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 | 66,606 | T→C | 4.7% | intergenic (‑56/+229) | araD ← / ← araA | L‑ribulose‑5‑phosphate 4‑epimerase/L‑arabinose isomerase |
| JC | 92,854 | (GCG)4→3 | 10.5% | coding (1442‑1444/1767 nt) | ftsI → | transpeptidase involved in septal peptidoglycan synthesis, penicillin‑binding protein 3 |
| RA | 115,416 | A→G | 4.1% | D103D (GAT→GAC) | hofC ← | assembly protein in type IV pilin biogenesis, transmembrane protein |
| RA | 209,217 | Δ1 bp | 4.6% | coding (597/960 nt) | accA → | acetyl‑CoA carboxylase, carboxytransferase, alpha subunit |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 357,657 | A→G | 4.6% | intergenic (+203/+134) | codA → / ← cynR | cytosine/isoguanine deaminase/transcriptional activator of cyn operon, autorepressor |
| RA | 424,700 | C→T | 3.0% | A73A (GCG→GCA) | acpH ← | acyl carrier protein (ACP) phosphodiesterase, ACP hydrolyase |
| RA | 612,292:1 | +A | 4.0% | coding (203/2241 nt) | fepA ← | ferrienterobactin outer membrane transporter |
| RA | 612,292:2 | +C | 4.0% | coding (203/2241 nt) | fepA ← | ferrienterobactin outer membrane transporter |
| RA | 623,643 | Δ1 bp | 2.7% | coding (868/957 nt) | fepB ← | ferrienterobactin ABC transporter periplasmic binding protein |
| RA | 918,105 | T→A | 3.5% | W545R (TGG→AGG) | ybjD → | putative OLD family ATP‑dependent endonuclease, DUF2813 family protein |
| RA | 1,029,472 | T→A | 3.7% | G166G (GGA→GGT) | rlmI ← | 23S rRNA m(5)C1962 methyltransferase, SAM‑dependent |
| RA | 1,153,109 | Δ1 bp | 3.8% | coding (1171/1242 nt) | fabF → | 3‑oxoacyl‑[acyl‑carrier‑protein] synthase II |
| RA | 1,202,115:1 | +G | 4.1% | intergenic (‑31/+144) | ymfJ ← / ← cohE | e14 prophage, uncharacterized protein/e14 prophage, repressor protein phage e14 |
| RA | 1,308,013 | Δ1 bp | 5.2% | coding (633/1461 nt) | clsA ← | cardiolipin synthase 1 |
| RA | 1,391,251 | Δ1 bp | 4.6% | coding (603/921 nt) | ycjY ← | S9 homolog non‑peptidase family protein |
| RA | 1,466,138 | G→A | 9.3% | pseudogene (747/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,144 | G→T | 7.5% | pseudogene (753/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,201 | T→C | 9.2% | pseudogene (810/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,210 | G→A | 10.9% | pseudogene (819/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,258 | G→C | 6.9% | pseudogene (867/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,729 | G→A | 6.4% | pseudogene (1338/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,538,462 | C→T | 4.3% | G131D (GGC→GAC) | narY ← | nitrate reductase 2 (NRZ), beta subunit |
| RA | 1,562,255:1 | +G | 4.3% | coding (227/1551 nt) | ddpA ← | D,D‑dipeptide ABC transporter periplasmic binding protein |
| RA | 1,598,904 | T→C | 55.6% | S436G (AGT→GGT) | lsrK ← | autoinducer‑2 (AI‑2) kinase |
| RA | 1,670,591 | Δ1 bp | 3.4% | coding (893/1254 nt) | ynfM → | putative arabinose efflux transporter |
| RA | 1,670,592 | Δ1 bp | 3.4% | coding (894/1254 nt) | ynfM → | putative arabinose efflux transporter |
| RA | 1,708,718 | G→A | 6.0% | A600A (GCG→GCA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,751 | A→G | 6.1% | E611E (GAA→GAG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,758 | G→C | 5.4% | E614Q (GAA→CAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,844 | C→G | 10.8% | A642A (GCC→GCG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,930 | C→A | 11.6% | P671Q (CCG→CAG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,833,785 | G→A | 4.3% | G129S (GGT→AGT) | ydjX → | TVP38/TMEM64 family inner membrane protein |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,246,123 | C→T | 4.6% | P215P (CCG→CCA) | cirA ← | colicin IA outer membrane receptor and translocator, ferric iron‑catecholate transporter |
| RA | 2,304,760 | T→C | 7.4% | intergenic (+369/+346) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,796 | T→C | 14.8% | intergenic (+405/+310) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,316,391 | T→C | 100% | Y73H (TAC→CAC) | rcsB → | response regulator in two‑component regulatory system with RcsC and YojN |
| RA | 2,316,758 | T→C | 100% | V195A (GTC→GCC) | rcsB → | response regulator in two‑component regulatory system with RcsC and YojN |
| RA | 2,383,798 | G→A | 15.4% | R363Q (CGA→CAA) | elaD → | protease, capable of cleaving an AMC‑ubiquitin model substrate |
| RA | 2,500,743 | Δ1 bp | 4.2% | coding (363/735 nt) | ypdB → | response regulator activating yhjX, pyruvate‑responsive YpdAB two‑component system |
| RA | 2,546,734 | A→G | 3.6% | N22D (AAT→GAT) | murP → | N‑acetylmuramic acid permease, EIIBC component, PTS system |
| RA | 2,660,944 | T→A | 4.0% | K196* (AAA→TAA) | iscS ← | cysteine desulfurase (tRNA sulfurtransferase), PLP‑dependent |
| RA | 2,817,761 | T→C | 4.1% | intergenic (‑260/+21) | yqaB ← / ← argQ | fructose‑1‑P and 6‑phosphogluconate phosphatase/tRNA‑Arg |
| RA | 2,817,768 | G→A | 4.0% | intergenic (‑267/+14) | yqaB ← / ← argQ | fructose‑1‑P and 6‑phosphogluconate phosphatase/tRNA‑Arg |
| RA | 2,817,771 | Δ1 bp | 4.1% | intergenic (‑270/+11) | yqaB ← / ← argQ | fructose‑1‑P and 6‑phosphogluconate phosphatase/tRNA‑Arg |
| RA | 2,817,775 | G→T | 5.1% | intergenic (‑274/+7) | yqaB ← / ← argQ | fructose‑1‑P and 6‑phosphogluconate phosphatase/tRNA‑Arg |
| RA | 2,817,873 | T→C | 5.0% | intergenic (‑15/+184) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,817,875 | C→T | 6.3% | intergenic (‑17/+182) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,818,047 | T→A | 5.5% | intergenic (‑189/+10) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,875,266 | G→T | 3.7% | T51N (ACC→AAC) | cysN ← | sulfate adenylyltransferase, subunit 1 |
| RA | 3,002,093 | C→T | 6.1% | P584L (CCT→CTT) | xdhA → | xanthine dehydrogenase, molybdenum binding subunit |
| RA | 3,017,889 | C→T | 3.0% | A611V (GCC→GTC) | ygfK → | putative Fe‑S subunit oxidoreductase subunit |
| RA | 3,184,969 | C→T | 4.7% | L44L (CTC→CTT) | yqiC → | BMFP family putative fusogenic protein |
| RA | 3,204,321:1 | +G | 3.7% | coding (267/369 nt) | folB ← | dihydroneopterin aldolase and dihydroneopterin triphosphate 2'‑epimerase |
| RA | 3,204,321:2 | +A | 3.7% | coding (267/369 nt) | folB ← | dihydroneopterin aldolase and dihydroneopterin triphosphate 2'‑epimerase |
| RA | 3,242,626 | A→G | 2.8% | D229D (GAT→GAC) | uxaA ← | altronate hydrolase |
| RA | 3,308,102 | G→A | 87.9% | A274V (GCA→GTA) | nlpI ← | lipoprotein involved in osmotic sensitivity and filamentation |
| RA | 3,415,874 | A→G | 3.9% | N282D (AAC→GAC) | acrF → | multidrug efflux system protein |
| MC JC | 3,527,656 | Δ5 bp | 100% | coding (1190‑1194/2136 nt) | yrfF → | putative RcsCDB‑response attenuator, inner membrane protein |
| RA | 3,692,445 | C→A | 2.8% | P54P (CCG→CCT) | bcsB ← | regulator of cellulose synthase, cyclic di‑GMP binding |
| RA | 3,754,283 | Δ1 bp | 3.8% | coding (145/324 nt) | yiaW ← | DUF3302 family inner membrane protein |
| RA | 3,754,284 | Δ1 bp | 3.8% | coding (144/324 nt) | yiaW ← | DUF3302 family inner membrane protein |
| RA | 3,766,526 | C→T | 6.8% | S64F (TCT→TTT) | yibA → | putative immunity protein for polymorphic toxin RhsA, HEAT‑domain protein, lethality reduction protein |
| RA | 3,812,703 | T→A | 4.1% | intergenic (‑145/‑27) | yicR ← / → dfp | UPF0758 family protein/fused 4'‑phosphopantothenoylcysteine decarboxylase/phosphopantothenoylcysteine synthetase, FMN‑binding |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,818,670 | C→G | 6.1% | intergenic (+87/‑203) | dinD → / → yicG | DNA damage‑inducible protein/UPF0126 family inner membrane protein |
| MC JC | 3,992,523 | (CGGGC)2→1 | 100% | coding (1372‑1376/2547 nt) | cyaA → | adenylate cyclase |
| MC JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,103,655 | Δ1 bp | 100% | coding (1320/1374 nt) | cpxA ← | sensory histidine kinase in two‑component regulatory system with CpxR |
| RA | 4,122,730 | A→G | 5.3% | S203S (TCT→TCC) | ftsN ← | essential cell division protein |
| RA | 4,136,505 | C→T | 4.7% | A133A (GCC→GCT) | yijE → | EamA‑like transporter family protein |
| RA | 4,153,569 | G→A | 3.8% | intergenic (‑472/+126) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,295,964 | A→C | 4.5% | intergenic (+171/+473) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,154 | T→C | 12.6% | intergenic (+361/+283) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,189 | A→G | 39.9% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 42.4% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,267 | T→C | 14.3% | intergenic (+474/+170) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,550,448 | G→A | 3.8% | R284C (CGT→TGT) | gntP ← | fructuronate transporter |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1978500 | 1979280 | 781 | 33 [31] | [31] 34 | insB1–insA | insB1, insA |
| * | * | ÷ | NC_000913 | 2533738 | 2536374 | 2637 | 33 [28] | [29] 33 | ptsH–crr | ptsH, ptsI, crr |
| * | * | ÷ | NC_000913 | 3423883–3424447 | 3424447 | 1–565 | 33 [30] | [31] 32 | rrlD | 23S ribosomal RNA of rrnD operon |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 79 (0.830) | 59/508 | 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 | 457693 = | 135 (1.420) | 3 (0.030) | 3/502 | NT | 2.6% | coding (268/1275 nt) | clpX | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease |
| ? | NC_000913 | 458482 = | 91 (0.970) | coding (1057/1275 nt) | clpX | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease | |||||
| * | ? | NC_000913 | 1207790 = | 33 (0.350) | 33 (0.370) | 30/476 | NT | 50.8% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 33 (0.370) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 31 (0.330) | 61 (0.690) | 45/476 | NT | 66.3% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 33 (0.370) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 2 (0.020) | 67 (0.710) | 50/508 | NT | 97.1% | 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) | 44 (0.470) | 34/500 | 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) | 29 (0.320) | 20/492 | 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) | 34 (0.360) | 28/508 | 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) | 57 (0.600) | 39/508 | 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 | 3220235 = | 87 (0.920) | 6 (0.070) | 3/488 | NT | 5.6% | coding (744/1380 nt) | patA | putrescine:2‑oxoglutaric acid aminotransferase, PLP‑dependent |
| ? | NC_000913 | 3220407 = | 118 (1.300) | coding (916/1380 nt) | patA | putrescine:2‑oxoglutaric acid aminotransferase, PLP‑dependent | |||||
| * | ? | NC_000913 | 3742296 = | 83 (0.880) | 3 (0.030) | 3/492 | NT | 3.8% | coding (236/849 nt) | yiaJ | transcriptional repressor for the yiaKLMNO‑lyxK‑sgbHUE operon |
| ? | NC_000913 | 3742330 = | 73 (0.790) | coding (202/849 nt) | yiaJ | transcriptional repressor for the yiaKLMNO‑lyxK‑sgbHUE operon | |||||
| * | ? | NC_000913 | = 4106252 | 90 (0.950) | 9 (0.090) | 9/508 | NT | 9.1% | coding (434/501 nt) | cpxP | inhibitor of the cpx response, periplasmic adaptor protein |
| ? | 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 | |||||