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 |
| RA | 32,767 | Δ1 bp | 3.6% | coding (1951/3222 nt) | carB → | carbamoyl‑phosphate synthase large subunit |
| RA | 32,768 | Δ1 bp | 3.6% | coding (1952/3222 nt) | carB → | carbamoyl‑phosphate synthase large subunit |
| RA | 187,969 | C→A | 7.8% | D228Y (GAT→TAT) | glnD ← | uridylyltransferase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 273,367 | T→C | 3.2% | pseudogene (521/1108 nt) | ykfC → | CP4‑6 prophage, conserved protein,Phage or Prophage Related |
| RA | 279,281 | T→C | 7.1% | Q134R (CAG→CGG) | insB1 ← | IS1 transposase B |
| RA | 519,322 | G→A | 4.1% | S148S (AGC→AGT) | tesA ← | acyl‑CoA thioesterase 1 and protease I and lysophospholipase L1 |
| RA | 541,525:1 | +A | 6.1% | coding (961/1302 nt) | ybbY → | putative uracil/xanthine transporter |
| RA | 645,189 | G→A | 4.6% | G464G (GGC→GGT) | citT ← | citrate/succinate antiporter, citrate carrier |
| RA | 763,346 | T→C | 4.2% | G111G (GGT→GGC) | sucC → | succinyl‑CoA synthetase, beta subunit |
| RA | 1,179,730 | C→T | 4.0% | R34W (CGG→TGG) | cobB → | deacetylase of acs and cheY, chemotaxis regulator |
| RA | 1,334,015 | A→G | 58.9% | K54R (AAG→AGG) | cysB → | N‑acetylserine‑responsive cysteine regulon transcriptional activator, autorepressor |
| RA | 1,354,687 | C→A | 4.7% | V262F (GTT→TTT) | sapB ← | antimicrobial peptide transport ABC transporter permease |
| RA | 1,453,135 | Δ1 bp | 4.0% | coding (508/2046 nt) | paaZ ← | oxepin‑CoA hydrolase and 3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase |
| RA | 1,698,314 | A→G | 5.0% | D289D (GAT→GAC) | malI ← | transcriptional repressor of Mal regulon |
| RA | 1,708,847 | G→A | 9.0% | E643E (GAG→GAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,854 | C→G | 10.3% | Q646E (CAA→GAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,852,970 | G→A | 4.5% | A337V (GCC→GTC) | ydjE ← | putative MFS sugar transporter, membrane protein |
| RA | 1,959,393 | Δ1 bp | 5.0% | coding (454/567 nt) | yecM ← | putative metal‑binding enzyme |
| RA | 1,967,541 | T→A | 6.0% | M321L (ATG→TTG) | cheB ← | fused chemotaxis regulator: protein‑glutamate methylesterase in two‑component regulatory system with CheA |
| JC | 2,121,532 | (TCGC)3→2 | 9.3% | coding (20‑23/1395 nt) | wcaJ ← | colanic biosynthesis UDP‑glucose lipid carrier transferase |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,146,825 | T→C | 4.4% | Y239C (TAT→TGT) | alkA ← | 3‑methyl‑adenine DNA glycosylase II |
| RA | 2,329,497:1 | +G | 4.8% | coding (299/1650 nt) | yfaQ ← | tandem DUF2300 domain protein, putative host defense protein |
| RA | 2,339,012 | G→A | 3.4% | A136V (GCC→GTC) | gyrA ← | DNA gyrase (type II topoisomerase), subunit A |
| RA | 3,180,972 | A→G | 4.0% | D185G (GAT→GGT) | ygiC → | ATP‑Grasp family ATPase |
| RA | 3,329,688 | C→T | 3.8% | P243L (CCG→CTG) | dacB → | D‑alanyl‑D‑alanine carboxypeptidase |
| RA | 3,400,524 | G→A | 7.9% | R188C (CGC→TGC) | mreB ← | cell wall structural complex MreBCD, actin‑like component MreB |
| RA | 3,402,648 | A→G | 3.3% | V228A (GTG→GCG) | csrD ← | targeting factor for csrBC sRNA degradation |
| RA | 3,579,182 | T→C | 3.7% | K155E (AAA→GAA) | yhhW ← | quercetinase activity in vitro |
| RA | 3,640,510 | T→C | 5.0% | M134T (ATG→ACG) | uspA → | universal stress global response regulator |
| RA | 3,707,229 | Δ1 bp | 4.1% | coding (476/1608 nt) | dppA ← | dipeptide/heme ABC transporter periplasmic binding protein, dipeptide chemotaxis receptor |
| RA | 3,748,879 | G→A | 3.9% | A102T (GCA→ACA) | sgbH → | 3‑keto‑L‑gulonate 6‑phosphate decarboxylase |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,968,508 | Δ1 bp | 9.2% | coding (594/1104 nt) | wecA → | UDP‑GlcNAc:undecaprenylphosphate GlcNAc‑1‑phosphate transferase |
| JC | 3,976,196 | Δ9 bp | 7.0% | coding (1052‑1060/1131 nt) | wecE → | TDP‑4‑oxo‑6‑deoxy‑D‑glucose transaminase |
| MC JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| JC | 4,180,673:1 | (CTG)4→5 | 61.6% | coding (115/366 nt) | rplL → | 50S ribosomal subunit protein L7/L12 |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,249,989 | Δ1 bp | 3.5% | coding (437/921 nt) | malM → | maltose regulon periplasmic protein |
| RA | 4,267,779 | G→A | 6.2% | E223K (GAA→AAA) | tyrB → | tyrosine aminotransferase, tyrosine‑repressible, PLP‑dependent |
| RA | 4,295,833 | T→C | 4.6% | intergenic (+40/+604) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,189 | A→G | 36.6% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 40.7% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 583130 | 584734 | 1605 | 28 [26] | [26] 28 | [tfaX]–[ompT] | [tfaX], appY, [ompT] |
| * | * | ÷ | NC_000913 | 1211062 | 1212808 | 1747 | 28 [27] | [27] 28 | [mcrA]–[ycgX] | [mcrA], icdC, iraM, [ycgX] |
| * | * | ÷ | NC_000913 | 1215950 | 1216802 | 853 | 28 [27] | [26] 28 | [ycgZ]–[ymgC] | [ycgZ], ymgA, ariR, [ymgC] |
| * | * | ÷ | NC_000913 | 1299468 | 1300729 | 1262 | 28 [27] | [27] 29 | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| * | * | ÷ | NC_000913 | 1529944 | 1530473 | 530 | 28 [27] | [27] 28 | [ydcD] | [ydcD] |
| * | * | ÷ | NC_000913 | 1978495 | 1979278 | 784 | 28 [26] | [4] 30 | insB1–insA | insB1, insA |
| * | * | ÷ | NC_000913 | 2455603 | 2456190 | 588 | 28 [26] | [24] 29 | [yfcV] | [yfcV] |
| * | * | ÷ | NC_000913 | 2774333 | 2775166 | 834 | 28 [27] | [26] 28 | [yfjW] | [yfjW] |
| * | * | ÷ | NC_000913 | 2785819 | 2786591 | 773 | 28 [27] | [27] 28 | [ileY]–[ygaQ] | [ileY], [ygaQ] |
| * | * | ÷ | NC_000913 | 2990615 | 2991426 | 812 | 28 [26] | [26] 28 | [ygeF]–[ygeG] | [ygeF], ygeF, [ygeG] |
| * | * | ÷ | NC_000913 | 2994930 | 2996008 | 1079 | 33 [27] | [27] 30 | [ygeK]–[ygeO] | [ygeK], ygeN, [ygeN], [ygeO] |
| * | * | ÷ | NC_000913 | 3268712 | 3269644 | 933 | 28 [27] | [27] 28 | [yhaC] | [yhaC] |
| * | * | ÷ | NC_000913 | 3769495 | 3770106 | 612 | 30 [27] | [27] 28 | [yibV]–[yibU] | [yibV], yibV, yibU, [yibU] |
| * | * | ÷ | NC_000913 | 3796823 | 3797412 | 590 | 31 [27] | [26] 29 | [waaC]–[waaL] | [waaC], [waaL] |
| * | * | ÷ | NC_000913 | 3798471 | 3800256 | 1786 | 28 [26] | [27] 29 | [waaU]–waaZ | [waaU], waaZ |
| * | * | ÷ | NC_000913 | 3804099 | 3805233 | 1135 | 28 [24] | [27] 29 | [waaB]–[waaP] | [waaB], waaS, [waaP] |
| * | * | ÷ | NC_000913 | 4476511 | 4477190 | 680 | 32 [26] | [27] 28 | yjgL | SopA‑central‑domain‑like hexapeptide repeat protein |
| * | * | ÷ | NC_000913 | 4556316 | 4556783 | 468 | 35 [24] | [26] 29 | [yjiC] | [yjiC] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 69 (0.850) | 54/500 | 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 | 1207790 = | 26 (0.320) | 61 (0.810) | 46/468 | NT | 67.7% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 34 (0.450) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 26 (0.320) | 47 (0.620) | 37/468 | NT | 61.7% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 34 (0.450) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 1 (0.010) | 83 (1.030) | 60/500 | NT | 98.8% | 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) | 20 (0.250) | 17/492 | 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 | = 1978502 | 0 (0.000) | 24 (0.310) | 20/484 | NT | 100% | intergenic (‑305/+16) | flhD/insB1 | flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B |
| ? | NC_000913 | 1979279 = | 0 (0.000) | intergenic (‑64/‑474) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 44 (0.540) | 39/500 | 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) | 52 (0.640) | 40/500 | 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 | 2097812 = | 39 (0.480) | 52 (0.640) | 45/500 | NT | 57.1% | coding (490/981 nt) | wzzB | regulator of length of O‑antigen component of lipopolysaccharide chains |
| ? | NC_000913 | = 2102943 | NA (NA) | intergenic (‑32/+1) | insH1/wbbL | IS5 transposase and trans‑activator/pseudogene, lipopolysaccharide biosynthesis protein | |||||
| * | ? | NC_000913 | = 2097815 | 38 (0.470) | 44 (0.540) | 34/500 | NT | 53.7% | coding (487/981 nt) | wzzB | regulator of length of O‑antigen component of lipopolysaccharide chains |
| ? | NC_000913 | 2101749 = | NA (NA) | intergenic (‑5/+146) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | 2288917 = | NA (NA) | 5 (0.060) | 5/500 | NT | 8.1% | 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 | 2876676 = | 57 (0.700) | coding (98/1038 nt) | iap | aminopeptidase in alkaline phosphatase isozyme conversion | |||||
| * | ? | NC_000913 | 2288920 = | NA (NA) | 6 (0.080) | 6/494 | NT | 8.8% | intergenic (‑8/+143) | 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 | = 2913667 | 63 (0.780) | intergenic (‑18/+30) | relA/rlmD | (p)ppGpp synthetase I/GTP pyrophosphokinase/23S rRNA m(5)U1939 methyltransferase, SAM‑dependent | |||||
| * | ? | NC_000913 | = 2290111 | NA (NA) | 12 (0.150) | 8/500 | NT | 17.9% | 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 | = 2876679 | 55 (0.680) | coding (101/1038 nt) | iap | aminopeptidase in alkaline phosphatase isozyme conversion | |||||
| * | ? | NC_000913 | 2375822 = | 79 (0.980) | 3 (0.040) | 3/492 | NT | 3.7% | coding (139/963 nt) | menC | O‑succinylbenzoyl‑CoA synthase |
| ? | NC_000913 | 2514275 = | NA (NA) | intergenic (+33/‑54) | nupC/insL1 | nucleoside (except guanosine) transporter/IS186 transposase | |||||
| * | ? | NC_000913 | 2642943 = | 45 (0.560) | 6 (0.070) | 6/500 | NT | 11.8% | intergenic (‑101/+184) | rodZ/rlmN | MreB assembly cytoskeletal protein/dual specificity 23S rRNA m(2)A2503, tRNA m(2)A37 methyltransferase, SAM‑dependent |
| ? | NC_000913 | = 3187424 | NA (NA) | intergenic (+11/‑1) | insD1/yqiG | IS2 transposase TnpB/pseudogene, fimbrial export usher family,putative membrane, Not classified, putative membrane protein | |||||
| * | ? | NC_000913 | = 2671660 | 79 (0.980) | 3 (0.040) | 3/488 | NT | 3.7% | coding (438/813 nt) | hcaB | 2,3‑dihydroxy‑2,3‑dihydrophenylpropionate dehydrogenase |
| ? | NC_000913 | = 2671669 | 81 (1.030) | coding (447/813 nt) | hcaB | 2,3‑dihydroxy‑2,3‑dihydrophenylpropionate dehydrogenase | |||||
| * | ? | NC_000913 | 2876676 = | 57 (0.700) | 4 (0.050) | 4/500 | NT | 6.6% | coding (98/1038 nt) | iap | aminopeptidase in alkaline phosphatase isozyme conversion |
| ? | NC_000913 | 3130144 = | NA (NA) | intergenic (‑3/‑32) | yghO/insH1 | pseudogene, IS‑interrupted/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | 3652035 = | NA (NA) | 5 (0.060) | 5/500 | NT | 27.8% | intergenic (+5/+146) | yhiS/insH1 | pseudogene/IS5 transposase and trans‑activator |
| ? | NC_000913 | 3802088 = | 13 (0.160) | coding (970/1020 nt) | waaO | UDP‑D‑galactose:(glucosyl)lipopolysaccharide‑ alpha‑1,3‑D‑galactosyltransferase | |||||
| * | ? | NC_000913 | 4295831 = | NA (NA) | 5 (0.070) | 3/422 | NT | NA | intergenic (+38/+606) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| ? | NC_000913 | = 4296395 | NA (NA) | noncoding (562/602 nt) | RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites | |||||