mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 |
| RA | 152,527 | T→A | 7.4% | T96S (ACT→TCT) | yadM ← | putative fimbrial‑like adhesin protein |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 292,362:1 | +C | 6.3% | coding (587/627 nt) | yagK ← | CP4‑6 prophage; conserved protein |
| RA | 292,362:2 | +A | 6.3% | coding (587/627 nt) | yagK ← | CP4‑6 prophage; conserved protein |
| RA | 349,615 | T→C | 7.0% | intergenic (+43/‑397) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 349,624 | C→T | 5.6% | intergenic (+52/‑388) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 349,642 | A→G | 9.2% | intergenic (+70/‑370) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 349,673 | G→C | 9.1% | intergenic (+101/‑339) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 349,676 | G→A | 9.1% | intergenic (+104/‑336) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 349,717 | T→C | 7.8% | intergenic (+145/‑295) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 374,972 | T→C | 7.6% | intergenic (+91/‑487) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 374,986 | T→C | 9.9% | intergenic (+105/‑473) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 374,999:1 | +C | 5.8% | intergenic (+118/‑460) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 375,000 | T→A | 5.4% | intergenic (+119/‑459) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 375,001 | T→A | 5.7% | intergenic (+120/‑458) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 375,019 | Δ1 bp | 5.9% | intergenic (+138/‑440) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 375,020 | T→G | 6.3% | intergenic (+139/‑439) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 700,948 | A→C | 100% | I216S (ATT→AGT) | nagC ← | N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor |
| RA | 985,712 | C→T | 6.3% | intergenic (‑3/+182) | aspC ← / ← ompF | aspartate aminotransferase, PLP‑dependent/outer membrane porin 1a (Ia;b;F) |
| RA | 1,269,766 | C→T | 6.0% | A15A (GCG→GCA) | ldrB ← | toxic polypeptide, small |
| 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 |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,571,973:1 | +G | 7.1% | coding (73/1401 nt) | gadB ← | glutamate decarboxylase B, PLP‑dependent |
| RA | 1,617,465 | A→G | 6.5% | T146T (ACA→ACG) | ydeA → | arabinose efflux transporter, arabinose‑inducible |
| RA | 1,708,814 | A→G | 9.8% | A632A (GCA→GCG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,762,280 | T→A | 5.7% | E78V (GAA→GTA) | sufC ← | SufBCD Fe‑S cluster assembly scaffold protein, ATP‑binding protein |
| RA | 1,787,828 | G→A | 8.7% | A128A (GCG→GCA) | ppsR → | PEP synthase kinase and PEP synthase pyrophosphorylase |
| RA | 1,880,008 | G→A | 5.7% | intergenic (‑60/+113) | yeaR ← / ← leuE | DUF1971 family protein, nitrate‑inducible/leucine efflux protein |
| RA | 1,933,865 | A→T | 5.3% | V247D (GTT→GAT) | edd ← | 6‑phosphogluconate dehydratase |
| RA | 1,952,107 | T→C | 5.9% | I238T (ATT→ACT) | yecE → | UPF0759 family protein |
| 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 | 2,131,940 | T→C | 5.8% | K44R (AAA→AGA) | wcaC ← | putative glycosyl transferase |
| 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 | 2,304,798 | T→C | 11.0% | intergenic (+405/+310) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| JC JC | 2,313,540 | Δ2 bp :: IS186 (+) +6 bp | 100% | coding (53‑58/2673 nt) | rcsD → | phosphotransfer intermediate protein in two‑component regulatory system with RcsBC |
| RA | 2,509,471 | G→A | 100% | intergenic (‑45/‑159) | glk ← / → yfeO | glucokinase/putative ion channel protein |
| RA | 2,960,264 | Δ1 bp | 6.2% | coding (2165/3369 nt) | recC ← | exonuclease V (RecBCD complex), gamma chain |
| RA | 2,977,580 | T→G | 100% | S328A (TCA→GCA) | galR → | galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor |
| RA | 3,045,998 | T→C | 5.6% | intergenic (‑97/+170) | ygfF ← / ← gcvP | putative NAD(P)‑dependent oxidoreductase/glycine decarboxylase, PLP‑dependent, subunit P of glycine cleavage complex |
| RA | 3,046,002 | A→G | 5.6% | intergenic (‑101/+166) | ygfF ← / ← gcvP | putative NAD(P)‑dependent oxidoreductase/glycine decarboxylase, PLP‑dependent, subunit P of glycine cleavage complex |
| JC JC | 3,526,449 | IS5 (+) +4 bp | 100% | intergenic (‑300/‑17) | nudE ← / → yrfF | adenosine nucleotide hydrolase; Ap3A/Ap2A/ADP‑ribose/NADH hydrolase/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 | 3,769,666 | Δ1 bp | 100% | pseudogene (322/327 nt) | yibV → | pseudogene, putative cryptic Rhs immunity protein |
| RA | 3,789,632 | C→A | 5.4% | P150P (CCG→CCT) | waaH ← | LPS(HepIII)‑glucuronic acid glycosyltransferase |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,875,538 | C→A | 12.2% | A34E (GCA→GAA) | yidX → | putative lipoprotein |
| RA | 3,876,895 | T→G | 5.9% | T20P (ACC→CCC) | yidA ← | sugar phosphate phosphatase |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,053,570 | G→T | 5.7% | intergenic (+152/+77) | hemN → / ← yshB | coproporphyrinogen III oxidase, SAM and NAD(P)H dependent, oxygen‑independent/uncharacterized protein |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,190 | A→G | 19.5% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 21.6% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 19.6% | intergenic (+474/+168) | 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 | 2533715 | 2536367 | 2653 | 22 [21] | [20] 22 | ptsH–crr | ptsH,ptsI,crr |
| * | * | ÷ | NC_000913 | 3423887–3424234 | 3424409–3424238 | 5–523 | 22 [21] | [21] 22 | 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 | 151088 = | 60 (0.790) | 4 (0.050) | 4/488 | NT | 7.3% | coding (512/597 nt) | yadK | putative fimbrial‑like adhesin protein |
| ? | NC_000913 | 151321 = | 43 (0.580) | coding (279/597 nt) | yadK | putative fimbrial‑like adhesin protein | |||||
| * | ? | NC_000913 | 172704 = | 69 (0.900) | 4 (0.050) | 3/490 | NT | 5.6% | coding (1243/1983 nt) | fhuB | iron(3+)‑hydroxamate import ABC transporter permease |
| ? | NC_000913 | 173004 = | 67 (0.910) | coding (1543/1983 nt) | fhuB | iron(3+)‑hydroxamate import ABC transporter permease | |||||
| * | ? | NC_000913 | 227918 = | NA (NA) | 3 (0.040) | 3/494 | NT | NA | noncoding (2160/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913 | 228067 = | NA (NA) | noncoding (2309/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | = 381278 | 39 (0.530) | 3 (0.040) | 3/490 | NT | 7.1% | noncoding (19/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382572 | NA (NA) | noncoding (1313/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 392579 = | NA (NA) | 4 (0.060) | 4/480 | NT | 15.5% | noncoding (388/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | 392779 = | 23 (0.300) | noncoding (188/1258 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 1051218 = | 59 (0.770) | 4 (0.050) | 4/498 | NT | 6.6% | intergenic (‑43/‑243) | cspH/cspG | stress protein, member of the CspA‑family/cold shock protein homolog, cold‑inducible |
| ? | NC_000913 | 1051370 = | 56 (0.750) | intergenic (‑195/‑91) | cspH/cspG | stress protein, member of the CspA‑family/cold shock protein homolog, cold‑inducible | |||||
| * | ? | NC_000913 | 1207790 = | 27 (0.350) | 41 (0.570) | 36/474 | NT | 62.5% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 24 (0.340) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 26 (0.340) | 55 (0.770) | 44/474 | NT | 69.5% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 24 (0.340) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1328280 = | 56 (0.730) | 4 (0.050) | 4/492 | NT | 5.4% | coding (78/591 nt) | btuR | cob(I)yrinic acid a,c‑diamide adenosyltransferase |
| ? | NC_000913 | 1329071 = | 86 (1.160) | coding (42/759 nt) | yciK | putative EmrKY‑TolC system oxoacyl‑(acyl carrier protein) reductase | |||||
| * | ? | NC_000913 | = 1853917 | 44 (0.580) | 4 (0.050) | 4/502 | NT | 8.8% | coding (63/1359 nt) | ydjE | putative MFS sugar transporter, membrane protein |
| ? | NC_000913 | = 1854271 | 39 (0.520) | coding (584/759 nt) | ydjF | putative DNA‑binding transcriptional regulator | |||||
| * | ? | NC_000913 | = 2428232 | 76 (1.000) | 4 (0.050) | 4/492 | NT | 5.4% | coding (395/570 nt) | ubiX | 3‑octaprenyl‑4‑hydroxybenzoate carboxy‑lyase |
| ? | NC_000913 | = 2428528 | 66 (0.890) | coding (99/570 nt) | ubiX | 3‑octaprenyl‑4‑hydroxybenzoate carboxy‑lyase | |||||
| * | ? | NC_000913 | = 3798187 | 11 (0.140) | 4 (0.050) | 4/496 | NT | 27.8% | coding (1240/1260 nt) | waaL | O‑antigen ligase |
| ? | NC_000913 | = 3798669 | 10 (0.130) | coding (644/1074 nt) | waaU | lipopolysaccharide core biosynthesis | |||||
| * | ? | NC_000913 | 3845531 = | 71 (0.930) | 77 (1.050) | 59/486 | NT | 52.3% | coding (1568/1767 nt) | adeD | cryptic adenine deaminase |
| ? | NC_000913 | = 3992760 | 72 (0.980) | coding (1608/2547 nt) | cyaA | adenylate cyclase | |||||
| * | ? | NC_000913 | = 4214796 | 64 (0.840) | 6 (0.080) | 4/484 | NT | 8.5% | coding (517/930 nt) | metA | homoserine O‑transsuccinylase |
| ? | NC_000913 | = 4214987 | 68 (0.930) | coding (708/930 nt) | metA | homoserine O‑transsuccinylase | |||||