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 | annotation | gene | description |
| RA | 8,621 | T→C | R128R (CGT→CGC) | talB → | transaldolase B |
| RA | 8,639 | T→C | A134A (GCT→GCC) | talB → | transaldolase B |
| RA | 8,642 | T→C | S135S (TCT→TCC) | talB → | transaldolase B |
| RA | 8,654 | T→C | G139G (GGT→GGC) | talB → | transaldolase B |
| RA | 8,657 | C→T | I140I (ATC→ATT) | talB → | transaldolase B |
| RA | 8,660 | T→C | R141R (CGT→CGC) | talB → | transaldolase B |
| RA | 8,663 | T→C | A142A (GCT→GCC) | talB → | transaldolase B |
| RA | 8,666 | A→T | A143A (GCA→GCT) | talB → | transaldolase B |
| RA | 8,690 | C→T | I151I (ATC→ATT) | talB → | transaldolase B |
| RA | 8,705 | C→G | T156T (ACC→ACG) | talB → | transaldolase B |
| RA | 8,732 | T→C | R165R (CGT→CGC) | talB → | transaldolase B |
| RA | 8,738 | T→C | C167C (TGT→TGC) | talB → | transaldolase B |
| RA | 8,741 | G→C | A168A (GCG→GCC) | talB → | transaldolase B |
| RA | 8,753 | G→C | V172V (GTG→GTC) | talB → | transaldolase B |
| RA | 8,762 | C→T | I175I (ATC→ATT) | talB → | transaldolase B |
| RA | 8,771 | T→C | F178F (TTT→TTC) | talB → | transaldolase B |
| RA | 8,783 | T→C | I182I (ATT→ATC) | talB → | transaldolase B |
| RA | 8,786 | T→C | L183L (CTT→CTC) | talB → | transaldolase B |
| RA | 8,801 | G→C | A188A (GCG→GCC) | talB → | transaldolase B |
| RA | 8,804 | T→C | N189N (AAT→AAC) | talB → | transaldolase B |
| RA | 8,810 | T→C | D191D (GAT→GAC) | talB → | transaldolase B |
| RA | 8,825 | T→A | A196A (GCT→GCA) | talB → | transaldolase B |
| RA | 8,852 | T→C | S205S (TCT→TCC) | talB → | transaldolase B |
| RA | 8,868 | C→G | Q211E (CAG→GAG) | talB → | transaldolase B |
| RA | 8,873 | C→T | Y212Y (TAC→TAT) | talB → | transaldolase B |
| RA | 8,879 | 2 bp→GC | coding (642‑643/954 nt) | talB → | transaldolase B |
| JC | 374,644 | +CCCG | coding (384/1110 nt) | frmA ← | alcohol dehydrogenase class III/glutathione‑dependent formaldehyde dehydrogenase |
| RA | 1,191,676 | C→T | H366H (CAC→CAT) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,484,227 | (T)6→7 | pseudogene (744/750 nt) | gapC ← | pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment) |
| RA | 1,484,236 | C→G | pseudogene (735/750 nt) | gapC ← | pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment) |
| RA | 1,484,239 | T→C | pseudogene (732/750 nt) | gapC ← | pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment) |
| RA | 1,484,245 | T→C | pseudogene (726/750 nt) | gapC ← | pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment) |
| RA | 1,484,404 | C→T | pseudogene (567/750 nt) | gapC ← | pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment) |
| RA | 1,484,856 | A→T | pseudogene (115/750 nt) | gapC ← | pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment) |
| RA | 1,484,919 | C→G | pseudogene (52/750 nt) | gapC ← | pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment) |
| RA | 1,485,017 | A→G | intergenic (‑47/‑142) | gapC ← / → cybB | pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment)/cytochrome b561 |
| RA | 1,909,758 | C→A | E12* (GAA→TAA) | proQ ← | RNA chaperone, putative ProP translation regulator |
| RA | 1,977,727 | A→C | I275R (ATA→AGA) | araG ← | fused L‑arabinose transporter subunits of ABC superfamily: ATP‑binding components |
| MC JC | 2,093,044 | Δ2,186 bp | IS5‑mediated | [ugd]–wbbL | [ugd], gnd, wbbL |
| JC JC | 2,527,064 | IS2 (+) +5 bp | intergenic (+325/‑55) | cysK → / → ptsH | cysteine synthase A, O‑acetylserine sulfhydrolase A subunit/phosphohistidinoprotein‑hexose phosphotransferase component of PTS system (Hpr) |
| JC | 2,758,822 | (TATGGCAC)6→7 | intergenic (‑310/+50) | yfjL ← / ← yfjM | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein/CP4‑57 prophage; uncharacterized protein |
| RA | 2,960,120 | +C | coding (1674/2247 nt) | ptsP ← | fused PTS enzyme: PEP‑protein phosphotransferase (enzyme I)/GAF domain containing protein |
| RA | 3,433,446 | C→A | G315C (GGC→TGC) | rpoA ← | RNA polymerase, alpha subunit |
| RA | 3,729,296 | A→C | K320Q (AAG→CAG) | xylR → | xylose divergent operon transcriptional activator |
| RA | 4,076,988 | Δ1 bp | coding (2195/3051 nt) | fdoG ← | formate dehydrogenase‑O, large subunit |
| RA | 4,097,480 | Δ1 bp | coding (1/963 nt) | pfkA → | 6‑phosphofructokinase I |
| MC JC | 4,097,486 | Δ962 bp | [pfkA] | [pfkA] | |
| RA | 4,177,475 | C→T | S733F (TCT→TTT) | rpoC → | RNA polymerase, beta prime subunit |
| MC JC | 4,224,391 | Δ12 bp | coding (706‑717/1650 nt) | pgi → | glucosephosphate isomerase |
| MC JC | 4,303,167 | Δ450 bp | coding (1‑450/450 nt) | rpiB → | ribose 5‑phosphate isomerase B/allose 6‑phosphate isomerase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 1191688 | 1206938 | 15251 | 82 [75] | [78] 82 | [icd]–[icdC] | [icd],ymfD,ymfE,lit,intE,xisE,ymfI,ymfJ,cohE,croE,ymfL,ymfM,oweE,aaaE,ymfR,beeE,jayE,ymfQ,stfP,tfaP,tfaE,stfE,pinE,mcrA,[icdC] |
| * | * | ÷ | CP009273 | 1308873 | 1308955 | 83 | 81 [80] | [0] 136 | [ompW] | [ompW] |
| * | * | ÷ | CP009273 | 1857028 | 1858030 | 1003 | 126 [0] | [0] 123 | [gapA] | [gapA] |
| * | * | ÷ | CP009273 | 3099974 | 3100016 | 43 | 81 [75] | [78] 81 | nupG | nucleoside transporter |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 360104 = | NA (NA) | 217 (1.420) | 148/296 | 0.0 | 61.5% | intergenic (‑38/+557) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | = 360286 | 136 (0.890) | intergenic (‑220/+375) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor | |||||
| * | ? | CP009273 | 376717 = | NA (NA) | 157 (1.030) | 110/294 | 0.2 | 95.8% | intergenic (‑2/‑90) | yaiX/insC1 | pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase/IS2 repressor TnpA |
| ? | CP009273 | 750105 = | 7 (0.050) | intergenic (‑181/‑528) | gltA/sdhC | citrate synthase/succinate dehydrogenase, membrane subunit, binds cytochrome b556 | |||||
| * | ? | CP009273 | = 378045 | NA (NA) | 138 (0.910) | 108/294 | 0.2 | 96.5% | intergenic (+10/+2) | insD1/yaiX | IS2 transposase TnpB/pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase |
| ? | CP009273 | = 750111 | 5 (0.030) | intergenic (‑187/‑522) | gltA/sdhC | citrate synthase/succinate dehydrogenase, membrane subunit, binds cytochrome b556 | |||||
| * | ? | CP009273 | = 378046 | NA (NA) | 218 (1.430) | 102/296 | 0.4 | 99.1% | intergenic (+11/+1) | insD1/yaiX | IS2 transposase TnpB/pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase |
| ? | CP009273 | 997360 = | 2 (0.010) | coding (98/1071 nt) | elfG | putative fimbrial‑like adhesin protein | |||||
| * | ? | CP009273 | 454244 = | 11 (0.070) | 138 (0.930) | 106/288 | 0.2 | 92.8% | intergenic (+88/‑100) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| ? | CP009273 | 603467 = | NA (NA) | intergenic (+23/‑54) | hokE/insL1 | toxic polypeptide, small/IS186 transposase | |||||
| * | ? | CP009273 | = 454255 | 9 (0.060) | 132 (0.890) | 104/288 | 0.3 | 93.8% | intergenic (+99/‑89) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| ? | CP009273 | = 604803 | NA (NA) | intergenic (+170/+112) | insL1/entD | IS186 transposase/phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex | |||||
| * | ? | CP009273 | = 997364 | 3 (0.020) | 147 (0.970) | 114/294 | 0.1 | 98.0% | coding (102/1071 nt) | elfG | putative fimbrial‑like adhesin protein |
| ? | CP009273 | = 1463497 | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||
| * | ? | CP009273 | 1308956 = | 0 (0.000) | 82 (0.920) +62 bp |
63/172 | 0.3 | 79.0% | intergenic (+41/+19) | ompW/yciE | outer membrane protein W/putative rubrerythrin/ferritin‑like metal‑binding protein |
| ? | CP009273 | = 4161777 | 75 (0.490) | intergenic (+93/‑208) | rrfB/murB | 5S ribosomal RNA of rrnB operon/UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding | |||||
| * | ? | CP009273 | = 1463497 | NA (NA) | 132 (0.860) | 99/296 | 0.6 | 97.1% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | CP009273 | 1639684 = | 4 (0.030) | coding (207/288 nt) | relE | Qin prophage; toxin of the RelE‑RelB toxin‑antitoxin system | |||||
| * | ? | CP009273 | 1483968 = | NA (NA) | 123 (0.810) | 96/296 | 0.7 | 100% | intergenic (+40/+2) | aldA/gapC | aldehyde dehydrogenase A, NAD‑linked/pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment) |
| ? | CP009273 | 1858031 = | 0 (0.000) | intergenic (+8/‑76) | gapA/yeaD | glyceraldehyde‑3‑phosphate dehydrogenase A/D‑hexose‑6‑phosphate epimerase‑like protein | |||||
| * | ? | CP009273 | = 1485085 | 135 (0.880) | 79 (0.810) +53 bp |
64/190 | 0.5 | 64.6% | intergenic (‑115/‑74) | gapC/cybB | pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment)/cytochrome b561 |
| ? | CP009273 | = 1857027 | 0 (0.000) | intergenic (‑341/‑1) | msrB/gapA | methionine sulfoxide reductase B/glyceraldehyde‑3‑phosphate dehydrogenase A | |||||
| * | ? | CP009273 | = 1639688 | 1 (0.010) | 139 (0.910) | 110/296 | 0.2 | 99.3% | coding (203/288 nt) | relE | Qin prophage; toxin of the RelE‑RelB toxin‑antitoxin system |
| ? | CP009273 | = 1645805 | NA (NA) | intergenic (+11/‑3) | insD1/intQ | IS2 transposase TnpB;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related/pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related | |||||
| * | ? | CP009273 | 2163652 = | NA (NA) | 142 (0.930) | 113/296 | 0.2 | 96.6% | intergenic (‑4/‑65) | gatR/insE1 | pseudogene, repressor for gat operon; interrupted by IS3; split galactitol utilization operon repressor, fragment 2; split galactitol utilization operon repressor, interrupted/IS3 transposase A |
| ? | CP009273 | = 2460975 | 5 (0.030) | coding (952/1158 nt) | intS | CPS‑53 (KpLE1) prophage; putative prophage CPS‑53 integrase | |||||
| * | ? | CP009273 | = 2164909 | NA (NA) | 125 (0.820) | 96/296 | 0.7 | 99.2% | intergenic (+30/+1) | insF1/gatR | IS3 transposase B/pseudogene, repressor for gat operon; interrupted by IS3; split galactitol utilization operon repressor, fragment 2; split galactitol utilization operon repressor, interrupted |
| ? | CP009273 | 2460973 = | 1 (0.010) | coding (950/1158 nt) | intS | CPS‑53 (KpLE1) prophage; putative prophage CPS‑53 integrase | |||||
| * | ? | CP009273 | 3052022 = | 29 (0.190) | 1162 (7.710) +AG |
207/292 | -0.0 | 97.6% | intergenic (‑253/+3) | serA/rpiA | D‑3‑phosphoglycerate dehydrogenase/ribose 5‑phosphate isomerase, constitutive |
| ? | CP009273 | 4161679 = | NA (NA) | noncoding (115/120 nt) | rrfB | 5S ribosomal RNA of rrnB operon | |||||
| * | ? | CP009273 | 3060603 = | 140 (0.920) | 454 (2.970) | 223/296 | -0.0 | 76.4% | intergenic (‑71/+96) | ygfI/yggE | putative DNA‑binding transcriptional regulator/oxidative stress defense protein |
| ? | CP009273 | = 3124699 | NA (NA) | intergenic (+146/+1) | insH1/yghQ | IS5 transposase and trans‑activator/putative inner membrane polysaccharide flippase | |||||
| * | ? | CP009273 | 3179455 = | NA (NA) | 366 (2.400) | 176/296 | 0.0 | 99.7% | intergenic (+7/‑91) | yqiG/insC1 | pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein/IS2 repressor TnpA |
| ? | CP009273 | = 3426721 | 1 (0.010) | coding (199/1125 nt) | smf | DNA recombination‑mediator A family protein | |||||
| * | ? | CP009273 | = 3180785 | NA (NA) | 250 (1.640) | 167/296 | 0.0 | 96.2% | pseudogene (6/2445 nt) | yqiG | pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein |
| ? | CP009273 | 3372448 = | 10 (0.070) | coding (909/1128 nt) | yhcM | putative AFG1‑like family P‑loop ATPase | |||||
| * | ? | CP009273 | = 3180785 | NA (NA) | 126 (0.820) | 100/296 | 0.5 | 90.6% | pseudogene (6/2445 nt) | yqiG | pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein |
| ? | CP009273 | 3426717 = | 13 (0.090) | coding (203/1125 nt) | smf | DNA recombination‑mediator A family protein | |||||
| * | ? | CP009273 | = 3372452 | 9 (0.060) | 266 (1.740) | 163/296 | 0.0 | 96.7% | coding (905/1128 nt) | yhcM | putative AFG1‑like family P‑loop ATPase |
| ? | CP009273 | 4487998 = | NA (NA) | intergenic (+241/‑91) | intB/insC1 | pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase/IS2 repressor TnpA | |||||