mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 |
| MC JC | 62,822 | Δ16 bp | 100% | coding (428‑443/2907 nt) | rapA ← | RNA polymerase remodeling/recycling factor ATPase, RNA polymerase‑associated, ATP‑dependent RNA translocase |
| RA | 92,250 | T→C | 6.3% | S280P (TCA→CCA) | ftsI → | transpeptidase involved in septal peptidoglycan synthesis, penicillin‑binding protein 3 |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 349,642 | A→G | 6.5% | intergenic (+70/‑370) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 349,673 | G→C | 5.2% | intergenic (+101/‑339) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 349,676 | G→A | 5.5% | intergenic (+104/‑336) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 349,717 | T→C | 4.3% | intergenic (+145/‑295) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 425,955 | C→T | 5.1% | A315A (GCC→GCT) | queA → | S‑adenosylmethionine:tRNA ribosyltransferase‑isomerase |
| RA | 450,272 | T→A | 3.7% | N124Y (AAC→TAC) | cyoB ← | cytochrome o ubiquinol oxidase subunit I |
| RA | 701,362 | G→T | 7.1% | S78Y (TCC→TAC) | nagC ← | N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor |
| RA | 790,599:1 | +G | 4.2% | coding (431/1047 nt) | galT ← | galactose‑1‑phosphate uridylyltransferase |
| RA | 801,946 | T→C | 5.7% | G20G (GGT→GGC) | ybhI → | putative DASS family tricarboxylate or dicarboxylate transporter |
| RA | 1,031,646 | A→G | 5.6% | noncoding (67/88 nt) | serT ← | tRNA‑Ser |
| RA | 1,073,967 | T→G | 6.4% | E15D (GAA→GAC) | rutA ← | pyrimidine oxygenase, FMN‑dependent |
| RA | 1,174,981 | A→G | 4.3% | F62S (TTT→TCT) | ycfT ← | inner membrane protein |
| RA | 1,196,305 | C→T | 100% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase |
| RA | 1,261,083 | C→T | 4.2% | V265I (GTA→ATA) | prs ← | phosphoribosylpyrophosphate synthase |
| RA | 1,270,261 | T→C | 3.5% | S29G (AGC→GGC) | ldrC ← | toxic polypeptide, small |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,402,502 | G→T | 5.5% | Q252K (CAG→AAG) | abgB ← | p‑aminobenzoyl‑glutamate hydrolase, B subunit |
| RA | 1,407,779 | A→G | 5.6% | F6S (TTC→TCC) | ydaM ← | diguanylate cyclase, csgD regulator |
| RA | 1,466,210 | G→A | 8.0% | pseudogene (819/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,258 | G→C | 7.0% | pseudogene (867/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,529,430 | G→T | 5.1% | pseudogene (1529/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,683,511 | Δ1 bp | 4.9% | coding (630/1302 nt) | rstB → | sensory histidine kinase of RstAB two‑component system |
| RA | 1,756,758 | T→C | 3.9% | I354T (ATT→ACT) | pykF → | pyruvate kinase I |
| RA | 1,854,578:1 | +T | 5.6% | coding (277/759 nt) | ydjF ← | putative DNA‑binding transcriptional regulator |
| RA | 1,936,308 | C→T | 100% | V3I (GTA→ATA) | zwf ← | glucose‑6‑phosphate 1‑dehydrogenase |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 1,985,718 | G→A | 5.1% | G137G (GGC→GGT) | araF ← | L‑arabinose ABC transporter periplasmic binding protein |
| RA | 2,046,045 | Δ1 bp | 7.1% | coding (1108/7077 nt) | yeeJ → | putative adhesin |
| RA | 2,113,831 | C→T | 6.3% | R166H (CGT→CAT) | wcaN ← | putative regulatory subunit for GalU |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,137,960 | A→T | 7.1% | E20V (GAA→GTA) | yegH → | inner membrane protein |
| RA | 2,185,973 | C→A | 5.9% | A20D (GCC→GAC) | rcnA → | membrane protein conferring nickel and cobalt resistance |
| RA | 2,272,634 | C→A | 7.1% | S91S (TCC→TCA) | yejA → | microcin C ABC transporter periplasmic binding protein |
| RA | 2,304,521 | G→C | 4.9% | intergenic (+130/+585) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,535 | A→G | 7.0% | intergenic (+144/+571) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,796 | T→C | 15.5% | intergenic (+405/+310) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,370,843 | T→C | 4.6% | V276V (GTT→GTC) | arnD → | undecaprenyl phosphate‑alpha‑L‑ara4FN deformylase |
| RA | 2,514,256 | A→G | 5.4% | intergenic (+14/‑73) | nupC → / → insL1 | nucleoside (except guanosine) transporter/IS186 transposase |
| RA | 2,625,210 | G→A | 5.7% | G33D (GGT→GAT) | ppx → | exopolyphosphatase |
| RA | 2,641,264 | A→G | 4.0% | V180A (GTG→GCG) | ispG ← | 1‑hydroxy‑2‑methyl‑2‑(E)‑butenyl 4‑diphosphate synthase |
| RA | 2,963,182 | G→A | 5.5% | A178V (GCC→GTC) | ppdB ← | putative prepilin peptidase‑dependent protein |
| RA | 3,151,446 | T→C | 4.0% | L179L (TTA→TTG) | exbB ← | membrane spanning protein in TonB‑ExbB‑ExbD complex |
| RA | 3,267,746:1 | +G | 6.0% | intergenic (+150/‑106) | tdcR → / → yhaB | L‑threonine dehydratase operon activator protein/uncharacterized protein |
| RA | 3,272,189 | C→T | 4.3% | A187A (GCG→GCA) | garR ← | tartronate semialdehyde reductase |
| RA | 3,486,706 | A→T | 11.1% | I197F (ATC→TTC) | crp → | cAMP‑activated global transcription factor, mediator of catabolite repression |
| RA | 3,495,036 | C→A | 9.7% | A343E (GCA→GAA) | nirB → | nitrite reductase, large subunit, NAD(P)H‑binding |
| RA | 3,624,828 | A→G | 4.5% | E151G (GAG→GGG) | yhhI → | putative transposase |
| RA | 3,655,363:1 | +T | 5.5% | coding (539/648 nt) | yhiD ← | putative Mg(2+) transport ATPase, inner membrane protein |
| RA | 3,744,990 | T→C | 5.5% | V63A (GTG→GCG) | yiaN → | 2,3‑diketo‑L‑gulonate TRAP transporter large permease protein |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,850,291 | C→T | 3.6% | V145V (GTG→GTA) | uhpA ← | response regulator in two‑component regulatory system wtih UhpB |
| MC JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,004,944 | G→A | 6.8% | V28V (GTG→GTA) | pldA → | outer membrane phospholipase A |
| RA | 4,183,730 | Δ1 bp | 3.4% | coding (2487/4029 nt) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,059 | C→T | 8.7% | intergenic (+266/+378) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,154 | T→C | 11.6% | intergenic (+361/+283) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,189 | A→G | 33.2% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 33.6% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,267 | T→C | 21.8% | intergenic (+474/+170) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,556,274 | A→G | 3.7% | D16D (GAT→GAC) | yjiC ← | uncharacterized protein |
| RA | 4,583,908 | T→A | 5.7% | H952L (CAC→CTC) | hsdR ← | endonuclease R Type I restriction enzyme |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423877–3424230 | 3424412–3424236 | 7–536 | 24 [22] | [22] 24 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 4233758 | 4235398 | 1641 | 24 [23] | [23] 24 | 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) | 58 (0.760) | 43/502 | 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 | 273955 = | NA (NA) | 31 (0.410) | 28/502 | NT | 66.0% | intergenic (+1/+146) | ykfC/insH1 | CP4‑6 prophage, conserved protein,Phage or Prophage Related/IS5 transposase and trans‑activator |
| ? | NC_000913 | 973271 = | 16 (0.210) | coding (131/780 nt) | elyC | envelope biogenesis factor, DUF218 superfamily protein | |||||
| * | ? | NC_000913 | = 275149 | NA (NA) | 37 (0.490) | 33/502 | NT | 69.8% | intergenic (‑32/‑176) | insH1/mmuP | IS5 transposase and trans‑activator/CP4‑6 prophage, putative S‑methylmethionine transporter |
| ? | NC_000913 | = 973274 | 16 (0.210) | coding (128/780 nt) | elyC | envelope biogenesis factor, DUF218 superfamily protein | |||||
| * | ? | NC_000913 | = 382153 | NA (NA) | 9 (0.120) | 4/490 | NT | NA | coding (480/906 nt) | insD1 | IS2 transposase TnpB |
| ? | NC_000913 | = 382246 | NA (NA) | coding (573/906 nt) | insD1 | IS2 transposase TnpB | |||||
| * | ? | NC_000913 | 1207790 = | 50 (0.660) | 44 (0.620) | 35/470 | NT | 57.6% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 18 (0.250) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 48 (0.630) | 56 (0.790) | 52/470 | NT | 64.0% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 18 (0.250) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 2 (0.030) | 100 (1.320) | 67/502 | NT | 98.0% | 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 | 1491823 = | 46 (0.610) | 4 (0.050) | 4/492 | NT | 5.7% | coding (147/174 nt) | ydcA | putative periplasmic protein |
| ? | NC_000913 | 1492363 = | 88 (1.180) | intergenic (+189/‑107) | sokB/trg | sRNA antisense regulator blocking mokB, and hence hokB, translation/methyl‑accepting chemotaxis protein III, ribose and galactose sensor receptor | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 50 (0.660) | 37/502 | 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) | 50 (0.660) | 37/502 | 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 | |||||
| * | ? | NC_000913 | 2288917 = | NA (NA) | 75 (0.990) | 64/502 | NT | 100% | intergenic (‑5/+146) | yejO/insH1 | pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system/IS5 transposase and trans‑activator |
| ? | NC_000913 | 3553101 = | 0 (0.000) | coding (19/2706 nt) | malT | mal regulon transcriptional activator | |||||
| * | ? | NC_000913 | = 2290110 | NA (NA) | 90 (1.190) | 58/500 | NT | 100% | intergenic (‑31/+2) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system |
| ? | NC_000913 | = 3553105 | 0 (0.000) | coding (23/2706 nt) | malT | mal regulon transcriptional activator | |||||
| * | ? | NC_000913 | 2477000 = | 71 (0.940) | 3 (0.040) | 3/478 | NT | 4.4% | coding (628/936 nt) | dsdC | dsd operon activator, autorepressor |
| ? | NC_000913 | 2477033 = | 64 (0.890) | coding (595/936 nt) | dsdC | dsd operon activator, autorepressor | |||||
| * | ? | NC_000913 | = 2498106 | 65 (0.860) | 6 (0.080) | 5/480 | NT | 10.1% | coding (188/1239 nt) | alaC | glutamate‑pyruvate aminotransferase, glutamic‑pyruvic transaminase (GPT), alanine transaminase |
| ? | NC_000913 | = 2498313 | 45 (0.620) | intergenic (‑20/‑356) | alaC/ypdA | glutamate‑pyruvate aminotransferase, glutamic‑pyruvic transaminase (GPT), alanine transaminase/sensor kinase regulating yhjX, pyruvate‑responsive YpdAB two‑component system | |||||
| * | ? | NC_000913 | 3276528 = | 67 (0.880) | 3 (0.040) | 3/486 | NT | 3.5% | coding (1249/1572 nt) | garD | D‑galactarate dehydrogenase |
| ? | NC_000913 | 3277294 = | 101 (1.380) | coding (295/336 nt) | prlF | antitoxin of the SohA(PrlF)‑YhaV toxin‑antitoxin system | |||||
| * | ? | NC_000913 | = 3560426 | 96 (1.270) | 4 (0.050) | 4/486 | NT | 4.2% | pseudogene (26/606 nt) | glpR | pseudogene, DNA‑binding transcriptional repressor,regulator, Energy metabolism, carbon: Anaerobic respiration, repressor of the glp operon |
| ? | NC_000913 | = 3560564 | 88 (1.200) | pseudogene (40/149 nt) | glpR | pseudogene, DNA‑binding transcriptional repressor,regulator, Energy metabolism, carbon: Anaerobic respiration, repressor of the glp operon | |||||
| * | ? | NC_000913 | 3680195 = | 98 (1.290) | 3 (0.040) | 3/492 | NT | 3.2% | coding (778/930 nt) | kdgK | 2‑dehydro‑3‑deoxygluconokinase |
| ? | NC_000913 | 3680518 = | 84 (1.130) | coding (1422/1497 nt) | yhjJ | putative periplasmic M16 family chaperone | |||||
| * | ? | NC_000913 | = 3972569 | 64 (0.840) | 3 (0.040) | 3/484 | NT | 4.8% | coding (49/1068 nt) | rffG | dTDP‑glucose 4,6‑dehydratase |
| ? | NC_000913 | = 3972982 | 57 (0.780) | coding (462/1068 nt) | rffG | dTDP‑glucose 4,6‑dehydratase | |||||
| * | ? | NC_000913 | 4049902 = | 0 (0.000) | 62 (0.820) | 49/502 | NT | 100% | noncoding (5/109 nt) | spf | Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent |
| ? | NC_000913 | 4498182 = | 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 | |||||
| * | ? | NC_000913 | = 4049906 | 0 (0.000) | 65 (0.860) | 48/502 | NT | 100% | noncoding (9/109 nt) | spf | Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent |
| ? | NC_000913 | = 4499512 | NA (NA) | intergenic (+11/+82) | insD1/yjgX | IS2 transposase TnpB/pseudogene fragment | |||||
| * | ? | NC_000913 | 4231909 = | 87 (1.150) | 4 (0.050) | 4/488 | NT | 4.6% | coding (1324/1350 nt) | lysC | lysine‑sensitive aspartokinase 3 |
| ? | NC_000913 | 4232298 = | 83 (1.130) | coding (935/1350 nt) | lysC | lysine‑sensitive aspartokinase 3 | |||||