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 | 32,344 | G→A | 3.1% | E510K (GAA→AAA) | carB → | carbamoyl‑phosphate synthase large subunit |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 375,168 | G→A | 6.1% | intergenic (+287/‑291) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 375,176 | A→G | 7.0% | intergenic (+295/‑283) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 451,518:1 | +C | 3.5% | coding (93/948 nt) | cyoA ← | cytochrome o ubiquinol oxidase subunit II |
| RA | 561,331 | A→G | 2.8% | S545S (TCA→TCG) | sfmD → | putative outer membrane export usher protein |
| RA | 854,163 | Δ1 bp | 2.7% | coding (517/1119 nt) | ybiR → | putative transporter |
| RA | 1,446,864 | T→A | 2.7% | R140S (AGA→AGT) | feaR ← | transcriptional activator for tynA and feaB |
| RA | 1,466,495 | C→T | 7.5% | pseudogene (1104/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,504 | A→G | 6.2% | pseudogene (1113/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,622,957 | A→G | 3.2% | intergenic (‑43/+3) | mgrR ← / ← dgcZ | sRNA antisense regulator down regulates YgdQ and EptB, PhoPQ‑regulated, Hfq‑dependent, affects sensitivity to antimicrobial peptides/diguanylate cyclase, zinc‑sensing |
| RA | 1,708,662 | C→G | 5.8% | Q582E (CAA→GAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,749,207 | Δ1 bp | 3.3% | coding (353/813 nt) | ydhT ← | FNR, Nar, NarP‑regulated protein, putative subunit of YdhYVWXUT oxidoreductase complex |
| RA | 1,749,208 | Δ1 bp | 3.3% | coding (352/813 nt) | ydhT ← | FNR, Nar, NarP‑regulated protein, putative subunit of YdhYVWXUT oxidoreductase complex |
| RA | 1,837,913 | Δ1 bp | 2.6% | coding (702/1536 nt) | ynjC → | putative ABC transporter permease |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 1,985,112 | C→G | 3.2% | intergenic (‑43/+27) | araG ← / ← araF | L‑arabinose ABC transporter ATPase/L‑arabinose ABC transporter periplasmic binding protein |
| RA | 2,024,254 | Δ1 bp | 5.4% | coding (287/624 nt) | rcsA → | transcriptional regulator of colanic acid capsular biosynthesis |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,150,809 | A→T | 3.9% | A59A (GCT→GCA) | yegI ← | protein kinase‑related putative non‑specific DNA‑binding protein |
| RA | 2,304,520 | G→T | 4.2% | intergenic (+129/+586) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,521 | G→C | 5.4% | intergenic (+130/+585) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,791 | C→T | 7.7% | intergenic (+400/+315) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,796 | T→C | 17.6% | intergenic (+405/+310) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,316,782:1 | +A | 13.7% | coding (608/651 nt) | rcsB → | response regulator in two‑component regulatory system with RcsC and YojN |
| RA | 2,509,469 | G→A | 36.8% | intergenic (‑45/‑159) | glk ← / → yfeO | glucokinase/putative ion channel protein |
| RA | 2,637,335 | A→G | 3.2% | L7P (CTT→CCT) | der ← | GTPase, multicopy suppressor of ftsJ |
| RA | 2,649,931 | A→C | 12.7% | G785G (GGT→GGG) | yfhM ← | bacterial alpha2‑macroglobulin colonization factor ECAM, anti‑host protease defense factor, periplasmic inner membrane‑anchored lipoprotein |
| RA | 2,976,723 | Δ1 bp | 7.1% | coding (127/1032 nt) | galR → | galactose‑inducible d‑galactose regulon transcriptional repressor, autorepressor |
| RA | 2,977,090 | G→A | 5.4% | W165* (TGG→TAG) | galR → | galactose‑inducible d‑galactose regulon transcriptional repressor, autorepressor |
| JC | 2,977,232 | Δ53 bp | 5.6% | coding (636‑688/1032 nt) | galR → | galactose‑inducible d‑galactose regulon transcriptional repressor, autorepressor |
| RA | 3,384,905 | Δ1 bp | 3.1% | coding (205/471 nt) | argR → | l‑arginine‑responsive arginine metabolism regulon transcriptional regulator |
| RA | 3,419,435 | C→A | 6.1% | pseudogene (331/960 nt) | yhdW → | pseudogene, ABC transporter periplasmic binding protein family,putative transport, Not classified, putative periplasmic binding transport protein, periplasmic‑binding component of ABC superfamily |
| RA | 3,457,526 | A→T | 3.1% | L384F (TTA→TTT) | gspD → | general secretory pathway component, cryptic |
| RA | 3,526,445 | G→A | 4.0% | intergenic (‑298/‑22) | nudE ← / → yrfF | adenosine nucleotide hydrolase, Ap3A/Ap2A/ADP‑ribose/NADH hydrolase/putative RcsCDB‑response attenuator, inner membrane protein |
| RA | 3,528,106 | T→G | 25.6% | L547R (CTG→CGG) | yrfF → | putative RcsCDB‑response attenuator, inner membrane protein |
| RA | 3,599,805 | G→A | 3.2% | intergenic (‑148/+123) | livJ ← / ← rpoH | branched‑chain amino acid ABC transporter periplasmic binding protein/RNA polymerase, sigma 32 (sigma H) factor |
| RA | 3,687,584 | T→C | 5.2% | E530G (GAG→GGG) | bcsC ← | cellulose synthase subunit |
| RA | 3,698,606:1 | +C | 3.6% | coding (394/1680 nt) | bcsG → | DUF3260 family cellulose production inner membrane protein |
| RA | 3,698,606:2 | +C | 2.9% | coding (394/1680 nt) | bcsG → | DUF3260 family cellulose production inner membrane protein |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,875,520 | T→C | 24.3% | A28A (GCT→GCC) | yidX → | putative lipoprotein |
| RA | 3,938,905 | A→G | 7.8% | D227G (GAC→GGC) | rbsR → | transcriptional repressor of ribose metabolism |
| RA | 3,953,534 | G→T | 9.9% | A20S (GCG→TCG) | ilvD → | dihydroxyacid dehydratase |
| RA | 3,992,437 | T→G | 11.7% | L429* (TTA→TGA) | cyaA → | adenylate cyclase |
| JC | 3,992,468 | Δ4 bp | 6.2% | coding (1317‑1320/2547 nt) | cyaA → | adenylate cyclase |
| MC JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,080,671 | T→C | 3.0% | Q186R (CAA→CGA) | fdhE ← | formate dehydrogenase formation protein |
| RA | 4,085,324 | A→G | 2.8% | A166A (GCT→GCC) | fdoG ← | formate dehydrogenase‑O, large subunit |
| RA | 4,153,471 | C→A | 6.5% | intergenic (‑374/+224) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,153,492 | T→C | 5.3% | intergenic (‑395/+203) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,186,322 | A→G | 2.7% | K325R (AAA→AGA) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,296,059 | C→T | 11.2% | intergenic (+266/+378) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,189 | A→G | 33.8% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 36.6% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,639,473 | C→T | 2.7% | P432L (CCG→CTG) | creD → | inner membrane protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2533706 | 2536391 | 2686 | 66 [62] | [64] 65 | ptsH–[pdxK] | ptsH, ptsI, crr, [pdxK] |
| * | * | ÷ | NC_000913 | 3423804–3424232 | 3424425–3424237 | 6–622 | 67 [63] | [63] 65 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 157 (1.130) | 98/516 | 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 | 622841 = | 138 (1.000) | 4 (0.030) | 3/504 | NT | 2.8% | coding (542/1251 nt) | entS | enterobactin exporter, iron‑regulated |
| ? | NC_000913 | 622906 = | 148 (1.090) | coding (607/1251 nt) | entS | enterobactin exporter, iron‑regulated | |||||
| * | ? | NC_000913 | = 693912 | 101 (0.730) | 4 (0.030) | 3/506 | NT | 3.6% | coding (1044/1425 nt) | miaB | tRNA‑i(6)A37 methylthiotransferase |
| ? | NC_000913 | = 694111 | 118 (0.870) | coding (845/1425 nt) | miaB | tRNA‑i(6)A37 methylthiotransferase | |||||
| * | ? | NC_000913 | 1207790 = | 47 (0.340) | 97 (0.750) | 69/484 | NT | 66.9% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 52 (0.400) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 47 (0.340) | 102 (0.790) | 67/484 | NT | 68.0% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 52 (0.400) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 0 (0.000) | 146 (1.050) | 89/516 | NT | 100% | 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) | 103 (0.760) | 70/508 | 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 | 1646853 = | 68 (0.490) | 3 (0.020) | 3/498 | NT | 2.8% | intergenic (+116/+321) | flxA/intK | Qin prophage, uncharacterized protein/pseudogene, integrase fragment, Qin prophage,Phage or Prophage Related |
| ? | NC_000913 | 1649105 = | 140 (1.050) | intergenic (+64/‑277) | ydfC/dicF | uncharacterized protein, Qin prophage/sRNA antisense regulator, inhibits ftsZ, Hfq‑dependent, Qin prophage | |||||
| * | ? | NC_000913 | 1800053 = | 119 (0.860) | 3 (0.020) | 3/506 | NT | 2.5% | intergenic (‑54/+43) | rpmI/infC | 50S ribosomal subunit protein L35/translation initiation factor IF‑3 |
| ? | NC_000913 | 1800077 = | 117 (0.860) | intergenic (‑78/+19) | rpmI/infC | 50S ribosomal subunit protein L35/translation initiation factor IF‑3 | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 115 (0.830) | 71/516 | 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) | 110 (0.790) | 61/516 | 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 | 1985101 = | 121 (0.870) | 4 (0.030) | 4/494 | NT | 3.4% | intergenic (‑32/+38) | araG/araF | L‑arabinose ABC transporter ATPase/L‑arabinose ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1985124 = | 112 (0.850) | intergenic (‑55/+15) | araG/araF | L‑arabinose ABC transporter ATPase/L‑arabinose ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 2288917 = | NA (NA) | 89 (0.640) | 59/516 | NT | 74.8% | 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 | 3526447 = | 30 (0.220) | intergenic (‑300/‑20) | nudE/yrfF | adenosine nucleotide hydrolase, Ap3A/Ap2A/ADP‑ribose/NADH hydrolase/putative RcsCDB‑response attenuator, inner membrane protein | |||||
| * | ? | NC_000913 | = 2290110 | NA (NA) | 147 (1.070) | 78/514 | NT | 82.6% | 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 | = 3526451 | 31 (0.220) | intergenic (‑304/‑16) | nudE/yrfF | adenosine nucleotide hydrolase, Ap3A/Ap2A/ADP‑ribose/NADH hydrolase/putative RcsCDB‑response attenuator, inner membrane protein | |||||
| * | ? | NC_000913 | = 2531963 | 130 (0.940) | 4 (0.030) | 3/496 | NT | 2.6% | coding (503/762 nt) | cysZ | sulfate transporter, sulfite inhibited |
| ? | NC_000913 | = 2532165 | 169 (1.270) | coding (705/762 nt) | cysZ | sulfate transporter, sulfite inhibited | |||||
| * | ? | NC_000913 | = 2713827 | 137 (0.990) | 5 (0.040) | 5/494 | NT | 3.7% | coding (934/1335 nt) | srmB | ATP‑dependent RNA helicase |
| ? | NC_000913 | = 2713906 | 126 (0.950) | coding (1013/1335 nt) | srmB | ATP‑dependent RNA helicase | |||||
| * | ? | NC_000913 | 3154343 = | 132 (0.950) | 4 (0.030) | 4/498 | NT | 3.1% | coding (874/957 nt) | yqhC | transcriptional activator of yqhD |
| ? | NC_000913 | 3154374 = | 126 (0.940) | coding (843/957 nt) | yqhC | transcriptional activator of yqhD | |||||
| * | ? | NC_000913 | 3526447 = | 30 (0.220) | 10 (0.070) | 8/516 | NT | 25.0% | intergenic (‑300/‑20) | nudE/yrfF | adenosine nucleotide hydrolase, Ap3A/Ap2A/ADP‑ribose/NADH hydrolase/putative RcsCDB‑response attenuator, inner membrane protein |
| ? | NC_000913 | = 3653229 | NA (NA) | intergenic (‑32/‑1) | insH1/yhiS | IS5 transposase and trans‑activator/pseudogene | |||||
| * | ? | NC_000913 | = 3526451 | 31 (0.220) | 5 (0.040) | 4/514 | NT | 13.9% | intergenic (‑304/‑16) | nudE/yrfF | adenosine nucleotide hydrolase, Ap3A/Ap2A/ADP‑ribose/NADH hydrolase/putative RcsCDB‑response attenuator, inner membrane protein |
| ? | NC_000913 | 3652036 = | NA (NA) | intergenic (+6/+145) | yhiS/insH1 | pseudogene/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | 3845530 = | 98 (0.710) | 84 (0.630) | 59/496 | NT | 45.4% | coding (1568/1767 nt) | adeD | cryptic adenine deaminase |
| ? | NC_000913 | = 3992759 | 108 (0.810) | coding (1608/2547 nt) | cyaA | adenylate cyclase | |||||
| * | ? | NC_000913 | = 4034101 | 129 (0.930) | 4 (0.030) | 3/498 | NT | 3.1% | coding (958/1452 nt) | trkH | potassium transporter |
| ? | NC_000913 | = 4034171 | 126 (0.940) | coding (1028/1452 nt) | trkH | potassium transporter | |||||
| * | ? | NC_000913 | 4295831 = | NA (NA) | 7 (0.060) | 7/438 | 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 | |||||