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 | 65,670 | T→G | 12.9% | A37A (GCA→GCC) | polB ← | DNA polymerase II |
| RA | 249,538 | T→G | 18.0% | pseudogene (533/1713 nt) | lfhA ← | pseudogene, flagellar system protein, promoterless fragment; flagellar biosynthesis |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 343,444 | A→G | 18.0% | G187G (GGA→GGG) | yahK → | broad specificity NADPH‑dependent aldehyde reductase, Zn‑containing |
| RA | 357,819 | G→C | 19.8% | A291G (GCG→GGG) | cynR ← | transcriptional activator of cyn operon; autorepressor |
| RA | 417,533 | T→G | 11.4% | V131G (GTG→GGG) | phoB → | response regulator in two‑component regulatory system with PhoR |
| RA | 421,608 | T→G | 11.0% | V208G (GTG→GGG) | proY → | proline‑specific permease |
| RA | 433,649 | T→G | 21.5% | G65G (GGT→GGG) | ribD → | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| JC JC | 458,790 | IS186 (–) +6 bp :: Δ1 bp | 41.8% | intergenic (+90/‑93) | clpX → / → lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| JC JC | 458,873 | IS5 (–) +4 bp | 5.7% | intergenic (+173/‑12) | clpX → / → lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| RA | 602,635 | A→G | 10.2% | E226G (GAG→GGG) | pheP → | phenylalanine transporter |
| RA | 811,721 | T→G | 25.1% | V67G (GTG→GGG) | bioC → | malonyl‑ACP O‑methyltransferase, SAM‑dependent |
| RA | 823,339 | T→C | 11.1% | E134G (GAG→GGG) | clsB ← | cardiolipin synthase 2 |
| RA | 827,507 | T→G | 32.8% | D492A (GAC→GCC) | ybhF ← | putative ABC transporter ATPase |
| RA | 954,354 | G→C | 10.8% | A38G (GCG→GGG) | focA ← | formate channel |
| RA | 989,901 | G→T | 17.0% | S152R (AGC→AGA) | pncB ← | nicotinate phosphoribosyltransferase |
| RA | 1,196,131 | G→A | 21.4% | A337T (GCC→ACC) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,305 | C→T | 60.0% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,270,419 | T→C | 5.7% | noncoding (27/68 nt) | rdlC → | sRNA antisense regulator affects LdrC translation; proposed addiction module in LDR‑C repeat, with toxic peptide LdrC |
| RA | 1,286,965 | A→G | 7.2% | intergenic (+439/+101) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,286,974 | C→T | 11.1% | intergenic (+448/+92) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,286,983 | A→G | 6.9% | intergenic (+457/+83) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,287,037 | C→T | 9.2% | intergenic (+511/+29) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| 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 |
| RA | 1,377,071 | A→C | 17.2% | S80S (TCA→TCC) | ycjS → | putative NADH‑binding oxidoreductase |
| RA | 1,466,201 | T→C | 6.9% | pseudogene (810/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,711 | T→C | 7.1% | pseudogene (1320/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,714 | T→C | 6.5% | pseudogene (1323/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,717 | C→T | 5.3% | pseudogene (1326/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,726 | G→A | 8.0% | pseudogene (1335/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,729 | G→A | 5.4% | pseudogene (1338/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,732 | G→T | 5.6% | pseudogene (1341/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,708,709 | T→C | 11.1% | R597R (CGT→CGC) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,805 | T→C | 17.4% | R629R (CGT→CGC) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,930 | C→A | 10.9% | P671Q (CCG→CAG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,764,648 | T→A | 12.8% | intergenic (‑262/+65) | sufA ← / ← rydB | Fe‑S cluster assembly protein/novel sRNA, function unknown |
| 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 | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,149,907 | A→C | 14.5% | V360G (GTG→GGG) | yegI ← | protein kinase‑related putative non‑specific DNA‑binding protein |
| RA | 2,151,681 | G→T | 19.0% | intergenic (+35/+30) | yegJ → / ← yegK | uncharacterized protein/ser/thr phosphatase‑related protein |
| RA | 2,151,689 | G→T | 30.0% | intergenic (+43/+22) | yegJ → / ← yegK | uncharacterized protein/ser/thr phosphatase‑related 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 | 2,228,256 | A→C | 22.2% | pseudogene (354/1287 nt) | mdtQ ← | pseudogene; putative channel/filament proteins |
| RA | 2,228,272 | A→C | 27.3% | pseudogene (338/1287 nt) | mdtQ ← | pseudogene; putative channel/filament proteins |
| RA | 2,257,490 | A→C | 13.9% | V293G (GTG→GGG) | psuG ← | pseudouridine 5'‑phosphate glycosidase |
| RA | 2,339,781 | A→G | 13.0% | E72G (GAG→GGG) | ubiG → | bifunctional 3‑demethylubiquinone‑9 3‑methyltransferase/ 2‑octaprenyl‑6‑hydroxy phenol methylase |
| RA | 2,608,226 | T→G | 17.3% | V437G (GTA→GGA) | hyfF → | hydrogenase 4, membrane subunit |
| RA | 2,807,369 | A→C | 15.6% | T80P (ACC→CCC) | proX → | glycine betaine/proline ABC transporter periplasmic binding protein; cold shock protein |
| RA | 2,859,434 | T→G | 12.8% | V781G (GTG→GGG) | mutS → | methyl‑directed mismatch repair protein |
| RA | 3,019,572 | A→C | 14.2% | T138P (ACA→CCA) | ssnA → | putative chlorohydrolase/aminohydrolase |
| RA | 3,097,511 | A→G | 13.6% | D82G (GAC→GGC) | yggW → | HemN family putative oxidoreductase |
| RA | 3,206,438 | G→A | 17.5% | intergenic (‑182/‑25) | ttdR ← / → ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,458 | T→G | 13.2% | intergenic (‑202/‑5) | ttdR ← / → ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,471 | C→G | 13.1% | S3R (AGC→AGG) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,476 | G→A | 11.7% | S5N (AGT→AAT) ‡ | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,477 | T→A | 16.2% | S5R (AGT→AGA) ‡ | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,483 | G→A | 21.2% | K7K (AAG→AAA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,487 | C→A | 20.5% | Q9K (CAG→AAG) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,506 | C→A | 17.8% | T15K (ACA→AAA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,518 | C→T | 14.7% | A19V (GCT→GTT) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,536,135 | G→C | 10.9% | R150R (CGC→CGG) | ompR ← | response regulator in two‑component regulatory system with EnvZ |
| 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 | 3,560,494 | G→A | 6.7% | pseudogene (112/150 nt) | glpR ← | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,760,384 | A→C | 27.0% | V289G (GTG→GGG) | selA ← | selenocysteine synthase |
| RA | 3,780,896 | T→G | 10.7% | V357G (GTG→GGG) | lldD → | L‑lactate dehydrogenase, FMN‑linked |
| RA | 3,781,912 | G→C | 13.0% | G217G (GGC→GGG) | cysE ← | serine acetyltransferase |
| RA | 3,781,966 | A→C | 25.0% | G199G (GGT→GGG) | cysE ← | serine acetyltransferase |
| RA | 3,782,913 | A→C | 15.0% | V250G (GTG→GGG) | gpsA ← | glycerol‑3‑phosphate dehydrogenase (NAD+) |
| RA | 3,783,215 | A→C | 13.4% | G149G (GGT→GGG) | gpsA ← | glycerol‑3‑phosphate dehydrogenase (NAD+) |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,840,638 | C→A | 10.7% | G368C (GGT→TGT) | nepI ← | putative transporter |
| RA | 3,862,661 | T→G | 33.7% | pseudogene (943/1617 nt) | glvC ← | pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component |
| RA | 3,862,662 | T→G | 18.8% | pseudogene (942/1617 nt) | glvC ← | pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component |
| RA | 3,862,670 | T→A | 28.7% | pseudogene (934/1617 nt) | glvC ← | pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component |
| RA | 3,862,674 | C→A | 16.2% | pseudogene (930/1617 nt) | glvC ← | pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component |
| RA | 3,947,831 | T→G | 16.6% | N46T (AAC→ACC) | hdfR ← | flhDC operon transcriptional repressor |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,023,735 | T→G | 15.8% | V61G (GTA→GGA) | tatD → | quality control of Tat‑exported FeS proteins; Mg‑dependent cytoplasmic DNase |
| RA | 4,088,429 | T→G | 9.3% | H476P (CAC→CCC) | frvR ← | putative frv operon regulator; contains a PTS EIIA domain |
| RA | 4,088,445 | G→T | 8.8% | Q471K (CAA→AAA) | frvR ← | putative frv operon regulator; contains a PTS EIIA domain |
| RA | 4,091,186 | T→G | 24.2% | Y394S (TAC→TCC) | frvB ← | putative PTS enzyme, IIB component/IIC component |
| RA | 4,091,193 | T→A | 19.3% | I392F (ATT→TTT) | frvB ← | putative PTS enzyme, IIB component/IIC component |
| RA | 4,151,329 | T→G | 19.9% | A590A (GCA→GCC) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,219,539 | C→T | 10.2% | A315V (GCG→GTG) | aceK → | isocitrate dehydrogenase kinase/phosphatase |
| RA | 4,223,614 | A→G | 18.4% | I5I (ATT→ATC) | iclR ← | transcriptional repressor |
| RA | 4,228,215 | T→G | 10.4% | V162G (GTG→GGG) | yjbB → | putative Na+/Pi‑cotransporter |
| RA | 4,296,060 | C→T | 22.5% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 19.3% | intergenic (+474/+168) | 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 | 4,325,948 | A→G | 6.0% | intergenic (‑207/+451) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,336,897 | T→C | 19.0% | G45G (GGA→GGG) | adiC ← | arginine:agmatine antiporter |
| RA | 4,412,890 | T→G | 10.3% | G168G (GGT→GGG) | yjfM → | DUF1190 family protein |
| RA | 4,434,554 | C→G | 5.3% | intergenic (+61/+68) | ytfH → / ← cpdB | DUF24 family HxlR‑type putative transcriptional regulator/2':3'‑cyclic‑nucleotide 2'‑phosphodiesterase |
| RA | 4,571,096 | A→G | 18.9% | L160P (CTC→CCC) | yjiR ← | putative DNA‑binding transcriptional regulator/putative aminotransferase |
| RA | 4,571,180 | A→C | 19.8% | V132G (GTG→GGG) | yjiR ← | putative DNA‑binding transcriptional regulator/putative aminotransferase |
| RA | 4,617,735 | T→G | 8.8% | V138G (GTG→GGG) | deoC → | 2‑deoxyribose‑5‑phosphate aldolase, NAD(P)‑linked |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423855–3424233 | 3424451–3424239 | 7–597 | 42 [40] | [39] 44 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 4233764 | 4235434 | 1671 | 45 [41] | [41] 42 | [pgi] | [pgi] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 381473 | 2 (0.020) | 3 (0.030) | 3/416 | NT | 61.2% | noncoding (214/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 381839 | NA (NA) | noncoding (580/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 23 (0.180) | 81 (0.700) | 60/406 | NT | 81.7% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 15 (0.130) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 23 (0.180) | 96 (0.830) | 67/406 | NT | 84.1% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 15 (0.130) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 44 (0.360) | 37/430 | 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 | |||||