriptional repressor; autorepressor |
| RA | 3,368,219 | G→A | 5.1% | T131T (ACG→ACA) | yhcG → | DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily |
| RA | 3,368,220 | C→G | 6.0% | L132V (CTG→GTG) | yhcG → | DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily |
| RA | 3,423,531 | T→G | 7.2% | noncoding (12/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,458,110 | C→A | 100% | T578T (ACC→ACA) | gspD → | general secretory pathway component, cryptic |
| RA | 3,482,325 | G→A | 100% | R346H (CGC→CAC) | yheS → | ABC‑F family protein predicted regulatory ATPase |
| 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 | 3,736,325 | A→C | 5.6% | intergenic (+168/+28) | xylR → / ← bax | xylose divergent operon transcriptional activator/putative glucosaminidase |
| RA | 3,738,534 | C→T | 5.1% | R346R (CGC→CGT) | malS → | alpha‑amylase |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,856,683 | C→T | 8.3% | A90V (GCG→GTG) | yidI → | inner membrane protein |
| RA | 3,898,844 | T→C | 8.2% | M184V (ATG→GTG) | yieK ← | putative 6‑phosphogluconolactonase |
| RA | 3,967,302 | C→T | 29.6% | R296C (CGT→TGT) | rho → | transcription termination factor |
| RA | 3,967,531 | C→T | 8.8% | T372M (ACG→ATG) | rho → | transcription termination factor |
| RA | 4,070,462 | T→A | 7.3% | intergenic (‑61/+53) | yihR ← / ← yihS | putative sulphoquinovose mutarotase/sulphoquinovose isomerase |
| RA | 4,070,463 | T→A | 7.6% | intergenic (‑62/+52) | yihR ← / ← yihS | putative sulphoquinovose mutarotase/sulphoquinovose isomerase |
| RA | 4,070,464 | T→A | 6.8% | intergenic (‑63/+51) | yihR ← / ← yihS | putative sulphoquinovose mutarotase/sulphoquinovose isomerase |
| RA | 4,070,469 | A→C | 9.0% | intergenic (‑68/+46) | yihR ← / ← yihS | putative sulphoquinovose mutarotase/sulphoquinovose isomerase |
| RA | 4,106,369 | T→G | 5.2% | intergenic (+49/‑100) | cpxP → / → fieF | inhibitor of the cpx response; periplasmic adaptor protein/ferrous iron and zinc transporter |
| RA | 4,153,616 | C→T | 5.2% | intergenic (‑518/+80) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,153,658 | C→T | 5.9% | intergenic (‑560/+38) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,270,142 | G→A | 6.7% | intergenic (+15/‑96) | aphA → / → yjbQ | acid phosphatase/phosphotransferase, class B, non‑specific/thiamine phosphate synthase |
| RA | 4,270,144 | G→C | 6.6% | intergenic (+17/‑94) | aphA → / → yjbQ | acid phosphatase/phosphotransferase, class B, non‑specific/thiamine phosphate synthase |
| RA | 4,270,146 | T→C | 6.6% | intergenic (+19/‑92) | aphA → / → yjbQ | acid phosphatase/phosphotransferase, class B, non‑specific/thiamine phosphate synthase |
| RA | 4,283,905 | G→A | 5.9% | A333V (GCG→GTG) | actP ← | acetate transporter |
| RA | 4,296,060 | C→T | 34.3% | 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 | 4,390,401 | C→A | 5.3% | intergenic (‑41/+56) | psd ← / ← rsgA | phosphatidylserine decarboxylase/ribosome small subunit‑dependent GTPase A |
| RA | 4,473,927 | C→A | 100% | A43S (GCC→TCC) | bdcA ← | c‑di‑GMP‑binding biofilm dispersal mediator protein |
| RA | 4,520,500 | Δ1 bp | 5.2% | intergenic (‑176/+171) | yjhU ← / ← yjhF | putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter |
| RA | 4,579,672 | C→T | 6.1% | A57T (GCG→ACG) | symE ← | toxic peptide regulated by antisense sRNA symR |
| RA | 4,627,993 | A→T | 5.9% | K227* (AAG→TAG) | nadR → | trifunctional protein: nicotinamide mononucleotide adenylyltransferase, ribosylnicotinamide kinase, transcriptional repressor |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 448611 | 450691 | 2081 | 39 [37] | [37] 40 | [cyoC]–[cyoA] | [cyoC],cyoB,[cyoA] |
| * | * | ÷ | NC_000913 | 1166013 | 1167479 | 1467 | 38 [37] | [37] 39 | ndh | ndh |
| * | * | ÷ | NC_000913 | 3423742–3424234 | 3424542–3424238 | 5–801 | 38 [36] | [37] 38 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 497841 = | 62 (0.740) | 4 (0.050) | 4/268 | NT | 6.5% | intergenic (+22/‑214) | adk/hemH | adenylate kinase/ferrochelatase |
| ? | NC_000913 | 497861 = | 55 (0.680) | intergenic (+42/‑194) | adk/hemH | adenylate kinase/ferrochelatase | |||||
| * | ? | NC_000913 | 781577 = | 53 (0.640) | 32 (0.400) +GAAG |
9/270 | NT | 40.7% | noncoding (1/76 nt) | lysQ | tRNA‑Lys |
| ? | NC_000913 | = 2521006 | 43 (0.520) | noncoding (76/76 nt) | valU | tRNA‑Val | |||||
| * | ? | NC_000913 | 1207790 = | 34 (0.410) | 41 (0.560) | 29/246 | NT | 52.9% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 43 (0.580) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 34 (0.410) | 28 (0.380) | 22/246 | NT | 43.4% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 43 (0.580) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1287084 | 53 (0.640) | 6 (0.080) | 4/238 | NT | 13.7% | noncoding (153/171 nt) | rttR | rtT sRNA, processed from tyrT transcript |
| ? | NC_000913 | 1287557 = | 30 (0.420) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 91 (1.120) | 63/270 | 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 | 2277865 = | 76 (0.910) | 5 (0.060) | 3/260 | NT | 7.1% | coding (1566/1590 nt) | yejF | microcin C ABC transporter ATPase |
| ? | NC_000913 | 2277893 = | 60 (0.770) | coding (345/345 nt) | yejG | uncharacterized protein | |||||
| * | ? | NC_000913 | 3247441 = | 81 (0.970) | 4 (0.050) | 3/262 | NT | 5.2% | intergenic (+13/‑332) | exuR/yqjA | hexuronate regulon transcriptional repressor; autorepressor/general envelope maintenance protein; DedA family inner membrane protein; putative multidrug efflux transporter |
| ? | NC_000913 | 3247463 = | 69 (0.880) | intergenic (+35/‑310) | exuR/yqjA | hexuronate regulon transcriptional repressor; autorepressor/general envelope maintenance protein; DedA family inner membrane protein; putative multidrug efflux transporter | |||||
| * | ? | NC_000913 | 4542682 = | 56 (0.670) | 3 (0.040) | 3/260 | NT | 5.1% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 60 (0.770) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 4542690 | 59 (0.710) | 9 (0.120) | 8/260 | NT | 13.5% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 60 (0.770) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||