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 | 126,168 | A→G | 3.0% | K158K (AAA→AAG) | aceF → | pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2 |
| RA | 141,444 | T→C | 3.0% | V5A (GTA→GCA) | hpt → | hypoxanthine phosphoribosyltransferase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 627,076 | A→G | 2.5% | E336G (GAA→GGA) | entE → | 2,3‑dihydroxybenzoate‑AMP ligase component of enterobactin synthase multienzyme complex |
| RA | 781,283 | T→A | 3.0% | intergenic (+61/‑86) | lysY → / → lysZ | tRNA‑Lys/tRNA‑Lys |
| RA | 1,196,305 | C→T | 93.9% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase |
| RA | 1,269,785 | G→A | 3.5% | T9I (ACT→ATT) | ldrB ← | toxic polypeptide, small |
| RA | 1,286,793 | A→G | 2.8% | intergenic (+267/+273) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,286,861 | T→G | 2.9% | intergenic (+335/+205) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,619,420 | A→G | 7.7% | T101A (ACC→GCC) | marR → | transcriptional repressor of multiple antibiotic resistance |
| JC | 1,707,863 | Δ4 bp | 3.5% | coding (945‑948/2223 nt) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,847 | G→A | 8.8% | E643E (GAG→GAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 2,066,465 | T→C | 100% | K286R (AAG→AGG) | insH1 ← | IS5 transposase and trans‑activator |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,194,234 | T→C | 2.7% | intergenic (‑68/‑64) | mrp ← / → metG | antiporter inner membrane protein/methionyl‑tRNA synthetase |
| RA | 2,304,547 | C→T | 3.2% | intergenic (+156/+559) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,686 | A→G | 5.5% | intergenic (+295/+420) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,449,326:1 | +G | 2.6% | coding (722/822 nt) | yfcO ← | DUF2544 family putative outer membrane protein |
| RA | 2,817,769 | G→A | 2.9% | intergenic (‑268/+13) | yqaB ← / ← argQ | fructose‑1‑P and 6‑phosphogluconate phosphatase/tRNA‑Arg |
| RA | 2,817,772 | A→T | 2.8% | intergenic (‑271/+10) | yqaB ← / ← argQ | fructose‑1‑P and 6‑phosphogluconate phosphatase/tRNA‑Arg |
| RA | 2,817,869 | C→T | 3.2% | intergenic (‑11/+188) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,817,875 | C→T | 3.9% | intergenic (‑17/+182) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,817,907 | A→G | 2.9% | intergenic (‑49/+150) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,817,914 | T→G | 4.6% | intergenic (‑56/+143) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 3,234,702 | G→A | 3.1% | intergenic (‑249/+35) | higB ← / ← rlmG | mRNA interferase toxin of the HigB‑HigA toxin‑antitoxin system/23S rRNA m(2)G1835 methyltransferase, SAM‑dependent |
| JC | 3,451,524 | (GACTTC)3→2 | 2.8% | coding (154‑159/303 nt) | rplW ← | 50S ribosomal subunit protein L23 |
| RA | 3,483,276 | Δ1 bp | 2.7% | coding (77/1023 nt) | yheT → | UPF0017 family putative hydrolase |
| RA | 3,560,493 | G→A | 5.0% | pseudogene (111/149 nt) | glpR ← | pseudogene, DNA‑binding transcriptional repressor,regulator, Energy metabolism, carbon: Anaerobic respiration, repressor of the glp operon |
| RA | 3,688,286 | A→C | 7.1% | V296G (GTG→GGG) | bcsC ← | cellulose synthase subunit |
| JC | 3,758,392:1 | (GCT)2→3 | 4.2% | coding (1469/1845 nt) | selB ← | selenocysteinyl‑tRNA‑specific translation factor |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,070,449 | T→C | 7.4% | intergenic (‑49/+65) | yihR ← / ← yihS | putative sulphoquinovose mutarotase/sulphoquinovose isomerase |
| RA | 4,118,096 | A→C | 8.4% | intergenic (‑7/‑418) | glpF ← / → zapB | glycerol facilitator/FtsZ stabilizer, septal ring assembly factor, cell division stimulator |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,295,833 | T→C | 4.4% | intergenic (+40/+604) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,059 | C→T | 6.5% | intergenic (+266/+378) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,154 | T→C | 13.2% | intergenic (+361/+283) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,189 | A→G | 32.9% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 36.1% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,325,949 | A→G | 4.0% | intergenic (‑207/+451) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,326,089 | T→G | 6.7% | intergenic (‑347/+311) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423826–3424233 | 3424446–3424237 | 5–621 | 103 [97] | [99] 103 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 4233744 | 4235438 | 1695 | 110 [101] | [101] 105 | pgi | pgi |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 15391 = | NA (NA) | 8 (0.030) | 8/432 | NT | 10.2% | intergenic (+93/‑54) | dnaJ/insL1 | chaperone Hsp40, DnaK co‑chaperone/IS186 transposase |
| ? | NC_000913 | = 458799 | 72 (0.280) | intergenic (+99/‑89) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La | |||||
| * | ? | NC_000913 | = 224395 | NA (NA) | 7 (0.030) | 6/428 | NT | NA | noncoding (625/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon |
| ? | NC_000913 | = 224600 | NA (NA) | noncoding (830/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | 257908 = | NA (NA) | 276 (1.090) | 128/440 | NT | 99.3% | 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 | 2 (0.010) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | 458787 = | 90 (0.360) | 173 (0.690) | 100/434 | NT | 66.1% | 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 | 458787 = | 90 (0.360) | 8 (0.030) | 8/434 | NT | 8.3% | intergenic (+87/‑101) | 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 | = 458799 | 72 (0.280) | 177 (0.710) | 92/432 | NT | 71.5% | 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 = | 76 (0.300) | 144 (0.610) | 76/408 | NT | 68.5% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 62 (0.260) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 72 (0.280) | 154 (0.660) | 87/408 | NT | 70.5% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 62 (0.260) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 13 (0.050) | 246 (0.970) | 127/440 | NT | 95.0% | 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 | = 1299498 | 0 (0.000) | 123 (0.500) | 79/432 | 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 | |||||
| * | ? | NC_000913 | = 1651548 | NA (NA) | 43 (0.170) | 33/440 | NT | 18.2% | 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 |
| ? | NC_000913 | = 1937140 | 193 (0.760) | coding (489/870 nt) | yebK | putative DNA‑binding transcriptional regulator | |||||
| * | ? | NC_000913 | 1710414 = | 207 (0.820) | 39 (0.150) | 18/440 | NT | 15.9% | coding (211/621 nt) | rsxG | SoxR iron‑sulfur cluster reduction factor component, putative membrane protein of electron transport complex |
| ? | 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 | = 1710418 | 206 (0.810) | 17 (0.070) | 11/438 | NT | 7.7% | coding (215/621 nt) | rsxG | SoxR iron‑sulfur cluster reduction factor component, putative membrane protein of electron transport complex |
| ? | NC_000913 | 2101750 = | NA (NA) | intergenic (‑6/+145) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | 1937136 = | 183 (0.720) | 28 (0.110) | 27/440 | NT | 13.3% | coding (485/870 nt) | yebK | putative DNA‑binding transcriptional regulator |
| ? | NC_000913 | = 2070271 | NA (NA) | intergenic (‑91/‑6) | insC1/yoeA | IS2 repressor TnpA/CP4‑44 prophage, putative disrupted hemin or colicin receptor,Phage or Prophage Related, interrupted by IS2 and C‑terminal deletion | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 131 (0.540) | 77/424 | 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) | 144 (0.570) | 78/440 | 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) | 217 (0.860) | 103/440 | 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 | = 2771960 | 168 (0.660) | 5 (0.020) | 5/436 | NT | 2.9% | intergenic (+347/+40) | yfjT/yfjU | CP4‑57 prophage, putative periplasmic protein/CP4‑57 prophage, conserved protein,Phage or Prophage Related |
| ? | NC_000913 | 2996361 = | NA (NA) | intergenic (‑3/+9) | ygeO/insD1 | pseudogene, orgA family, part of T3SS PAI ETT2 remnant/IS2 transposase TnpB | |||||
| * | ? | NC_000913 | 2814161 = | 213 (0.840) | 6 (0.020) | 6/418 | NT | 2.8% | intergenic (+9/+55) | emrB/luxS | multidrug efflux system protein/S‑ribosylhomocysteine lyase |
| ? | NC_000913 | 2814185 = | 210 (0.870) | intergenic (+33/+31) | emrB/luxS | multidrug efflux system protein/S‑ribosylhomocysteine lyase | |||||
| * | ? | NC_000913 | 3868319 = | 231 (0.910) | 6 (0.020) | 5/426 | NT | 2.7% | coding (990/1248 nt) | yidR | DUF3748 family protein |
| ? | NC_000913 | 3868340 = | 205 (0.840) | coding (969/1248 nt) | yidR | DUF3748 family protein | |||||
| * | ? | NC_000913 | 4148373 = | 350 (1.380) | 11 (0.040) | 11/440 | NT | 2.6% | intergenic (‑57/+158) | yijO/eptC | AraC family putative transcriptional activator/LPS heptose I phosphoethanolamine transferase |
| ? | NC_000913 | = 4503516 | 468 (1.850) | intergenic (‑84/‑543) | insG/yjhB | IS4 transposase/putative MFS transporter, membrane protein | |||||
| * | ? | NC_000913 | 4295831 = | NA (NA) | 19 (0.090) | 11/362 | 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 | |||||