mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 375,168 | G→A | 6.5% | 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 | 6.9% | intergenic (+295/‑283) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| RA | 1,466,495 | C→T | 5.4% | pseudogene (1104/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,504 | A→G | 5.2% | pseudogene (1113/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,024,253 | Δ1 bp | 5.4% | coding (286/624 nt) | rcsA → | transcriptional regulator of colanic acid capsular biosynthesis |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,304,523 | G→C | 5.7% | intergenic (+130/+585) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,798 | T→C | 10.1% | 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 (606/651 nt) | rcsB → | response regulator in two‑component regulatory system with RcsC and YojN |
| RA | 2,509,471 | G→A | 36.8% | intergenic (‑45/‑159) | glk ← / → yfeO | glucokinase/putative ion channel protein |
| RA | 2,976,725 | Δ1 bp | 7.1% | coding (127/1032 nt) | galR → | galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor |
| RA | 2,977,092 | G→A | 5.4% | W165* (TGG→TAG) | galR → | galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor |
| JC | 2,977,234 | Δ53 bp | 5.6% | coding (636‑688/1032 nt) | galR → | galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor |
| RA | 3,419,437 | 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 |
| JC JC | 3,526,449 | IS5 (–) +4 bp | 17.8% | intergenic (‑300/‑17) | nudE ← / → yrfF | adenosine nucleotide hydrolase; Ap3A/Ap2A/ADP‑ribose/NADH hydrolase/putative RcsCDB‑response attenuator, inner membrane protein |
| JC JC | 3,526,449 | IS5 (+) +4 bp | 79.6% | intergenic (‑300/‑17) | nudE ← / → yrfF | adenosine nucleotide hydrolase; Ap3A/Ap2A/ADP‑ribose/NADH hydrolase/putative RcsCDB‑response attenuator, inner membrane protein |
| RA | 3,528,108 | T→G | 25.6% | L547R (CTG→CGG) | yrfF → | putative RcsCDB‑response attenuator, inner membrane protein |
| RA | 3,560,455:1 | +G | 100% | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,687,585 | T→C | 5.4% | E530G (GAG→GGG) | bcsC ← | cellulose synthase subunit |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,953,535 | G→T | 9.4% | A20S (GCG→TCG) | ilvD → | dihydroxyacid dehydratase |
| RA | 3,992,438 | T→G | 11.8% | L429* (TTA→TGA) | cyaA → | adenylate cyclase |
| JC | 3,992,469 | Δ4 bp | 6.2% | coding (1317‑1320/2547 nt) | cyaA → | adenylate cyclase |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,153,472 | C→A | 5.0% | intergenic (‑374/+224) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,060 | C→T | 10.6% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→G | 17.0% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 20.0% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 22.3% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 17.7% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | 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 | 2533701 | 2536448 | 2748 | 64 [63] | [62] 64 | ptsH–[pdxK] | ptsH,ptsI,crr,[pdxK] |
| * | * | ÷ | NC_000913 | 3423806–3424234 | 3424427–3424239 | 6–622 | 65 [61] | [63] 65 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 47 (0.340) | 97 (0.750) | 69/484 | NT | 67.1% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 51 (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) | 101 (0.790) | 66/484 | NT | 68.0% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 51 (0.400) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | 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 | 3845531 = | 96 (0.700) | 80 (0.610) | 57/496 | NT | 44.4% | coding (1568/1767 nt) | adeD | cryptic adenine deaminase |
| ? | NC_000913 | = 3992760 | 108 (0.820) | coding (1608/2547 nt) | cyaA | adenylate cyclase | |||||