mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.32.0 revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 11,427 | C→T | 12.7% | V120V (GTG→GTA) | yaaI ← | UPF0412 family protein |
| RA | 12,484 | C→A | 19.0% | Q108K (CAG→AAG) | dnaK → | chaperone Hsp70, with co‑chaperone DnaJ |
| RA | 149,436 | A→G | 9.2% | S56P (TCC→CCC) | panB ← | 3‑methyl‑2‑oxobutanoate hydroxymethyltransferase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 272,636 | T→G | 18.9% | noncoding (57/75 nt) | eyeA → | novel sRNA, function unknown, CP4‑6 propahge |
| RA | 404,848 | A→G | 16.2% | L266P (CTC→CCC) | proC ← | pyrroline‑5‑carboxylate reductase, NAD(P)‑binding |
| RA | 419,111 | A→G | 15.4% | E408G (GAG→GGG) | phoR → | sensory histidine kinase in two‑component regulatory system with PhoB |
| RA | 507,782 | T→G | 23.1% | H100P (CAC→CCC) | ybaP ← | TraB family protein |
| RA | 677,006 | C→G | 8.0% | A99G (GCG→GGG) | ybeR → | uncharacterized protein |
| RA | 729,603 | G→C | 13.4% | A7A (GCG→GCC) | rhsC → | Rhs protein with putative toxin domain, putative neighboring cell growth inhibitor |
| RA | 817,815 | G→C | 14.7% | A258P (GCC→CCC) | moaA → | molybdopterin biosynthesis protein A |
| RA | 854,311 | A→G | 26.1% | E222G (GAG→GGG) | ybiR → | putative transporter |
| RA | 908,290 | T→C | 15.0% | intergenic (‑8/+3) | ybjT ← / ← ltaE | putative NAD‑dependent oxidoreductase/L‑allo‑threonine aldolase, PLP‑dependent |
| RA | 1,058,486 | T→C | 19.5% | S135P (TCG→CCG) | torC → | trimethylamine N‑oxide (TMAO) reductase I, cytochrome c‑type subunit |
| RA | 1,196,305 | C→T | 100% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase |
| RA | 1,400,230 | T→C | 16.6% | R3G (AGA→GGA) | ogt ← | O‑6‑alkylguanine‑DNA:cysteine‑protein methyltransferase |
| RA | 1,424,240 | G→T | 34.8% | L153F (TTG→TTT) | trkG → | Rac prophage, potassium transporter subunit |
| RA | 1,520,060 | A→T | 22.5% | D345V (GAT→GTT) | curA → | curcumin/dihydrocurcumin reductase, NADPH‑dependent |
| RA | 1,520,084 | G→A | 32.1% | intergenic (+20/‑178) | curA → / → mcbR | curcumin/dihydrocurcumin reductase, NADPH‑dependent/colanic acid and biofilm gene transcriptional regulator, MqsR‑controlled |
| RA | 1,616,800 | G→A | 23.4% | V346V (GTG→GTA) | yneK → | uncharacterized protein |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,223,934 | A→C | 18.9% | intergenic (+36/+2) | dld → / ← pbpG | D‑lactate dehydrogenase, FAD‑binding, NADH independent/D‑alanyl‑D‑alanine endopeptidase |
| RA | 2,354,498 | T→C | 18.5% | L79P (CTC→CCC) | glpB → | anaerobic sn‑glycerol‑3‑phosphate dehydrogenase membrane anchor subunit |
| RA | 2,411,023 | T→C | 11.6% | S110G (AGT→GGT) | yfbS ← | putative transporter |
| RA | 2,419,689 | A→C | 20.7% | V33G (GTG→GGG) | yfcE ← | phosphodiesterase activity on bis‑pNPP |
| RA | 2,550,536 | Δ1 bp | 5.4% | coding (8/900 nt) | yfeX ← | porphyrinogen oxidase, cytoplasmic |
| RA | 2,565,350 | T→C | 15.6% | intergenic (+20/+129) | yffS → / ← eutA | CPZ‑55 prophage, uncharacterized protein/reactivating factor for ethanolamine ammonia lyase |
| RA | 2,596,612 | T→C | 18.1% | I42V (ATA→GTA) | ypfJ ← | putative neutral zinc metallopeptidase |
| RA | 2,913,611 | A→C | 18.1% | G13G (GGT→GGG) | relA ← | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| RA | 2,934,872 | Δ1 bp | 8.3% | coding (640/1317 nt) | fucP → | L‑fucose transporter |
| RA | 3,081,407 | T→G | 15.3% | H76P (CAC→CCC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,206,436 | G→A | 29.4% | intergenic (‑182/‑25) | ttdR ← / → ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| RA | 3,210,859 | T→G | 19.2% | G27G (GGT→GGG) | rpsU → | 30S ribosomal subunit protein S21 |
| RA | 3,217,528 | T→C | 23.5% | intergenic (+128/+26) | yqjI → / ← aer | PadR family putative transcriptional regulator/fused signal transducer for aerotaxis sensory component/methyl accepting chemotaxis component |
| RA | 3,364,402 | G→A | 17.0% | R533K (AGA→AAA) | yhcD → | putative outer membrane fimbrial subunit usher protein |
| RA | 3,457,073 | T→A | 22.0% | D233E (GAT→GAA) | gspD → | general secretory pathway component, cryptic |
| RA | 3,489,442 | Δ1 bp | 5.8% | coding (737/1221 nt) | argD ← | bifunctional acetylornithine aminotransferase and succinyldiaminopimelate aminotransferase |
| RA | 3,514,936 | T→G | 17.6% | H41P (CAC→CCC) | rpe ← | D‑ribulose‑5‑phosphate 3‑epimerase |
| RA | 3,590,223 | T→G | 26.1% | T230P (ACC→CCC) | ugpA ← | sn‑glycerol‑3‑phosphate ABC transporter permease |
| RA | 3,728,949 | T→C | 15.0% | E141G (GAG→GGG) | xylB ← | xylulokinase |
| RA | 3,809,085 | C→A | 9.5% | Q183K (CAA→AAA) | waaA → | 3‑deoxy‑D‑manno‑octulosonic‑acid transferase (KDO transferase) |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| JC | 4,001,644 | Δ5 bp | 92.6% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,065,172 | G→A | 11.6% | G198G (GGC→GGT) | yihO ← | putative sulphoquinovose importer |
| RA | 4,076,841 | A→C | 18.2% | T233P (ACC→CCC) | yihY → | BrkB family putative transporter, inner membrane protein |
| RA | 4,163,577 | T→C | 6.3% | intergenic (‑308/‑61) | trmA ← / → btuB | tRNA m(5)U54 methyltransferase, SAM‑dependent, tmRNA m(5)U341 methyltransferase/vitamin B12/cobalamin outer membrane transporter |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,304,822 | T→C | 5.7% | N593D (AAC→GAC) | yjcS ← | metallo‑beta‑lactamase superfamily protein |
| RA | 4,305,424:1 | +G | 7.8% | coding (1175/1986 nt) | yjcS ← | metallo‑beta‑lactamase superfamily protein |
| RA | 4,540,284 | T→G | 26.7% | intergenic (‑782/‑674) | nanC ← / → fimB | N‑acetylnuraminic acid outer membrane channel protein/tyrosine recombinase/inversion of on/off regulator of fimA |
| RA | 4,579,657 | A→C | 18.6% | V62G (GTG→GGG) | symE ← | toxic peptide regulated by antisense sRNA symR |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 583371 | 583684 | 314 | 12 [11] | [11] 12 | [appY] | [appY] |
| * | * | ÷ | NC_000913 | 720912 | 721091 | 180 | 14 [11] | [11] 12 | [kdpE] | [kdpE] |
| * | * | ÷ | NC_000913 | 1212022 | 1212355 | 334 | 14 [10] | [11] 12 | iraM/ycgX | RpoS stabilzer during Mg starvation, anti‑RssB factor/DUF1398 family protein |
| * | * | ÷ | NC_000913 | 1640955 | 1641044 | 90 | 12 [10] | [11] 13 | essQ/cspB | Qin prophage, putative S lysis protein/Qin prophage, cold shock protein |
| * | * | ÷ | NC_000913 | 2470134 | 2470399 | 266 | 12 [11] | [11] 12 | gtrS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| * | * | ÷ | NC_000913 | 3799007 | 3799510 | 504 | 12 [11] | [11] 13 | [waaU]–[waaZ] | [waaU], [waaZ] |
| * | * | ÷ | NC_000913 | 3804741 | 3805137 | 397 | 14 [10] | [9] 12 | [waaS] | [waaS] |
| * | * | ÷ | NC_000913 | 4233765 | 4235396 | 1632 | 12 [11] | [10] 12 | pgi | glucosephosphate isomerase |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 64 (1.200) | 43/408 | NT | 100% | intergenic (+9/‑768) | crl/crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers |
| ? | NC_000913 | = 1293039 | 0 (0.000) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | 458787 = | 7 (0.130) | 54 (1.020) | 43/402 | NT | 88.7% | intergenic (+87/‑101) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| ? | NC_000913 | 608011 = | NA (NA) | intergenic (+23/‑54) | hokE/insL1 | toxic polypeptide, small/IS186 transposase | |||||
| * | ? | NC_000913 | = 458799 | 4 (0.070) | 75 (1.430) | 53/400 | NT | 95.0% | intergenic (+99/‑89) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| ? | NC_000913 | = 609347 | NA (NA) | intergenic (+170/+112) | insL1/entD | IS186 transposase/phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex | |||||
| * | ? | NC_000913 | 1207790 = | 16 (0.300) | 49 (0.990) | 37/376 | NT | 82.5% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 6 (0.120) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 15 (0.280) | 51 (1.030) | 41/376 | NT | 83.7% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 6 (0.120) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 1 (0.020) | 44 (0.820) | 29/408 | NT | 97.8% | intergenic (‑110/‑495) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| ? | NC_000913 | = 1979270 | NA (NA) | intergenic (‑55/‑483) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 24 (0.460) | 18/400 | 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 | 1979486 = | 0 (0.000) | 31 (0.580) | 20/408 | NT | 100% | intergenic (‑271/‑267) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | 2101749 = | NA (NA) | intergenic (‑5/+146) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | = 1979489 | 0 (0.000) | 62 (1.160) | 43/408 | NT | 100% | intergenic (‑274/‑264) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | = 2290111 | NA (NA) | intergenic (‑32/+1) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system | |||||