mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 360,362 | T→G | 16.4% | V124G (GTG→GGG) | cynX → | putative cyanate transporter |
| RA | 433,649 | T→G | 26.7% | G65G (GGT→GGG) | ribD → | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| JC JC | 458,790 | IS186 (–) +6 bp :: Δ1 bp | 83.6% | intergenic (+90/‑93) | clpX → / → lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| RA | 509,371 | A→C | 16.7% | V670G (GTG→GGG) | copA ← | copper transporter |
| RA | 538,370 | C→G | 15.8% | S246R (AGC→AGG) | ybbW → | putative allantoin transporter |
| RA | 599,579 | T→G | 20.2% | V289G (GTG→GGG) | cusA → | copper/silver efflux system, membrane component |
| RA | 630,153 | T→G | 17.3% | V87G (GTG→GGG) | cstA → | carbon starvation protein involved in peptide utilization; APC peptide transporter family protein |
| RA | 770,213 | A→G | 10.3% | S746G (AGT→GGT) | mngB → | alpha‑mannosidase |
| RA | 954,374 | C→G | 22.8% | P31P (CCG→CCC) | focA ← | formate channel |
| RA | 981,253 | T→G | 18.9% | G69G (GGT→GGG) | ldtD → | murein L,D‑transpeptidase |
| RA | 989,945 | A→G | 21.4% | S138P (TCA→CCA) | pncB ← | nicotinate phosphoribosyltransferase |
| RA | 1,137,238 | T→G | 15.7% | V322G (GTA→GGA) | flgI → | putative flagellar basal body protein |
| RA | 1,196,305 | C→T | 90.6% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,239,823 | T→G | 23.4% | G315G (GGT→GGG) | dadX → | alanine racemase, catabolic, PLP‑binding |
| RA | 1,239,840 | A→G | 11.5% | E321G (GAG→GGG) | dadX → | alanine racemase, catabolic, PLP‑binding |
| 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 | 1,466,336 | C→G | 7.2% | pseudogene (945/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,345 | T→C | 7.7% | pseudogene (954/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,513,778 | T→G | 14.3% | V321G (GTG→GGG) | ydcT → | putative ABC transporter ATPase |
| RA | 1,616,757 | T→A | 13.9% | V332E (GTA→GAA) | yneK → | uncharacterized protein |
| RA | 1,739,952 | G→T | 13.5% | L14F (TTG→TTT) | ydhC → | putative arabinose efflux transporter |
| RA | 1,877,629 | C→T | 18.8% | intergenic (‑97/‑86) | yoaF ← / → yeaP | DUF333 family outer membrane lipoprotein/diguanylate cyclase |
| RA | 1,911,547 | A→G | 13.3% | G424G (GGA→GGG) | yebQ → | putative transporter |
| 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 | 2,014,202 | T→C | 16.5% | I325T (ATC→ACC) | fliF → | flagellar basal‑body MS‑ring and collar protein |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| 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 | 2,185,199 | T→G | 17.9% | T35P (ACC→CCC) | thiM ← | hydoxyethylthiazole kinase |
| RA | 2,395,466 | G→C | 13.0% | A144G (GCT→GGT) | nuoJ ← | NADH:ubiquinone oxidoreductase, membrane subunit J |
| RA | 2,459,225 | T→C | 24.5% | G415G (GGA→GGG) | fadI ← | beta‑ketoacyl‑CoA thiolase, anaerobic, subunit |
| RA | 2,464,499 | T→A | 12.3% | Y170F (TAC→TTC) | mlaA ← | ABC transporter maintaining OM lipid asymmetry, OM lipoprotein component |
| RA | 2,525,239 | G→T | 12.9% | W38L (TGG→TTG) | yfeN → | putative outer membrane protein |
| JC | 2,765,412 | Δ8 bp | 8.4% | intergenic (‑259/+94) | yfjL ← / ← yfjM | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein/CP4‑57 prophage; uncharacterized protein |
| JC JC | 2,771,956 | IS2 (–) +5 bp | 7.6% | intergenic (+341/+42) | yfjT → / ← yfjU | CP4‑57 prophage; putative periplasmic protein/CP4‑57 prophage; conserved protein;Phage or Prophage Related |
| RA | 2,828,506 | T→G | 16.0% | V257G (GTG→GGG) | srlD → | sorbitol‑6‑phosphate dehydrogenase |
| RA | 2,859,434 | T→G | 15.7% | V781G (GTG→GGG) | mutS → | methyl‑directed mismatch repair protein |
| RA | 3,026,901 | A→C | 11.8% | N379T (AAC→ACC) | guaD → | guanine deaminase |
| RA | 3,206,436 | C→A | 14.6% | intergenic (‑180/‑27) | ttdR ← / → ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,438 | G→A | 21.5% | intergenic (‑182/‑25) | ttdR ← / → ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,466 | A→G | 15.0% | M2V (ATG→GTG) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,471 | C→G | 17.0% | S3R (AGC→AGG) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,506 | C→A | 25.2% | T15K (ACA→AAA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,277,499 | G→A | 17.5% | V55M (GTG→ATG) | yhaV → | toxin of the SohB(PrlF)‑YhaV toxin‑antitoxin system |
| RA | 3,499,694 | G→T | 15.3% | intergenic (+79/‑216) | yhfL → / → frlA | small lipoprotein/putative fructoselysine transporter |
| RA | 3,531,454 | A→C | 11.8% | V329G (GTG→GGG) | yhgE ← | DUF4153 family putative inner membrane protein |
| RA | 3,536,135 | G→C | 11.4% | 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 | 5.4% | pseudogene (112/150 nt) | glpR ← | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,615,865 | A→C | 16.3% | T209P (ACC→CCC) | nikB → | nickel ABC transporter permease |
| RA | 3,638,228 | A→G | 12.7% | E196G (GAG→GGG) | pitA → | phosphate transporter, low‑affinity; tellurite importer |
| RA | 3,661,663 | A→G | 11.9% | E417G (GAG→GGG) | mdtF → | anaerobic multidrug efflux transporter, ArcA‑regulated |
| RA | 3,680,185 | T→G | 10.4% | V256G (GTG→GGG) | kdgK → | 2‑dehydro‑3‑deoxygluconokinase |
| RA | 3,731,720 | C→A | 18.4% | A197E (GCA→GAA) | xylF → | D‑xylose transporter subunit |
| RA | 3,733,274 | T→G | 12.8% | G358G (GGT→GGG) | xylG → | D‑xylose ABC transporter dual domain ATPase |
| RA | 3,760,384 | A→C | 31.3% | V289G (GTG→GGG) | selA ← | selenocysteine synthase |
| RA | 3,781,966 | A→C | 21.6% | G199G (GGT→GGG) | cysE ← | serine acetyltransferase |
| RA | 3,782,919 | T→C | 30.8% | D248G (GAT→GGT) | gpsA ← | glycerol‑3‑phosphate dehydrogenase (NAD+) |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,864,875 | T→C | 7.6% | I467V (ATT→GTT) | yidE ← | putative transporter |
| RA | 3,875,537 | G→A | 19.4% | A34T (GCA→ACA) | yidX → | putative lipoprotein |
| RA | 3,895,556 | T→C | 13.3% | M352V (ATG→GTG) | adeP ← | adenine permease, high affinity; adenine:H+ symporter |
| RA | 3,904,286 | C→A | 11.0% | A438S (GCC→TCC) | bglF ← | fused beta‑glucoside‑specific PTS enzymes: IIA component/IIB component/IIC component |
| RA | 3,947,831 | T→G | 14.6% | N46T (AAC→ACC) | hdfR ← | flhDC operon transcriptional repressor |
| RA | 3,976,145 | G→T | 9.1% | G334C (GGT→TGT) | wecE → | TDP‑4‑oxo‑6‑deoxy‑D‑glucose transaminase |
| RA | 3,977,527 | G→T | 17.5% | *417L (TGA→TTA) M1M (ATG→ATT) † |
wzxE → wecF → |
O‑antigen translocase TDP‑Fuc4NAc:lipidIIFuc4NAc transferase |
| RA | 3,977,593 | C→T | 14.2% | F23F (TTC→TTT) | wecF → | TDP‑Fuc4NAc:lipidIIFuc4NAc transferase |
| JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,003,509 | T→G | 22.3% | T224P (ACC→CCC) | rarD ← | putative chloramphenical resistance permease |
| RA | 4,088,438 | A→G | 9.7% | V473A (GTC→GCC) | frvR ← | putative frv operon regulator; contains a PTS EIIA domain |
| RA | 4,099,985 | A→C | 10.7% | C181G (TGC→GGC) | rhaT ← | L‑rhamnose:proton symporter |
| RA | 4,115,218 | T→C | 10.5% | E121G (GAG→GGG) | glpX ← | fructose 1,6‑bisphosphatase II |
| RA | 4,145,050 | T→C | 11.6% | Y352Y (TAT→TAC) | pflD → | putative glycine radical domain‑containing pyruvate formate‑lyase |
| RA | 4,145,065 | A→C | 16.5% | L357F (TTA→TTC) | pflD → | putative glycine radical domain‑containing pyruvate formate‑lyase |
| RA | 4,145,088 | G→C | 11.4% | R365P (CGC→CCC) | pflD → | putative glycine radical domain‑containing pyruvate formate‑lyase |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,201,278 | A→C | 14.8% | G137G (GGT→GGG) | zraP ← | Zn‑dependent periplasmic chaperone |
| RA | 4,296,060 | C→T | 16.3% | 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 | 4,394,334 | T→G | 16.9% | V90G (GTC→GGC) | nnr → | bifunctional NAD(P)H‑hydrate repair enzyme; C‑terminal domain ADP‑dependent (S)‑NAD(P)H‑hydrate dehydratase and N‑terminal domain NAD(P)H‑hydrate epimerase |
| RA | 4,395,304 | T→G | 12.9% | G413G (GGT→GGG) | nnr → | bifunctional NAD(P)H‑hydrate repair enzyme; C‑terminal domain ADP‑dependent (S)‑NAD(P)H‑hydrate dehydratase and N‑terminal domain NAD(P)H‑hydrate epimerase |
| RA | 4,421,192 | A→G | 16.4% | S405G (AGT→GGT) | ulaA → | L‑ascorbate‑specific enzyme IIC permease component of PTS |
| RA | 4,449,045 | T→G | 18.8% | intergenic (+3/+77) | chpB → / ← ppa | toxin of the ChpB‑ChpS toxin‑antitoxin system/inorganic pyrophosphatase |
| RA | 4,548,864 | C→T | 16.5% | A19A (GCC→GCT) | fimH → | minor component of type 1 fimbriae |
| RA | 4,582,478 | A→C | 13.3% | S191A (TCG→GCG) | hsdM ← | DNA methyltransferase M |
| RA | 4,626,668 | A→C | 14.1% | T253P (ACC→CCC) | radA → | DNA repair protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 583130 | 583887 | 758 | 37 [32] | [29] 33 | [tfaX]–[appY] | [tfaX],[appY] |
| * | * | ÷ | NC_000913 | 1299442 | 1300737 | 1296 | 33 [29] | [31] 33 | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| * | * | ÷ | NC_000913 | 2455615 | 2456146 | 532 | 34 [32] | [31] 33 | [yfcV] | [yfcV] |
| * | * | ÷ | NC_000913 | 3798898 | 3799562 | 665 | 33 [32] | [28] 35 | [waaU]–[waaZ] | [waaU],[waaZ] |
| * | * | ÷ | NC_000913 | 4233764 | 4235435 | 1672 | 34 [32] | [31] 34 | [pgi] | [pgi] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 20 (0.180) | 87 (0.850) | 56/408 | NT | 83.8% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 15 (0.150) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 20 (0.180) | 77 (0.760) | 53/408 | NT | 82.1% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 15 (0.150) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 19 (0.180) | 16/432 | 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 | |||||